This is a list of selected publications by EVBC members. For a full list of publications from EVBC members, see PubMed.

Authors: Type:

2021

  • [DOI] L. Chen, D. Wang, S. Garmaeva, A. Kurilshikov, A. V. Vila, R. Gacesa, T. Sinha, E. Segal, R. K. Weersma, C. Wijmenga, A. Zhernakova, and J. Fu, “The long-term genetic stability and individual specificity of the human gut microbiome,” Cell, 2021.
    [Bibtex]
    @Article{Chen:21a,
    author = {Lianmin Chen and Daoming Wang and Sanzhima Garmaeva and Alexander Kurilshikov and Arnau Vich Vila and Ranko Gacesa and Trishla Sinha and Eran Segal and Rinse K. Weersma and Cisca Wijmenga and Alexandra Zhernakova and Jingyuan Fu},
    journal = {Cell},
    title = {The long-term genetic stability and individual specificity of the human gut microbiome},
    year = {2021},
    doi = {10.1016/j.cell.2021.03.024},
    publisher = {Elsevier {BV}},
    }
  • [DOI] A. N. Aziz, V. M. Corman, A. K. C. Echterhoff, M. A. Müller, A. Richter, A. Schmandke, M. L. Schmidt, T. H. Schmidt, F. M. de Vries, C. Drosten, and M. M. B. Breteler, “Seroprevalence and correlates of SARS-CoV-2 neutralizing antibodies from a population-based study in Bonn, Germany,” Nat Commun, vol. 12, iss. 1, 2021.
    [Bibtex]
    @Article{Aziz:21,
    author = {N. Ahmad Aziz and Victor M. Corman and Antje K. C. Echterhoff and Marcel A. Müller and Anja Richter and Antonio Schmandke and Marie Luisa Schmidt and Thomas H. Schmidt and Folgerdiena M. de Vries and Christian Drosten and Monique M. B. Breteler},
    journal = {{Nat Commun}},
    title = {Seroprevalence and correlates of {SARS}-{CoV}-2 neutralizing antibodies from a population-based study in {B}onn, {G}ermany},
    year = {2021},
    number = {1},
    volume = {12},
    doi = {10.1038/s41467-021-22351-5},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] S. L. Hong, P. Lemey, M. A. Suchard, and G. Baele, “Bayesian phylogeographic analysis incorporating predictors and individual travel histories in BEAST,” Current protocols, vol. 1, iss. 4, 2021.
    [Bibtex]
    @Article{Hong:21,
    author = {Samuel L. Hong and Philippe Lemey and Marc A. Suchard and Guy Baele},
    journal = {Current Protocols},
    title = {Bayesian Phylogeographic Analysis Incorporating Predictors and Individual Travel Histories in {BEAST}},
    year = {2021},
    number = {4},
    volume = {1},
    doi = {10.1002/cpz1.98},
    publisher = {Wiley},
    }
  • [DOI] T. Schwarz, K. Heiss, Y. Mahendran, F. Casilag, F. Kurth, L. E. Sander, C. Wendtner, M. A. Hoechstetter, M. A. Müller, R. Sekul, C. Drosten, V. Stadler, and V. M. Corman, “SARS-CoV-2 proteome-wide analysis revealed significant epitope signatures in COVID-19 patients,” Front Immunol, vol. 12, 2021.
    [Bibtex]
    @Article{Schwarz:21,
    author = {Tatjana Schwarz and Kirsten Heiss and Yuvaraj Mahendran and Fiordiligie Casilag and Florian Kurth and Leif E. Sander and Clemens-Martin Wendtner and Manuela A. Hoechstetter and Marcel A. Müller and Renate Sekul and Christian Drosten and Volker Stadler and Victor M. Corman},
    journal = {{Front Immunol}},
    title = {{SARS}-{CoV}-2 Proteome-Wide Analysis Revealed Significant Epitope Signatures in {COVID}-19 Patients},
    year = {2021},
    volume = {12},
    doi = {10.3389/fimmu.2021.629185},
    publisher = {Frontiers Media {SA}},
    }
  • [DOI] J. J. C. de Vries, J. R. Brown, N. Couto, M. Beer, P. L. Mercier, I. Sidorov, A. Papa, N. Fischer, B. O. B. Munnink, C. Rodriquez, M. Zaheri, A. Sayiner, M. Hönemann, A. Pérez-Cataluña, E. C. Carbo, C. Bachofen, J. Kubacki, D. Schmitz, K. Tsioka, S. Matamoros, D. Höper, M. Hernandez, E. Puchhammer-Stöckl, A. Lebrand, M. Huber, P. Simmonds, E. C. J. Claas, and X. F. López-Labrador, “Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting,” J Clin Virol, vol. 138, p. 104812, 2021.
    [Bibtex]
    @Article{Vries:21,
    author = {Jutte J.C. de Vries and Julianne R. Brown and Natacha Couto and Martin Beer and Philippe Le Mercier and Igor Sidorov and Anna Papa and Nicole Fischer and Bas B. Oude Munnink and Christophe Rodriquez and Maryam Zaheri and Arzu Sayiner and Mario Hönemann and Alba Pérez-Cataluña and Ellen C. Carbo and Claudia Bachofen and Jakub Kubacki and Dennis Schmitz and Katerina Tsioka and S{\'{e}}bastien Matamoros and Dirk Höper and Marta Hernandez and Elisabeth Puchhammer-Stöckl and Aitana Lebrand and Michael Huber and Peter Simmonds and Eric C.J. Claas and F. Xavier L{\'{o}}pez-Labrador},
    journal = {{J Clin Virol}},
    title = {Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part {II}: bioinformatic analysis and reporting},
    year = {2021},
    pages = {104812},
    volume = {138},
    doi = {10.1016/j.jcv.2021.104812},
    publisher = {Elsevier {BV}},
    }
  • [DOI] N. R. Faria, T. A. Mellan, C. Whittaker, I. M. Claro, D. S. da Candido, S. Mishra, M. A. E. Crispim, F. C. S. Sales, I. Hawryluk, J. T. McCrone, R. J. G. Hulswit, L. A. M. Franco, M. S. Ramundo, J. G. de Jesus, P. S. Andrade, T. M. Coletti, G. M. Ferreira, C. A. M. Silva, E. R. Manuli, R. H. M. Pereira, P. S. Peixoto, M. U. G. Kraemer, N. Gaburo, C. C. da Camilo, H. Hoeltgebaum, W. M. Souza, E. C. Rocha, L. M. de Souza, M. C. de Pinho, L. J. T. Araujo, F. S. V. Malta, A. B. de Lima, J. P. do Silva, D. A. G. Zauli, A. C. S. de Ferreira, R. P. Schnekenberg, D. J. Laydon, P. G. T. Walker, H. M. Schlüter, A. L. P. dos Santos, M. S. Vidal, V. D. S. Caro, R. M. F. Filho, H. M. dos Santos, R. S. Aguiar, J. L. Proença-Modena, B. Nelson, J. A. Hay, M. Monod, X. Miscouridou, H. Coupland, R. Sonabend, M. Vollmer, A. Gandy, C. A. Prete, V. H. Nascimento, M. A. Suchard, T. A. Bowden, S. L. K. Pond, C. Wu, O. Ratmann, N. M. Ferguson, C. Dye, N. J. Loman, P. Lemey, A. Rambaut, N. A. Fraiji, M. P. S. S. do Carvalho, O. G. Pybus, S. Flaxman, S. Bhatt, and E. C. Sabino, “Genomics and epidemiology of the p.1 SARS-CoV-2 lineage in Manaus, Brazil,” Science, p. eabh2644, 2021.
    [Bibtex]
    @Article{Faria:21,
    author = {Nuno R. Faria and Thomas A. Mellan and Charles Whittaker and Ingra M. Claro and Darlan da S. Candido and Swapnil Mishra and Myuki A. E. Crispim and Flavia C. S. Sales and Iwona Hawryluk and John T. McCrone and Ruben J. G. Hulswit and Lucas A. M. Franco and Mariana S. Ramundo and Jaqueline G. de Jesus and Pamela S. Andrade and Thais M. Coletti and Giulia M. Ferreira and Camila A. M. Silva and Erika R. Manuli and Rafael H. M. Pereira and Pedro S. Peixoto and Moritz U. G. Kraemer and Nelson Gaburo and Cecilia da C. Camilo and Henrique Hoeltgebaum and William M. Souza and Esmenia C. Rocha and Leandro M. de Souza and Mariana C. de Pinho and Leonardo J. T Araujo and Frederico S. V. Malta and Aline B. de Lima and Joice do P. Silva and Danielle A. G. Zauli and Alessandro C. de S. Ferreira and Ricardo P Schnekenberg and Daniel J. Laydon and Patrick G. T. Walker and Hannah M. Schlüter and Ana L. P. dos Santos and Maria S. Vidal and Valentina S. Del Caro and Rosinaldo M. F. Filho and Helem M. dos Santos and Renato S. Aguiar and Jos{\'{e}} L. Proen{\c{c}}a-Modena and Bruce Nelson and James A. Hay and M{\'{e}}lodie Monod and Xenia Miscouridou and Helen Coupland and Raphael Sonabend and Michaela Vollmer and Axel Gandy and Carlos A. Prete and Vitor H. Nascimento and Marc A. Suchard and Thomas A. Bowden and Sergei L. K. Pond and Chieh-Hsi Wu and Oliver Ratmann and Neil M. Ferguson and Christopher Dye and Nick J. Loman and Philippe Lemey and Andrew Rambaut and Nelson A. Fraiji and Maria do P. S. S. Carvalho and Oliver G. Pybus and Seth Flaxman and Samir Bhatt and Ester C. Sabino},
    journal = {Science},
    title = {Genomics and epidemiology of the P.1 {SARS}-{CoV}-2 lineage in {M}anaus, {B}razil},
    year = {2021},
    pages = {eabh2644},
    doi = {10.1126/science.abh2644},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
  • [DOI] O. Zablocki, M. Michelsen, M. Burris, N. Solonenko, J. Warwick-Dugdale, R. Ghosh, J. Pett-Ridge, M. B. Sullivan, and B. Temperton, “VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature,” PeerJ, vol. 9, p. e11088, 2021.
    [Bibtex]
    @Article{Zablocki:21,
    author = {Olivier Zablocki and Michelle Michelsen and Marie Burris and Natalie Solonenko and Joanna Warwick-Dugdale and Romik Ghosh and Jennifer Pett-Ridge and Matthew B. Sullivan and Ben Temperton},
    journal = {{PeerJ}},
    title = {{VirION}2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature},
    year = {2021},
    pages = {e11088},
    volume = {9},
    doi = {10.7717/peerj.11088},
    publisher = {{PeerJ}},
    }
  • [DOI] A. Steiner, M. Pletz, B. Löffler, and M. Baier, “A novel SARS-CoV-2 IgG line-blot for evaluating discrepant IgG test results – observations in pre-pandemic and follow-up samples of five patients,” Journal of microbiology, immunology and infection, 2021.
    [Bibtex]
    @Article{Steiner:21,
    author = {Andrea Steiner and Mathias Pletz and Bettina Löffler and Michael Baier},
    journal = {Journal of Microbiology, Immunology and Infection},
    title = {A novel {SARS}-{CoV}-2 {IgG} line-blot for evaluating discrepant {IgG} test results {\textendash} Observations in pre-pandemic and follow-up samples of five patients},
    year = {2021},
    doi = {10.1016/j.jmii.2021.03.004},
    publisher = {Elsevier {BV}},
    }
  • [DOI] V. M. Corman, V. C. Haage, T. Bleicker, M. L. Schmidt, B. Mühlemann, M. Zuchowski, W. K. Jo, P. Tscheak, E. Möncke-Buchner, M. A. Müller, A. Krumbholz, J. F. Drexler, and C. Drosten, “Comparison of seven commercial SARS-CoV-2 rapid point-of-care antigen tests: a single-centre laboratory evaluation study,” Lancet Microbe, 2021.
    [Bibtex]
    @Article{Corman:21,
    author = {Victor M Corman and Verena Claudia Haage and Tobias Bleicker and Marie Luisa Schmidt and Barbara Mühlemann and Marta Zuchowski and Wendy K Jo and Patricia Tscheak and Elisabeth Möncke-Buchner and Marcel A Müller and Andi Krumbholz and Jan Felix Drexler and Christian Drosten},
    journal = {{Lancet Microbe}},
    title = {Comparison of seven commercial {SARS}-{CoV}-2 rapid point-of-care antigen tests: a single-centre laboratory evaluation study},
    year = {2021},
    doi = {10.1016/s2666-5247(21)00056-2},
    publisher = {Elsevier {BV}},
    }
  • [DOI] A. Stukalov, V. Girault, V. Grass, O. Karayel, V. Bergant, C. Urban, D. A. Haas, Y. Huang, L. Oubraham, A. Wang, S. M. Hamad, A. Piras, F. M. Hansen, M. C. Tanzer, I. Paron, L. Zinzula, T. Enghleitner, M. Reinecke, T. M. Lavacca, R. Ehmann, R. Wölfel, J. Jores, B. Kuster, U. Protzer, R. Rad, J. Ziebuhr, V. Thiel, P. Scaturro, M. Mann, and A. Pichlmair, “Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV,” Nature, 2021.
    [Bibtex]
    @Article{Stukalov:21,
    author = {Alexey Stukalov and Virginie Girault and Vincent Grass and Ozge Karayel and Valter Bergant and Christian Urban and Darya A. Haas and Yiqi Huang and Lila Oubraham and Anqi Wang and M. Sabri Hamad and Antonio Piras and Fynn M. Hansen and Maria C. Tanzer and Igor Paron and Luca Zinzula and Thomas Enghleitner and Maria Reinecke and Teresa M. Lavacca and Rosina Ehmann and Roman Wölfel and Jörg Jores and Bernhard Kuster and Ulrike Protzer and Roland Rad and John Ziebuhr and Volker Thiel and Pietro Scaturro and Matthias Mann and Andreas Pichlmair},
    journal = {Nature},
    title = {Multilevel proteomics reveals host perturbations by {SARS}-{CoV}-2 and {SARS}-{CoV}},
    year = {2021},
    doi = {10.1038/s41586-021-03493-4},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] I. Wagenhäuser, K. Knies, V. Rauschenberger, M. Eisenmann, M. McDonogh, N. Petri, O. Andres, S. Flemming, M. Gawlik, M. Papsdorf, R. Taurines, H. Böhm, J. Forster, D. Weismann, B. Weißbrich, L. Dölken, J. Liese, O. Kurzai, U. Vogel, and M. Krone, “Clinical performance evaluation of SARS-CoV-2 rapid antigen testing in point of care usage in comparison to RT-qPCR,” medRxiv, 2021.
    [Bibtex]
    @Article{Wagenhaeuser:21,
    author = {Isabell Wagenhäuser and Kerstin Knies and Vera Rauschenberger and Michael Eisenmann and Miriam McDonogh and Nils Petri and Oliver Andres and Sven Flemming and Micha Gawlik and Michael Papsdorf and Regina Taurines and Hartmut Böhm and Johannes Forster and Dirk Weismann and Benedikt Wei{\ss}brich and Lars Dölken and Johannes Liese and Oliver Kurzai and Ulrich Vogel and Manuel Krone},
    journal = {{medRxiv}},
    title = {Clinical performance evaluation of {SARS}-{CoV}-2 rapid antigen testing in point of care usage in comparison to {RT}-{qPCR}},
    year = {2021},
    doi = {10.1101/2021.03.27.21253966},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] B. Sposito, A. Broggi, L. Pandolfi, S. Crotta, R. Ferrarese, S. Sisti, N. Clementi, A. Ambrosi, E. Liu, V. Frangipane, L. Saracino, L. Marongiu, F. A. Facchini, A. Bottazzi, T. Fossali, R. Colombo, M. Clementi, E. Tagliabue, A. E. Pontiroli, F. Meloni, A. Wack, N. Mancini, and I. Zanoni, “Severity of SARS-CoV-2 infection as a function of the interferon landscape across the respiratory tract of COVID-19 patients,” bioRxiv, 2021.
    [Bibtex]
    @Article{Sposito:21,
    author = {Benedetta Sposito and Achille Broggi and Laura Pandolfi and Stefania Crotta and Roberto Ferrarese and Sofia Sisti and Nicola Clementi and Alessandro Ambrosi and Enju Liu and Vanessa Frangipane and Laura Saracino and Laura Marongiu and Fabio A Facchini and Andrea Bottazzi and Tommaso Fossali and Riccardo Colombo and Massimo Clementi and Elena Tagliabue and Antonio E Pontiroli and Federica Meloni and Andreas Wack and Nicasio Mancini and Ivan Zanoni},
    journal = {{bioRxiv}},
    title = {Severity of {SARS}-{CoV}-2 infection as a function of the interferon landscape across the respiratory tract of {COVID}-19 patients},
    year = {2021},
    doi = {10.1101/2021.03.30.437173},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] L. Loyal, J. Braun, L. Henze, B. Kruse, M. Dingeldey, U. Reimer, F. Kern, T. Schwarz, M. Mangold, C. Unger, F. Dörfler, S. Kadler, J. Rosowski, K. Gürcan, Z. Uyar-Aydin, M. Frentsch, F. Kurth, K. Schnatbaum, M. Eckey, S. Hippenstiel, A. Hocke, M. A. Müller, B. Sawitzki, S. Miltenyi, F. Paul, M. A. Mall, H. Wenschuh, S. Voigt, C. Drosten, R. Lauster, N. Lachman, L. Sander, V. M. Corman, J. Röhmel, L. Meyer-Arndt, A. Thiel, and C. G. and, “Cross-reactive CD4+ t cells enhance SARS-CoV-2 immune responses upon infection and vaccination,” medRxiv, 2021.
    [Bibtex]
    @Article{Loyal:21,
    author = {Lucie Loyal and Julian Braun and Larissa Henze and Beate Kruse and Manuela Dingeldey and Ulf Reimer and Florian Kern and Tatjana Schwarz and Maike Mangold and Clara Unger and Friederike Dörfler and Shirin Kadler and Jennifer Rosowski and Kübrah Gürcan and Zehra Uyar-Aydin and Marco Frentsch and Florian Kurth and Karsten Schnatbaum and Maren Eckey and Stefan Hippenstiel and Andreas Hocke and Marcel A. Müller and Birgit Sawitzki and Stefan Miltenyi and Friedemann Paul and Marcus A. Mall and Holger Wenschuh and Sebastian Voigt and Christian Drosten and Roland Lauster and Nils Lachman and Leif-Erik Sander and Victor M. Corman and Jobst Röhmel and Lil Meyer-Arndt and Andreas Thiel and Claudia Giesecke-Thiel and},
    journal = {{medRxiv}},
    title = {Cross-reactive {CD}4+ T cells enhance {SARS}-{CoV}-2 immune responses upon infection and vaccination},
    year = {2021},
    doi = {10.1101/2021.04.01.21252379},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] E. Cuevas-Ferrando, W. Randazzo, A. Pérez-Cataluña, I. Falcó, D. Navarro, S. Martin-Latin, A. Díaz-Reolid, I. Girón-Guzmán, A. Allende, and G. Sánchez, “Viability RT-PCR for SARS-CoV-2: a step forward to solve the infectivity quandary,” medRxiv, 2021.
    [Bibtex]
    @Article{CuevasFerrando:21,
    author = {Enric Cuevas-Ferrando and Walter Randazzo and Alba Pérez-Cataluña and Irene Falc{\'{o}} and David Navarro and Sandra Martin-Latin and Azahara D{\'{\i}}az-Reolid and In{\'{e}}s Gir{\'{o}}n-Guzm{\'{a}}n and Ana Allende and Gloria S{\'{a}}nchez},
    journal = {{medRxiv}},
    title = {Viability {RT}-{PCR} for {SARS}-{CoV}-2: a step forward to solve the infectivity quandary},
    year = {2021},
    doi = {10.1101/2021.03.22.21253818},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. Cotten, D. L. Robertson, and M. V. T. Phan, “Unique protein features of SARS-CoV-2 relative to other Sarbecoviruses,” bioRxiv, 2021.
    [Bibtex]
    @Article{Cotten:21,
    author = {Matthew Cotten and David L. Robertson and My V.T. Phan},
    journal = {{bioRxiv}},
    title = {Unique protein features of {SARS}-{CoV}-2 relative to other {S}arbecoviruses},
    year = {2021},
    doi = {10.1101/2021.04.06.438675},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] N. Zuckerman, S. Fleishon, E. Bucris, D. Bar-Ilan, M. Linial, I. Bar-Or, V. Indenbaum, M. Weil, E. Mendelson, M. Mandelboim, and O. M. and, “A unique SARS-CoV-2 spike protein P681H strain detected in Israel,” medRxiv, 2021.
    [Bibtex]
    @Article{Zuckerman:21,
    author = {Neta Zuckerman and Shay Fleishon and Efrat Bucris and Dana Bar-Ilan and Michal Linial and Itay Bar-Or and Victoria Indenbaum and Merav Weil and Ella Mendelson and Michal Mandelboim and Orna Mor and},
    journal = {{medRxiv}},
    title = {A unique {SARS}-{CoV}-2 spike protein {P681H} strain detected in {I}srael},
    year = {2021},
    doi = {10.1101/2021.03.25.21253908},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] D. Todt, T. L. Meister, B. Tamele, J. Howes, D. Paulmann, B. Becker, F. H. Brill, M. Wind, J. Schijven, B. Mhlekude, C. Goffinet, A. Krawczyk, J. Steinmann, S. Pfaender, Y. Brüggemann, and E. Steinmann, “A realistic touch-transfer method reveals low risk of transmission for SARS-CoV-2 by contaminated coins and bank notes,” bioRxiv, 2021.
    [Bibtex]
    @Article{Todt:21,
    author = {Daniel Todt and Toni Luise Meister and Barbora Tamele and John Howes and Dajana Paulmann and Britta Becker and Florian H. Brill and Mark Wind and Jack Schijven and Baxolele Mhlekude and Christine Goffinet and Adalbert Krawczyk and Jörg Steinmann and Stephanie Pfaender and Yannick Brüggemann and Eike Steinmann},
    journal = {{bioRxiv}},
    title = {A realistic touch-transfer method reveals low risk of transmission for {SARS}-{CoV}-2 by contaminated coins and bank notes},
    year = {2021},
    doi = {10.1101/2021.04.02.438182},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. Huber, P. W. Schreiber, T. Scheier, A. Audigé, R. Buonomano, A. Rudiger, D. L. Braun, G. Eich, D. I. Keller, B. Hasse, J. Böni, C. Berger, H. F. Günthard, A. Manrique, and A. Trkola, “High efficacy of saliva in detecting SARS-CoV-2 by RT-PCR in adults and children,” Microorganisms, vol. 9, iss. 3, p. 642, 2021.
    [Bibtex]
    @Article{Huber:21,
    author = {Michael Huber and Peter Werner Schreiber and Thomas Scheier and Annette Audig{\'{e}} and Roberto Buonomano and Alain Rudiger and Dominique L. Braun and Gerhard Eich and Dagmar I. Keller and Barbara Hasse and Jürg Böni and Christoph Berger and Huldrych F. Günthard and Amapola Manrique and Alexandra Trkola},
    journal = {Microorganisms},
    title = {High Efficacy of Saliva in Detecting {SARS}-{CoV}-2 by {RT}-{PCR} in Adults and Children},
    year = {2021},
    number = {3},
    pages = {642},
    volume = {9},
    doi = {10.3390/microorganisms9030642},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] G. Taroncher-Oldenburg, C. Müller, W. Obermann, J. Ziebuhr, R. K. Hartmann, and A. Grünweller, “Targeting the DEAD-box RNA helicase eIF4a with rocaglates—a pan-antiviral strategy for minimizing the impact of future RNA virus pandemics,” Microorganisms, vol. 9, iss. 3, p. 540, 2021.
    [Bibtex]
    @Article{TaroncherOldenburg:21,
    author = {Gaspar Taroncher-Oldenburg and Christin Müller and Wiebke Obermann and John Ziebuhr and Roland K. Hartmann and Arnold Grünweller},
    journal = {Microorganisms},
    title = {Targeting the {DEAD}-Box {RNA} Helicase {eIF}4A with Rocaglates{\textemdash}A Pan-Antiviral Strategy for Minimizing the Impact of Future {RNA} Virus Pandemics},
    year = {2021},
    number = {3},
    pages = {540},
    volume = {9},
    doi = {10.3390/microorganisms9030540},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] C. Liang, E. Bencurova, E. Psota, P. Neurgaonkar, M. Prelog, C. Scheller, and T. Dandekar, “Population-predicted MHC class II epitope presentation of SARS-CoV-2 structural proteins correlates to the case fatality rates of COVID-19 in different countries,” Int J Mol Sci, vol. 22, iss. 5, p. 2630, 2021.
    [Bibtex]
    @Article{Liang:21,
    author = {Chunguang Liang and Elena Bencurova and Eric Psota and Priya Neurgaonkar and Martina Prelog and Carsten Scheller and Thomas Dandekar},
    journal = {{Int J Mol Sci}},
    title = {Population-Predicted {MHC} Class {II} Epitope Presentation of {SARS}-{CoV}-2 Structural Proteins Correlates to the Case Fatality Rates of {COVID}-19 in Different Countries},
    year = {2021},
    number = {5},
    pages = {2630},
    volume = {22},
    doi = {10.3390/ijms22052630},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] L. M. Zaeck, D. Scheibner, J. Sehl, M. Müller, D. Hoffmann, M. Beer, E. M. Abdelwhab, T. C. Mettenleiter, A. Breithaupt, and S. Finke, “Light sheet microscopy-assisted 3d analysis of SARS-CoV-2 infection in the respiratory tract of the ferret model,” Viruses, vol. 13, iss. 3, p. 529, 2021.
    [Bibtex]
    @Article{Zaeck:21,
    author = {Luca M. Zaeck and David Scheibner and Julia Sehl and Martin Müller and Donata Hoffmann and Martin Beer and Elsayed M. Abdelwhab and Thomas C. Mettenleiter and Angele Breithaupt and Stefan Finke},
    journal = {Viruses},
    title = {Light Sheet Microscopy-Assisted 3D Analysis of {SARS}-{CoV}-2 Infection in the Respiratory Tract of the Ferret Model},
    year = {2021},
    number = {3},
    pages = {529},
    volume = {13},
    doi = {10.3390/v13030529},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] A. R. G. Cabecinhas, T. Roloff, M. Stange, C. Bertelli, M. Huber, A. Ramette, C. Chen, S. Nadeau, Y. Gerth, S. Yerly, O. Opota, T. Pillonel, T. Schuster, C. M. J. A. Metzger, J. Sieber, M. Bel, N. Wohlwend, C. Baumann, M. C. Koch, P. Bittel, K. Leuzinger, M. Brunner, F. Suter-Riniker, L. Berlinger, K. K. S. o, C. Beckmann, C. Noppen, M. Redondo, I. Steffen, H. M. B. Seth-Smith, A. Mari, R. Lienhard, M. Risch, O. Nolte, I. Eckerle, G. M. Lucchini, E. B. Hodcroft, R. A. Neher, T. Stadler, H. H. Hirsch, S. L. Leib, L. Risch, L. Kaiser, A. Trkola, G. Greub, and A. Egli, “SARS-CoV-2 n501y introductions and transmissions in switzerland from beginning of october 2020 to february 2021—implementation of swiss-wide diagnostic screening and whole genome sequencing,” Microorganisms, vol. 9, iss. 4, p. 677, 2021.
    [Bibtex]
    @Article{Cabecinhas:21,
    author = {Ana Rita Goncalves Cabecinhas and Tim Roloff and Madlen Stange and Claire Bertelli and Michael Huber and Alban Ramette and Chaoran Chen and Sarah Nadeau and Yannick Gerth and Sabine Yerly and Onya Opota and Trestan Pillonel and Tobias Schuster and Cesar M. J. A. Metzger and Jonas Sieber and Michael Bel and Nadia Wohlwend and Christian Baumann and Michel C. Koch and Pascal Bittel and Karoline Leuzinger and Myrta Brunner and Franziska Suter-Riniker and Livia Berlinger and Kirstine K. S{\o}gaard and Christiane Beckmann and Christoph Noppen and Maurice Redondo and Ingrid Steffen and Helena M. B. Seth-Smith and Alfredo Mari and Reto Lienhard and Martin Risch and Oliver Nolte and Isabella Eckerle and Gladys Martinetti Lucchini and Emma B. Hodcroft and Richard A. Neher and Tanja Stadler and Hans H. Hirsch and Stephen L. Leib and Lorenz Risch and Laurent Kaiser and Alexandra Trkola and Gilbert Greub and Adrian Egli},
    journal = {Microorganisms},
    title = {{SARS}-{CoV}-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021{\textemdash}Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing},
    year = {2021},
    number = {4},
    pages = {677},
    volume = {9},
    doi = {10.3390/microorganisms9040677},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] K. Fink, A. Nitsche, M. Neumann, M. Grossegesse, K. Eisele, and W. Danysz, “Amantadine inhibits SARS-CoV-2 in vitro,” Viruses, vol. 13, iss. 4, p. 539, 2021.
    [Bibtex]
    @Article{Fink:21,
    author = {Klaus Fink and Andreas Nitsche and Markus Neumann and Marica Grossegesse and Karl-Heinz Eisele and Wojciech Danysz},
    journal = {Viruses},
    title = {Amantadine Inhibits {SARS}-{CoV}-2 In Vitro},
    year = {2021},
    number = {4},
    pages = {539},
    volume = {13},
    doi = {10.3390/v13040539},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] R. Velázquez-Moctezuma, E. H. Augestad, M. Castelli, C. H. Olesen, N. Clementi, M. Clementi, N. Mancini, and J. Prentoe, “Mechanisms of hepatitis C virus escape from vaccine-relevant neutralizing antibodies,” Vaccines, vol. 9, iss. 3, p. 291, 2021.
    [Bibtex]
    @Article{VelazquezMoctezuma:21,
    author = {Rodrigo Vel{\'{a}}zquez-Moctezuma and Elias H. Augestad and Matteo Castelli and Christina Holmboe Olesen and Nicola Clementi and Massimo Clementi and Nicasio Mancini and Jannick Prentoe},
    journal = {Vaccines},
    title = {Mechanisms of Hepatitis {C} Virus Escape from Vaccine-Relevant Neutralizing Antibodies},
    year = {2021},
    number = {3},
    pages = {291},
    volume = {9},
    doi = {10.3390/vaccines9030291},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] R. H. J. Lorenzo, D. Cadar, F. R. Koundouno, J. Juste, A. Bialonski, H. Baum, J. L. García-Mudarra, H. Hakamaki, A. Bencsik, E. V. Nelson, M. W. Carroll, N. Magassouba, S. Günther, J. Schmidt-Chanasit, C. M. Fontela, and B. Escudero-Pérez, “Metagenomic snapshots of viral components in guinean bats,” Microorganisms, vol. 9, iss. 3, p. 599, 2021.
    [Bibtex]
    @Article{Lorenzo:21,
    author = {Roberto J. Hermida Lorenzo and D{\'{a}}niel Cadar and Fara Raymond Koundouno and Javier Juste and Alexandra Bialonski and Heike Baum and Juan Luis Garc{\'{\i}}a-Mudarra and Henry Hakamaki and Andr{\'{a}}s Bencsik and Emily V. Nelson and Miles W. Carroll and N'Faly Magassouba and Stephan Günther and Jonas Schmidt-Chanasit and C{\'{e}}sar Mu{\~{n}}oz Fontela and Beatriz Escudero-P{\'{e}}rez},
    journal = {Microorganisms},
    title = {Metagenomic Snapshots of Viral Components in Guinean Bats},
    year = {2021},
    number = {3},
    pages = {599},
    volume = {9},
    doi = {10.3390/microorganisms9030599},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] D. Turner, A. M. Kropinski, and E. M. Adriaenssens, “A roadmap for genome-based phage taxonomy,” Viruses, vol. 13, iss. 3, p. 506, 2021.
    [Bibtex]
    @Article{Turner:21,
    author = {Dann Turner and Andrew M. Kropinski and Evelien M. Adriaenssens},
    journal = {Viruses},
    title = {A Roadmap for Genome-Based Phage Taxonomy},
    year = {2021},
    number = {3},
    pages = {506},
    volume = {13},
    doi = {10.3390/v13030506},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] M. Bousali, A. Dimadi, E. Kostaki, S. Tsiodras, G. K. Nikolopoulos, D. N. Sgouras, G. Magiorkinis, G. Papatheodoridis, V. Pogka, G. Lourida, A. Argyraki, E. Angelakis, G. Sourvinos, A. Beloukas, D. Paraskevis, and T. Karamitros, “SARS-CoV-2 molecular transmission clusters and containment measures in ten european regions during the first pandemic wave,” Life, vol. 11, iss. 3, p. 219, 2021.
    [Bibtex]
    @Article{Bousali:21,
    author = {Maria Bousali and Aristea Dimadi and Evangelia-Georgia Kostaki and Sotirios Tsiodras and Georgios K. Nikolopoulos and Dionyssios N. Sgouras and Gkikas Magiorkinis and George Papatheodoridis and Vasiliki Pogka and Giota Lourida and Aikaterini Argyraki and Emmanouil Angelakis and George Sourvinos and Apostolos Beloukas and Dimitrios Paraskevis and Timokratis Karamitros},
    journal = {Life},
    title = {{SARS}-{CoV}-2 Molecular Transmission Clusters and Containment Measures in Ten European Regions during the First Pandemic Wave},
    year = {2021},
    number = {3},
    pages = {219},
    volume = {11},
    doi = {10.3390/life11030219},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] O. E. Tsitsilonis, D. Paraskevis, E. Lianidou, E. Terpos, A. Akalestos, V. Pierros, E. G. Kostaki, E. Kastritis, P. Moutsatsou, M. Politou, A. Scorilas, T. Sphicopoulos, N. Thomaidis, I. P. Trougakos, A. Tsakris, N. Voulgaris, C. C. Daskalaki, Z. Evangelakou, C. Fouki, D. D. Gianniou, S. Gumeni, I. V. Kostopoulos, M. S. Manola, N. Orologas-Stavrou, C. Panteli, E. Papanagnou, P. Rousakis, A. D. Sklirou, S. Smilkou, D. Stergiopoulou, S. Tsiodras, M. Dimopoulos, and P. P. Sfikakis, “SARS-CoV-2 infection is asymptomatic in nearly half of adults with robust anti-spike protein receptor-binding domain antibody response,” Vaccines, vol. 9, iss. 3, p. 207, 2021.
    [Bibtex]
    @Article{Tsitsilonis:21,
    author = {Ourania E. Tsitsilonis and Dimitrios Paraskevis and Evi Lianidou and Evangelos Terpos and Athanasios Akalestos and Vassilios Pierros and Evangelia Georgia Kostaki and Efstathios Kastritis and Paraskevi Moutsatsou and Marianna Politou and Andreas Scorilas and Thomas Sphicopoulos and Nikolaos Thomaidis and Ioannis P. Trougakos and Athanassios Tsakris and Nikolaos Voulgaris and Christina C. Daskalaki and Zoi Evangelakou and Christina Fouki and Despoina D. Gianniou and Sentiljana Gumeni and Ioannis V. Kostopoulos and Maria S. Manola and Nikolaos Orologas-Stavrou and Chrysanthi Panteli and Eleni-Dimitra Papanagnou and Pantelis Rousakis and Aimilia D. Sklirou and Stavroula Smilkou and Dimitra Stergiopoulou and Sotirios Tsiodras and Meletios-Athanasios Dimopoulos and Petros P. Sfikakis},
    journal = {Vaccines},
    title = {{SARS}-{CoV}-2 Infection Is Asymptomatic in Nearly Half of Adults with Robust Anti-Spike Protein Receptor-Binding Domain Antibody Response},
    year = {2021},
    number = {3},
    pages = {207},
    volume = {9},
    doi = {10.3390/vaccines9030207},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] C. Kohl, A. Brinkmann, A. Radonić, P. W. Dabrowski, K. Mühldorfer, A. Nitsche, G. Wibbelt, and A. Kurth, “The virome of German bats: comparing virus discovery approaches,” Sci Rep, vol. 11, iss. 1, 2021.
    [Bibtex]
    @Article{Kohl:21,
    author = {Claudia Kohl and Annika Brinkmann and Aleksandar Radoni{\'{c}} and Piotr Wojtek Dabrowski and Kristin Mühldorfer and Andreas Nitsche and Gudrun Wibbelt and Andreas Kurth},
    journal = {{Sci Rep}},
    title = {The virome of {G}erman bats: comparing virus discovery approaches},
    year = {2021},
    number = {1},
    volume = {11},
    doi = {10.1038/s41598-021-86435-4},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] A. Berger, M. T. N. Nsoga, F. J. Perez-Rodriguez, Y. A. Aad, P. Sattonnet-Roche, A. Gayet-Ageron, C. Jaksic, G. Torriani, E. Boehm, I. Kronig, J. A. Sacks, M. de Vos, F. J. Bausch, F. Chappuis, A. Renzoni, L. Kaiser, M. Schibler, and I. Eckerle, “Diagnostic accuracy of two commercial SARS-CoV-2 antigen-detecting rapid tests at the point of care in community-based testing centers,” PLoS One, vol. 16, iss. 3, p. e0248921, 2021.
    [Bibtex]
    @Article{Berger:21,
    author = {Alice Berger and Marie Therese Ngo Nsoga and Francisco Javier Perez-Rodriguez and Yasmine Abi Aad and Pascale Sattonnet-Roche and Ang{\`{e}}le Gayet-Ageron and Cyril Jaksic and Giulia Torriani and Erik Boehm and Ilona Kronig and Jilian A. Sacks and Margaretha de Vos and Fr{\'{e}}d{\'{e}}rique Jacquerioz Bausch and Fran{\c{c}}ois Chappuis and Adriana Renzoni and Laurent Kaiser and Manuel Schibler and Isabella Eckerle},
    journal = {{PLoS One}},
    title = {Diagnostic accuracy of two commercial {SARS}-{CoV}-2 antigen-detecting rapid tests at the point of care in community-based testing centers},
    year = {2021},
    number = {3},
    pages = {e0248921},
    volume = {16},
    doi = {10.1371/journal.pone.0248921},
    editor = {Nei-yuan Hsiao},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] S. Deinhardt-Emmer, D. Wittschieber, J. Sanft, S. Kleemann, S. Elschner, K. F. Haupt, V. Vau, C. Häring, J. Rödel, A. Henke, C. Ehrhardt, M. Bauer, M. Philipp, N. Gaßler, S. Nietzsche, B. Löffler, and G. Mall, “Early postmortem mapping of SARS-CoV-2 RNA in patients with COVID-19 and the correlation with tissue damage,” eLife, vol. 10, 2021.
    [Bibtex]
    @Article{DeinhardtEmmer:21a,
    author = {Stefanie Deinhardt-Emmer and Daniel Wittschieber and Juliane Sanft and Sandra Kleemann and Stefan Elschner and Karoline Frieda Haupt and Vanessa Vau and Clio Häring and Jürgen Rödel and Andreas Henke and Christina Ehrhardt and Michael Bauer and Mike Philipp and Nikolaus Ga{\ss}ler and Sandor Nietzsche and Bettina Löffler and Gita Mall},
    journal = {{eLife}},
    title = {Early postmortem mapping of {SARS}-{CoV}-2 {RNA} in patients with {COVID}-19 and the correlation with tissue damage},
    year = {2021},
    volume = {10},
    doi = {10.7554/elife.60361},
    publisher = {{eLife} Sciences Publications, Ltd},
    }
  • [DOI] P. V’kovski, M. Gultom, J. N. Kelly, S. Steiner, J. Russeil, B. Mangeat, E. Cora, J. Pezoldt, M. Holwerda, A. Kratzel, L. Laloli, M. Wider, J. Portmann, T. Tran, N. Ebert, H. Stalder, R. Hartmann, V. Gardeux, D. Alpern, B. Deplancke, V. Thiel, and R. Dijkman, “Disparate temperature-dependent virus-host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epithelium.,” PLoS Biol, vol. 19, p. e3001158, 2021.
    [Bibtex]
    @Article{Vkovski:21,
    author = {V'kovski, Philip and Gultom, Mitra and Kelly, Jenna N. and Steiner, Silvio and Russeil, Julie and Mangeat, Bastien and Cora, Elisa and Pezoldt, Joern and Holwerda, Melle and Kratzel, Annika and Laloli, Laura and Wider, Manon and Portmann, Jasmine and Tran, Thao and Ebert, Nadine and Stalder, Hanspeter and Hartmann, Rune and Gardeux, Vincent and Alpern, Daniel and Deplancke, Bart and Thiel, Volker and Dijkman, Ronald},
    journal = {{PLoS Biol}},
    title = {Disparate temperature-dependent virus-host dynamics for {SARS-CoV-2} and {SARS-CoV} in the human respiratory epithelium.},
    year = {2021},
    pages = {e3001158},
    volume = {19},
    abstract = {Since its emergence in December 2019, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread globally and become a major public health burden. Despite its close phylogenetic relationship to SARS-CoV, SARS-CoV-2 exhibits increased human-to-human transmission dynamics, likely due to efficient early replication in the upper respiratory epithelium of infected individuals. Since different temperatures encountered in the human upper and lower respiratory tract (33°C and 37°C, respectively) have been shown to affect the replication kinetics of several respiratory viruses, as well as host innate immune response dynamics, we investigated the impact of temperature on SARS-CoV-2 and SARS-CoV infection using the primary human airway epithelial cell culture model. SARS-CoV-2, in contrast to SARS-CoV, replicated to higher titers when infections were performed at 33°C rather than 37°C. Although both viruses were highly sensitive to type I and type III interferon pretreatment, a detailed time-resolved transcriptome analysis revealed temperature-dependent interferon and pro-inflammatory responses induced by SARS-CoV-2 that were inversely proportional to its replication efficiency at 33°C or 37°C. These data provide crucial insight on pivotal virus-host interaction dynamics and are in line with characteristic clinical features of SARS-CoV-2 and SARS-CoV, as well as their respective transmission efficiencies.},
    doi = {10.1371/journal.pbio.3001158},
    issue = {3},
    pmid = {33780434},
    pubstate = {epublish},
    }
  • [DOI] C. Chen, S. Nadeau, I. Topolsky, M. Manceau, J. S. Huisman, K. P. Jablonski, L. Fuhrmann, D. Dreifuss, K. Jahn, C. Beckmann, M. Redondo, O. Kobel, C. Noppen, L. Risch, M. Risch, N. Wohlwend, S. Kas, T. Bodmer, T. Roloff, M. Stange, A. Egli, I. Eckerle, R. Denes, M. Feldkamp, I. Nissen, N. Santacroce, E. Burcklen, C. Aquino, A. C. de Gouvea, M. D. Moccia, S. Grüter, T. Sykes, L. Opitz, G. White, L. Neff, D. Popovic, A. Patrignani, J. Tracy, R. Schlapbach, E. T. Dermitzakis, K. Harshman, I. Xenarios, H. Pegeot, L. Cerutti, D. Penet, A. Blin, M. Elies, C. Althaus, C. Beisel, N. Beerenwinkel, M. Ackermann, and T. Stadler, “Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland,” medRxiv, 2021.
    [Bibtex]
    @Article{Chen:21,
    author = {Chaoran Chen and Sarah Nadeau and Ivan Topolsky and Marc Manceau and Jana S. Huisman and Kim Philipp Jablonski and Lara Fuhrmann and David Dreifuss and Katharina Jahn and Christiane Beckmann and Maurice Redondo and Olivier Kobel and Christoph Noppen and Lorenz Risch and Martin Risch and Nadia Wohlwend and Sinem Kas and Thomas Bodmer and Tim Roloff and Madlen Stange and Adrian Egli and Isabella Eckerle and Rebecca Denes and Mirjam Feldkamp and Ina Nissen and Natascha Santacroce and Elodie Burcklen and Catharine Aquino and Andreia Cabral de Gouvea and Maria Domenica Moccia and Simon Grüter and Timothy Sykes and Lennart Opitz and Griffin White and Laura Neff and Doris Popovic and Andrea Patrignani and Jay Tracy and Ralph Schlapbach and Emmanouil T. Dermitzakis and Keith Harshman and Ioannis Xenarios and Henri Pegeot and Lorenzo Cerutti and Deborah Penet and Anthony Blin and Melyssa Elies and Christian Althaus and Christian Beisel and Niko Beerenwinkel and Martin Ackermann and Tanja Stadler},
    journal = {{medRxiv}},
    title = {Quantification of the spread of {SARS}-{CoV}-2 variant {B}.1.1.7 in {S}witzerland},
    year = {2021},
    doi = {10.1101/2021.03.05.21252520},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] K. T. T. Kwok, M. M. T. de Rooij, A. B. Messink, I. M. Wouters, L. A. M. Smit, D. J. J. Heederik, M. P. G. Koopmans, and M. V. T. Phan, “Comparative viral metagenomics from chicken feces and farm dust in the Netherlands,” bioRxiv, 2021.
    [Bibtex]
    @Article{Kwok:21,
    author = {Kirsty T. T. Kwok and Myrna M. T. de Rooij and Aniek B. Messink and Inge M. Wouters and Lidwien A. M. Smit and Dick J.J. Heederik and Marion P. G. Koopmans and My V. T. Phan},
    journal = {{bioRxiv}},
    title = {Comparative viral metagenomics from chicken feces and farm dust in the {N}etherlands},
    year = {2021},
    doi = {10.1101/2021.03.09.434704},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] L. Van Espen, E. G. Bak, L. Beller, L. Close, W. Deboutte, H. Bæk. Juel, T. Nielsen, D. Sinar, L. D. Coninck, C. F. o, C. E. Fonvig, S. Jacobsen, M. Kjærgaard, M. Thiele, A. Fullam, M. Kuhn, J. Holm, P. Bork, A. Krag, T. Hansen, M. Arumugam, and J. Matthijnssens, “A previously undescribed highly prevalent phage identified in a Danish enteric virome catalogue,” Research Square, 2021.
    [Bibtex]
    @Article{Espen:21,
    author = {Lore {Van Espen} and Emilie Glad Bak and Leen Beller and Lila Close and Ward Deboutte and Helene B{\ae}k Juel and Trine Nielsen and Deniz Sinar and Lander De Coninck and Christine Frithioff-B{\o}js{\o}e and Cilius Esmann Fonvig and Suganya Jacobsen and Maria Kj{\ae}rgaard and Maja Thiele and Anthony Fullam and Michael Kuhn and Jens-Christian Holm and Peer Bork and Aleksander Krag and Torben Hansen and Manimozhiyan Arumugam and Jelle Matthijnssens},
    journal = {{Research Square}},
    title = {A previously undescribed highly prevalent phage identified in a {D}anish enteric virome catalogue},
    year = {2021},
    doi = {10.21203/rs.3.rs-273865/v1},
    publisher = {Research Square},
    }
  • [DOI] B. Schepens, L. van Schie, W. Nerinckx, K. Roose, W. V. Breedam, D. Fijalkowska, S. Devos, W. Weyts, S. D. Cae, S. Vanmarcke, C. Lonigro, H. Eeckhaut, D. V. Herpe, J. Borloo, A. F. Oliveira, J. P. Catani, S. Creytens, D. D. Vlieger, G. Michielsen, J. C. Z. Marchan, G. D. Moschonas, I. Rossey, K. Sedeyn, A. V. Hecke, X. Zhang, L. Langendries, S. Jacobs, S. ter Horst, L. Seldeslachts, L. Liesenborghs, R. Boudewijns, H. J. Thibaut, K. Dallmeier, G. V. Velde, B. Weynand, J. Beer, D. Schnepf, A. Ohnemus, I. Remory, C. S. Foo, R. Abdelnabi, P. Maes, S. J. F. Kaptein, J. Rocha-Pereira, D. Jochmans, L. Delang, F. Peelman, P. Staeheli, M. Schwemmle, N. Devoogdt, D. Tersago, M. Germani, J. Heads, A. Henry, A. Popplewell, M. Ellis, K. Brady, A. Turner, B. Dombrecht, C. Stortelers, J. Neyts, N. Callewaert, and X. Saelens, “Drug development of an affinity enhanced, broadly neutralizing heavy chain-only antibody that restricts SARS-CoV-2 in rodents,” bioRxiv, 2021.
    [Bibtex]
    @Article{Schepens:21,
    author = {Bert Schepens and Loes van Schie and Wim Nerinckx and Kenny Roose and Wander Van Breedam and Daria Fijalkowska and Simon Devos and Wannes Weyts and Sieglinde De Cae and Sandrine Vanmarcke and Chiara Lonigro and Hannah Eeckhaut and Dries Van Herpe and Jimmy Borloo and Ana Filipa Oliveira and Joao Paulo Catani and Sarah Creytens and Dorien De Vlieger and Gitte Michielsen and Jackeline Cecilia Zavala Marchan and George D. Moschonas and Iebe Rossey and Koen Sedeyn and Annelies Van Hecke and Xin Zhang and Lana Langendries and Sofie Jacobs and Sebastiaan ter Horst and Laura Seldeslachts and Laurens Liesenborghs and Robbert Boudewijns and Hendrik Jan Thibaut and Kai Dallmeier and Greetje Vande Velde and Birgit Weynand and Julius Beer and Daniel Schnepf and Annette Ohnemus and Isabel Remory and Caroline S. Foo and Rana Abdelnabi and Piet Maes and Suzanne J. F. Kaptein and Joana Rocha-Pereira and Dirk Jochmans and Leen Delang and Frank Peelman and Peter Staeheli and Martin Schwemmle and Nick Devoogdt and Dominique Tersago and Massimiliano Germani and James Heads and Alistair Henry and Andrew Popplewell and Mark Ellis and Kevin Brady and Alison Turner and Bruno Dombrecht and Catelijne Stortelers and Johan Neyts and Nico Callewaert and Xavier Saelens},
    journal = {{bioRxiv}},
    title = {Drug development of an affinity enhanced, broadly neutralizing heavy chain-only antibody that restricts {SARS}-{CoV}-2 in rodents},
    year = {2021},
    doi = {10.1101/2021.03.08.433449},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] D. Hoffmann, B. Corleis, S. Rauch, N. Roth, J. Mühe, N. J. Halwe, L. Ulrich, C. Fricke, J. Schön, A. Kraft, A. Breithaupt, K. Wernike, A. Michelitsch, F. Sick, C. Wylezich, S. O. Müller, T. C. Mettenleiter, B. Petsch, A. Dorhoi, and M. Beer, “CVnCoV protects human ACE2 transgenic mice from ancestral B BavPat1 and emerging B.1.351 SARS-CoV-2,” bioRxiv, 2021.
    [Bibtex]
    @Article{Hoffmann:21,
    author = {Donata Hoffmann and Björn Corleis and Susanne Rauch and Nicole Roth and Janine Mühe and Nico Joel Halwe and Lorenz Ulrich and Charlie Fricke and Jacob Schön and Anna Kraft and Angele Breithaupt and Kerstin Wernike and Anna Michelitsch and Franziska Sick and Claudia Wylezich and Stefan O. Müller and Thomas C. Mettenleiter and Benjamin Petsch and Anca Dorhoi and Martin Beer},
    journal = {{bioRxiv}},
    title = {{CVnCoV} protects human {ACE}2 transgenic mice from ancestral {B} {BavPat}1 and emerging {B}.1.351 {SARS}-{CoV}-2},
    year = {2021},
    doi = {10.1101/2021.03.22.435960},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] I. Jungreis, C. W. Nelson, Z. Ardern, Y. Finkel, N. J. Krogan, K. Sato, J. Ziebuhr, N. Stern-Ginossar, A. Pavesi, A. E. Firth, A. E. Gorbalenya, and M. Kellis, “Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: a homology-based resolution,” Virology, vol. 558, p. 145–151, 2021.
    [Bibtex]
    @Article{Jungreis:21,
    author = {Irwin Jungreis and Chase W. Nelson and Zachary Ardern and Yaara Finkel and Nevan J. Krogan and Kei Sato and John Ziebuhr and Noam Stern-Ginossar and Angelo Pavesi and Andrew E. Firth and Alexander E. Gorbalenya and Manolis Kellis},
    journal = {Virology},
    title = {Conflicting and ambiguous names of overlapping {ORFs} in the {SARS}-{CoV}-2 genome: A homology-based resolution},
    year = {2021},
    pages = {145--151},
    volume = {558},
    doi = {10.1016/j.virol.2021.02.013},
    publisher = {Elsevier {BV}},
    }
  • [DOI] W. K. Jo, C. Drosten, and J. F. Drexler, “The evolutionary dynamics of endemic human coronaviruses,” Virus Evol, vol. 7, iss. 1, 2021.
    [Bibtex]
    @Article{Jo:21,
    author = {Wendy K Jo and Christian Drosten and Jan Felix Drexler},
    journal = {{Virus Evol}},
    title = {The evolutionary dynamics of endemic human coronaviruses},
    year = {2021},
    number = {1},
    volume = {7},
    doi = {10.1093/ve/veab020},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] N. Huang, P. and Pérez, T. Kato, Y. Mikami, K. Okuda, R. C. Gilmore, C. D. Conde, B. Gasmi, S. Stein, M. Beach, E. Pelayo, J. O. Maldonado, B. A. Lafont, S. Jang, N. Nasir, R. J. Padilla, V. A. Murrah, R. Maile, W. Lovell, S. M. Wallet, N. M. Bowman, S. L. Meinig, M. C. Wolfgang, S. N. Choudhury, M. Novotny, B. D. Aevermann, R. H. Scheuermann, G. Cannon, C. W. Anderson, R. E. Lee, J. T. Marchesan, M. Bush, M. Freire, A. J. Kimple, D. L. Herr, J. Rabin, A. Grazioli, S. Das, B. N. French, T. Pranzatelli, J. A. Chiorini, D. E. Kleiner, S. Pittaluga, S. M. Hewitt, P. D. Burbelo, D. Chertow, K. Frank, J. Lee, R. C. Boucher, S. A. Teichmann, B. M. Warner, and K. B. M. and, “SARS-CoV-2 infection of the oral cavity and saliva,” Nat Med, 2021.
    [Bibtex]
    @Article{Huang:21,
    author = {Ni Huang and and Paola P{\'{e}}rez and Takafumi Kato and Yu Mikami and Kenichi Okuda and Rodney C. Gilmore and Cecilia Dom{\'{\i}}nguez Conde and Billel Gasmi and Sydney Stein and Margaret Beach and Eileen Pelayo and Jose O. Maldonado and Bernard A. Lafont and Shyh-Ing Jang and Nadia Nasir and Ricardo J. Padilla and Valerie A. Murrah and Robert Maile and William Lovell and Shannon M. Wallet and Natalie M. Bowman and Suzanne L. Meinig and Matthew C. Wolfgang and Saibyasachi N. Choudhury and Mark Novotny and Brian D. Aevermann and Richard H. Scheuermann and Gabrielle Cannon and Carlton W. Anderson and Rhianna E. Lee and Julie T. Marchesan and Mandy Bush and Marcelo Freire and Adam J. Kimple and Daniel L. Herr and Joseph Rabin and Alison Grazioli and Sanchita Das and Benjamin N. French and Thomas Pranzatelli and John A. Chiorini and David E. Kleiner and Stefania Pittaluga and Stephen M. Hewitt and Peter D. Burbelo and Daniel Chertow and Karen Frank and Janice Lee and Richard C. Boucher and Sarah A. Teichmann and Blake M. Warner and Kevin M. Byrd and},
    journal = {{Nat Med}},
    title = {{SARS}-{CoV}-2 infection of the oral cavity and saliva},
    year = {2021},
    doi = {10.1038/s41591-021-01296-8},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] M. O. Pohl, I. Busnadiego, V. Kufner, I. Glas, U. Karakus, S. Schmutz, M. Zaheri, I. Abela, A. Trkola, M. Huber, S. Stertz, and B. G. Hale, “SARS-CoV-2 variants reveal features critical for replication in primary human cells,” PLoS Biol, vol. 19, iss. 3, p. e3001006, 2021.
    [Bibtex]
    @Article{Pohl:21,
    author = {Marie O. Pohl and Idoia Busnadiego and Verena Kufner and Irina Glas and Umut Karakus and Stefan Schmutz and Maryam Zaheri and Irene Abela and Alexandra Trkola and Michael Huber and Silke Stertz and Benjamin G. Hale},
    journal = {{PLoS Biol}},
    title = {{SARS}-{CoV}-2 variants reveal features critical for replication in primary human cells},
    year = {2021},
    number = {3},
    pages = {e3001006},
    volume = {19},
    doi = {10.1371/journal.pbio.3001006},
    editor = {Stacey Schultz-Cherry},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] L. Ulrich, A. Michelitsch, N. Halwe, K. Wernike, D. Hoffmann, and M. Beer, “Experimental SARS-CoV-2 infection of bank voles,” Emerg Infect Dis., vol. 27, iss. 4, p. 1193–1195, 2021.
    [Bibtex]
    @Article{Ulrich:21,
    author = {Lorenz Ulrich and Anna Michelitsch and Nico Halwe and Kerstin Wernike and Donata Hoffmann and Martin Beer},
    journal = {{Emerg Infect Dis.}},
    title = {Experimental {SARS}-{CoV}-2 Infection of Bank Voles},
    year = {2021},
    number = {4},
    pages = {1193--1195},
    volume = {27},
    doi = {10.3201/eid2704.204945},
    publisher = {Centers for Disease Control and Prevention ({CDC})},
    }
  • [DOI] J. Beck, S. Seitz, C. Lauber, and M. Nassal, “Conservation of the HBV RNA element epsilon in nackednaviruses reveals ancient origin of protein-primed reverse transcription,” Proc Natl Acad Sci USA, vol. 118, iss. 13, p. e2022373118, 2021.
    [Bibtex]
    @Article{Beck:21,
    author = {Jürgen Beck and Stefan Seitz and Chris Lauber and Michael Nassal},
    journal = {{Proc Natl Acad Sci USA}},
    title = {Conservation of the {HBV} {RNA} element epsilon in nackednaviruses reveals ancient origin of protein-primed reverse transcription},
    year = {2021},
    number = {13},
    pages = {e2022373118},
    volume = {118},
    doi = {10.1073/pnas.2022373118},
    publisher = {Proceedings of the National Academy of Sciences},
    }
  • [DOI] P. Barrat-Charlaix, J. Huddleston, T. Bedford, and R. A. Neher, “Limited predictability of amino acid substitutions in seasonal influenza viruses,” Mol Biol Evol, 2021.
    [Bibtex]
    @Article{BarratCharlaix:21,
    author = {Pierre Barrat-Charlaix and John Huddleston and Trevor Bedford and Richard A Neher},
    journal = {{Mol Biol Evol}},
    title = {Limited Predictability of Amino Acid Substitutions in Seasonal Influenza Viruses},
    year = {2021},
    doi = {10.1093/molbev/msab065},
    editor = {Thomas Leitner},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] S. Lytras, G. Arriagada, and R. J. Gifford, “Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes,” Virus Evol, vol. 7, iss. 1, 2021.
    [Bibtex]
    @Article{Lytras:21a,
    author = {Spyros Lytras and Gloria Arriagada and Robert J Gifford},
    journal = {{Virus Evol}},
    title = {Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes},
    year = {2021},
    number = {1},
    volume = {7},
    doi = {10.1093/ve/veab012},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] A. Bataille, H. Salami, I. Seck, M. M. Lo, A. Ba, M. Diop, B. Sall, C. Faye, M. Lo, L. Kaba, Y. Sidime, M. Keyra, A. O. S. Diallo, M. Niang, C. A. K. Sidibe, A. Sery, M. Dakouo, A. B. E. Mamy, A. S. E. Arbi, Y. Barry, E. Isselmou, H. Habiboullah, A. S. Lella, B. Doumbia, M. B. Gueya, C. Coste, C. S. Diaw, O. Kwiatek, G. Libeau, and A. Apolloni, “Combining viral genetic and animal mobility network data to unravel peste des petits ruminants transmission dynamics in West Africa,” PLoS Pathog, vol. 17, iss. 3, p. e1009397, 2021.
    [Bibtex]
    @Article{Bataille:21,
    author = {Arnaud Bataille and Habib Salami and Ismaila Seck and Modou Moustapha Lo and Aminata Ba and Mariame Diop and Baba Sall and Coumba Faye and Mbargou Lo and Lanceï Kaba and Youssouf Sidime and Mohamed Keyra and Alpha Oumar Sily Diallo and Mamadou Niang and Cheick Abou Kounta Sidibe and Amadou Sery and Martin Dakouo and Ahmed Bezeid El Mamy and Ahmed Salem El Arbi and Yahya Barry and Ekaterina Isselmou and Habiboullah Habiboullah and Abdellahi Salem Lella and Baba Doumbia and Mohamed Baba Gueya and Caroline Coste and C{\'{e}}cile Squarzoni Diaw and Olivier Kwiatek and Genevi{\`{e}}ve Libeau and Andrea Apolloni},
    journal = {{PLoS Pathog}},
    title = {Combining viral genetic and animal mobility network data to unravel peste des petits ruminants transmission dynamics in {W}est {A}frica},
    year = {2021},
    number = {3},
    pages = {e1009397},
    volume = {17},
    doi = {10.1371/journal.ppat.1009397},
    editor = {Guillaume Fourni{\'{e}}},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] S. Mantip, A. Sigismeau, D. Shamaki, T. Y. Woma, O. Kwiatek, G. Libeau, S. Farougou, and A. Bataille, “Molecular epidemiology of peste des petits ruminants virus in Nigeria: an update,” Transbound Emerg Dis, 2021.
    [Bibtex]
    @Article{Mantip:21,
    author = {Samuel Mantip and Anthony Sigismeau and David Shamaki and Timothy Yusuf Woma and Olivier Kwiatek and Genevieve Libeau and Souabou Farougou and Arnaud Bataille},
    journal = {{Transbound Emerg Dis}},
    title = {Molecular epidemiology of peste des petits ruminants virus in {N}igeria: an update},
    year = {2021},
    doi = {10.1111/tbed.14073},
    publisher = {Wiley},
    }
  • [DOI] B. W. Haak, R. Argelaguet, C. M. Kinsella, R. F. J. Kullberg, J. M. Lankelma, M. Deijs, M. Klein, M. F. Jebbink, F. Hugenholtz, S. Kostidis, M. Giera, T. B. M. Hakvoort, W. J. de Jonge, M. J. Schultz, T. van Gool, T. van der Poll, W. M. de Vos, L. M. van der Hoek, and J. W. Wiersinga, “Integrative transkingdom analysis of the gut microbiome in antibiotic perturbation and critical illness,” mSystems, vol. 6, iss. 2, 2021.
    [Bibtex]
    @Article{Haak:21,
    author = {Bastiaan W. Haak and Ricard Argelaguet and Cormac M. Kinsella and Robert F. J. Kullberg and Jacqueline M. Lankelma and Martin Deijs and Michelle Klein and Maarten F. Jebbink and Floor Hugenholtz and Sarantos Kostidis and Martin Giera and Theodorus B. M. Hakvoort and Wouter J. de Jonge and Marcus J. Schultz and Tom van Gool and Tom van der Poll and Willem M. de Vos and Lia M. van der Hoek and W. Joost Wiersinga},
    journal = {{mSystems}},
    title = {Integrative Transkingdom Analysis of the Gut Microbiome in Antibiotic Perturbation and Critical Illness},
    year = {2021},
    number = {2},
    volume = {6},
    doi = {10.1128/msystems.01148-20},
    editor = {Nicholas Chia},
    publisher = {American Society for Microbiology},
    }
  • [DOI] J. O. Wertheim, R. Hostager, D. Ryu, K. Merkel, S. Angedakin, M. Arandjelovic, E. A. Ayimisin, F. Babweteera, M. Bessone, K. J. Brun-Jeffery, P. Dieguez, W. Eckardt, B. Fruth, I. Herbinger, S. Jones, H. Kuehl, K. E. Langergraber, K. Lee, N. F. Madinda, S. Metzger, L. J. Ormsby, M. M. Robbins, V. Sommer, T. Stoinski, E. G. Wessling, R. M. Wittig, Y. G. Yuh, F. H. Leendertz, and S. Calvignac-Spencer, “Discovery of novel herpes simplexviruses in wild gorillas, bonobos, and chimpanzees supports zoonotic origin of HSV-2,” Mol Biol Evol, 2021.
    [Bibtex]
    @Article{Wertheim:21,
    author = {Joel O Wertheim and Reilly Hostager and Diane Ryu and Kevin Merkel and Samuel Angedakin and Mimi Arandjelovic and Emmanuel Ayuk Ayimisin and Fred Babweteera and Mattia Bessone and Kathryn J Brun-Jeffery and Paula Dieguez and Winnie Eckardt and Barbara Fruth and Ilka Herbinger and Sorrel Jones and Hjalmar Kuehl and Kevin E Langergraber and Kevin Lee and Nadege F Madinda and Sonja Metzger and Lucy Jayne Ormsby and Martha M Robbins and Volker Sommer and Tara Stoinski and Erin G Wessling and Roman M Wittig and Yisa Ginath Yuh and Fabian H Leendertz and S{\'{e}}bastien Calvignac-Spencer},
    journal = {{Mol Biol Evol}},
    title = {Discovery of novel herpes simplexviruses in wild gorillas, bonobos, and chimpanzees supports zoonotic origin of {HSV}-2},
    year = {2021},
    doi = {10.1093/molbev/msab072},
    editor = {Tal Pupko},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] C. S. Jürges, L. Dölken, and F. Erhard, “Integrative transcription start site identification with iTiSS,” Bioinformatics, 2021.
    [Bibtex]
    @Article{Juerges:21,
    author = {Christopher S Jürges and Lars Dölken and Florian Erhard},
    journal = {Bioinformatics},
    title = {Integrative transcription start site identification with {iTiSS}},
    year = {2021},
    doi = {10.1093/bioinformatics/btab170},
    editor = {Alfonso Valencia},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] D. F. Nieuwenhuijse, B. O. B. Munnink, and M. P. G. Koopmans, “viromeBrowser: a shiny app for browsing virome sequencing analysis results,” Viruses, vol. 13, iss. 3, p. 437, 2021.
    [Bibtex]
    @Article{Nieuwenhuijse:21,
    author = {David F. Nieuwenhuijse and Bas B. Oude Munnink and Marion P. G. Koopmans},
    journal = {Viruses},
    title = {{viromeBrowser}: A Shiny App for Browsing Virome Sequencing Analysis Results},
    year = {2021},
    number = {3},
    pages = {437},
    volume = {13},
    doi = {10.3390/v13030437},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] M. Rueca, A. Fontana, B. Bartolini, P. Piselli, A. Mazzarelli, M. Copetti, E. Binda, F. Perri, C. E. M. Gruber, E. Nicastri, L. Marchioni, G. Ippolito, M. R. Capobianchi, A. D. Caro, and V. Pazienza, “Investigation of nasal/oropharyngeal microbial community of COVID-19 patients by 16s rDNA sequencing,” Int J Environ Res Public Health, vol. 18, iss. 4, p. 2174, 2021.
    [Bibtex]
    @Article{Rueca:21,
    author = {Martina Rueca and Andrea Fontana and Barbara Bartolini and Pierluca Piselli and Antonio Mazzarelli and Massimiliano Copetti and Elena Binda and Francesco Perri and Cesare Ernesto Maria Gruber and Emanuele Nicastri and Luisa Marchioni and Giuseppe Ippolito and Maria Rosaria Capobianchi and Antonino Di Caro and Valerio Pazienza},
    journal = {{Int J Environ Res Public Health}},
    title = {Investigation of Nasal/Oropharyngeal Microbial Community of {COVID}-19 Patients by 16S {rDNA} Sequencing},
    year = {2021},
    number = {4},
    pages = {2174},
    volume = {18},
    doi = {10.3390/ijerph18042174},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] J. N. Hakizimana, C. Yona, O. Kamana, H. Nauwynck, and G. Misinzo, “African swine fever virus circulation between Tanzania and neighboring countries: a systematic review and meta-analysis,” Viruses, vol. 13, iss. 2, p. 306, 2021.
    [Bibtex]
    @Article{Hakizimana:21,
    author = {Jean N. Hakizimana and Clara Yona and Olivier Kamana and Hans Nauwynck and Gerald Misinzo},
    journal = {Viruses},
    title = {African Swine Fever Virus Circulation between {T}anzania and Neighboring Countries: A Systematic Review and Meta-Analysis},
    year = {2021},
    number = {2},
    pages = {306},
    volume = {13},
    doi = {10.3390/v13020306},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] F. Varghese, E. van Woudenbergh, G. Overheul, M. Eleveld, L. Kurver, N. van Heerbeek, A. van Laarhoven, P. Miesen, G. den Hartog, M. de Jonge, and R. van Rij, “Berberine and Obatoclax inhibit SARS-cov-2 replication in primary human nasal epithelial cells in vitro,” Viruses, vol. 13, iss. 2, p. 282, 2021.
    [Bibtex]
    @Article{Varghese:21,
    author = {Finny Varghese and Esther van Woudenbergh and Gijs Overheul and Marc Eleveld and Lisa Kurver and Niels van Heerbeek and Arjan van Laarhoven and Pascal Miesen and Gerco den Hartog and Marien de Jonge and Ronald van Rij},
    journal = {Viruses},
    title = {{B}erberine and {O}batoclax Inhibit {SARS}-Cov-2 Replication in Primary Human Nasal Epithelial Cells In Vitro},
    year = {2021},
    number = {2},
    pages = {282},
    volume = {13},
    doi = {10.3390/v13020282},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] B. Agerer, M. Koblischke, V. Gudipati, L. F. Montaño-Gutierrez, M. Smyth, A. Popa, J. Genger, L. Endler, D. M. Florian, V. Mühlgrabner, M. Graninger, S. W. Aberle, A. Husa, L. E. Shaw, A. Lercher, P. Gattinger, R. Torralba-Gombau, D. Trapin, T. Penz, D. Barreca, I. Fae, S. Wenda, M. Traugott, G. Walder, W. F. Pickl, V. Thiel, F. Allerberger, H. Stockinger, E. Puchhammer-Stöckl, W. Weninger, G. Fischer, W. Hoepler, E. Pawelka, A. Zoufaly, R. Valenta, C. Bock, W. Paster, R. Geyeregger, M. Farlik, F. Halbritter, J. B. Huppa, J. H. Aberle, and A. Bergthaler, “SARS-CoV-2 mutations in MHC-I-restricted epitopes evade CD8+ T cell responses,” Sci Immunol, vol. 6, iss. 57, p. eabg6461, 2021.
    [Bibtex]
    @Article{Agerer:21,
    author = {Benedikt Agerer and Maximilian Koblischke and Venugopal Gudipati and Luis Fernando Monta{\~{n}}o-Gutierrez and Mark Smyth and Alexandra Popa and Jakob-Wendelin Genger and Lukas Endler and David M. Florian and Vanessa Mühlgrabner and Marianne Graninger and Stephan W. Aberle and Anna-Maria Husa and Lisa Ellen Shaw and Alexander Lercher and Pia Gattinger and Ricard Torralba-Gombau and Doris Trapin and Thomas Penz and Daniele Barreca and Ingrid Fae and Sabine Wenda and Marianna Traugott and Gernot Walder and Winfried F. Pickl and Volker Thiel and Franz Allerberger and Hannes Stockinger and Elisabeth Puchhammer-Stöckl and Wolfgang Weninger and Gottfried Fischer and Wolfgang Hoepler and Erich Pawelka and Alexander Zoufaly and Rudolf Valenta and Christoph Bock and Wolfgang Paster and Ren{\'{e}} Geyeregger and Matthias Farlik and Florian Halbritter and Johannes B. Huppa and Judith H. Aberle and Andreas Bergthaler},
    journal = {{Sci Immunol}},
    title = {{SARS}-{CoV}-2 mutations in {MHC}-{I}-restricted epitopes evade {CD}8+ {T} cell responses},
    year = {2021},
    number = {57},
    pages = {eabg6461},
    volume = {6},
    doi = {10.1126/sciimmunol.abg6461},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
  • [DOI] A. E. Gorbalenya and S. G. Siddell, “Recognizing species as a new focus of virus research,” PLoS Pathog, vol. 17, iss. 3, p. e1009318, 2021.
    [Bibtex]
    @Article{Gorbalenya:21,
    author = {Alexander E. Gorbalenya and Stuart G. Siddell},
    journal = {{PLoS Pathog}},
    title = {Recognizing species as a new focus of virus research},
    year = {2021},
    number = {3},
    pages = {e1009318},
    volume = {17},
    doi = {10.1371/journal.ppat.1009318},
    editor = {Thomas E. Morrison},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] B. Krichel, G. Bylapudi, C. Schmidt, C. Blanchet, R. Schubert, L. Brings, M. Koehler, R. Zenobi, D. Svergun, K. Lorenzen, R. Madhugiri, J. Ziebuhr, and C. Uetrecht, “Hallmarks of Alpha- and Betacoronavirus non-structural protein 7+8 complexes,” Science advances, vol. 7, iss. 10, p. eabf1004, 2021.
    [Bibtex]
    @Article{Krichel:21,
    author = {Boris Krichel and Ganesh Bylapudi and Christina Schmidt and Clement Blanchet and Robin Schubert and Lea Brings and Martin Koehler and Renato Zenobi and Dmitri Svergun and Kristina Lorenzen and Ramakanth Madhugiri and John Ziebuhr and Charlotte Uetrecht},
    journal = {Science Advances},
    title = {Hallmarks of {A}lpha- and {B}etacoronavirus non-structural protein 7+8 complexes},
    year = {2021},
    number = {10},
    pages = {eabf1004},
    volume = {7},
    doi = {10.1126/sciadv.abf1004},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
  • [DOI] F. Meyer, T. Lesker, D. Koslicki, A. Fritz, A. Gurevich, A. E. Darling, A. Sczyrba, A. Bremges, and A. C. McHardy, “Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit,” Nat Protoc, 2021.
    [Bibtex]
    @Article{Meyer:21,
    author = {Fernando Meyer and Till-Robin Lesker and David Koslicki and Adrian Fritz and Alexey Gurevich and Aaron E. Darling and Alexander Sczyrba and Andreas Bremges and Alice C. McHardy},
    journal = {{Nat Protoc}},
    title = {Tutorial: assessing metagenomics software with the {CAMI} benchmarking toolkit},
    year = {2021},
    doi = {10.1038/s41596-020-00480-3},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] E. B. Hodcroft, N. De Maio, R. Lanfear, D. R. MacCannell, B. Q. Minh, H. A. Schmidt, A. Stamatakis, N. Goldman, and C. Dessimoz, “Want to track pandemic variants faster? fix the bioinformatics bottleneck.,” Nature, vol. 591, p. 30–33, 2021.
    [Bibtex]
    @Article{Hodcroft:21,
    author = {Hodcroft, Emma B. and De Maio, Nicola and Lanfear, Rob and MacCannell, Duncan R. and Minh, Bui Quang and Schmidt, Heiko A. and Stamatakis, Alexandros and Goldman, Nick and Dessimoz, Christophe},
    journal = {Nature},
    title = {Want to track pandemic variants faster? Fix the bioinformatics bottleneck.},
    year = {2021},
    pages = {30--33},
    volume = {591},
    doi = {10.1038/d41586-021-00525-x},
    issue = {7848},
    keywords = {Animals; Automation, methods; Basic Reproduction Number; COVID-19, epidemiology, immunology, transmission, virology; COVID-19 Vaccines, immunology; Evolution, Molecular; Genome, Viral, genetics; Genomics, methods, trends; Humans; Mink, virology; Mutation; Pandemics, statistics & numerical data; Phylogeny; Public Health, methods, trends; SARS-CoV-2, genetics, immunology, isolation & purification, pathogenicity; Social Media; Uncertainty; Bioinformatics; Genomics; Public health; SARS-CoV-2},
    pmid = {33649511},
    pubstate = {ppublish},
    }
  • [DOI] M. Desdouits, J. Piquet, C. Wacrenier, C. L. Mennec, S. Parnaudeau, S. Jousse, S. Rocq, L. Bigault, M. Contrant, P. Garry, F. Chavanon, R. Gabellec, L. Lamort, L. Lebrun, P. L. Gall, C. Meteigner, A. Schmitt, J. L. Seugnet, O. Serais, C. Peltier, C. Bressolette-Bodin, Y. Blanchard, and F. L. S. Guyader, “Can shellfish be used to monitor SARS-CoV-2 in the coastal environment?,” Sci Total Environ, vol. 778, p. 146270, 2021.
    [Bibtex]
    @Article{Desdouits:21,
    author = {Marion Desdouits and Jean-C{\^{o}}me Piquet and Candice Wacrenier and C{\'{e}}cile Le Mennec and Sylvain Parnaudeau and Sarah Jousse and Sophie Rocq and Lionel Bigault and Maud Contrant and Pascal Garry and Fabienne Chavanon and Raoul Gabellec and Laure Lamort and Luc Lebrun and Patrik Le Gall and Claire Meteigner and Anne Schmitt and Jean Luc Seugnet and Oph{\'{e}}lie Serais and C{\'{e}}cile Peltier and C{\'{e}}line Bressolette-Bodin and Yannick Blanchard and Fran{\c{c}}oise S. Le Guyader},
    journal = {{Sci Total Environ}},
    title = {Can shellfish be used to monitor {SARS}-{CoV}-2 in the coastal environment?},
    year = {2021},
    pages = {146270},
    volume = {778},
    doi = {10.1016/j.scitotenv.2021.146270},
    publisher = {Elsevier {BV}},
    }
  • [DOI] O. A. MacLean, S. Lytras, S. Weaver, J. B. Singer, M. F. Boni, P. Lemey, S. K. L. Pond, and D. L. Robertson, “Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen,” PLoS Biol, vol. 19, iss. 3, p. e3001115, 2021.
    [Bibtex]
    @Article{MacLean:21,
    author = {Oscar A. MacLean and Spyros Lytras and Steven Weaver and Joshua B. Singer and Maciej F. Boni and Philippe Lemey and Sergei L. Kosakovsky Pond and David L. Robertson},
    journal = {{PLoS Biol}},
    title = {Natural selection in the evolution of {SARS}-{CoV}-2 in bats created a generalist virus and highly capable human pathogen},
    year = {2021},
    number = {3},
    pages = {e3001115},
    volume = {19},
    doi = {10.1371/journal.pbio.3001115},
    editor = {Damien Tully},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] K. A. Lythgoe, M. Hall, L. Ferretti, M. de Cesare, G. MacIntyre-Cockett, A. Trebes, M. Andersson, N. Otecko, E. L. Wise, N. Moore, J. Lynch, S. Kidd, N. Cortes, M. Mori, R. Williams, G. Vernet, A. Justice, A. Green, S. M. Nicholls, A. M. Ansari, L. Abeler-Dörner, C. E. Moore, T. E. A. Peto, D. W. Eyre, R. Shaw, P. Simmonds, D. Buck, J. A. Todd, T. R. Connor, S. Ashraf, A. S. da Filipe, J. Shepherd, E. C. Thomson, D. Bonsall, C. Fraser, T. Golubchik, and and, “SARS-CoV-2 within-host diversity and transmission,” Science, p. eabg0821, 2021.
    [Bibtex]
    @Article{Lythgoe:21,
    author = {Katrina A. Lythgoe and Matthew Hall and Luca Ferretti and Mariateresa de Cesare and George MacIntyre-Cockett and Amy Trebes and Monique Andersson and Newton Otecko and Emma L. Wise and Nathan Moore and Jessica Lynch and Stephen Kidd and Nicholas Cortes and Matilde Mori and Rebecca Williams and Gabrielle Vernet and Anita Justice and Angie Green and Samuel M. Nicholls and M. Azim Ansari and Lucie Abeler-Dörner and Catrin E. Moore and Timothy E. A. Peto and David W. Eyre and Robert Shaw and Peter Simmonds and David Buck and John A. Todd and Thomas R. Connor and Shirin Ashraf and Ana da Silva Filipe and James Shepherd and Emma C. Thomson and David Bonsall and Christophe Fraser and Tanya Golubchik and and},
    journal = {Science},
    title = {{SARS}-{CoV}-2 within-host diversity and transmission},
    year = {2021},
    pages = {eabg0821},
    doi = {10.1126/science.abg0821},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
  • [DOI] A. Kratzel, J. N. Kelly, Y. Brueggemann, J. Portmann, P. V’kovski, D. Todt, N. Ebert, E. Steinmann, R. Dijkman, G. Zimmer, S. Pfaender, and V. Thiel, “A genome-wide CRISPR screen identifies interactors of the autophagy pathway as conserved coronavirus targets,” bioRxiv, 2021.
    [Bibtex]
    @Article{Kratzel:21,
    author = {Annika Kratzel and Jenna N. Kelly and Yannick Brueggemann and Jasmine Portmann and Philip V'kovski and Daniel Todt and Nadine Ebert and Eike Steinmann and Ronald Dijkman and Gert Zimmer and Stephanie Pfaender and Volker Thiel},
    journal = {{bioRxiv}},
    title = {A genome-wide {CRISPR} screen identifies interactors of the autophagy pathway as conserved coronavirus targets},
    year = {2021},
    doi = {10.1101/2021.02.24.432634},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. Widera, A. Wilhelm, S. Hoehl, C. Pallas, N. Kohmer, T. Wolf, H. F. Rabenau, V. Corman, C. Drosten, M. J. Vehreschild, U. Goetsch, R. Gottschalk, and S. Ciesek, “Bamlanivimab does not neutralize two SARS-CoV-2 variants carrying E484K in vitro,” medRxiv, 2021.
    [Bibtex]
    @Article{Widera:21,
    author = {Marek Widera and Alexander Wilhelm and Sebastian Hoehl and Christiane Pallas and Niko Kohmer and Timo Wolf and Holger F Rabenau and Victor Corman and Christian Drosten and Maria JGT Vehreschild and Udo Goetsch and Rene Gottschalk and Sandra Ciesek},
    journal = {{medRxiv}},
    title = {Bamlanivimab does not neutralize two {SARS}-{CoV}-2 variants carrying {E484K} in vitro},
    year = {2021},
    doi = {10.1101/2021.02.24.21252372},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] L. Marongiu, G. Protti, F. A. Facchini, M. Valache, F. Mingozzi, V. Ranzani, A. R. Putignano, L. Salviati, V. Bevilacqua, S. Curti, M. Crosti, M. D’Angiò, L. R. Bettini, A. Biondi, L. Nespoli, N. Tamini, N. Mancini, N. Clementi, S. Abrignani, R. Spreafico, and F. Granucci, “Maturation signatures of conventional dendritic cells in COVID-19 reflect direct viral sensing,” bioRxiv, 2021.
    [Bibtex]
    @Article{Marongiu:21,
    author = {Laura Marongiu and Giulia Protti and Fabio A. Facchini and Mihai Valache and Francesca Mingozzi and Valeria Ranzani and Anna Rita Putignano and Lorenzo Salviati and Valeria Bevilacqua and Serena Curti and Mariacristina Crosti and Mariella D'Angi{\`{o}} and Laura Rachele Bettini and Andrea Biondi and Luca Nespoli and Nicol{\`{o}} Tamini and Nicasio Mancini and Nicola Clementi and Sergio Abrignani and Roberto Spreafico and Francesca Granucci},
    journal = {{bioRxiv}},
    title = {Maturation signatures of conventional dendritic cells in {COVID}-19 reflect direct viral sensing},
    year = {2021},
    doi = {10.1101/2021.03.03.433597},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] W. Xia, J. Hughes, D. Robertson, and X. Jiang, “How one pandemic led to another: ASFV, the disruption contributing to SARS-CoV-2 emergence in Wuhan,” Preprints, 2021.
    [Bibtex]
    @Article{Xia:21,
    author = {Wei Xia and Joseph Hughes and David Robertson and Xiaowei Jiang},
    journal = {{Preprints}},
    title = {How One Pandemic Led To Another: {ASFV}, the Disruption Contributing To {SARS-CoV}-2 Emergence in {W}uhan},
    year = {2021},
    doi = {10.20944/preprints202102.0590.v1},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] H. Bastani, K. Drakopoulos, V. Gupta, J. Vlachogiannis, C. Hadjicristodoulou, P. Lagiou, G. Magiorkinis, D. Paraskevis, and S. Tsiodras, “Deploying an artificial intelligence system for COVID-19 testing at the Greek border,” SSRN, 2021.
    [Bibtex]
    @Article{Bastani:21,
    author = {Hamsa Bastani and Kimon Drakopoulos and Vishal Gupta and Jon Vlachogiannis and Christos Hadjicristodoulou and Pagona Lagiou and Gkikas Magiorkinis and Dimitrios Paraskevis and Sotirios Tsiodras},
    journal = {{SSRN}},
    title = {Deploying an Artificial Intelligence System for {COVID}-19 Testing at the {G}reek Border},
    year = {2021},
    doi = {10.2139/ssrn.3789038},
    publisher = {Elsevier {BV}},
    }
  • [DOI] D. P. Martin, S. Weaver, H. Tegally, E. J. San, S. D. Shank, E. Wilkinson, J. Giandhari, S. Naidoo, Y. Pillay, L. Singh, R. J. Lessells, R. K. Gupta, J. O. Wertheim, A. Nekturenko, B. Murrell, G. W. Harkins, P. Lemey, O. A. MacLean, D. L. Robertson, T. de Oliveira, S. K. L. Pond, and and, “The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape,” medRxiv, 2021.
    [Bibtex]
    @Article{Martin:21,
    author = {Darren P Martin and Steven Weaver and Houryiah Tegally and Emmanuel James San and Stephen D Shank and Eduan Wilkinson and Jennifer Giandhari and Sureshnee Naidoo and Yeshnee Pillay and Lavanya Singh and Richard J Lessells and Ravindra K Gupta and Joel O Wertheim and Anton Nekturenko and Ben Murrell and Gordon W Harkins and Philippe Lemey and Oscar A MacLean and David L Robertson and Tulio de Oliveira and Sergei L Kosakovsky Pond and and},
    journal = {{medRxiv}},
    title = {The emergence and ongoing convergent evolution of the {N501Y} lineages coincides with a major global shift in the {SARS}-{CoV}-2 selective landscape},
    year = {2021},
    doi = {10.1101/2021.02.23.21252268},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] K. McLaughlin, D. Bojkova, M. Bechtel, J. Kandler, P. Reus, T. Le, J. U. Wagner, S. Ciesek, M. N. Wass, M. Michaelis, and J. N. Cinatl, “CD47 as a potential biomarker for the early diagnosis of severe COVID-19,” bioRxiv, 2021.
    [Bibtex]
    @Article{McLaughlin:21,
    author = {Katie-May McLaughlin and Denisa Bojkova and Marco Bechtel and Joshua Kandler and Philipp Reus and Trang Le and Julian UG Wagner and Sandra Ciesek and Mark N Wass and Martin Michaelis and Jindrich N Cinatl},
    journal = {{bioRxiv}},
    title = {{CD}47 as a potential biomarker for the early diagnosis of severe {COVID}-19},
    year = {2021},
    doi = {10.1101/2021.03.01.433404},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] A. Tarke, J. Sidney, N. Methot, Y. Zhang, J. M. Dan, B. Goodwin, P. Rubiro, A. Sutherland, R. S. da Antunes, A. Fraizer, S. A. Rawlings, D. M. Smith, B. Peters, R. H. Scheuermann, D. Weiskopf, S. Crotty, A. Grifoni, and A. Sette, “Negligible impact of SARS-CoV-2 variants on CD4+ and CD8+ t cell reactivity in COVID-19 exposed donors and vaccinees.,” bioRxiv, 2021.
    [Bibtex]
    @Article{Tarke:21,
    author = {Alison Tarke and John Sidney and Nils Methot and Yun Zhang and Jennifer M Dan and Benjamin Goodwin and Paul Rubiro and Aaron Sutherland and Ricardo da Silva Antunes and April Fraizer and Stephen A. Rawlings and Davey M. Smith and Bjoern Peters and Richard H. Scheuermann and Daniela Weiskopf and Shane Crotty and Alba Grifoni and Alessandro Sette},
    journal = {{bioRxiv}},
    title = {Negligible impact of {SARS}-{CoV}-2 variants on {CD}4+ and {CD}8+ T cell reactivity in {COVID}-19 exposed donors and vaccinees.},
    year = {2021},
    doi = {10.1101/2021.02.27.433180},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] J. Ratcliff, D. Nguyen, M. Fish, J. Rhynne, A. Jennings, S. Williams, F. Al-Beidh, D. Bonsall, A. Evans, T. Golubchik, A. C. Gordon, A. Lamikanra, P. Tsang, N. Ciccone, U. Leuscher, W. Slack, E. Laing, P. R. Mouncey, S. Ziyenge, M. Olivera, R. Ploeg, K. M. Rowan, M. Shankar-Hari, D. J. Roberts, D. K. Menon, L. Estcourt, P. Simmonds, and H. Harvala, “Virological and serological characterization of critically ill patients with COVID-19 in the UK: a special focus on variant detection,” bioRxiv, 2021.
    [Bibtex]
    @Article{Ratcliff:21a,
    author = {Jeremy Ratcliff and Dung Nguyen and Matthew Fish and Jennifer Rhynne and Aislinn Jennings and Sarah Williams and Farah Al-Beidh and David Bonsall and Amy Evans and Tanya Golubchik and Anthony C Gordon and Abigail Lamikanra and Pat Tsang and Nick Ciccone and Ullrich Leuscher and Wendy Slack and Emma Laing and Paul R Mouncey and Sheba Ziyenge and Marta Olivera and Rutger Ploeg and Kathryn M Rowan and Manu Shankar-Hari and David J. Roberts and David K Menon and Lise Estcourt and Peter Simmonds and Heli Harvala},
    journal = {{bioRxiv}},
    title = {Virological and serological characterization of critically ill patients with {COVID}-19 in the {UK}: a special focus on variant detection},
    year = {2021},
    doi = {10.1101/2021.02.24.21251989},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] E. C. Thomson, L. E. Rosen, J. G. Shepherd, R. Spreafico, A. da Silva Filipe, J. A. Wojcechowskyj, C. Davis, L. Piccoli, D. J. Pascall, J. Dillen, S. Lytras, N. Czudnochowski, R. Shah, M. Meury, N. Jesudason, A. De Marco, K. Li, J. Bassi, A. O’Toole, D. Pinto, R. M. Colquhoun, K. Culap, B. Jackson, F. Zatta, A. Rambaut, S. Jaconi, V. B. Sreenu, J. Nix, I. Zhang, R. F. Jarrett, W. G. Glass, M. Beltramello, K. Nomikou, M. Pizzuto, L. Tong, E. Cameroni, T. I. Croll, N. Johnson, J. Di Iulio, A. Wickenhagen, A. Ceschi, A. M. Harbison, D. Mair, P. Ferrari, K. Smollett, F. Sallusto, S. Carmichael, C. Garzoni, J. Nichols, M. Galli, J. Hughes, A. Riva, A. Ho, M. Schiuma, M. G. Semple, P. J. M. Openshaw, E. Fadda, K. J. Baillie, J. D. Chodera, The ISARIC4C Investigators, COVID-19 Genomics UK (COG-UK) consortium, S. J. Rihn, S. J. Lycett, H. W. Virgin, A. Telenti, D. Corti, D. L. Robertson, and G. Snell, “Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity.,” Cell, 2021.
    [Bibtex]
    @Article{Thomson:21,
    author = {Thomson, Emma C. and Rosen, Laura E. and Shepherd, James G. and Spreafico, Roberto and da Silva Filipe, Ana and Wojcechowskyj, Jason A. and Davis, Chris and Piccoli, Luca and Pascall, David J. and Dillen, Josh and Lytras, Spyros and Czudnochowski, Nadine and Shah, Rajiv and Meury, Marcel and Jesudason, Natasha and De Marco, Anna and Li, Kathy and Bassi, Jessica and O'Toole, Aine and Pinto, Dora and Colquhoun, Rachel M. and Culap, Katja and Jackson, Ben and Zatta, Fabrizia and Rambaut, Andrew and Jaconi, Stefano and Sreenu, Vattipally B. and Nix, Jay and Zhang, Ivy and Jarrett, Ruth F. and Glass, William G. and Beltramello, Martina and Nomikou, Kyriaki and Pizzuto, Matteo and Tong, Lily and Cameroni, Elisabetta and Croll, Tristan I. and Johnson, Natasha and Di Iulio, Julia and Wickenhagen, Arthur and Ceschi, Alessandro and Harbison, Aoife M. and Mair, Daniel and Ferrari, Paolo and Smollett, Katherine and Sallusto, Federica and Carmichael, Stephen and Garzoni, Christian and Nichols, Jenna and Galli, Massimo and Hughes, Joseph and Riva, Agostino and Ho, Antonia and Schiuma, Marco and Semple, Malcolm G. and Openshaw, Peter J. M. and Fadda, Elisa and Baillie, J. Kenneth and Chodera, John D. and {The ISARIC4C Investigators} and {COVID-19 Genomics UK (COG-UK) consortium} and Rihn, Suzannah J. and Lycett, Samantha J. and Virgin, Herbert W. and Telenti, Amalio and Corti, Davide and Robertson, David L. and Snell, Gyorgy},
    journal = {Cell},
    title = {Circulating {SARS-CoV-2} spike {N439K} variants maintain fitness while evading antibody-mediated immunity.},
    year = {2021},
    abstract = {SARS-CoV-2 can mutate and evade immunity, with consequences for efficacy of emerging vaccines and antibody therapeutics. Here, we demonstrate that the immunodominant SARS-CoV-2 spike (S) receptor binding motif (RBM) is a highly variable region of S and provide epidemiological, clinical, and molecular characterization of a prevalent, sentinel RBM mutation, N439K. We demonstrate N439K S protein has enhanced binding affinity to the hACE2 receptor, and N439K viruses have similar in vitro replication fitness and cause infections with similar clinical outcomes as compared to wild type. We show the N439K mutation confers resistance against several neutralizing monoclonal antibodies, including one authorized for emergency use by the US Food and Drug Administration (FDA), and reduces the activity of some polyclonal sera from persons recovered from infection. Immune evasion mutations that maintain virulence and fitness such as N439K can emerge within SARS-CoV-2 S, highlighting the need for ongoing molecular surveillance to guide development and usage of vaccines and therapeutics.},
    doi = {10.1016/j.cell.2021.01.037},
    keywords = {COVID-19; N439K; SARS-CoV-2; Spike; monoclonal antibody escape; mutation; protein structure; receptor binding motif; variant},
    pmid = {33621484},
    pubstate = {aheadofprint},
    }
  • [DOI] S. J. Rihn, A. Merits, S. Bakshi, M. L. Turnbull, A. Wickenhagen, A. J. T. Alexander, C. Baillie, B. Brennan, F. Brown, K. Brunker, S. R. Bryden, K. A. Burness, S. Carmichael, S. J. Cole, V. M. Cowton, P. Davies, C. Davis, G. De Lorenzo, C. L. Donald, M. Dorward, J. I. Dunlop, M. Elliott, M. Fares, A. da Silva Filipe, J. R. Freitas, W. Furnon, R. J. Gestuveo, A. Geyer, D. Giesel, D. M. Goldfarb, N. Goodman, R. Gunson, J. C. Hastie, V. Herder, J. Hughes, C. Johnson, N. Johnson, A. Kohl, K. Kerr, H. Leech, L. S. Lello, K. Li, G. Lieber, X. Liu, R. Lingala, C. Loney, D. Mair, M. J. McElwee, S. McFarlane, J. Nichols, K. Nomikou, A. Orr, R. J. Orton, M. Palmarini, Y. A. Parr, R. M. Pinto, S. Raggett, E. Reid, D. L. Robertson, J. Royle, N. Cameron-Ruiz, J. G. Shepherd, K. Smollett, D. G. Stewart, M. Stewart, E. Sugrue, A. M. Szemiel, A. Taggart, E. C. Thomson, L. Tong, L. S. Torrie, R. Toth, M. Varjak, S. Wang, S. G. Wilkinson, P. G. Wyatt, E. Zusinaite, D. R. Alessi, A. H. Patel, A. Zaid, S. J. Wilson, and S. Mahalingam, “A plasmid DNA-launched SARS-CoV-2 reverse genetics system and coronavirus toolkit for COVID-19 research.,” PLoS Biol, vol. 19, p. e3001091, 2021.
    [Bibtex]
    @Article{Rihn:21,
    author = {Rihn, Suzannah J. and Merits, Andres and Bakshi, Siddharth and Turnbull, Matthew L. and Wickenhagen, Arthur and Alexander, Akira J. T. and Baillie, Carla and Brennan, Benjamin and Brown, Fiona and Brunker, Kirstyn and Bryden, Steven R. and Burness, Kerry A. and Carmichael, Stephen and Cole, Sarah J. and Cowton, Vanessa M. and Davies, Paul and Davis, Chris and De Lorenzo, Giuditta and Donald, Claire L. and Dorward, Mark and Dunlop, James I. and Elliott, Matthew and Fares, Mazigh and da Silva Filipe, Ana and Freitas, Joseph R. and Furnon, Wilhelm and Gestuveo, Rommel J. and Geyer, Anna and Giesel, Daniel and Goldfarb, Daniel M. and Goodman, Nicola and Gunson, Rory and Hastie, C. James and Herder, Vanessa and Hughes, Joseph and Johnson, Clare and Johnson, Natasha and Kohl, Alain and Kerr, Karen and Leech, Hannah and Lello, Laura Sandra and Li, Kathy and Lieber, Gauthier and Liu, Xiang and Lingala, Rajendra and Loney, Colin and Mair, Daniel and McElwee, Marion J. and McFarlane, Steven and Nichols, Jenna and Nomikou, Kyriaki and Orr, Anne and Orton, Richard J. and Palmarini, Massimo and Parr, Yasmin A. and Pinto, Rute Maria and Raggett, Samantha and Reid, Elaine and Robertson, David L. and Royle, Jamie and Cameron-Ruiz, Natalia and Shepherd, James G. and Smollett, Katherine and Stewart, Douglas G. and Stewart, Meredith and Sugrue, Elena and Szemiel, Agnieszka M. and Taggart, Aislynn and Thomson, Emma C. and Tong, Lily and Torrie, Leah S. and Toth, Rachel and Varjak, Margus and Wang, Sainan and Wilkinson, Stuart G. and Wyatt, Paul G. and Zusinaite, Eva and Alessi, Dario R. and Patel, Arvind H. and Zaid, Ali and Wilson, Sam J. and Mahalingam, Suresh},
    journal = {{PLoS Biol}},
    title = {A plasmid {DNA}-launched {SARS-CoV-2} reverse genetics system and coronavirus toolkit for {COVID-19} research.},
    year = {2021},
    pages = {e3001091},
    volume = {19},
    abstract = {The recent emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the underlying cause of Coronavirus Disease 2019 (COVID-19), has led to a worldwide pandemic causing substantial morbidity, mortality, and economic devastation. In response, many laboratories have redirected attention to SARS-CoV-2, meaning there is an urgent need for tools that can be used in laboratories unaccustomed to working with coronaviruses. Here we report a range of tools for SARS-CoV-2 research. First, we describe a facile single plasmid SARS-CoV-2 reverse genetics system that is simple to genetically manipulate and can be used to rescue infectious virus through transient transfection (without in vitro transcription or additional expression plasmids). The rescue system is accompanied by our panel of SARS-CoV-2 antibodies (against nearly every viral protein), SARS-CoV-2 clinical isolates, and SARS-CoV-2 permissive cell lines, which are all openly available to the scientific community. Using these tools, we demonstrate here that the controversial ORF10 protein is expressed in infected cells. Furthermore, we show that the promising repurposed antiviral activity of apilimod is dependent on TMPRSS2 expression. Altogether, our SARS-CoV-2 toolkit, which can be directly accessed via our website at https://mrcppu-covid.bio/, constitutes a resource with considerable potential to advance COVID-19 vaccine design, drug testing, and discovery science.},
    doi = {10.1371/journal.pbio.3001091},
    issue = {2},
    pmid = {33630831},
    pubstate = {epublish},
    }
  • [DOI] S. Rüeger, C. Hammer, A. Loetscher, P. J. McLaren, D. Lawless, O. Naret, D. P. Depledge, S. Morfopoulou, J. Breuer, E. Zdobnov, J. Fellay, and S. C. H. I. V. Study, “The influence of human genetic variation on Epstein-barr virus sequence diversity.,” Sci Rep, vol. 11, p. 4586, 2021.
    [Bibtex]
    @Article{Rueeger:21,
    author = {Rüeger, Sina and Hammer, Christian and Loetscher, Alexis and McLaren, Paul J. and Lawless, Dylan and Naret, Olivier and Depledge, Daniel P. and Morfopoulou, Sofia and Breuer, Judith and Zdobnov, Evgeny and Fellay, Jacques and Study, Swiss H.I.V. Cohort},
    journal = {{Sci Rep}},
    title = {The influence of human genetic variation on {E}pstein-Barr virus sequence diversity.},
    year = {2021},
    pages = {4586},
    volume = {11},
    abstract = {Epstein-Barr virus (EBV) is one of the most common viruses latently infecting humans. Little is known about the impact of human genetic variation on the large inter-individual differences observed in response to EBV infection. To search for a potential imprint of host genomic variation on the EBV sequence, we jointly analyzed paired viral and human genomic data from 268 HIV-coinfected individuals with CD4 + T cell count < 200/mm and elevated EBV viremia. We hypothesized that the reactivated virus circulating in these patients could carry sequence variants acquired during primary EBV infection, thereby providing a snapshot of early adaptation to the pressure exerted on EBV by the individual immune response. We searched for associations between host and pathogen genetic variants, taking into account human and EBV population structure. Our analyses revealed significant associations between human and EBV sequence variation. Three polymorphic regions in the human genome were found to be associated with EBV variation: one at the amino acid level (BRLF1:p.Lys316Glu); and two at the gene level (burden testing of rare variants in BALF5 and BBRF1). Our findings confirm that jointly analyzing host and pathogen genomes can identify sites of genomic interactions, which could help dissect pathogenic mechanisms and suggest new therapeutic avenues.},
    doi = {10.1038/s41598-021-84070-7},
    investigator = {Aebi-Popp, Karoline and Anagnostopoulos, Alexia and Battegay, Manuel and Bernasconi, Enos and Böni, Jürg and Braun, Dominique and Bucher, Heiner and Calmy, Alexandra and Cavassini, Matthias and Ciuffi, Angela and Dollenmaier, Guenter and Egger, Matthias and Elzi, Luigia and Fehr, Jan and Fellay, Jacques and Furrer, Hansjakob and Fux, Christoph and Günthard, Huldrych and Haerry, David and Hasse, Barbara and Hirsch, Hans and Hoffmann, Matthias and Hösli, Irene and Huber, Michael and Kahlert, Christian and Kaiser, Laurent and Keiser, Olivia and Klimkait, Thomas and Kottanattu, Lisa and Kouyos, Roger and Kovari, Helen and Ledergerber, Bruno and Martinetti, Gladys and de Tejada, Begoña Martinez and Marzolini, Catia and Metzner, Karin and Müller, Nicolas and Nicca, Dunja and Paioni, Paolo and Pantaleo, Giuseppe and Perreau, Matthieu and Rauch, Andri and Rudin, Christoph and Scherrer, Alexandra and Schmid, Patrick and Speck, Roberto and Stöckle, Marcel and Tarr, Philip and Trkola, Alexandra and Vernazza, Pietro and Wagner, Noémie and Wandeler, Gilles and Weber, Rainer and Yerly, Sabine},
    issue = {1},
    pmid = {33633271},
    pubstate = {epublish},
    }
  • [DOI] B. Zhou, T. Thi Nhu Thao, D. Hoffmann, A. Taddeo, N. Ebert, F. Labroussaa, A. Pohlmann, J. King, S. Steiner, J. N. Kelly, J. Portmann, N. J. Halwe, L. Ulrich, B. S. Trüeb, X. Fan, B. Hoffmann, L. Wang, L. Thomann, X. Lin, H. Stalder, B. Pozzi, S. de Brot, N. Jiang, D. Cui, J. Hossain, M. Wilson, M. Keller, T. J. Stark, J. R. Barnes, R. Dijkman, J. Jores, C. Benarafa, D. E. Wentworth, V. Thiel, and M. Beer, "SARS-CoV-2 spike D614G change enhances replication and transmission.," Nature, 2021.
    [Bibtex]
    @Article{Zhou:21,
    author = {Zhou, Bin and Thi Nhu Thao, Tran and Hoffmann, Donata and Taddeo, Adriano and Ebert, Nadine and Labroussaa, Fabien and Pohlmann, Anne and King, Jacqueline and Steiner, Silvio and Kelly, Jenna N. and Portmann, Jasmine and Halwe, Nico Joel and Ulrich, Lorenz and Trüeb, Bettina Salome and Fan, Xiaoyu and Hoffmann, Bernd and Wang, Li and Thomann, Lisa and Lin, Xudong and Stalder, Hanspeter and Pozzi, Berta and de Brot, Simone and Jiang, Nannan and Cui, Dan and Hossain, Jaber and Wilson, Malania and Keller, Matthew and Stark, Thomas J. and Barnes, John R. and Dijkman, Ronald and Jores, Joerg and Benarafa, Charaf and Wentworth, David E. and Thiel, Volker and Beer, Martin},
    journal = {Nature},
    title = {{SARS-CoV-2} spike {D614G} change enhances replication and transmission.},
    year = {2021},
    abstract = {During the evolution of SARS-CoV-2 in humans a D614G substitution in the spike (S) protein emerged and became the predominant circulating variant (S-614G) of the COVID-19 pandemic . However, whether the increasing prevalence of the S-614G variant represents a fitness advantage that improves replication and/or transmission in humans or is merely due to founder effects remains elusive. Here, we generated isogenic SARS-CoV-2 variants and demonstrate that the S-614G variant has (i) enhanced binding to human host cell surface receptor angiotensin-converting enzyme 2 (ACE2), (ii) increased replication in primary human bronchial and nasal airway epithelial cultures as well as in a novel human ACE2 knock-in mouse model, and (iii) markedly increased replication and transmissibility in hamster and ferret models of SARS-CoV-2 infection. Collectively, our data show that while the S-614G substitution results in subtle increases in binding and replication in vitro, it provides a real competitive advantage in vivo, particularly during the transmission bottle neck, providing an explanation for the global predominance of S-614G variant among the SARS-CoV-2 viruses currently circulating.},
    doi = {10.1038/s41586-021-03361-1},
    pmid = {33636719},
    pubstate = {aheadofprint},
    }
  • [DOI] S. Deinhardt-Emmer, S. Böttcher, C. Häring, L. Giebeler, A. Henke, R. Zell, J. Jungwirth, P. M. Jordan, O. Werz, F. Hornung, C. Brandt, M. Marquet, A. S. Mosig, M. W. Pletz, M. Schacke, J. Rödel, R. Heller, S. Nietzsche, B. Löffler, and C. Ehrhardt, "SARS-CoV-2 causes severe epithelial inflammation and barrier dysfunction.," J Virol, 2021.
    [Bibtex]
    @Article{DeinhardtEmmer:21,
    author = {Deinhardt-Emmer, Stefanie and Böttcher, Sarah and Häring, Clio and Giebeler, Liane and Henke, Andreas and Zell, Roland and Jungwirth, Johannes and Jordan, Paul M. and Werz, Oliver and Hornung, Franziska and Brandt, Christian and Marquet, Mike and Mosig, Alexander S. and Pletz, Mathias W. and Schacke, Michael and Rödel, Jürgen and Heller, Regine and Nietzsche, Sandor and Löffler, Bettina and Ehrhardt, Christina},
    journal = {{J Virol}},
    title = {{SARS-CoV-2} causes severe epithelial inflammation and barrier dysfunction.},
    year = {2021},
    abstract = {Infections with SARS-CoV-2 can be asymptomatic, but they can also be accompanied by a variety of symptoms that result in mild to severe coronavirus disease-19 (COVID-19) and are sometimes associated with systemic symptoms. Although the viral infection originates in the respiratory system, it is unclear how the virus can overcome the alveolar barrier, which is observed in severe COVID-19 disease courses. To elucidate the viral effects on the barrier integrity and immune reactions, we used mono-cell culture systems and a complex human chip model composed of epithelial, endothelial, and mononuclear cells. Our data show that SARS-CoV-2 efficiently infected epithelial cells with high viral loads and inflammatory response, including interferon expression. By contrast, the adjacent endothelial layer was neither infected nor did it show productive virus replication or interferon release. With prolonged infection, both cell types were damaged, and the barrier function was deteriorated, allowing the viral particles to overbear. In our study, we demonstrate that although SARS-CoV-2 is dependent on the epithelium for efficient replication, the neighboring endothelial cells are affected, e.g., by the epithelial cytokines or components induced during infection, which further results in the damage of the epithelial/endothelial barrier function and viral dissemination. SARS-CoV-2 challenges healthcare systems and societies worldwide in unprecedented ways. Although numerous new studies have been conducted, research to better understand the molecular pathogen-host interactions are urgently needed. For this, experimental models have to be developed and adapted. In the present study we used mono cell-culture systems and we established a complex chip model, where epithelial and endothelial cells are cultured in close proximity. We demonstrate that epithelial cells can be infected with SARS-CoV-2, while the endothelium did not show any infection signs. Since SARS-CoV-2 is able to establish viremia, the link to thromboembolic events in severe COVID-19 courses is evident. However, whether the endothelial layer is damaged by the viral pathogens or whether other endothelial-independent homeostatic factors are induced by the virus is essential for understanding the disease development. Therefore, our study is important as it demonstrates that the endothelial layer could not be infected by SARS-CoV-2 in our experiments, but we were able to show the destruction of the epithelial-endothelial barrier in our chip model. From our experiments we can assume that virus-induced host factors disturbed the epithelial-endothelial barrier function and thereby promote viral spread.},
    doi = {10.1128/JVI.00110-21},
    pmid = {33637603},
    pubstate = {aheadofprint},
    }
  • [DOI] N. I. Vlachogiannis, K. Verrou, K. Stellos, P. P. Sfikakis, and D. Paraskevis, "The role of A-to-I RNA editing in infections by RNA viruses: possible implications for SARS-CoV-2 infection.," Clin Immunol, p. 108699, 2021.
    [Bibtex]
    @Article{Vlachogiannis:21,
    author = {Vlachogiannis, Nikolaos I. and Verrou, Kleio-Maria and Stellos, Konstantinos and Sfikakis, Petros P. and Paraskevis, Dimitrios},
    journal = {{Clin Immunol}},
    title = {The role of {A}-to-{I} {RNA} editing in infections by {RNA} viruses: Possible implications for {SARS-CoV-2} infection.},
    year = {2021},
    pages = {108699},
    abstract = {RNA editing is a fundamental biological process with 2 major forms, namely adenosine-to-inosine (A-to-I, recognized as A-to-G) and cytosine-to-uracil (C-to-U) deamination, mediated by ADAR and APOBEC enzyme families, respectively. A-to-I RNA editing has been shown to directly affect the genome/transcriptome of RNA viruses with significant repercussions for viral protein synthesis, proliferation and infectivity, while it also affects recognition of double-stranded RNAs by cytosolic receptors controlling the host innate immune response. Recent evidence suggests that RNA editing may be present in SARS-CoV-2 genome/transcriptome. The majority of mapped mutations in SARS-CoV-2 genome are A-to-G/U-to-C(opposite strand) and C-to-U/G-to-A(opposite strand) substitutions comprising potential ADAR-/APOBEC-mediated deamination events. A single nucleotide substitution can have dramatic effects on SARS-CoV-2 infectivity as shown by the D614G(A-to-G) substitution in the spike protein. Future studies utilizing serial sampling from patients with COVID-19 are warranted to delineate whether RNA editing affects viral replication and/or the host immune response to SARS-CoV-2.},
    doi = {10.1016/j.clim.2021.108699},
    keywords = {A-to-I RNA editing; Innate immunity; Mutations; SARS-CoV-2; Viral infections},
    pmid = {33639276},
    pubstate = {aheadofprint},
    }
  • [DOI] N. Marty, S. Saeng-Aroon, E. Heger, A. Thielen, M. Obermeier, N. Pfeifer, R. Kaiser, and T. Klimkait, "Adapting the geno2pheno[coreceptor] tool to HIV-1 subtype CRF01_AE by phenotypic validation using clinical isolates from South-East Asia.," J Clin Virol, vol. 136, p. 104755, 2021.
    [Bibtex]
    @Article{Marty:21,
    author = {Marty, Nina and Saeng-Aroon, Siriphan and Heger, Eva and Thielen, Alexander and Obermeier, Martin and Pfeifer, Nico and Kaiser, Rolf and Klimkait, Thomas},
    journal = {{J Clin Virol}},
    title = {Adapting the geno2pheno[coreceptor] tool to {HIV}-1 subtype {CRF01\_AE} by phenotypic validation using clinical isolates from {S}outh-{E}ast {A}sia.},
    year = {2021},
    pages = {104755},
    volume = {136},
    abstract = {Geno2pheno[coreceptor] is a widely used tool for the prediction of coreceptor usage (viral tropism) of HIV-1 samples. For HIV-1 CRF01_AE, a significant overcalling of X4-tropism is observed when using the standard settings of Geno2pheno[coreceptor]. The aim of this study was to provide the experimental backing for adaptations to the geno2pheno[coreceptor] algorithm in order to improve coreceptor usage predictions of clinical HIV-1 CRF01_AE isolates STUDY DESIGN: V3-sequences of 20 clinical HIV-1 subtype CRF01_AE samples were sequenced and analyzed by geno2pheno[coreceptor]. In parallel, coreceptor usage was determined for these samples by replicative phenotyping in human cells in the presence of specific X4- or R5-inhibitors. The sole introduction of the CRF01_AE V3 region into a full-length otherwise subtype B provirus failed to produce replication-competent viral progeny. A successive genome-replacement strategy revealed that also CRF01_AE derived gag and pol sequences are necessary to generate HIV genomes with sufficient replication competence. Subsequent phenotypic analysis confirmed overcalling of X4-tropism for CRF01_AE viruses using the current version and the standard cut-off at 10% false positive rate (FPR) of geno2pheno[coreceptor]. Lowering the FPR cut-off to 2.5% reduced the X4-overcalling in our sample collection, while still allowing a safe administration of Maraviroc (MCV). This study demonstrates the successful adjustment of geno2pheno[coreceptor] rules for subtype CRF01_AE. It also supports the unique strength of combining complementing methods, namely phenotyping and genotyping, for validating new bioinformatics tools prior to application in diagnostics.},
    doi = {10.1016/j.jcv.2021.104755},
    keywords = {Coreceptor; HIV-1; Phenotyping; Subtype CRF01_AE; Tropism; geno2pheno},
    pmid = {33639408},
    pubstate = {aheadofprint},
    }
  • [DOI] P. Vetter, S. Cordey, M. Schibler, L. Vieux, L. Despres, F. Laubscher, D. O. Andrey, R. Martischang, S. Harbarth, C. Cuvelier, M. Bekliz, I. Eckerle, C. Siegrist, A. M. Didierlaurent, C. S. Eberhardt, B. Meyer, and L. Kaiser, "Clinical, virological and immunological features of a mild case of SARS-CoV-2 re-infection," Clin Microbiol Infec, 2021.
    [Bibtex]
    @Article{Vetter:21,
    author = {Pauline Vetter and Samuel Cordey and Manuel Schibler and Laure Vieux and Lena Despres and Florian Laubscher and Diego O. Andrey and Romain Martischang and Stephan Harbarth and Cl{\'{e}}mence Cuvelier and Meriem Bekliz and Isabella Eckerle and Claire-Anne Siegrist and Arnaud M. Didierlaurent and Christiane S. Eberhardt and Benjamin Meyer and Laurent Kaiser},
    journal = {{Clin Microbiol Infec}},
    title = {Clinical, virological and immunological features of a mild case of {SARS}-{CoV}-2 re-infection},
    year = {2021},
    doi = {10.1016/j.cmi.2021.02.010},
    publisher = {Elsevier {BV}},
    }
  • [DOI] M. Grossegesse, A. Nitsche, L. Schaade, and J. Doellinger, "Application of spectral library prediction for parallel reaction monitoring of viral peptides," Proteomics, p. 2000226, 2021.
    [Bibtex]
    @Article{Grossegesse:21,
    author = {Marica Grossegesse and Andreas Nitsche and Lars Schaade and Joerg Doellinger},
    journal = {{Proteomics}},
    title = {Application of spectral library prediction for parallel reaction monitoring of viral peptides},
    year = {2021},
    pages = {2000226},
    doi = {10.1002/pmic.202000226},
    publisher = {Wiley},
    }
  • [DOI] J. A. H. Masoli, A. Jeffries, B. Temperton, C. Auckland, M. Michelsen, J. Warwick-Dugdale, R. Manley, A. Farbos, S. Ellard, B. Knight, C. Bewshea, C. Sambles, J. Harrison, B. Bunce, A. Carr, A. T. Hattersley, S. L. Michell, and D. J. Studholme, "Viral genetic sequencing identifies staff transmission of COVID-19 is important in a community hospital outbreak," medRxiv, 2021.
    [Bibtex]
    @Article{Masoli:21,
    author = {Jane A.H. Masoli and Aaron Jeffries and Ben Temperton and Cressida Auckland and Michelle Michelsen and Joanna Warwick-Dugdale and Robyn Manley and Audrey Farbos and Sian Ellard and Beatrice Knight and Claire Bewshea and Christine Sambles and James Harrison and Ben Bunce and Alexis Carr and Andrew T. Hattersley and Stephen Ll. Michell and David J. Studholme},
    journal = {{medRxiv}},
    title = {Viral genetic sequencing identifies staff transmission of {COVID}-19 is important in a community hospital outbreak},
    year = {2021},
    doi = {10.1101/2021.02.18.21250737},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] C. Wylezich, S. Calvelage, K. Schlottau, U. Ziegler, A. Pohlmann, D. Höper, and M. Beer, "Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including SARS-CoV-2," Microbiome, vol. 9, iss. 1, 2021.
    [Bibtex]
    @Article{Wylezich:21,
    author = {Claudia Wylezich and Sten Calvelage and Kore Schlottau and Ute Ziegler and Anne Pohlmann and Dirk Höper and Martin Beer},
    journal = {Microbiome},
    title = {Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including {SARS}-{CoV}-2},
    year = {2021},
    number = {1},
    volume = {9},
    doi = {10.1186/s40168-020-00973-z},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] C. Bahrs, A. Kimmig, S. Weis, J. Ankert, S. Hagel, J. Maschmann, A. Stallmach, A. Steiner, M. Bauer, W. Behringer, M. Baier, M. Kesselmeier, C. Richert, F. Zepf, M. Walter, A. Scherag, M. Kiehntopf, B. Löffler, and M. W. Pletz, "Prospective surveillance study in a 1,400-bed university hospital: COVID-19 exposure at home was the main risk factor for SARS-CoV-2 point seroprevalence among hospital staff," Transbound Emerg Dis, 2021.
    [Bibtex]
    @Article{Bahrs:21,
    author = {Christina Bahrs and Aurelia Kimmig and Sebastian Weis and Juliane Ankert and Stefan Hagel and Jens Maschmann and Andreas Stallmach and Andrea Steiner and Michael Bauer and Wilhelm Behringer and Michael Baier and Miriam Kesselmeier and Cora Richert and Florian Zepf and Martin Walter and Andr{\'{e}} Scherag and Michael Kiehntopf and Bettina Löffler and Mathias W. Pletz},
    journal = {{Transbound Emerg Dis}},
    title = {Prospective surveillance study in a 1,400-bed university hospital: {COVID}-19 exposure at home was the main risk factor for {SARS}-{CoV}-2 point seroprevalence among hospital staff},
    year = {2021},
    doi = {10.1111/tbed.14041},
    publisher = {Wiley},
    }
  • [DOI] A. M. Szemiel, A. Merits, R. J. Orton, O. MacLean, R. M. Pinto, A. Wickenhagen, G. Lieber, M. L. Turnbull, S. Wang, D. Mair, A. S. da Filipe, B. J. Willett, S. J. Wilson, A. H. Patel, E. C. Thomson, M. Palmarini, A. Kohl, and M. E. Stewart, "In vitro evolution of Remdesivir resistance reveals genome plasticity of SARS-CoV-2," bioRxiv, 2021.
    [Bibtex]
    @Article{Szemiel:21,
    author = {Agnieszka M. Szemiel and Andres Merits and Richard J. Orton and Oscar MacLean and Rute Maria Pinto and Arthur Wickenhagen and Gauthier Lieber and Matthew L. Turnbull and Sainan Wang and Daniel Mair and Ana da Silva Filipe and Brian J. Willett and Sam J. Wilson and Arvind H. Patel and Emma C. Thomson and Massimo Palmarini and Alain Kohl and Meredith E. Stewart},
    journal = {{bioRxiv}},
    title = {In vitro evolution of {R}emdesivir resistance reveals genome plasticity of {SARS}-{CoV}-2},
    year = {2021},
    doi = {10.1101/2021.02.01.429199},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] A. Pérez-Cataluña, Á. Chiner-Oms, E. Cuevas-Ferrando, A. Díaz-Reolid, I. Falcó, W. Randazzo, I. Girón-Guzmán, A. Allende, M. A. Bracho, I. Comas, and G. Sánchez, "Detection of genomic variants of SARS-CoV-2 circulating in wastewater by high-throughput sequencing," bioRxiv, 2021.
    [Bibtex]
    @Article{PerezCataluna:21,
    author = {Alba Pérez-Cataluña and {\'{A}}lvaro Chiner-Oms and Enric Cuevas-Ferrando and Azahara D{\'{\i}}az-Reolid and Irene Falc{\'{o}} and Walter Randazzo and In{\'{e}}s Gir{\'{o}}n-Guzm{\'{a}}n and Ana Allende and Mar{\'{\i}}a A. Bracho and I{\~{n}}aki Comas and Gloria S{\'{a}}nchez},
    journal = {{bioRxiv}},
    title = {Detection Of Genomic Variants Of {SARS}-{CoV}-2 Circulating In Wastewater By High-Throughput Sequencing},
    year = {2021},
    doi = {10.1101/2021.02.08.21251355},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] P. Lemey, N. Ruktanonchai, S. Hong, V. Colizza, C. Poletto, F. V. den Broeck, M. Gill, X. Ji, A. Levasseur, A. Sadilek, S. Lai, A. Tatem, G. Baele, M. Suchard, and S. Dellicour, "SARS-CoV-2 european resurgence foretold: interplay of introductions and persistence by leveraging genomic and mobility data," Research Square, 2021.
    [Bibtex]
    @Article{Lemey:21,
    author = {Philippe Lemey and Nick Ruktanonchai and Samuel Hong and Vittoria Colizza and Chiara Poletto and Frederik Van den Broeck and Mandev Gill and Xiang Ji and Anthony Levasseur and Adam Sadilek and Shengjie Lai and Andrew Tatem and Guy Baele and Marc Suchard and Simon Dellicour},
    journal = {{Research Square}},
    title = {{SARS}-{CoV}-2 European resurgence foretold: interplay of introductions and persistence by leveraging genomic and mobility data},
    year = {2021},
    doi = {10.21203/rs.3.rs-208849/v1},
    publisher = {Research Square},
    }
  • [DOI] D. L. Bugembe, M. V. T. Phan, I. Ssewanyana, P. Semanda, H. Nansumba, B. Dhaala, S. Nabadda, Á. N. O'Toole, A. Rambaut, P. Kaleebu, and M. Cotten, "A SARS-CoV-2 lineage A variant (A.23.1) with altered spike has emerged and is dominating the current Uganda epidemic," medRxiv, 2021.
    [Bibtex]
    @Article{Bugembe:21,
    author = {Daniel Lule Bugembe and My V.T. Phan and Isaac Ssewanyana and Patrick Semanda and Hellen Nansumba and Beatrice Dhaala and Susan Nabadda and {\'{A}}ine Niamh O'Toole and Andrew Rambaut and Pontiano Kaleebu and Matthew Cotten},
    journal = {{medRxiv}},
    title = {A {SARS}-{CoV}-2 lineage {A} variant ({A}.23.1) with altered spike has emerged and is dominating the current {U}ganda epidemic},
    year = {2021},
    doi = {10.1101/2021.02.08.21251393},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] E. Petter, O. Mor, N. Zuckerman, D. Oz-Levi, A. Younger, D. Aran, and Y. Erlich, "Initial real world evidence for lower viral load of individuals who have been vaccinated by BNT162b2," medRxiv, 2021.
    [Bibtex]
    @Article{Petter:21,
    author = {Ella Petter and Orna Mor and Neta Zuckerman and Danit Oz-Levi and Asaf Younger and Dvir Aran and Yaniv Erlich},
    journal = {{medRxiv}},
    title = {Initial real world evidence for lower viral load of individuals who have been vaccinated by {BNT}162b2},
    year = {2021},
    doi = {10.1101/2021.02.08.21251329},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] P. Simmonds and A. M. Ansari, "Mutation bias implicates RNA editing in a wide range of mammalian RNA viruses," bioRxiv, 2021.
    [Bibtex]
    @Article{Simmonds:21,
    author = {Peter Simmonds and M. Azim Ansari},
    journal = {{bioRxiv}},
    title = {Mutation bias implicates {RNA} editing in a wide range of mammalian {RNA} viruses},
    year = {2021},
    doi = {10.1101/2021.02.09.430395},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. Ghafari, P. Simmonds, O. G. Pybus, and A. Katzourakis, "Prisoner of war dynamics explains the time-dependent pattern of substitution rates in viruses," bioRxiv, 2021.
    [Bibtex]
    @Article{Ghafari:21,
    author = {Mahan Ghafari and Peter Simmonds and Oliver G Pybus and Aris Katzourakis},
    journal = {{bioRxiv}},
    title = {Prisoner of War dynamics explains the time-dependent pattern of substitution rates in viruses},
    year = {2021},
    doi = {10.1101/2021.02.09.430479},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] D. A. Hoagland, R. Møller, S. A. Uhl, K. Oishi, J. Frere, I. Golynker, S. Horiuchi, M. Panis, D. Blanco-Melo, D. Sachs, K. Arkun, J. K. Lim, and B. R. tenOever, "Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity.," Immunity, 2021.
    [Bibtex]
    @Article{Hoagland:21,
    author = {Hoagland, Daisy A. and Møller, Rasmus and Uhl, Skyler A. and Oishi, Kohei and Frere, Justin and Golynker, Ilona and Horiuchi, Shu and Panis, Maryline and Blanco-Melo, Daniel and Sachs, David and Arkun, Knarik and Lim, Jean K. and tenOever, Benjamin R.},
    journal = {Immunity},
    title = {Leveraging the antiviral type {I} interferon system as a first line of defense against {SARS-CoV-2} pathogenicity.},
    year = {2021},
    abstract = {The emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in significant global morbidity, mortality, and societal disruption. A better understanding of virus-host interactions may potentiate therapeutic insights toward limiting this infection. Here we investigated the dynamics of the systemic response to SARS-CoV-2 in hamsters by histological analysis and transcriptional profiling. Infection resulted in consistently high levels of virus in the upper and lower respiratory tracts and sporadic occurrence in other distal tissues. A longitudinal cohort revealed a wave of inflammation, including a type I interferon (IFN-I) response, that was evident in all tissues regardless of viral presence but was insufficient to prevent disease progression. Bolstering the antiviral response with intranasal administration of recombinant IFN-I reduced viral disease, prevented transmission, and lowered inflammation in vivo. This study defines the systemic host response to SARS-CoV-2 infection and supports use of intranasal IFN-I as an effective means of early treatment.},
    doi = {10.1016/j.immuni.2021.01.017},
    keywords = {COVID-19; IFN-I; cytokine; hamster; intranasal; mRNA-seq; pandemic; prophylactic; therapeutic; transcriptomics},
    pmid = {33577760},
    pubstate = {aheadofprint},
    }
  • [DOI] J. M. Bartoszewicz, A. Seidel, and B. Y. Renard, "Interpretable detection of novel human viruses from genome sequencing data.," NAR Genom Bioinform, vol. 3, p. lqab004, 2021.
    [Bibtex]
    @Article{Bartoszewicz:21a,
    author = {Bartoszewicz, Jakub M. and Seidel, Anja and Renard, Bernhard Y.},
    journal = {{NAR Genom Bioinform}},
    title = {Interpretable detection of novel human viruses from genome sequencing data.},
    year = {2021},
    pages = {lqab004},
    volume = {3},
    abstract = {Viruses evolve extremely quickly, so reliable methods for viral host prediction are necessary to safeguard biosecurity and biosafety alike. Novel human-infecting viruses are difficult to detect with standard bioinformatics workflows. Here, we predict whether a virus can infect humans directly from next-generation sequencing reads. We show that deep neural architectures significantly outperform both shallow machine learning and standard, homology-based algorithms, cutting the error rates in half and generalizing to taxonomic units distant from those presented during training. Further, we develop a suite of interpretability tools and show that it can be applied also to other models beyond the host prediction task. We propose a new approach for convolutional filter visualization to disentangle the information content of each nucleotide from its contribution to the final classification decision. Nucleotide-resolution maps of the learned associations between pathogen genomes and the infectious phenotype can be used to detect regions of interest in novel agents, for example, the SARS-CoV-2 coronavirus, unknown before it caused a COVID-19 pandemic in 2020. All methods presented here are implemented as easy-to-install packages not only enabling analysis of NGS datasets without requiring any deep learning skills, but also allowing advanced users to easily train and explain new models for genomics.},
    doi = {10.1093/nargab/lqab004},
    issue = {1},
    pmid = {33554119},
    pubstate = {epublish},
    }
  • [DOI] A. Ebinger, S. Fischer, and D. Höper, "A theoretical and generalized approach for the assessment of the sample-specific limit of detection for clinical metagenomics.," Comput Struct Biotechnol J, vol. 19, p. 732–742, 2021.
    [Bibtex]
    @Article{Ebinger:21,
    author = {Ebinger, Arnt and Fischer, Susanne and Höper, Dirk},
    journal = {{Comput Struct Biotechnol J}},
    title = {A theoretical and generalized approach for the assessment of the sample-specific limit of detection for clinical metagenomics.},
    year = {2021},
    pages = {732--742},
    volume = {19},
    abstract = {Metagenomics is a powerful tool to identify novel or unexpected pathogens, since it is generic and relatively unbiased. The limit of detection (LOD) is a critical parameter for the routine application of methods in the clinical diagnostic context. Although attempts for the determination of LODs for metagenomics next-generation sequencing (mNGS) have been made previously, these were only applicable for specific target species in defined samples matrices. Therefore, we developed and validated a generalized probability-based model to assess the sample-specific LOD of mNGS experiments (LOD ). Initial rarefaction analyses with datasets of Borna disease virus 1 human encephalitis cases revealed a stochastic behavior of virus read detection. Based on this, we transformed the Bernoulli formula to predict the minimal necessary dataset size to detect one virus read with a probability of 99%. We validated the formula with 30 datasets from diseased individuals, resulting in an accuracy of 99.1% and an average of 4.5 ± 0.4 viral reads found in the calculated minimal dataset size. We demonstrated by modeling the virus genome size, virus-, and total RNA-concentration that the main determinant of mNGS sensitivity is the virus-sample background ratio. The predicted LOD for the respective pathogenic virus in the datasets were congruent with the virus-concentration determined by RT-qPCR. Theoretical assumptions were further confirmed by correlation analysis of mNGS and RT-qPCR data from the samples of the analyzed datasets. This approach should guide standardization of mNGS application, due to the generalized concept of LOD .},
    doi = {10.1016/j.csbj.2020.12.040},
    keywords = {Bernoulli process; Detection limit; Metagenomics; Next-generation sequencing; Sensitivity; qPCR},
    pmid = {33552445},
    pubstate = {epublish},
    }
  • [DOI] J. Ratcliff and P. Simmonds, "Potential APOBEC-mediated RNA editing of the genomes of SARS-CoV-2 and other coronaviruses and its impact on their longer term evolution.," Virology, vol. 556, p. 62–72, 2021.
    [Bibtex]
    @Article{Ratcliff:21,
    author = {Ratcliff, Jeremy and Simmonds, Peter},
    journal = {Virology},
    title = {Potential {APOBEC}-mediated {RNA} editing of the genomes of {SARS-CoV-2} and other coronaviruses and its impact on their longer term evolution.},
    year = {2021},
    pages = {62--72},
    volume = {556},
    abstract = {Members of the APOBEC family of cytidine deaminases show antiviral activities in mammalian cells through lethal editing in the genomes of small DNA viruses, herpesviruses and retroviruses, and potentially those of RNA viruses such as coronaviruses. Consistent with the latter, APOBEC-like directional C→U transitions of genomic plus-strand RNA are greatly overrepresented in SARS-CoV-2 genome sequences of variants emerging during the COVID-19 pandemic. A C→U mutational process may leave evolutionary imprints on coronavirus genomes, including extensive homoplasy from editing and reversion at targeted sites and the occurrence of driven amino acid sequence changes in viral proteins. If sustained over longer periods, this process may account for the previously reported marked global depletion of C and excess of U bases in human seasonal coronavirus genomes. This review synthesizes the current knowledge on APOBEC evolution and function and the evidence of their role in APOBEC-mediated genome editing of SARS-CoV-2 and other coronaviruses.},
    doi = {10.1016/j.virol.2020.12.018},
    keywords = {APOBEC; Coronavirus; Innate immunity; SARS-CoV-2; Virus evolution},
    pmid = {33545556},
    pubstate = {aheadofprint},
    }
  • [DOI] S. Dellicour, M. S. Gill, N. R. Faria, A. Rambaut, O. G. Pybus, M. A. Suchard, and P. Lemey, "Relax, keep walking-a practical guide to continuous phylogeographic inference with BEAST.," Mol Biol Evol, 2021.
    [Bibtex]
    @Article{Dellicour:21,
    author = {Dellicour, Simon and Gill, Mandev S. and Faria, Nuno R. and Rambaut, Andrew and Pybus, Oliver G. and Suchard, Marc A. and Lemey, Philippe},
    journal = {{Mol Biol Evol}},
    title = {Relax, keep walking-a practical guide to continuous phylogeographic inference with {BEAST}.},
    year = {2021},
    abstract = {Spatially-explicit phylogeographic analyses can be performed with an inference framework that employs relaxed random walks to reconstruct phylogenetic dispersal histories in continuous space. This core model was first implemented ten years ago and has opened up new opportunities in the field of phylodynamics, allowing researchers to map and analyse the spatial dissemination of rapidly evolving pathogens. We here provide a detailed and step-by-step guide on how to set up, run, and interpret continuous phylogeographic analyses using the programs BEAUti, BEAST, Tracer, and TreeAnnotator.},
    doi = {10.1093/molbev/msab031},
    keywords = {BEAST; continuous phylogeography; relaxed random walk; viruses},
    pmid = {33528560},
    pubstate = {aheadofprint},
    }
  • [DOI] F. Stefaniak and J. M. Bujnicki, "AnnapuRNA: a scoring function for predicting RNA-small molecule binding poses.," PLoS Comput Biol, vol. 17, p. e1008309, 2021.
    [Bibtex]
    @Article{Stefaniak:21,
    author = {Stefaniak, Filip and Bujnicki, Janusz M.},
    journal = {{PLoS Comput Biol}},
    title = {{AnnapuRNA}: A scoring function for predicting {RNA}-small molecule binding poses.},
    year = {2021},
    pages = {e1008309},
    volume = {17},
    abstract = {RNA is considered as an attractive target for new small molecule drugs. Designing active compounds can be facilitated by computational modeling. Most of the available tools developed for these prediction purposes, such as molecular docking or scoring functions, are parametrized for protein targets. The performance of these methods, when applied to RNA-ligand systems, is insufficient. To overcome these problems, we developed AnnapuRNA, a new knowledge-based scoring function designed to evaluate RNA-ligand complex structures, generated by any computational docking method. We also evaluated three main factors that may influence the structure prediction, i.e., the starting conformer of a ligand, the docking program, and the scoring function used. We applied the AnnapuRNA method for a post-hoc study of the recently published structures of the FMN riboswitch. Software is available at https://github.com/filipspl/AnnapuRNA.},
    doi = {10.1371/journal.pcbi.1008309},
    issue = {2},
    pmid = {33524009},
    pubstate = {epublish},
    }
  • [DOI] F. Aubry, S. Jacobs, M. Darmuzey, S. Lequime, L. Delang, A. Fontaine, N. Jupatanakul, E. F. Miot, S. Dabo, C. Manet, X. Montagutelli, A. Baidaliuk, F. Gámbaro, E. Simon-Lorière, M. Gilsoul, C. M. Romero-Vivas, V. Cao-Lormeau, R. G. Jarman, C. T. Diagne, O. Faye, O. Faye, A. A. Sall, J. Neyts, L. Nguyen, S. J. F. Kaptein, and L. Lambrechts, "Recent african strains of Zika virus display higher transmissibility and fetal pathogenicity than Asian strains.," Nat Commun, vol. 12, p. 916, 2021.
    [Bibtex]
    @Article{Aubry:21,
    author = {Aubry, Fabien and Jacobs, Sofie and Darmuzey, Maïlis and Lequime, Sebastian and Delang, Leen and Fontaine, Albin and Jupatanakul, Natapong and Miot, Elliott F. and Dabo, Stéphanie and Manet, Caroline and Montagutelli, Xavier and Baidaliuk, Artem and Gámbaro, Fabiana and Simon-Lorière, Etienne and Gilsoul, Maxime and Romero-Vivas, Claudia M. and Cao-Lormeau, Van-Mai and Jarman, Richard G. and Diagne, Cheikh T. and Faye, Oumar and Faye, Ousmane and Sall, Amadou A. and Neyts, Johan and Nguyen, Laurent and Kaptein, Suzanne J. F. and Lambrechts, Louis},
    journal = {{Nat Commun}},
    title = {Recent African strains of {Zika} virus display higher transmissibility and fetal pathogenicity than {A}sian strains.},
    year = {2021},
    pages = {916},
    volume = {12},
    abstract = {The global emergence of Zika virus (ZIKV) revealed the unprecedented ability for a mosquito-borne virus to cause congenital birth defects. A puzzling aspect of ZIKV emergence is that all human outbreaks and birth defects to date have been exclusively associated with the Asian ZIKV lineage, despite a growing body of laboratory evidence pointing towards higher transmissibility and pathogenicity of the African ZIKV lineage. Whether this apparent paradox reflects the use of relatively old African ZIKV strains in most laboratory studies is unclear. Here, we experimentally compare seven low-passage ZIKV strains representing the recently circulating viral genetic diversity. We find that recent African ZIKV strains display higher transmissibility in mosquitoes and higher lethality in both adult and fetal mice than their Asian counterparts. We emphasize the high epidemic potential of African ZIKV strains and suggest that they could more easily go unnoticed by public health surveillance systems than Asian strains due to their propensity to cause fetal loss rather than birth defects.},
    doi = {10.1038/s41467-021-21199-z},
    issue = {1},
    pmid = {33568638},
    pubstate = {epublish},
    }
  • [DOI] T. Spicher, M. Delitz, A. B. de Schneider, and M. T. Wolfinger, "Dynamic molecular epidemiology reveals lineage-associated single-nucleotide variants that alter RNA structure in Chikungunya virus.," Genes, vol. 12, 2021.
    [Bibtex]
    @Article{Spicher:21,
    author = {Spicher, Thomas and Delitz, Markus and Schneider, Adriano de Bernardi and Wolfinger, Michael T.},
    journal = {Genes},
    title = {Dynamic Molecular Epidemiology Reveals Lineage-Associated Single-Nucleotide Variants That Alter {RNA} Structure in {C}hikungunya Virus.},
    year = {2021},
    volume = {12},
    abstract = {Chikungunya virus (CHIKV) is an emerging which causes millions of human infections every year. Outbreaks have been reported in Africa and Asia since the early 1950s, from three CHIKV lineages: West African, East Central South African, and Asian Urban. As new outbreaks occurred in the Americas, individual strains from the known lineages have evolved, creating new monophyletic groups that generated novel geographic-based lineages. Building on a recently updated phylogeny of CHIKV, we report here the availability of an interactive CHIKV phylodynamics dataset, which is based on more than 900 publicly available CHIKV genomes. We provide an interactive view of CHIKV molecular epidemiology built on Nextstrain, a web-based visualization framework for real-time tracking of pathogen evolution. CHIKV molecular epidemiology reveals single nucleotide variants that change the stability and fold of locally stable RNA structures. We propose alternative RNA structure formation in different CHIKV lineages by predicting more than a dozen RNA elements that are subject to perturbation of the structure ensemble upon variation of a single nucleotide.},
    doi = {10.3390/genes12020239},
    issue = {2},
    keywords = {Chikungunya virus; RNA structure; molecular epidemiology; mutation},
    pmid = {33567556},
    pubstate = {epublish},
    }
  • [DOI] A. Dastjerdi, D. J. Everest, H. Davies, D. Denk, and R. Zell, "A novel dicistrovirus in a captive red squirrel (Sciurus vulgaris)," J Gen Virol, 2021.
    [Bibtex]
    @Article{Dastjerdi:21,
    author = {Dastjerdi, Akbar and Everest, David J. and Davies, Hannah and Denk, Daniela and Zell, Roland},
    journal = {{J Gen Virol}},
    title = {A novel dicistrovirus in a captive red squirrel ({S}ciurus vulgaris)},
    year = {2021},
    abstract = {Dicistroviruses are single-stranded RNA viruses in the family . The viruses have mainly been detected in arthropods and are the cause of several devastating diseases in many of these species such as honeybees. Increasingly, dicistroviruses have also been detected in both mammalian and avian species in faeces, blood and liver, but with unconfirmed pathology. Here, we report a novel dicistrovirus detected in the intestinal content of a captive red squirrel with enteritis along with the disease history, pathology and genomic characterisation of the virus. Virus particle morphology resembled those of picornaviruses with a diameter of 28-32 nm but failed to be detected using a mammalian/avian pan viral microarray. Next-generation sequencing confirmed a dicistrovirus having a typical dicistrovirus genome organization, but with the polyprotein 1 being shorter by about 100 amino acids, compared to that of other dicistroviruses. Phylogenetic analysis of ORF1 and ORF2 sequences clustered the virus with two yet unassigned dicistroviruses detected in and a freshwater arthropod and likely to be designated to a new genus. Our data further highlights the ever-growing diversity of dicistroviruses, but the clinical significance of the virus in mammalian species and particularly red squirrels has yet to be established.},
    doi = {10.1099/jgv.0.001555},
    keywords = {dicistrovirus; enteritis; genomic organisation; phylogeny; red squirrel},
    pmid = {33565956},
    pubstate = {aheadofprint},
    }
  • [DOI] D. J. Baker, A. Aydin, T. Le-Viet, G. L. Kay, S. Rudder, L. de Oliveira Martins, A. P. Tedim, A. Kolyva, M. Diaz, N. Alikhan, L. Meadows, A. Bell, A. V. Gutierrez, A. J. Trotter, N. M. Thomson, R. Gilroy, L. Griffith, E. M. Adriaenssens, R. Stanley, I. G. Charles, N. Elumogo, J. Wain, R. Prakash, E. Meader, A. E. Mather, M. A. Webber, S. Dervisevic, A. J. Page, and J. O'Grady, "CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes.," Genome Med, vol. 13, p. 21, 2021.
    [Bibtex]
    @Article{Baker:21,
    author = {Baker, Dave J. and Aydin, Alp and Le-Viet, Thanh and Kay, Gemma L. and Rudder, Steven and de Oliveira Martins, Leonardo and Tedim, Ana P. and Kolyva, Anastasia and Diaz, Maria and Alikhan, Nabil-Fareed and Meadows, Lizzie and Bell, Andrew and Gutierrez, Ana Victoria and Trotter, Alexander J. and Thomson, Nicholas M. and Gilroy, Rachel and Griffith, Luke and Adriaenssens, Evelien M. and Stanley, Rachael and Charles, Ian G. and Elumogo, Ngozi and Wain, John and Prakash, Reenesh and Meader, Emma and Mather, Alison E. and Webber, Mark A. and Dervisevic, Samir and Page, Andrew J. and O'Grady, Justin},
    journal = {{Genome Med}},
    title = {{CoronaHiT}: high-throughput sequencing of {SARS-CoV-2} genomes.},
    year = {2021},
    pages = {21},
    volume = {13},
    abstract = {We present CoronaHiT, a platform and throughput flexible method for sequencing SARS-CoV-2 genomes (≤ 96 on MinION or > 96 on Illumina NextSeq) depending on changing requirements experienced during the pandemic. CoronaHiT uses transposase-based library preparation of ARTIC PCR products. Method performance was demonstrated by sequencing 2 plates containing 95 and 59 SARS-CoV-2 genomes on nanopore and Illumina platforms and comparing to the ARTIC LoCost nanopore method. Of the 154 samples sequenced using all 3 methods, ≥ 90% genome coverage was obtained for 64.3% using ARTIC LoCost, 71.4% using CoronaHiT-ONT and 76.6% using CoronaHiT-Illumina, with almost identical clustering on a maximum likelihood tree. This protocol will aid the rapid expansion of SARS-CoV-2 genome sequencing globally.},
    doi = {10.1186/s13073-021-00839-5},
    issue = {1},
    keywords = {ARTIC; Genetic; Genome; Multiplexing; NGS; Nanopore; SARS-CoV-2; Sequencing},
    pmid = {33563320},
    pubstate = {epublish},
    }
  • [DOI] R. Van Damme, M. Hölzer, A. Viehweger, B. Müller, E. Bongcam-Rudloff, and C. Brandt, "Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN).," PLoS Comput Biol, vol. 17, p. e1008716, 2021.
    [Bibtex]
    @Article{VanDamme:21,
    author = {Van Damme, Renaud and Hölzer, Martin and Viehweger, Adrian and Müller, Bettina and Bongcam-Rudloff, Erik and Brandt, Christian},
    journal = {{PLoS Comput Biol}},
    title = {Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis ({MUFFIN}).},
    year = {2021},
    pages = {e1008716},
    volume = {17},
    abstract = {Metagenomics has redefined many areas of microbiology. However, metagenome-assembled genomes (MAGs) are often fragmented, primarily when sequencing was performed with short reads. Recent long-read sequencing technologies promise to improve genome reconstruction. However, the integration of two different sequencing modalities makes downstream analyses complex. We, therefore, developed MUFFIN, a complete metagenomic workflow that uses short and long reads to produce high-quality bins and their annotations. The workflow is written by using Nextflow, a workflow orchestration software, to achieve high reproducibility and fast and straightforward use. This workflow also produces the taxonomic classification and KEGG pathways of the bins and can be further used for quantification and annotation by providing RNA-Seq data (optionally). We tested the workflow using twenty biogas reactor samples and assessed the capacity of MUFFIN to process and output relevant files needed to analyze the microbial community and their function. MUFFIN produces functional pathway predictions and, if provided de novo metatranscript annotations across the metagenomic sample and for each bin. MUFFIN is available on github under GNUv3 licence: https://github.com/RVanDamme/MUFFIN.},
    doi = {10.1371/journal.pcbi.1008716},
    issue = {2},
    pmid = {33561126},
    pubstate = {aheadofprint},
    }
  • [DOI] D. Bojkova, J. E. McGreig, K. McLaughlin, S. G. Masterson, M. Antczak, M. Widera, V. Krähling, S. Ciesek, M. N. Wass, M. Michaelis, and J. Cinatl, "Differentially conserved amino acid positions may reflect differences in SARS-CoV-2 and SARS-CoV behaviour.," Bioinformatics, 2021.
    [Bibtex]
    @Article{Bojkova:21,
    author = {Bojkova, Denisa and McGreig, Jake E. and McLaughlin, Katie-May and Masterson, Stuart G. and Antczak, Magdalena and Widera, Marek and Krähling, Verena and Ciesek, Sandra and Wass, Mark N. and Michaelis, Martin and Cinatl, Jindrich},
    journal = {{Bioinformatics}},
    title = {Differentially conserved amino acid positions may reflect differences in {SARS-CoV-2} and {SARS-CoV} behaviour.},
    year = {2021},
    abstract = {SARS-CoV-2 is a novel coronavirus currently causing a pandemic. Here, we performed a combined in-silico and cell culture comparison of SARS-CoV-2 and the closely related SARS-CoV. Many amino acid positions are differentially conserved between SARS-CoV-2 and SARS-CoV, which reflects the discrepancies in virus behaviour, i.e. more effective human-to-human transmission of SARS-CoV-2 and higher mortality associated with SARS-CoV. Variations in the S protein (mediates virus entry) were associated with differences in its interaction with ACE2 (cellular S receptor) and sensitivity to TMPRSS2 (enables virus entry via S cleavage) inhibition. Anti-ACE2 antibodies more strongly inhibited SARS-CoV than SARS-CoV-2 infection, probably due to a stronger SARS-CoV-2 S-ACE2 affinity relative to SARS-CoV S. Moreover, SARS-CoV-2 and SARS-CoV displayed differences in cell tropism. Cellular ACE2 and TMPRSS2 levels did not indicate susceptibility to SARS-CoV-2. In conclusion, we identified genomic variation between SARS-CoV-2 and SARS-CoV that may reflect the differences in their clinical and biological behaviour. Supplementary data are available at Bioinformatics online.},
    doi = {10.1093/bioinformatics/btab094},
    pmid = {33560365},
    pubstate = {aheadofprint},
    }
  • [DOI] S. S. Good, J. Westover, K. H. Jung, X. Zhou, A. Moussa, P. La Colla, G. Collu, B. Canard, and J. Sommadossi, "AT-527, a double prodrug of a guanosine nucleotide analog, is a potent inhibitor of SARS-CoV-2 in vitro and a promising oral antiviral for treatment of COVID-19.," Antimicrob Agents Chemother, 2021.
    [Bibtex]
    @Article{Good:21,
    author = {Good, Steven S. and Westover, Jonna and Jung, Kie Hoon and Zhou, Xiao-Jian and Moussa, Adel and La Colla, Paolo and Collu, Gabriella and Canard, Bruno and Sommadossi, Jean-Pierre},
    journal = {{Antimicrob Agents Chemother}},
    title = {{AT}-527, a double prodrug of a guanosine nucleotide analog, is a potent inhibitor of {SARS-CoV-2} in vitro and a promising oral antiviral for treatment of {COVID-19}.},
    year = {2021},
    abstract = {The impact of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of COVID-19, is global and unprecedented. Although remdesivir has recently been approved by the FDA to treat SARS-CoV-2 infection, no oral antiviral is available for outpatient treatment. AT-527, an orally administered double prodrug of a guanosine nucleotide analog, was previously shown to be highly efficacious and well tolerated in HCV-infected subjects. Here, we report the potent activity of AT-511, the free base of AT-527, against several coronaviruses, including SARS-CoV-2. In normal human airway epithelial cells, the concentration of AT-511 required to inhibit replication of SARS-CoV-2 by 90% (EC ) was 0.47 μM, very similar to its EC against HCoV-229E, HCoV-OC43 and SARS-CoV in Huh-7 cells. Little to no cytotoxicity was observed for AT-511 at concentrations up to 100 μM. Substantial levels of the active triphosphate metabolite AT-9010 were formed in normal human bronchial and nasal epithelial cells incubated with 10 μM AT-511 (698 ± 15 and 236 ± 14 μM, respectively), with a half-life of at least 38 h. Results from steady-state pharmacokinetic and tissue distribution studies of non-human primates administered oral doses of AT-527, as well as pharmacokinetic data from subjects given daily oral doses of AT-527, predict that twice daily oral doses of 550 mg AT-527 will produce AT-9010 trough concentrations in human lung that exceed the EC observed for the prodrug against SARS-CoV-2 replication. This suggests that AT-527 may be an effective treatment option for COVID-19.},
    doi = {10.1128/AAC.02479-20},
    pmid = {33558299},
    pubstate = {aheadofprint},
    }
  • [DOI] P. P. Mathkar, X. Chen, A. Sulovari, and D. Li, "Characterization of hepatitis B virus integrations identified in hepatocellular carcinoma genomes.," Viruses, vol. 13, 2021.
    [Bibtex]
    @Article{Mathkar:21,
    author = {Mathkar, Pranav P. and Chen, Xun and Sulovari, Arvis and Li, Dawei},
    journal = {Viruses},
    title = {Characterization of Hepatitis {B} Virus Integrations Identified in Hepatocellular Carcinoma Genomes.},
    year = {2021},
    volume = {13},
    abstract = {Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality. Almost half of HCC cases are associated with hepatitis B virus (HBV) infections, which often lead to HBV sequence integrations in the human genome. Accurate identification of HBV integration sites at a single nucleotide resolution is critical for developing a better understanding of the cancer genome landscape and of the disease itself. Here, we performed further analyses and characterization of HBV integrations identified by our recently reported VIcaller platform in recurrent or known HCC genes (such as , , and ) as well as non-recurrent cancer-related genes (such as , , and ). Our pathway enrichment analysis revealed multiple pathways involving the alcohol dehydrogenase 4 gene, such as the metabolism pathways of retinol, tyrosine, and fatty acid. Further analysis of the HBV integration sites revealed distinct patterns involving the integration upper breakpoints, integrated genome lengths, and integration allele fractions between tumor and normal tissues. Our analysis also implies that the VIcaller method has diagnostic potential through discovering novel clonal integrations in cancer-related genes. In conclusion, although VIcaller is a hypothesis free virome-wide approach, it can still be applied to accurately identify genome-wide integration events of a specific candidate virus and their integration allele fractions.},
    doi = {10.3390/v13020245},
    issue = {2},
    keywords = {VIcaller; hepatitis B virus (HBV); hepatocellular carcinoma (HCC); integration allele fraction; viral integration; virome-wide detection},
    pmid = {33557409},
    pubstate = {epublish},
    }
  • [DOI] A. Oulas, M. Zanti, M. Tomazou, M. Zachariou, G. Minadakis, M. M. Bourdakou, P. Pavlidis, and G. M. Spyrou, "Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains," PLoS One, vol. 16, iss. 1, p. e0238665, 2021.
    [Bibtex]
    @Article{Oulas:21,
    author = {Anastasis Oulas and Maria Zanti and Marios Tomazou and Margarita Zachariou and George Minadakis and Marilena M. Bourdakou and Pavlos Pavlidis and George M. Spyrou},
    journal = {{PLoS One}},
    title = {Generalized linear models provide a measure of virulence for specific mutations in {SARS}-{CoV}-2 strains},
    year = {2021},
    number = {1},
    pages = {e0238665},
    volume = {16},
    doi = {10.1371/journal.pone.0238665},
    editor = {Jean-Luc EPH Darlix},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] F. Briand, E. Niqueux, A. Schmitz, C. Martenot, M. Cherbonnel, P. Massin, F. Kerbrat, M. Chatel, C. Guillemoto, C. Guillou-Cloarec, K. Ogor, A. L. Prioux, C. Allée, V. Beven, E. Hirchaud, Y. Blanchard, A. Scoizec, S. L. Bouquin, N. Eterradossi, and B. Grasland, "Highly pathogenic avian influenza A(H5N8) virus spread by short- and long-range transmission, France, 2016–17," Emerg Infect Dis, vol. 27, iss. 2, p. 508–516, 2021.
    [Bibtex]
    @Article{Briand:21,
    author = {Fran{\c{c}}ois-Xavier Briand and Eric Niqueux and Audrey Schmitz and Claire Martenot and Martine Cherbonnel and Pascale Massin and Florian Kerbrat and Marina Chatel and Carole Guillemoto and Cecile Guillou-Cloarec and Katell Ogor and Aur{\'{e}}lie Le Prioux and Chantal All{\'{e}}e and V{\'{e}}ronique Beven and Edouard Hirchaud and Yannick Blanchard and Axelle Scoizec and Sophie Le Bouquin and Nicolas Eterradossi and B{\'{e}}atrice Grasland},
    journal = {{Emerg Infect Dis}},
    title = {Highly Pathogenic Avian Influenza {A(H5N8)} Virus Spread by Short- and Long-Range Transmission, {F}rance, 2016--17},
    year = {2021},
    number = {2},
    pages = {508--516},
    volume = {27},
    doi = {10.3201/eid2702.202920},
    publisher = {Centers for Disease Control and Prevention ({CDC})},
    }
  • [DOI] V. Sypsa, S. Roussos, D. Paraskevis, T. Lytras, S. Tsiodras, and A. Hatzakis, "Effects of social distancing measures during the first epidemic wave of Severe Acute Respiratory Syndrome infection, Greece," Emerg Infect Dis, vol. 27, iss. 2, p. 452–462, 2021.
    [Bibtex]
    @Article{Sypsa:21,
    author = {Vana Sypsa and Sotirios Roussos and Dimitrios Paraskevis and Theodore Lytras and Sotirios Tsiodras and Angelos Hatzakis},
    journal = {{Emerg Infect Dis}},
    title = {Effects of Social Distancing Measures during the First Epidemic Wave of {S}evere {A}cute {R}espiratory {S}yndrome Infection, {G}reece},
    year = {2021},
    number = {2},
    pages = {452--462},
    volume = {27},
    doi = {10.3201/eid2702.203412},
    publisher = {Centers for Disease Control and Prevention ({CDC})},
    }
  • [DOI] H. H. Buchholz, M. L. Michelsen, L. M. Bolaños, E. Browne, M. J. Allen, and B. Temperton, "Efficient dilution-to-extinction isolation of novel virus–host model systems for fastidious heterotrophic bacteria," ISME J, 2021.
    [Bibtex]
    @Article{Buchholz:21,
    author = {Holger H. Buchholz and Michelle L. Michelsen and Luis M. Bola{\~{n}}os and Emily Browne and Michael J. Allen and Ben Temperton},
    journal = {{ISME J}},
    title = {Efficient dilution-to-extinction isolation of novel virus{\textendash}host model systems for fastidious heterotrophic bacteria},
    year = {2021},
    doi = {10.1038/s41396-020-00872-z},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] G. Nouailles, E. Wyler, P. Pennitz, D. Postmus, D. Vladrimirova, J. Kazmierski, F. Pott, K. Dietert, M. Mülleder, V. Farztdinov, B. Obermayer, S. Wienhold, S. Andreotti, T. Hoefler, B. Sawitzki, C. Drosten, L. Sander, N. Suttorp, M. Ralser, D. Beule, A. Gruber, C. Goffinet, M. Landthaler, J. Trimpert, and M. Witzenrath, "Longitudinal omics in syrian hamsters integrated with human data unravel cellular effector responses to moderate covid-19," Research Square, 2021.
    [Bibtex]
    @Article{Nouailles:21,
    author = {Nouailles, Geraldine and Wyler, Emanuel and Pennitz, Peter and Postmus, Dylan and Vladrimirova, Daria and Kazmierski, Julia and Pott, Fabian and Dietert, Kristina and Mülleder, Michael and Farztdinov, Vadim and Obermayer, Benedikt and Wienhold, Sandra-Maria and Andreotti, Sandro and Hoefler, Thomas and Sawitzki, Birgit and Drosten, Christian and Sander, Leif and Suttorp, Norbert and Ralser, Markus and Beule, Dieter and Gruber, Achim and Goffinet, Christine and Landthaler, Markus and Trimpert, Jakob and Witzenrath, Martin},
    journal = {{Research Square}},
    title = {Longitudinal omics in Syrian hamsters integrated with human data unravel cellular effector responses to moderate COVID-19},
    year = {2021},
    abstract = {In COVID-19, immune responses are key in determining disease severity. However, cellular mechanisms at the onset of inflammatory lung injury in SARS-CoV-2 infection, particularly involving endothelial cells, remain ill-defined. Using Syrian hamsters as model for moderate COVID-19, we conducted a detailed longitudinal analysis of systemic and pulmonary cellular responses, and corroborated it with datasets from COVID-19 patients. Monocyte-derived macrophages in lungs exerted the earliest and strongest transcriptional response to infection, including induction of pro-inflammatory genes, while epithelial cells showed weak activation. Without evidence for productive infection, endothelial cells reacted, depending on cell subtypes, by strong and early expression of anti-viral, pro-inflammatory, and T cell recruiting genes. Recruitment of cytotoxic T cells as well as emergence of IgM antibodies preceded viral clearance at day 5 post infection. Investigating SARS-CoV-2 infected Syrian hamsters can thus identify cell type-specific effector functions, provide detailed insights into pathomechanisms of COVID-19, and inform therapeutic strategies.},
    doi = {10.21203/rs.3.rs-148392/v1},
    url = {https://doi.org/10.21203/rs.3.rs-148392/v1},
    }
  • [DOI] V. Haage, A. Moreira-Soto, J. A. Sacks, V. Corman, C. Drosten, and F. Drexler, "Limited specificity of SARS-CoV-2 antigen-detecting rapid diagnostic tests at low temperatures," medRxiv, 2021.
    [Bibtex]
    @Article{Haage:21,
    author = {Verena Haage and Andres Moreira-Soto and Jilian A. Sacks and Victor Corman and Christian Drosten and Felix Drexler},
    journal = {{medRxiv}},
    title = {Limited specificity of {SARS}-{CoV}-2 antigen-detecting rapid diagnostic tests at low temperatures},
    year = {2021},
    doi = {10.1101/2021.02.01.21250904},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] C. Brandt, R. Spott, M. Hölzer, D. Kühnert, S. Fuchs, M. Lohde, M. Marquet, A. Viehweger, D. Rimek, and M. W. Pletz, "Molecular epidemiology of SARS-CoV-2 - a regional to global perspective," medRxiv, 2021.
    [Bibtex]
    @Article{Brandt:21,
    author = {Christian Brandt and Riccardo Spott and Martin Hölzer and Denise Kühnert and Stephan Fuchs and Mara Lohde and Mike Marquet and Adrian Viehweger and Dagmar Rimek and Mathias W. Pletz},
    journal = {{medRxiv}},
    title = {Molecular epidemiology of {SARS}-{CoV}-2 - a regional to global perspective},
    year = {2021},
    doi = {10.1101/2021.01.25.21250447},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] E. G. Kostaki, G. A. Pavlopoulos, K. Verrou, G. Ampatziadis-Michailidis, V. Harokopos, P. Hatzis, P. Moulos, N. Siafakas, S. Pournaras, C. Hadjichristodoulou, F. Chatzopoulou, D. Chatzidimitriou, P. Panagopoulos, P. Lourida, A. Argyraki, T. Lytras, S. Sapounas, G. Gerolymatos, G. Panagiotakopoulos, P. Prezerakos, S. Tsiodras, V. Sypsa, A. Hatzakis, C. Anastassopoulou, N. Spanakis, A. Tsakris, M. A. Dimopoulos, A. Kotanidou, P. Sfikakis, G. Kollias, G. Magiorkinis, and D. Paraskevis, "Molecular epidemiology of SARS-CoV-2 in greece reveals low rates of onward virus transmission after lifting of travel restrictions based on risk assessment during summer 2020," medRxiv, 2021.
    [Bibtex]
    @Article{Kostaki:21,
    author = {Evangelia Georgia Kostaki and Georgios A. Pavlopoulos and Kleio-Maria Verrou and Giannis Ampatziadis-Michailidis and Vaggelis Harokopos and Pantelis Hatzis and Panagiotis Moulos and Nikolaos Siafakas and Spyridon Pournaras and Christos Hadjichristodoulou and Fani Chatzopoulou and Dimitrios Chatzidimitriou and Periklis Panagopoulos and Panagiota Lourida and Aikaterini Argyraki and Theodoros Lytras and Spyros Sapounas and Gerasimos Gerolymatos and Georgios Panagiotakopoulos and Panagiotis Prezerakos and Sotirios Tsiodras and Vana Sypsa and Angelos Hatzakis and Cleo Anastassopoulou and Nikolaos Spanakis and Athanasios Tsakris and Meletios Athanasios Dimopoulos and Anastasia Kotanidou and Petros Sfikakis and Georgios Kollias and Gkikas Magiorkinis and Dimitrios Paraskevis},
    journal = {{medRxiv}},
    title = {Molecular epidemiology of {SARS}-{CoV}-2 in Greece reveals low rates of onward virus transmission after lifting of travel restrictions based on risk assessment during summer 2020},
    year = {2021},
    doi = {10.1101/2021.01.31.21250868},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] A. Wittig, F. Miranda, M. Tang, M. Hölzer, B. Y. Renard, and S. Fuchs, "CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillance," bioRxiv, 2021.
    [Bibtex]
    @Article{Wittig:21,
    author = {Alice Wittig and F{\'{a}}bio Miranda and Ming Tang and Martin Hölzer and Bernhard Y. Renard and Stephan Fuchs},
    journal = {{bioRxiv}},
    title = {{CovRadar}: Continuously tracking and filtering {SARS}-{CoV}-2 mutations for molecular surveillance},
    year = {2021},
    doi = {10.1101/2021.02.03.429146},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] K. Vanshylla, V. D. Cristanziano, F. Kleipass, F. Dewald, P. Schommers, L. Gieselmann, H. Gruell, M. Schlotz, M. S. Ercanoglu, R. Stumpf, P. Mayer, E. Heger, W. Johannis, C. Horn, I. Suárez, N. Jung, S. Salomon, K. A. Eberhardt, G. Fätkenheuer, N. Pfeifer, R. Eggeling, M. Augustin, C. Lehmann, and F. Klein, "Kinetics and correlates of the neutralizing antibody response to SARS-CoV-2," bioRxiv, 2021.
    [Bibtex]
    @Article{Vanshylla:21,
    author = {Kanika Vanshylla and Veronica Di Cristanziano and Franziska Kleipass and Felix Dewald and Philipp Schommers and Lutz Gieselmann and Henning Gruell and Maike Schlotz and Meryem S Ercanoglu and Ricarda Stumpf and Petra Mayer and Eva Heger and Wibke Johannis and Carola Horn and Isabelle Su{\'{a}}rez and Norma Jung and Susanne Salomon and Kirsten Alexandra Eberhardt and Gerd Fätkenheuer and Nico Pfeifer and Ralf Eggeling and Max Augustin and Clara Lehmann and Florian Klein},
    journal = {{bioRxiv}},
    title = {Kinetics and correlates of the neutralizing antibody response to {SARS}-{CoV}-2},
    year = {2021},
    doi = {10.1101/2021.01.26.428207},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] J. M. Bartoszewicz, U. Genske, and B. Y. Renard, "A deep learning framework for real-time detection of novel pathogens during sequencing," bioRxiv, 2021.
    [Bibtex]
    @Article{Bartoszewicz:21,
    author = {Jakub M. Bartoszewicz and Ulrich Genske and Bernhard Y. Renard},
    journal = {{bioRxiv}},
    title = {A deep learning framework for real-time detection of novel pathogens during sequencing},
    year = {2021},
    doi = {10.1101/2021.01.26.428301},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] C. B. F. Vogels, M. Breban, T. Alpert, M. E. Petrone, A. E. Watkins, E. B. Hodcroft, C. E. Mason, G. Khullar, J. Metti, J. T. Dudley, M. J. MacKay, M. Nash, J. Wang, C. Liu, P. Hui, S. Murphy, C. Neal, E. Laszlo, M. L. Landry, A. Muyombwe, R. Downing, J. Razeq, R. A. Neher, J. R. Fauver, and N. D. Grubaugh, "PCR assay to enhance global surveillance for SARS-CoV-2 variants of concern," medRxiv, 2021.
    [Bibtex]
    @Article{Vogels:21,
    author = {Chantal B.F. Vogels and Mallery Breban and Tara Alpert and Mary E. Petrone and Anne E. Watkins and Emma B. Hodcroft and Christopher E. Mason and Gaurav Khullar and Jessica Metti and Joel T. Dudley and Matthew J. MacKay and Megan Nash and Jianhui Wang and Chen Liu and Pei Hui and Steven Murphy and Caleb Neal and Eva Laszlo and Marie L. Landry and Anthony Muyombwe and Randy Downing and Jafar Razeq and Richard A. Neher and Joseph R. Fauver and Nathan D. Grubaugh},
    journal = {{medRxiv}},
    title = {{PCR} assay to enhance global surveillance for {SARS}-{CoV}-2 variants of concern},
    year = {2021},
    doi = {10.1101/2021.01.28.21250486},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] B. Tönshoff, B. Müller, R. Elling, H. Renk, P. Meissner, H. Hengel, S. F. Garbade, M. Kieser, K. Jeltsch, J. Grulich-Henn, J. Euler, M. Stich, K. Chobanyan-Jürgens, M. Zernickel, A. Janda, L. Wölfle, T. Stamminger, T. Iftner, T. Ganzenmueller, C. Schmitt, T. Görne, V. Laketa, S. Olberg, A. Plaszczyca, M. Cortese, R. Bartenschlager, C. Pape, R. Remme, D. Huzly, M. Panning, S. Weigang, S. Giese, K. Ciminski, J. Ankerhold, G. Kochs, M. Schwemmle, R. Handgretinger, C. M. Niemeyer, C. Engel, W. V. Kern, G. F. Hoffmann, A. R. Franz, P. Henneke, K. Debatin, and H. Kräusslich, "Prevalence of SARS-CoV-2 infection in children and their parents in Southwest Germany," JAMA Pediatr, 2021.
    [Bibtex]
    @Article{Toenshoff:21,
    author = {Burkhard Tönshoff and Barbara Müller and Roland Elling and Hanna Renk and Peter Meissner and Hartmut Hengel and Sven F. Garbade and Meinhard Kieser and Kathrin Jeltsch and Jürgen Grulich-Henn and Julia Euler and Maximilian Stich and Kristine Chobanyan-Jürgens and Maria Zernickel and Ale{\v{s}} Janda and Lena Wölfle and Thomas Stamminger and Thomas Iftner and Tina Ganzenmueller and Christian Schmitt and Tessa Görne and Vibor Laketa and Sylvia Olberg and Anna Plaszczyca and Mirko Cortese and Ralf Bartenschlager and Constantin Pape and Roman Remme and Daniela Huzly and Marcus Panning and Sebastian Weigang and Sebastian Giese and Kevin Ciminski and Jakob Ankerhold and Georg Kochs and Martin Schwemmle and Rupert Handgretinger and Charlotte M. Niemeyer and Corinna Engel and Winfried V. Kern and Georg Friedrich Hoffmann and Axel R. Franz and Philipp Henneke and Klaus-Michael Debatin and Hans-Georg Kräusslich},
    journal = {{JAMA Pediatr}},
    title = {Prevalence of {SARS}-{CoV}-2 Infection in Children and Their Parents in {S}outhwest {G}ermany},
    year = {2021},
    doi = {10.1001/jamapediatrics.2021.0001},
    publisher = {American Medical Association ({AMA})},
    }
  • [DOI] H. Slanina, R. Madhugiri, G. Bylapudi, K. Schultheiß, N. Karl, A. Gulyaeva, A. E. Gorbalenya, U. Linne, and J. Ziebuhr, "Coronavirus replication–transcription complex: Vital and selective NMPylation of a conserved site in nsp9 by the NiRAN-RdRp subunit," Proc Natl Acad Sci USA, vol. 118, iss. 6, p. e2022310118, 2021.
    [Bibtex]
    @Article{Slanina:21,
    author = {Heiko Slanina and Ramakanth Madhugiri and Ganesh Bylapudi and Karin Schulthei{\ss} and Nadja Karl and Anastasia Gulyaeva and Alexander E. Gorbalenya and Uwe Linne and John Ziebuhr},
    journal = {{Proc Natl Acad Sci USA}},
    title = {Coronavirus replication{\textendash}transcription complex: {V}ital and selective {NMPylation} of a conserved site in nsp9 by the {NiRAN}-{RdRp} subunit},
    year = {2021},
    number = {6},
    pages = {e2022310118},
    volume = {118},
    doi = {10.1073/pnas.2022310118},
    publisher = {Proceedings of the National Academy of Sciences},
    }
  • [DOI] S. Posada-Céspedes, D. Seifert, I. Topolsky, K. P. Jablonski, K. J. Metzner, and N. Beerenwinkel, "V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data," Bioinformatics, 2021.
    [Bibtex]
    @Article{PosadaCespedes:21,
    author = {Susana Posada-C{\'{e}}spedes and David Seifert and Ivan Topolsky and Kim Philipp Jablonski and Karin J Metzner and Niko Beerenwinkel},
    journal = {Bioinformatics},
    title = {V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data},
    year = {2021},
    doi = {10.1093/bioinformatics/btab015},
    editor = {Jinbo Xu},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] C. Simsek, V. M. Corman, H. U. Everling, A. N. Lukashev, A. Rasche, G. D. Maganga, T. Binger, D. Jansen, L. Beller, W. Deboutte, F. Gloza-Rausch, A. Seebens-Hoyer, S. Yordanov, A. Sylverken, S. Oppong, Y. A. Sarkodie, P. Vallo, E. M. Leroy, M. Bourgarel, K. C. Yinda, M. V. Ranst, C. Drosten, J. F. Drexler, and J. Matthijnssens, "At least seven distinct rotavirus genotype constellations in bats with evidence of reassortment and zoonotic transmissions," mBio, vol. 12, iss. 1, 2021.
    [Bibtex]
    @Article{Simsek:21,
    author = {Ceren Simsek and Victor Max Corman and Hermann Ulrich Everling and Alexander N. Lukashev and Andrea Rasche and Gael Darren Maganga and Tabea Binger and Daan Jansen and Leen Beller and Ward Deboutte and Florian Gloza-Rausch and Antje Seebens-Hoyer and Stoian Yordanov and Augustina Sylverken and Samuel Oppong and Yaw Adu Sarkodie and Peter Vallo and Eric M. Leroy and Mathieu Bourgarel and Kwe Claude Yinda and Marc Van Ranst and Christian Drosten and Jan Felix Drexler and Jelle Matthijnssens},
    journal = {{mBio}},
    title = {At Least Seven Distinct Rotavirus Genotype Constellations in Bats with Evidence of Reassortment and Zoonotic Transmissions},
    year = {2021},
    number = {1},
    volume = {12},
    doi = {10.1128/mbio.02755-20},
    editor = {John T. Patton},
    publisher = {American Society for Microbiology},
    }
  • [DOI] K. Jahn, D. Dreifuss, I. Topolsky, A. Kull, P. Ganesanandamoorthy, X. Fernandez-Cassi, C. Bänziger, E. Stachler, L. Fuhrmann, K. P. Jablonski, C. Chen, C. Aquino, T. Stadler, C. Ort, T. Kohn, T. R. Julian, and N. Beerenwinkel, "Detection of SARS-CoV-2 variants in Switzerland by genomic analysis of wastewater samples," medRxiv, 2021.
    [Bibtex]
    @Article{Jahn:21,
    author = {Katharina Jahn and David Dreifuss and Ivan Topolsky and Anina Kull and Pravin Ganesanandamoorthy and Xavier Fernandez-Cassi and Carola Bänziger and Elyse Stachler and Lara Fuhrmann and Kim Philipp Jablonski and Chaoran Chen and Catharine Aquino and Tanja Stadler and Christoph Ort and Tamar Kohn and Timothy R. Julian and Niko Beerenwinkel},
    journal = {{medRxiv}},
    title = {Detection of {SARS}-{CoV}-2 variants in {S}witzerland by genomic analysis of wastewater samples},
    year = {2021},
    doi = {10.1101/2021.01.08.21249379},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] A. Tscherne, J. H. Schwarz, C. Rohde, A. Kupke, G. Kalodimou, L. Limpinsel, N. M. A. Okba, B. Bošnjak, I. Sandrock, S. Halwe, L. Sauerhering, K. Brosinski, N. Liangliang, E. Duell, S. Jany, A. Freudenstein, J. Schmidt, A. Werner, M. G. Sera, M. Klüver, W. Guggemos, M. Seilmaier, C. Wendtner, R. Förster, B. L. Haagmans, S. Becker, G. Sutter, and A. Volz, "Immunogenicity and efficacy of the COVID-19 candidate vector vaccine MVA-SARS-2-S in preclinical vaccination," bioRxiv, 2021.
    [Bibtex]
    @Article{Tscherne:21,
    author = {Alina Tscherne and Jan Hendrik Schwarz and Cornelius Rohde and Alexandra Kupke and Georgia Kalodimou and Leonard Limpinsel and Nisreen M.A. Okba and Berislav Bo{\v{s}}njak and Inga Sandrock and Sandro Halwe and Lucie Sauerhering and Katrin Brosinski and Nan Liangliang and Elke Duell and Sylvia Jany and Astrid Freudenstein and Jörg Schmidt and Anke Werner and Michelle Gellhorn Sera and Michael Klüver and Wolfgang Guggemos and Michael Seilmaier and Clemens-Martin Wendtner and Reinhold Förster and Bart L. Haagmans and Stephan Becker and Gerd Sutter and Asisa Volz},
    journal = {{bioRxiv}},
    title = {Immunogenicity and efficacy of the {COVID}-19 candidate vector vaccine {MVA-SARS-2-S} in preclinical vaccination},
    year = {2021},
    doi = {10.1101/2021.01.09.426032},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] S. J. Lycett, J. Hughes, M. P. McHugh, A. S. da Filipe, R. Dewar, L. Lu, T. Doherty, A. Shepherd, R. Inward, G. Rossi, D. Balaz, R. R. Kao, S. Rooke, S. Cotton, M. D. Gallagher, C. B. Lopez, Á. O'Toole, E. Scher, V. Hill, J. T. McCrone, R. M. Colquhoun, B. Jackson, T. C. Williams, K. A. Williamson, N. Johnson, K. Smollett, D. Mair, S. Carmichael, L. Tong, J. Nichols, K. Brunker, J. G. Shepherd, K. Li, E. Aranday-Cortes, Y. A. Parr, A. Broos, K. Nomikou, S. E. McDonald, M. Niebel, P. Asamaphan, I. Starinskij, N. Jesudason, R. Shah, V. B. Sreenu, T. Stanton, S. Shaaban, A. MacLean, M. Woolhouse, R. Gunson, K. Templeton, E. C. Thomson, A. Rambaut, M. T. G. Holden, and D. R. L. and, "Epidemic waves of COVID-19 in Scotland: a genomic perspective on the impact of the introduction and relaxation of lockdown on SARS-CoV-2," medRxiv, 2021.
    [Bibtex]
    @Article{Lycett:21,
    author = {Samantha J Lycett and Joseph Hughes and Martin P McHugh and Ana da Silva Filipe and Rebecca Dewar and Lu Lu and Thomas Doherty and Amy Shepherd and Rhys Inward and Gianluigi Rossi and Daniel Balaz and Rowland R Kao and Stefan Rooke and Seb Cotton and Michael D Gallagher and Carlos Balcazar Lopez and {\'{A}}ine O'Toole and Emily Scher and Verity Hill and John T McCrone and Rachel M Colquhoun and Ben Jackson and Thomas C Williams and Kathleen A Williamson and Natasha Johnson and Katherine Smollett and Daniel Mair and Stephen Carmichael and Lily Tong and Jenna Nichols and Kirstyn Brunker and James G Shepherd and Kathy Li and Elihu Aranday-Cortes and Yasmin A Parr and Alice Broos and Kyriaki Nomikou and Sarah E McDonald and Marc Niebel and Patawee Asamaphan and Igor Starinskij and Natasha Jesudason and Rajiv Shah and Vattipally B Sreenu and Tom Stanton and Sharif Shaaban and Alasdair MacLean and Mark Woolhouse and Rory Gunson and Kate Templeton and Emma C Thomson and Andrew Rambaut and Matthew T.G. Holden and David L Robertson and},
    journal = {{medRxiv}},
    title = {Epidemic waves of {COVID}-19 in {S}cotland: a genomic perspective on the impact of the introduction and relaxation of lockdown on {SARS}-{CoV}-2},
    year = {2021},
    doi = {10.1101/2021.01.08.20248677},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] S. Modha, D. L. Robertson, J. Hughes, and R. J. Orton, "Quantifying and cataloguing unknown sequences within human microbiomes," bioRxiv, 2021.
    [Bibtex]
    @Article{Modha:21,
    author = {Sejal Modha and David L. Robertson and Joseph Hughes and Richard J. Orton},
    journal = {{bioRxiv}},
    title = {Quantifying and cataloguing unknown sequences within human microbiomes},
    year = {2021},
    doi = {10.1101/2021.01.22.427751},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] S. Lytras, J. Hughes, W. Xia, X. Jiang, and D. L. Robertson, "Exploring the natural origins of SARS-CoV-2," bioRxiv, 2021.
    [Bibtex]
    @Article{Lytras:21,
    author = {Spyros Lytras and Joseph Hughes and Wei Xia and Xiaowei Jiang and David L Robertson},
    journal = {{bioRxiv}},
    title = {Exploring the natural origins of {SARS}-{CoV}-2},
    year = {2021},
    doi = {10.1101/2021.01.22.427830},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. Möckel, V. M. Corman, M. S. Stegemann, J. Hofmann, A. Stein, T. C. Jones, P. Gastmeier, J. Seybold, R. Offermann, U. Bachmann, T. Lindner, W. Bauer, C. Drosten, A. Rosen, and R. Somasundaram, "SARS-CoV-2 antigen rapid immunoassay for diagnosis of COVID-19 in the emergency department.," Biomarkers, p. 1–13, 2021.
    [Bibtex]
    @Article{Moeckel:21,
    author = {Möckel, Martin and Corman, Victor M. and Stegemann, Miriam S. and Hofmann, Jörg and Stein, Angela and Jones, Terry C. and Gastmeier, Petra and Seybold, Joachim and Offermann, Ralf and Bachmann, Ulrike and Lindner, Tobias and Bauer, Wolfgang and Drosten, Christian and Rosen, Alexander and Somasundaram, Rajan},
    journal = {{Biomarkers}},
    title = {{SARS-CoV-2} Antigen Rapid Immunoassay for Diagnosis of {COVID-19} in the Emergency Department.},
    year = {2021},
    pages = {1--13},
    abstract = {In the emergency department (ED) setting, rapid testing for SARS-CoV-2 is likely associated with advantages to patients and healthcare workers, for example enabling early but rationale use of limited isolation resources. Most recently, several SARS-CoV-2 rapid point-of-care antigen tests (AGTEST) became available. There is a growing need for data regarding their clinical utility and performance in the diagnosis of SARS-CoV-2 infection in the real life setting of 5 EDs. We implemented AGTEST (here: Roche/SD Biosensor) in all four adult and the one pediatric EDs at Charité - Universitätsmedizin Berlin in our diagnostic testing strategy. Test indication was limited to symptomatic suspected COVID-19 patients. Detailed written instructions on who to test were distributed and testing personnel were trained in proper specimen collection and handling. In each suspected COVID-19 patient, two sequential deep oro-nasopharyngeal swabs were obtained for viral tests. The first swab was collected for nucleic acid testing through SARS-CoV-2 Real-Time Reverse Transcriptase (rt)-PCR diagnostic panel (PCRTEST) in the central laboratory. The second swab was collected to perform the AGTEST. Analysis of routine data was prospectively planned and data were retrieved from the medical records after the inclusion period in the adult or pediatric ED. Diagnostic performance was calculated using the PCRTEST as reference standard. False negative and false positive AGTEST results were analyzed individually and compared with viral concentrations derived from the calibrated PCRTEST. We included n = 483 patients including n= 202 from the pediatric ED. N = 10 patients had to be excluded due to missing data and finally n = 473 patients were analyzed. In the adult cohort, the sensitivity of the AGTEST was 75.3 (95%CI: 65.8/83.4)% and the specificity was 100 (95%CI: 98.4/100)% with a SARS-CoV-2 prevalence of 32.8%; the positive predictive value was 100 (95%CI: 95.7/100)% and the negative predictive value 89.2 (95%CI: 84.5/93.9)%. In the pediatric cohort the sensitivity was 72.0 (95%CI: 53.3/86.7)%, the specificity was 99.4 (95%CI:97.3/99.9)% with a prevalence of 12.4%; the positive predictive value was 94.7 (95%CI: 78.3/99.7)% and the negative predictive value was 96.2 (95%CI:92.7/98.3)%.Thus, n = 22 adult and n = 7 pediatric patients showed false negative AGTEST results and only one false positive AGTEST occurred, in the pediatric cohort. Calculated viral concentrations from the rt-PCR lay between 3.16 and 9.51 log10 RNA copies/mL buffer. All false negative patients in the adult ED cohort, who had confirmed symptom onset at least seven days earlier had less than 5x 10^5 RNA copies/mL buffer. We conclude that the use of AGTEST among symptomatic patients in the emergency setting is useful for the early identification of COVID-19, but patients who test negative require confirmation by PCRTEST and must stay isolated until this result becomes available. Adult patients with a false negative AGTEST and symptom onset at least one week earlier have typically a low SARS-CoV-2 RNA concentration and likely pass the infectious period.},
    doi = {10.1080/1354750X.2021.1876769},
    pmid = {33455451},
    pubstate = {aheadofprint},
    }
  • [DOI] A. Osterman, H. Baldauf, M. Eletreby, J. M. Wettengel, S. Q. Afridi, T. Fuchs, E. Holzmann, A. Maier, J. Döring, N. Grzimek-Koschewa, M. Muenchhoff, U. Protzer, L. Kaderali, and O. T. Keppler, "Evaluation of two rapid antigen tests to detect SARS-CoV-2 in a hospital setting.," Med Microbiol Immunol, 2021.
    [Bibtex]
    @Article{Osterman:21,
    author = {Osterman, Andreas and Baldauf, Hanna-Mari and Eletreby, Marwa and Wettengel, Jochen M. and Afridi, Suliman Q. and Fuchs, Thimo and Holzmann, Elena and Maier, Anton and Döring, Johanna and Grzimek-Koschewa, Natascha and Muenchhoff, Maximilian and Protzer, Ulrike and Kaderali, Lars and Keppler, Oliver T.},
    journal = {{Med Microbiol Immunol}},
    title = {Evaluation of two rapid antigen tests to detect {SARS-CoV-2} in a hospital setting.},
    year = {2021},
    abstract = {Successful containment strategies for the SARS-CoV-2 pandemic will depend on reliable diagnostic assays. Point-of-care antigen tests (POCT) may provide an alternative to time-consuming PCR tests to rapidly screen for acute infections on site. Here, we evaluated two SARS-CoV-2 antigen tests: the STANDARD™ F COVID-19 Ag FIA (FIA) and the SARS-CoV-2 Rapid Antigen Test (RAT). For diagnostic assessment, we used a large set of PCR-positive and PCR-negative respiratory swabs from asymptomatic and symptomatic patients and health care workers in the setting of two University Hospitals in Munich, Germany, i.e. emergency rooms, patient care units or employee test centers. For FIA, overall clinical sensitivity and specificity were 45.4% (n = 381) and 97.8% (n = 360), respectively, and for RAT, 50.3% (n = 445) and 97.7% (n = 386), respectively. For primary diagnosis of asymptomatic and symptomatic individuals, diagnostic sensitivities were 60.9% (FIA) (n = 189) and 64.5% (RAT) (n = 256). This questions these tests' utility for the reliable detection of acute SARS-CoV-2-infected individuals, in particular in high-risk settings. We support the proposal that convincing high-quality outcome data on the impact of false-negative and false-positive antigen test results need to be obtained in a POCT setting. Moreover, the efficacy of alternative testing strategies to complement PCR assays must be evaluated by independent laboratories, prior to widespread implementation in national and international test strategies.},
    doi = {10.1007/s00430-020-00698-8},
    keywords = {COVID-19 point-of-care; Diagnostic test; SARS-CoV-2 antigen test; Sensitivity; Specificity},
    pmid = {33452927},
    pubstate = {aheadofprint},
    }
  • [DOI] M. Bárcena, C. O. Barnes, M. Beck, P. J. Bjorkman, B. Canard, G. F. Gao, Y. Gao, R. Hilgenfeld, G. Hummer, A. Patwardhan, G. Santoni, E. O. Saphire, C. Schaffitzel, S. L. Schendel, J. L. Smith, A. Thorn, D. Veesler, P. Zhang, and Q. Zhou, "Structural biology in the fight against COVID-19.," Nat Struct Mol Biol, vol. 28, p. 2–7, 2021.
    [Bibtex]
    @Article{Barcena:21,
    author = {Bárcena, Montserrat and Barnes, Christopher O. and Beck, Martin and Bjorkman, Pamela J. and Canard, Bruno and Gao, George F. and Gao, Yunyun and Hilgenfeld, Rolf and Hummer, Gerhard and Patwardhan, Ardan and Santoni, Gianluca and Saphire, Erica Ollmann and Schaffitzel, Christiane and Schendel, Sharon L. and Smith, Janet L. and Thorn, Andrea and Veesler, David and Zhang, Peijun and Zhou, Qiang},
    journal = {{Nat Struct Mol Biol}},
    title = {Structural biology in the fight against {COVID-19}.},
    year = {2021},
    pages = {2--7},
    volume = {28},
    doi = {10.1038/s41594-020-00544-8},
    issue = {1},
    keywords = {Computational Biology, methods; Cryoelectron Microscopy, methods; Databases, Protein; Epitopes, chemistry, immunology; Host-Pathogen Interactions; Humans; Linoleic Acid, chemistry, metabolism, pharmacology; Molecular Biology, methods; SARS-CoV-2, chemistry, genetics, pathogenicity; Spike Glycoprotein, Coronavirus, chemistry, metabolism; Viral Proteins, chemistry, metabolism; Viral Vaccines, immunology, pharmacology; Virus Replication, physiology},
    pmid = {33437043},
    pubstate = {ppublish},
    }
  • [DOI] D. A. Hofmaenner, P. D. Wendel Garcia, B. Duvnjak, B. Chakrakodi, J. D. Maier, M. Huber, J. Huder, A. Wolfensberger, P. W. Schreiber, R. A. Schuepbach, A. S. Zinkernagel, P. K. Buehler, S. D. Brugger, and COVID-19 ICU-Research Group Zurich, "Bacterial but no SARS-CoV-2 contamination after terminal disinfection of tertiary care intensive care units treating COVID-19 patients.," Antimicrob Resist Infect Control, vol. 10, p. 11, 2021.
    [Bibtex]
    @Article{Hofmaenner:21,
    author = {Hofmaenner, Daniel A. and Wendel Garcia, Pedro David and Duvnjak, Branko and Chakrakodi, Bhavya and Maier, Julian D. and Huber, Michael and Huder, Jon and Wolfensberger, Aline and Schreiber, Peter W. and Schuepbach, Reto A. and Zinkernagel, Annelies S. and Buehler, Philipp K. and Brugger, Silvio D. and {COVID-19 ICU-Research Group Zurich}},
    journal = {{Antimicrob Resist Infect Control}},
    title = {Bacterial but no {SARS-CoV-2} contamination after terminal disinfection of tertiary care intensive care units treating {COVID-19} patients.},
    year = {2021},
    pages = {11},
    volume = {10},
    abstract = {In intensive care units (ICUs) treating patients with Coronavirus disease 2019 (COVID-19) invasive ventilation poses a high risk for aerosol and droplet formation. Surface contamination of severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) or bacteria can result in nosocomial transmission. Two tertiary care COVID-19 intensive care units treating 53 patients for 870 patient days were sampled after terminal cleaning and preparation for regular use to treat non-COVID-19 patients. A total of 176 swabs were sampled of defined locations covering both ICUs. No SARS-CoV-2 ribonucleic acid (RNA) was detected. Gram-negative bacterial contamination was mainly linked to sinks and siphons. Skin flora was isolated from most swabbed areas and Enterococcus faecium was detected on two keyboards. After basic cleaning with standard disinfection measures no remaining SARS-CoV-2 RNA was detected. Bacterial contamination was low and mainly localised in sinks and siphons.},
    doi = {10.1186/s13756-021-00885-z},
    investigator = {Bartussek, Jan and Buehler, Phillip and Heuberger, Dorothea Monika and Hilty, Matthias Peter and Hofmänner, Daniel Andrea and Maibach, Martina and Andreas, Schuepbach Reto and Wendel Garcia, Pedro David},
    issue = {1},
    keywords = {Aerosols, analysis; Bacteria, classification, genetics, growth & development, isolation & purification; COVID-19, therapy, virology; Cross Infection, microbiology, prevention & control, virology; Disinfection, methods; Equipment Contamination, statistics & numerical data; Female; Humans; Intensive Care Units, statistics & numerical data; Male; Middle Aged; SARS-CoV-2, genetics, isolation & purification, physiology; Tertiary Healthcare, statistics & numerical data; Disinfection; Hospital epidemiology; Hydrogen peroxide nebulisation; ICU; Nosocomial infection; SARS-CoV-2},
    pmid = {33436105},
    pubstate = {epublish},
    }
  • [DOI] U. Teichgräber, A. Malouhi, M. Ingwersen, R. Neumann, M. Reljic, S. Deinhardt-Emmer, B. Löffler, W. Behringer, J. Lewejohann, A. Stallmach, and P. Reuken, "Ruling out COVID-19 by chest CT at emergency admission when prevalence is low: the prospective, observational SCOUT study.," Respir Res, vol. 22, p. 13, 2021.
    [Bibtex]
    @Article{Teichgraeber:21,
    author = {Teichgräber, Ulf and Malouhi, Amer and Ingwersen, Maja and Neumann, Rotraud and Reljic, Marina and Deinhardt-Emmer, Stefanie and Löffler, Bettina and Behringer, Wilhelm and Lewejohann, Jan-Christoph and Stallmach, Andreas and Reuken, Philipp},
    journal = {{Respir Res}},
    title = {Ruling out {COVID-19} by chest {CT} at emergency admission when prevalence is low: the prospective, observational {SCOUT} study.},
    year = {2021},
    pages = {13},
    volume = {22},
    abstract = {It is essential to avoid admission of patients with undetected corona virus disease 2019 (COVID-19) to hospitals' general wards. Even repeated negative reverse transcription polymerase chain reaction (RT-PCR) results do not rule-out COVID-19 with certainty. The study aimed to evaluate a rule-out strategy for COVID-19 using chest computed tomography (CT) in adults being admitted to the emergency department and suspected of COVID-19. In this prospective, single centre, diagnostic accuracy cohort study, consecutive adults (≥ 18 years) presenting with symptoms consistent with COVID-19 or previous contact to infected individuals, admitted to the emergency department and supposed to be referred to general ward were included in March and April 2020. All participants underwent low-dose chest CT. RT-PCR- and specific antibody tests were used as reference standard. Main outcome measures were sensitivity and specificity of chest CT. Predictive values were calculated based on the theorem of Bayes using Fagan's nomogram. Of 165 participants (56.4% male, 71 ± 16 years) included in the study, the diagnosis of COVID-19 was confirmed with RT-PCR and AB tests in 13 participants (prevalence 7.9%). Sensitivity and specificity of chest CT were 84.6% (95% confidence interval [CI], 54.6-98.1) and 94.7% (95% CI, 89.9-97.7), respectively. Positive and negative likelihood ratio of chest CT were 16.1 (95% CI, 7.9-32.8) and 0.16 (95% CI, 0.05-0.58) and positive and negative predictive value were 57.9% (95% CI, 40.3-73.7) and 98.6% (95% CI, 95.3-99.6), respectively. At a low prevalence of COVID-19, chest CT could be used as a complement to repeated RT-PCR testing for early COVID-19 exclusion in adults with suspected infection before referral to hospital's general wards. Trial registration ClinicalTrials.gov: NCT04357938 April 22, 2020.},
    doi = {10.1186/s12931-020-01611-w},
    issue = {1},
    keywords = {Aged; Aged, 80 and over; COVID-19, blood, diagnostic imaging, epidemiology; Cohort Studies; Emergency Service, Hospital, trends; Female; Germany, epidemiology; Humans; Male; Middle Aged; Patient Admission, trends; Prevalence; Prospective Studies; Quarantine, methods, trends; Tomography, X-Ray Computed, methods, trends; COVID-19; Computed tomography; Prevalence; Reverse transcriptase polymerase chain reaction; Sensitivity and specificity; Severe acute respiratory syndrome coronavirus 2},
    pmid = {33435973},
    pubstate = {epublish},
    }
  • [DOI] I. P. Trougakos, K. Stamatelopoulos, E. Terpos, O. E. Tsitsilonis, E. Aivalioti, D. Paraskevis, E. Kastritis, G. N. Pavlakis, and M. A. Dimopoulos, "Insights to SARS-CoV-2 life cycle, pathophysiology, and rationalized treatments that target COVID-19 clinical complications.," J Biomed Sci, vol. 28, p. 9, 2021.
    [Bibtex]
    @Article{Trougakos:21,
    author = {Trougakos, Ioannis P. and Stamatelopoulos, Kimon and Terpos, Evangelos and Tsitsilonis, Ourania E. and Aivalioti, Evmorfia and Paraskevis, Dimitrios and Kastritis, Efstathios and Pavlakis, George N. and Dimopoulos, Meletios A.},
    journal = {{J Biomed Sci}},
    title = {Insights to {SARS-CoV-2} life cycle, pathophysiology, and rationalized treatments that target {COVID-19} clinical complications.},
    year = {2021},
    pages = {9},
    volume = {28},
    abstract = {Gaining further insights into SARS-CoV-2 routes of infection and the underlying pathobiology of COVID-19 will support the design of rational treatments targeting the life cycle of the virus and/or the adverse effects (e.g., multi-organ collapse) that are triggered by COVID-19-mediated adult respiratory distress syndrome (ARDS) and/or other pathologies. COVID-19 is a two-phase disease being marked by (phase 1) increased virus transmission and infection rates due to the wide expression of the main infection-related ACE2, TMPRSS2 and CTSB/L human genes in tissues of the respiratory and gastrointestinal tract, as well as by (phase 2) host- and probably sex- and/or age-specific uncontrolled inflammatory immune responses which drive hyper-cytokinemia, aggressive inflammation and (due to broad organotropism of SARS-CoV-2) collateral tissue damage and systemic failure likely because of imbalanced ACE/ANGII/AT1R and ACE2/ANG(1-7)/MASR axes signaling. Here we discuss SARS-CoV-2 life cycle and a number of approaches aiming to suppress viral infection rates or propagation; increase virus antigen presentation in order to activate a robust and durable adaptive immune response from the host, and/or mitigate the ARDS-related "cytokine storm" and collateral tissue damage that triggers the severe life-threatening complications of COVID-19.},
    doi = {10.1186/s12929-020-00703-5},
    issue = {1},
    keywords = {COVID-19, complications, drug therapy, physiopathology, virology; Humans; Life Cycle Stages; SARS-CoV-2, isolation & purification, physiology; ACE2; ARDS; COVID-19; SARS-CoV-2; TMPRSS2},
    pmid = {33435929},
    pubstate = {epublish},
    }
  • [DOI] C. M. Crava, F. S. Varghese, E. Pischedda, R. Halbach, U. Palatini, M. Marconcini, L. Gasmi, S. Redmond, Y. Afrane, D. Ayala, C. Paupy, R. Carballar-Lejarazu, P. Miesen, R. P. van Rij, and M. Bonizzoni, "Population genomics in the arboviral vector Aedes aegypti reveals the genomic architecture and evolution of endogenous viral elements.," Mol Ecol, 2021.
    [Bibtex]
    @Article{Crava:21,
    author = {Crava, Cristina M. and Varghese, Finny S. and Pischedda, Elisa and Halbach, Rebecca and Palatini, Umberto and Marconcini, Michele and Gasmi, Leila and Redmond, Seth and Afrane, Yaw and Ayala, Diego and Paupy, Christophe and Carballar-Lejarazu, Rebeca and Miesen, Pascal and van Rij, Ronald P. and Bonizzoni, Mariangela},
    journal = {{Mol Ecol}},
    title = {Population genomics in the arboviral vector {A}edes aegypti reveals the genomic architecture and evolution of endogenous viral elements.},
    year = {2021},
    abstract = {Horizontal gene transfer from viruses to eukaryotic cells is a pervasive phenomenon. Somatic viral integrations are linked to persistent viral infection whereas integrations into germline cells are maintained in host genomes by vertical transmission and may be co-opted for host functions. In the arboviral vector Aedes aegypti, an endogenous viral element from a non-retroviral RNA virus (nrEVE) was shown to produce PIWI-interacting RNAs (piRNAs) to limit infection with a cognate virus. Thus, nrEVEs may constitute a heritable, sequence-specific mechanism for antiviral immunity, analogous to piRNA-mediated silencing of transposable elements. Here, we intersect population genomics and evolutionary approaches to analyze the genomic architecture of nrEVEs in Ae. aegypti. We conducted a genome-wide screen for adaptive nrEVEs and searched for novel population-specific nrEVEs in the genomes of eighty individual wild-caught mosquitoes from five geographical populations. We show a dynamic landscape of nrEVEs in mosquito genomes and identified five novel nrEVEs derived from two currently circulating viruses, providing evidence of the environmental-dependent modification of a piRNA cluster. Overall, our results show that virus endogenization events are complex events with only few nrEVEs contributing to adaptive evolution in Ae. aegypti.},
    doi = {10.1111/mec.15798},
    keywords = {Aedes aegypti ; endogenous viral elements; mosquito genomes; piRNA cluster},
    pmid = {33432714},
    pubstate = {aheadofprint},
    }
  • [DOI] S. R. Vaidya, S. M. Kasibhatla, M. B. Kamble, A. Munivenkatappa, N. S. Kumbhar, M. M. Jayaswamy, M. R. Ramtirthkar, M. M. Kale, and U. Kulkarni-Kale, "Genetic and antigenic characterization of wild type rubella viruses isolated from India.," Vaccine, 2021.
    [Bibtex]
    @Article{Vaidya21,
    author = {Vaidya, Sunil R. and Kasibhatla, Sunitha M. and Kamble, Madhukar B. and Munivenkatappa, Ashok and Kumbhar, Neelakshi S. and Jayaswamy, Manjunatha M. and Ramtirthkar, Mukund R. and Kale, Mohan M. and Kulkarni-Kale, Urmila},
    journal = {Vaccine},
    title = {Genetic and antigenic characterization of wild type rubella viruses isolated from {I}ndia.},
    year = {2021},
    abstract = {Rubella, is a contagious disease caused by Rubella virus (RuV) that manifests as fever with skin-rashes in children and adults along with complications in pregnant women. WHO-SEAR has set a target for Rubella elimination by 2023. This is the first report of antigenic characterization and genome sequencing of nine RuVs sampled during 1992, 2007-9, and 2015-17 from four Indian states. Comparative analysis of Indian RuVs (2B) with that of global isolates and vaccine strain RA 27/3 (1a) revealed that the observed mutations in structural proteins have no major impact on the 3D structure, function and antigenicity. Indian RuVs formed three major clusters (Pune-1992, Kannur-2009 and Chitradurg-2007) in genome-based phylogeny of global isolates. Neutralizing antibody titers in a panel of serum samples from measles negative cases were significantly higher to the vaccine strain compared to a wild-type 2B isolate (Kannur) with concordance of 91.9%, thereby substantiating the use of current vaccines.},
    doi = {10.1016/j.vaccine.2020.12.063},
    keywords = {Complete genome; Epitopes; Indian rubella virus isolates; Neutralization test; Rubella vaccine strain; Rubella virus bioinformatics},
    pmid = {33423836},
    pubstate = {aheadofprint},
    }
  • [DOI] C. Müller, W. Obermann, N. Karl, H. Wendel, G. Taroncher-Oldenburg, S. Pleschka, R. K. Hartmann, A. Grünweller, and J. Ziebuhr, "The rocaglate CR-31-B (-) inhibits SARS-CoV-2 replication at non-cytotoxic, low nanomolar concentrations in vitro and ex vivo.," Antiviral Res, vol. 186, p. 105012, 2021.
    [Bibtex]
    @Article{Mueller:21,
    author = {Müller, Christin and Obermann, Wiebke and Karl, Nadja and Wendel, Hans-Guido and Taroncher-Oldenburg, Gaspar and Pleschka, Stephan and Hartmann, Roland K. and Grünweller, Arnold and Ziebuhr, John},
    journal = {{Antiviral Res}},
    title = {The rocaglate {CR-31-B} (-) inhibits {SARS-CoV-2} replication at non-cytotoxic, low nanomolar concentrations in vitro and ex vivo.},
    year = {2021},
    pages = {105012},
    volume = {186},
    abstract = {Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of COVID-19, a severe respiratory disease with varying clinical presentations and outcomes, and responsible for a major pandemic that started in early 2020. With no vaccines or effective antiviral treatments available, the quest for novel therapeutic solutions remains an urgent priority. Rocaglates, a class of plant-derived cyclopenta[b]benzofurans, exhibit broad-spectrum antiviral activity against multiple RNA viruses including coronaviruses. Specifically, rocaglates inhibit eukaryotic initiation factor 4A (eIF4A)-dependent mRNA translation initiation, resulting in strongly reduced viral RNA translation. Here, we assessed the antiviral activity of the synthetic rocaglate CR-31-B (-) against SARS-CoV-2 using both in vitro and ex vivo cell culture models. In Vero E6 cells, CR-31-B (-) inhibited SARS-CoV-2 replication with an EC of ~1.8 nM. In primary human airway epithelial cells, CR-31-B (-) reduced viral titers to undetectable levels at a concentration of 100 nM. Reduced virus reproduction was accompanied by substantially reduced viral protein accumulation and replication/transcription complex formation. The data reveal a potent anti-SARS-CoV-2 activity by CR-31-B (-), corroborating previous results obtained for other coronaviruses and supporting the idea that rocaglates may be used in first-line antiviral intervention strategies against novel and emerging RNA virus outbreaks.},
    doi = {10.1016/j.antiviral.2021.105012},
    keywords = {Antiviral activity; COVID-19; Rocaglate; SARS-CoV-2; Translation initiation; eIF4A},
    pmid = {33422611},
    pubstate = {aheadofprint},
    }
  • [DOI] E. Criscuolo, R. A. Diotti, R. Ferrarese, C. Alippi, G. Viscardi, C. Signorelli, N. Mancini, M. Clementi, and N. Clementi, "Fast inactivation of SARS-CoV-2 by UV-C and ozone exposure on different materials.," Emerg Microbes Infect, p. 1–18, 2021.
    [Bibtex]
    @Article{Criscuolo:21,
    author = {Criscuolo, Elena and Diotti, Roberta A. and Ferrarese, Roberto and Alippi, Cesare and Viscardi, Gabriele and Signorelli, Carlo and Mancini, Nicasio and Clementi, Massimo and Clementi, Nicola},
    journal = {{Emerg Microbes Infect}},
    title = {Fast inactivation of {SARS-CoV-2} by {UV-C} and ozone exposure on different materials.},
    year = {2021},
    pages = {1--18},
    doi = {10.1080/22221751.2021.1872354},
    keywords = {SARS-CoV-2; UV-C; contact transmission; inactivation; ozone},
    pmid = {33399524},
    pubstate = {aheadofprint},
    }
  • [DOI] T. Tu, B. Zehnder, B. Qu, and S. Urban, "De novo synthesis of hepatitis B virus nucleocapsids is dispensable for the maintenance and transcriptional regulation of cccDNA," JHEP Rep, vol. 3, p. 100195, 2021.
    [Bibtex]
    @Article{Tu21,
    author = {Tu, Thomas and Zehnder, Benno and Qu, Bingqian and Urban, Stephan},
    journal = {{JHEP Rep}},
    title = {{D}e novo synthesis of hepatitis {B} virus nucleocapsids is dispensable for the maintenance and transcriptional regulation of {cccDNA}},
    year = {2021},
    pages = {100195},
    volume = {3},
    abstract = {Chronic HBV infection cannot be cured by current therapeutics owing to their limited ability to reduce covalently closed circular (ccc)DNA levels in the livers of infected individuals. Therefore, greater understanding of the molecular determinants of cccDNA formation and persistence is required. One key issue is the extent to which nucleocapsid-mediated replenishment (reimport) contributes to cccDNA levels in an infected hepatocyte. We engineered an infectious HBV mutant with a genome encoding a stop codon at position T67 in the HBV core open reading frame (ΔHBc HBV). Importantly, ΔHBc HBV virions cannot initiate nucleocapsid synthesis upon infection. Long-term HBV infection markers were followed for up for 9 weeks in HepG2-NTCP cells (A3 clone) and HBV DNA was quantified using a newly-developed, highly-precise PCR assay (cccDNA inversion quantitative PCR). ΔHBc and wild-type (WT) HBV resulted in comparable expression of HBV surface antigen (HBsAg), which could be blocked using the entry inhibitor Myrcludex B, confirming infection via the receptor sodium taurocholate cotransporting polypeptide (NTCP). In primary human hepatocytes, Huh7-NTCP, HepG2-NTCP, and HepaRG-NTCP cells, comparable copy numbers of cccDNA were formed. cccDNA levels, transcription of viral RNA, and HBsAg secretion remained comparably stable in WT and ΔHBc HBV-infected cells for at least 9 weeks. Our results imply that synthesised HBc plays a minor role in transcriptional regulation of cccDNA. Importantly, we show that initially-formed cccDNA is stable in hepatocytes without requiring continuous replenishment in infection systems and contribution from DNA-containing nucleocapsids is not required. Thus, short-term therapeutic targeting of capsid-reimport is likely an inefficient strategy in eliminating cccDNA in chronically infected hepatocytes. The hepatitis B virus can maintain itself in the liver for a patient's lifetime, causing liver injury and cancer. We have clarified exactly how it maintains itself in an infected cell. This now means we have a better idea at how to target the virus and cure a chronic infection.},
    doi = {10.1016/j.jhepr.2020.100195},
    issue = {1},
    keywords = {ALT, alanine aminotransferase; Antivirals; Bulevirtide; CIs, capsid inhibitors; Capsid inhibitors; Core protein; Covalently closed circular DNA; DHBV, duck hepatitis B virus; HBV DNA integration; HBV persistence; HBV, hepatitis B virus; HBcAg; HBsAg, hepatitis B virus surface antigen; Hepcludex; Myrcludex B; NC, naked capsids; NTCP, sodium taurocholate cotransporting polypeptide; NUCs, nucleos(t)ide analogues; ORF, open reading frame; PEG, polyethylene glycol; PHH, primary human hepatocytes; SN, supernatant; VP, virions; WT, wild-type; cccDNA, covalently closed circular DNA; dpi, days post inoculation; mge, multiplicity of genomic equivalent; pgRNA, pregenomic RNA; rcDNA, relaxed circular DNA; vge, viral genome equivalents},
    pmid = {33385130},
    pubstate = {epublish},
    }
  • [DOI] T. Toptan, L. Eckermann, A. E. Pfeiffer, S. Hoehl, S. Ciesek, C. Drosten, and V. M. Corman, "Evaluation of a SARS-CoV-2 rapid antigen test: potential to help reduce community spread?," J Clin Virol, vol. 135, p. 104713, 2021.
    [Bibtex]
    @Article{Toptan:21,
    author = {Tuna Toptan and Lisa Eckermann and Annika E. Pfeiffer and Sebastian Hoehl and Sandra Ciesek and Christian Drosten and Victor M. Corman},
    title = {Evaluation of a {SARS}-{CoV}-2 rapid antigen test: Potential to help reduce community spread?},
    journal = {{J Clin Virol}},
    year = {2021},
    volume = {135},
    pages = {104713},
    doi = {10.1016/j.jcv.2020.104713},
    publisher = {Elsevier {BV}},
    }
  • [DOI] A. Pérez-Cataluña, E. Cuevas-Ferrando, W. Randazzo, I. Falcó, A. Allende, and G. Sánchez, "Comparing analytical methods to detect SARS-CoV-2 in wastewater," Sci Total Environ, vol. 758, p. 143870, 2021.
    [Bibtex]
    @Article{Perez-Cataluna:21,
    author = {Alba Pérez-Cataluña and Enric Cuevas-Ferrando and Walter Randazzo and Irene Falc{\'{o}} and Ana Allende and Gloria Sánchez},
    journal = {{Sci Total Environ}},
    title = {Comparing analytical methods to detect {SARS}-{CoV}-2 in wastewater},
    year = {2021},
    pages = {143870},
    volume = {758},
    doi = {10.1016/j.scitotenv.2020.143870},
    publisher = {Elsevier {BV}},
    }

2020

  • [DOI] M. Desdouits, M. de Graaf, S. Strubbia, B. O. B. Munnink, A. Kroneman, F. L. S. Guyader, and M. P. G. Koopmans, "Novel opportunities for NGS-based one health surveillance of foodborne viruses," One health outlook, vol. 2, iss. 1, 2020.
    [Bibtex]
    @Article{Desdouits:20,
    author = {Marion Desdouits and Miranda de Graaf and Sofia Strubbia and Bas B. Oude Munnink and Annelies Kroneman and Fran{\c{c}}oise S. Le Guyader and Marion P. G. Koopmans},
    journal = {One Health Outlook},
    title = {Novel opportunities for {NGS}-based one health surveillance of foodborne viruses},
    year = {2020},
    number = {1},
    volume = {2},
    doi = {10.1186/s42522-020-00015-6},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] U. Ashraf, C. Benoit-Pilven, V. Navratil, C. Ligneau, G. Fournier, S. Munier, O. Sismeiro, J. Coppée, V. Lacroix, and N. Naffakh, "Influenza virus infection induces widespread alterations of host cell splicing.," NAR Genom Bioinform, vol. 2, p. lqaa095, 2020.
    [Bibtex]
    @Article{Ashraf:20,
    author = {Ashraf, Usama and Benoit-Pilven, Clara and Navratil, Vincent and Ligneau, Cécile and Fournier, Guillaume and Munier, Sandie and Sismeiro, Odile and Coppée, Jean-Yves and Lacroix, Vincent and Naffakh, Nadia},
    journal = {{NAR Genom Bioinform}},
    title = {Influenza virus infection induces widespread alterations of host cell splicing.},
    year = {2020},
    pages = {lqaa095},
    volume = {2},
    abstract = {Influenza A viruses (IAVs) use diverse mechanisms to interfere with cellular gene expression. Although many RNA-seq studies have documented IAV-induced changes in host mRNA abundance, few were designed to allow an accurate quantification of changes in host mRNA splicing. Here, we show that IAV infection of human lung cells induces widespread alterations of cellular splicing, with an overall increase in exon inclusion and decrease in intron retention. Over half of the mRNAs that show differential splicing undergo no significant changes in abundance or in their 3' end termination site, suggesting that IAVs can specifically manipulate cellular splicing. Among a randomly selected subset of 21 IAV-sensitive alternative splicing events, most are specific to IAV infection as they are not observed upon infection with VSV, induction of interferon expression or induction of an osmotic stress. Finally, the analysis of splicing changes in RED-depleted cells reveals a limited but significant overlap with the splicing changes in IAV-infected cells. This observation suggests that hijacking of RED by IAVs to promote splicing of the abundant viral NS1 mRNAs could partially divert RED from its target mRNAs. All our RNA-seq datasets and analyses are made accessible for browsing through a user-friendly Shiny interface (http://virhostnet.prabi.fr:3838/shinyapps/flu-splicing or https://github.com/cbenoitp/flu-splicing).},
    doi = {10.1093/nargab/lqaa095},
    issue = {4},
    pmid = {33575639},
    pubstate = {epublish},
    }
  • [DOI] S. Schlickeiser, T. Schwarz, S. Steiner, K. Wittke, N. Al Besher, O. Meyer, U. Kalus, A. Pruß, F. Kurth, T. Zoller, M. Witzenrath, L. E. Sander, M. A. Müller, C. Scheibenbogen, H. Volk, C. Drosten, V. M. Corman, and L. G. Hanitsch, "Disease severity, fever, age, and sex correlate with SARS-CoV-2 neutralizing antibody responses.," Front Immunol, vol. 11, p. 628971, 2020.
    [Bibtex]
    @Article{Schlickeiser:20,
    author = {Schlickeiser, Stephan and Schwarz, Tatjana and Steiner, Sophie and Wittke, Kirsten and Al Besher, Nabeel and Meyer, Oliver and Kalus, Ulrich and Pruß, Axel and Kurth, Florian and Zoller, Thomas and Witzenrath, Martin and Sander, Leif Erik and Müller, Marcel A. and Scheibenbogen, Carmen and Volk, Hans-Dieter and Drosten, Christian and Corman, Victor M. and Hanitsch, Leif G.},
    journal = {{Front Immunol}},
    title = {Disease Severity, Fever, Age, and Sex Correlate With {SARS-CoV-2} Neutralizing Antibody Responses.},
    year = {2020},
    pages = {628971},
    volume = {11},
    abstract = {Clinical trials on the use of COVID-19 convalescent plasma remain inconclusive. While data on safety is increasingly available, evidence for efficacy is still sparse. Subgroup analyses hint to a dose-response relationship between convalescent plasma neutralizing antibody levels and mortality. In particular, patients with primary and secondary antibody deficiency might benefit from this approach. However, testing of neutralizing antibodies is limited to specialized biosafety level 3 laboratories and is a time- and labor-intense procedure. In this single center study of 206 COVID-19 convalescent patients, clinical data, results of commercially available ELISA testing of SARS-CoV-2 spike-IgG and -IgA, and levels of neutralizing antibodies, determined by plaque reduction neutralization testing (PRNT), were analyzed. At a medium time point of 58 days after symptom onset, only 12.6% of potential plasma donors showed high levels of neutralizing antibodies (PRNT50 ≥ 1:320). Multivariable proportional odds logistic regression analysis revealed need for hospitalization due to COVID-19 (odds ratio 6.87; -value 0.0004) and fever (odds ratio 3.00; -value 0.0001) as leading factors affecting levels of SARS-CoV-2 neutralizing antibody titers in convalescent plasma donors. Using penalized estimation, a predictive proportional odds logistic regression model including the most important variables hospitalization, fever, age, sex, and anosmia or dysgeusia was developed. The predictive discrimination for PRNT50 ≥ 1:320 was reasonably good with AUC: 0.86 (with 95% CI: 0.79-0.92). Combining clinical and ELISA-based pre-screening, assessment of neutralizing antibodies could be spared in 75% of potential donors with a maximal loss of 10% of true positives (PRNT50 ≥ 1:320).},
    doi = {10.3389/fimmu.2020.628971},
    keywords = {COVID-19; SARS-CoV-2; SARS-CoV-2 neutralizing antibody; antibody deficiency; convalescent plasma; coronavirus disease 2019; immunodeficiency; plaque reduction neutralization test},
    pmid = {33584731},
    pubstate = {epublish},
    }
  • [DOI] V. Puller, P. Sagulenko, and R. A. Neher, "Efficient inference, potential, and limitations of site-specific substitution models.," Virus Evol, vol. 6, p. veaa066, 2020.
    [Bibtex]
    @Article{Puller:20,
    author = {Puller, Vadim and Sagulenko, Pavel and Neher, Richard A.},
    journal = {{Virus Evol}},
    title = {Efficient inference, potential, and limitations of site-specific substitution models.},
    year = {2020},
    pages = {veaa066},
    volume = {6},
    abstract = {Natural selection imposes a complex filter on which variants persist in a population resulting in evolutionary patterns that vary greatly along the genome. Some sites evolve close to neutrally, while others are highly conserved, allow only specific states, or only change in concert with other sites. On one hand, such constraints on sequence evolution can be to infer biological function, one the other hand they need to be accounted for in phylogenetic reconstruction. Phylogenetic models often account for this complexity by partitioning sites into a small number of discrete classes with different rates and/or state preferences. Appropriate model complexity is typically determined by model selection procedures. Here, we present an efficient algorithm to estimate more complex models that allow for different preferences at every site and explore the accuracy at which such models can be estimated from simulated data. Our iterative approximate maximum likelihood scheme uses information in the data efficiently and accurately estimates site-specific preferences from large data sets with moderately diverged sequences and known topology. However, the joint estimation of site-specific rates, and site-specific preferences, and phylogenetic branch length can suffer from identifiability problems, while ignoring variation in preferences across sites results in branch length underestimates. Site-specific preferences estimated from large HIV alignments show qualitative concordance with intra-host estimates of fitness costs. Analysis of these substitution models suggests near saturation of divergence after a few hundred years. Such saturation can explain the inability to infer deep divergence times of HIV and SIVs using molecular clock approaches and time-dependent rate estimates.},
    doi = {10.1093/ve/veaa066},
    issue = {2},
    keywords = {algorithms; fitness landscapes; phylogenetics},
    pmid = {33343922},
    pubstate = {epublish},
    }
  • [DOI] L. van der Hoek, "SARS-CoV-2 re-infections: lessons from other coronaviruses," Med, vol. 1, iss. 1, p. 23–28, 2020.
    [Bibtex]
    @Article{Hoek:20,
    author = {Lia van der Hoek},
    journal = {Med},
    title = {{SARS}-{CoV}-2 Re-infections: Lessons from Other Coronaviruses},
    year = {2020},
    number = {1},
    pages = {23--28},
    volume = {1},
    doi = {10.1016/j.medj.2020.12.005},
    publisher = {Elsevier {BV}},
    }
  • [DOI] S. Kuchi, Q. Gu, M. Palmarini, S. J. Wilson, and D. L. Robertson, "Meta-analysis of virus-induced host gene expression reveals unique signatures of immune dysregulation induced by SARS-CoV-2," bioRxiv, 2020.
    [Bibtex]
    @Article{Kuchi:20,
    author = {Srikeerthana Kuchi and Quan Gu and Massimo Palmarini and Sam J Wilson and David L Robertson},
    journal = {{bioRxiv}},
    title = {Meta-analysis of virus-induced host gene expression reveals unique signatures of immune dysregulation induced by {SARS}-{CoV}-2},
    year = {2020},
    doi = {10.1101/2020.12.29.424739},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] D. Paraskevis, E. Kostaki, N. Alygizakis, N. S. Thomaidis, C. Cartalis, S. Tsiodras, and M. A. Dimopoulos, "A review of the impact of weather and climate variables to COVID-19: in the absence of public health measures high temperatures cannot probably mitigate outbreaks.," Sci Total Environ, vol. 768, p. 144578, 2020.
    [Bibtex]
    @Article{Paraskevis:20a,
    author = {Paraskevis, Dimitrios and Kostaki, Evangelia-Georgia and Alygizakis, Nikiforos and Thomaidis, Nikolaos S. and Cartalis, Constantinos and Tsiodras, Sotirios and Dimopoulos, Meletios Athanasios},
    journal = {{Sci Total Environ}},
    title = {A review of the impact of weather and climate variables to {COVID-19}: In the absence of public health measures high temperatures cannot probably mitigate outbreaks.},
    year = {2020},
    pages = {144578},
    volume = {768},
    abstract = {The new severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) pandemic was first recognized at the end of 2019 and has caused one of the most serious global public health crises in the last years. In this paper, we review current literature on the effect of weather (temperature, humidity, precipitation, wind, etc.) and climate (temperature as an essential climate variable, solar radiation in the ultraviolet, sunshine duration) variables on SARS-CoV-2 and discuss their impact to the COVID-19 pandemic; the review also refers to respective effect of urban parameters and air pollution. Most studies suggest that a negative correlation exists between ambient temperature and humidity on the one hand and the number of COVID-19 cases on the other, while there have been studies which support the absence of any correlation or even a positive one. The urban environment and specifically the air ventilation rate, as well as air pollution, can probably affect, also, the transmission dynamics and the case fatality rate of COVID-19. Due to the inherent limitations in previously published studies, it remains unclear if the magnitude of the effect of temperature or humidity on COVID-19 is confounded by the public health measures implemented widely during the first pandemic wave. The effect of weather and climate variables, as suggested previously for other viruses, cannot be excluded, however, under the conditions of the first pandemic wave, it might be difficult to be uncovered. The increase in the number of cases observed during summertime in the Northern hemisphere, and especially in countries with high average ambient temperatures, demonstrates that weather and climate variables, in the absence of public health interventions, cannot mitigate the resurgence of COVID-19 outbreaks.},
    doi = {10.1016/j.scitotenv.2020.144578},
    keywords = {Air pollution; Climate and weather variables; Outbreak; Pandemic; Public health interventions; SARS-CoV-2; Urban environment},
    pmid = {33450689},
    pubstate = {aheadofprint},
    }
  • [DOI] A. Pérez-Cataluña, E. Cuevas-Ferrando, W. Randazzo, and G. Sánchez, "Bias of library preparation for virome characterization in untreated and treated wastewaters.," The science of the total environment, vol. 767, p. 144589, 2020.
    [Bibtex]
    @Article{PerezCataluna20,
    author = {Pérez-Cataluña, Alba and Cuevas-Ferrando, Enric and Randazzo, Walter and Sánchez, Gloria},
    journal = {The Science of the total environment},
    title = {Bias of library preparation for virome characterization in untreated and treated wastewaters.},
    year = {2020},
    pages = {144589},
    volume = {767},
    abstract = {The use of metagenomics for virome characterization and its implementation for wastewater analyses, including wastewater-based epidemiology, has increased in the last years. However, the lack of standardized methods can led to highly different results. The aim of this work was to analyze virome profiles in upstream and downstream wastewater samples collected from four wastewater treatment plants (WWTPs) using two different library preparation kits. Viral particles were enriched from wastewater concentrates using a filtration and nuclease digestion procedure prior to total nucleic acid (NA) extraction. Sequencing was performed using the ScriptSeq v2 RNA-Seq (LS) and the NEBNext Ultra II RNA (NB) library preparation kits. Cleaned reads and contigs were annotated using a curated in-house database composed by reads assigned to viruses at NCBI. Significant differences in viral families and in the ratio of detection were shown between the two library kits used. The use of LS library showed Virgaviridae, Microviridae and Siphoviridae as the most abundant families; while Ackermannviridae and Helleviridae were highly represented within the NB library. Additionally, the two sequencing libraries produced outcomes that differed in the detection of viral indicators. These results highlighted the importance of library selection for studying viruses in untreated and treated wastewater. Our results underline the need for further studies to elucidate the influence of sequencing procedures in virome profiles in wastewater matrices in order to improve the knowledge of the virome in the water environment.},
    doi = {10.1016/j.scitotenv.2020.144589},
    keywords = {Enteric viruses; Metagenomics; Viability RT-qPCR; Wastewater},
    pmid = {33422963},
    pubstate = {aheadofprint},
    }
  • [DOI] A. A. Gulyaeva and A. E. Gorbalenya, "A nidovirus perspective on SARS-CoV-2.," Biochem Biophys Res Commun, 2020.
    [Bibtex]
    @Article{Gulyaeva20a,
    author = {Gulyaeva, Anastasia A. and Gorbalenya, Alexander E.},
    journal = {{Biochem Biophys Res Commun}},
    title = {A nidovirus perspective on {SARS}-{CoV}-2.},
    year = {2020},
    abstract = {Two pandemics of respiratory distress diseases associated with zoonotic introductions of the species Severe acute respiratory syndrome-related coronavirus in the human population during 21st century raised unprecedented interest in coronavirus research and assigned it unseen urgency. The two viruses responsible for the outbreaks, SARS-CoV and SARS-CoV-2, respectively, are in the spotlight, and SARS-CoV-2 is the focus of the current fast-paced research. Its foundation was laid down by studies of many corona- and related viruses that collectively form the vast order Nidovirales. Comparative genomics of nidoviruses played a key role in this advancement over more than 30 years. It facilitated the transfer of knowledge from characterized to newly identified viruses, including SARS-CoV and SARS-CoV-2, as well as contributed to the dissection of the nidovirus proteome and identification of patterns of variations between different taxonomic groups, from species to families. This review revisits selected cases of protein conservation and variation that define nidoviruses, illustrates the remarkable plasticity of the proteome during nidovirus adaptation, and asks questions at the interface of the proteome and processes that are vital for nidovirus reproduction and could inform the ongoing research of SARS-CoV-2.},
    doi = {10.1016/j.bbrc.2020.11.015},
    keywords = {Comparative genomics; Coronaviruses; Evolution; Nidoviruses; Proteome},
    pmid = {33413979},
    pubstate = {aheadofprint},
    }
  • [DOI] O. M. Allicock, N. Sahadeo, P. Lemey, A. J. Auguste, M. A. Suchard, A. Rambaut, and C. V. F. Carrington, "Determinants of dengue virus dispersal in the Americas.," Virus Evol, vol. 6, p. veaa074, 2020.
    [Bibtex]
    @Article{Allicock20,
    author = {Allicock, Orchid M. and Sahadeo, Nikita and Lemey, Philippe and Auguste, Albert J. and Suchard, Marc A. and Rambaut, Andrew and Carrington, Christine V. F.},
    journal = {{Virus Evol}},
    title = {Determinants of dengue virus dispersal in the {A}mericas.},
    year = {2020},
    pages = {veaa074},
    volume = {6},
    abstract = {Dengue viruses (DENVs) are classified into four serotypes, each of which contains multiple genotypes. DENV genotypes introduced into the Americas over the past five decades have exhibited different rates and patterns of spatial dispersal. In order to understand factors underlying these patterns, we utilized a statistical framework that allows for the integration of ecological, socioeconomic, and air transport mobility data as predictors of viral diffusion while inferring the phylogeographic history. Predictors describing spatial diffusion based on several covariates were compared using a generalized linear model approach, where the support for each scenario and its contribution is estimated simultaneously from the data set. Although different predictors were identified for different serotypes, our analysis suggests that overall diffusion of DENV-1, -2, and -3 in the Americas was associated with airline traffic. The other significant predictors included human population size, the geographical distance between countries and between urban centers and the density of people living in urban environments.},
    doi = {10.1093/ve/veaa074},
    issue = {2},
    keywords = {Bayesian phylogeography; dengue virus; hypothesis testing; spatial diffusion},
    pmid = {33408877},
    pubstate = {epublish},
    }
  • [DOI] A. Brinkmann, C. Kohl, A. Radonic, P. W. Dabrowski, K. Mühldorfer, A. Nitsche, G. Wibbelt, and A. Kurth, "First detection of bat-borne Issyk-Kul virus in Europe," Sci Rep, vol. 10, iss. 1, 2020.
    [Bibtex]
    @Article{Brinkmann20a,
    author = {Annika Brinkmann and Claudia Kohl and Aleksandar Radonic and Piotr Wojtek Dabrowski and Kristin Mühldorfer and Andreas Nitsche and Gudrun Wibbelt and Andreas Kurth},
    journal = {{Sci Rep}},
    title = {First detection of bat-borne {I}ssyk-{K}ul virus in {E}urope},
    year = {2020},
    number = {1},
    volume = {10},
    doi = {10.1038/s41598-020-79468-8},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] H. Blake, J. Corner, C. Cirelli, J. Hassard, L. Briggs, J. M. Daly, M. Bennett, J. G. Chappell, L. Fairclough, P. C. McClure, A. Tarr, P. Tighe, A. Favier, W. Irving, and J. Ball, "Perceptions and experiences of the University of Nottingham pilot SARS-CoV-2 asymptomatic testing service: a mixed-methods study.," Int J Environ Res Public Health, vol. 18, 2020.
    [Bibtex]
    @Article{Blake20,
    author = {Blake, Holly and Corner, Jessica and Cirelli, Cecilia and Hassard, Juliet and Briggs, Lydia and Daly, Janet M. and Bennett, Malcolm and Chappell, Joseph G. and Fairclough, Lucy and McClure, C. Patrick and Tarr, Alexander and Tighe, Patrick and Favier, Alex and Irving, William and Ball, Jonathan},
    journal = {{Int J Environ Res Public Health}},
    title = {Perceptions and Experiences of the {U}niversity of {N}ottingham Pilot {SARS-CoV-2} Asymptomatic Testing Service: A Mixed-Methods Study.},
    year = {2020},
    volume = {18},
    abstract = {We aimed to explore student and staff perceptions and experiences of a pilot SARS-CoV-2 asymptomatic testing service (P-ATS) in a UK university campus setting. This was a mixed-method study comprised of an online survey, and thematic analysis of qualitative data from interviews and focus groups conducted at the mid-point and end of the 12-week P-ATS programme. Ninety-nine students (84.8% female, 70% first year; 93.9% P-ATS participants) completed an online survey, 41 individuals attended interviews or focus groups, including 31 students (21 first year; 10 final year) and 10 staff. All types of testing and logistics were highly acceptable ( : swab, saliva; : finger prick) and 94.9% would participate again. Reported adherence to weekly virus testing was high (92.4% completed ≥6 tests; 70.8% submitted all 10 swabs; 89.2% completed ≥1 saliva sample) and 76.9% submitted ≥3 blood samples. Students tested to "keep campus safe", "contribute to national efforts to control COVID-19", and "protect others". In total, 31.3% had high anxiety as measured by the Generalized Anxiety Disorder scale (GAD-7) (27.1% of first year). Students with lower levels of anxiety and greater satisfaction with university communications around P-ATS were more likely to adhere to virus and antibody tests. Increased adherence to testing was associated with higher perceived risk of COVID-19 to self and others. Qualitative findings revealed 5 themes and 13 sub-themes: "emotional responses to COVID-19", "university life during COVID-19", "influences on testing participation", "testing physical and logistical factors" and "testing effects on mental wellbeing". Asymptomatic COVID-19 testing (SARS-CoV-2 virus/antibodies) is highly acceptable to students and staff in a university campus setting. Clear communications and strategies to reduce anxiety are likely to be important for testing uptake and adherence. Strategies are needed to facilitate social connections and mitigate the mental health impacts of COVID-19 and self-isolation.},
    doi = {10.3390/ijerph18010188},
    issue = {1},
    keywords = {Asymptomatic Infections; COVID-19, diagnosis, psychology; COVID-19 Testing; Female; Humans; Male; Specimen Handling; Surveys and Questionnaires; United Kingdom; Universities; Young Adult; COVID-19; SARS-CoV-2; coronavirus; disease outbreaks; health promotion; students; virus; young people},
    pmid = {33383781},
    pubstate = {epublish},
    }
  • [DOI] S. Lequime, J. Dehecq, S. Matheus, F. de Laval, L. Almeras, S. Briolant, and A. Fontaine, "Modeling intra-mosquito dynamics of Zika virus and its dose-dependence confirms the low epidemic potential of Aedes albopictus," PLoS Pathog, vol. 16, iss. 12, p. e1009068, 2020.
    [Bibtex]
    @Article{Lequime20a,
    author = {Sebastian Lequime and Jean-S{\'{e}}bastien Dehecq and S{\'{e}}verine Matheus and Franck de Laval and Lionel Almeras and S{\'{e}}bastien Briolant and Albin Fontaine},
    journal = {{PLoS Pathog}},
    title = {Modeling intra-mosquito dynamics of {Z}ika virus and its dose-dependence confirms the low epidemic potential of {A}edes albopictus},
    year = {2020},
    number = {12},
    pages = {e1009068},
    volume = {16},
    doi = {10.1371/journal.ppat.1009068},
    editor = {Elizabeth Ann McGraw},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] S. Trump, S. Lukassen, M. S. Anker, R. L. Chua, J. Liebig, L. Thürmann, V. M. Corman, M. Binder, J. Loske, C. Klasa, T. Krieger, B. P. Hennig, M. Messingschlager, F. Pott, J. Kazmierski, S. Twardziok, J. P. Albrecht, J. Eils, S. Hadzibegovic, A. Lena, B. Heidecker, T. Bürgel, J. Steinfeldt, C. Goffinet, F. Kurth, M. Witzenrath, M. T. Völker, S. D. Müller, U. G. Liebert, N. Ishaque, L. Kaderali, L. Sander, C. Drosten, S. Laudi, R. Eils, C. Conrad, U. Landmesser, and I. Lehmann, "Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19.," Nat Biotechnol, 2020.
    [Bibtex]
    @Article{Trump20,
    author = {Trump, Saskia and Lukassen, Soeren and Anker, Markus S. and Chua, Robert Lorenz and Liebig, Johannes and Thürmann, Loreen and Corman, Victor Max and Binder, Marco and Loske, Jennifer and Klasa, Christina and Krieger, Teresa and Hennig, Bianca P. and Messingschlager, Marey and Pott, Fabian and Kazmierski, Julia and Twardziok, Sven and Albrecht, Jan Philipp and Eils, Jürgen and Hadzibegovic, Sara and Lena, Alessia and Heidecker, Bettina and Bürgel, Thore and Steinfeldt, Jakob and Goffinet, Christine and Kurth, Florian and Witzenrath, Martin and Völker, Maria Theresa and Müller, Sarah Dorothea and Liebert, Uwe Gerd and Ishaque, Naveed and Kaderali, Lars and Sander, Leif-Erik and Drosten, Christian and Laudi, Sven and Eils, Roland and Conrad, Christian and Landmesser, Ulf and Lehmann, Irina},
    journal = {{Nat Biotechnol}},
    title = {Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with {COVID}-19.},
    year = {2020},
    abstract = {In coronavirus disease 2019 (COVID-19), hypertension and cardiovascular diseases are major risk factors for critical disease progression. However, the underlying causes and the effects of the main anti-hypertensive therapies-angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs)-remain unclear. Combining clinical data (n = 144) and single-cell sequencing data of airway samples (n = 48) with in vitro experiments, we observed a distinct inflammatory predisposition of immune cells in patients with hypertension that correlated with critical COVID-19 progression. ACEI treatment was associated with dampened COVID-19-related hyperinflammation and with increased cell intrinsic antiviral responses, whereas ARB treatment related to enhanced epithelial-immune cell interactions. Macrophages and neutrophils of patients with hypertension, in particular under ARB treatment, exhibited higher expression of the pro-inflammatory cytokines CCL3 and CCL4 and the chemokine receptor CCR1. Although the limited size of our cohort does not allow us to establish clinical efficacy, our data suggest that the clinical benefits of ACEI treatment in patients with COVID-19 who have hypertension warrant further investigation.},
    doi = {10.1038/s41587-020-00796-1},
    pmid = {33361824},
    pubstate = {aheadofprint},
    }
  • [DOI] J. Nkengasong, A. Iwasaki, C. Victora, J. Oh, G. F. Gao, A. Agrawal, C. Drosten, C. Söderberg-Naucler, E. López-Collazo, A. M. Pollock, A. Viola, and M. Baker, "The global response to the COVID-19 pandemic.," Med (NY), vol. 1, p. 3–8, 2020.
    [Bibtex]
    @Article{Nkengasong20,
    author = {Nkengasong, John and Iwasaki, Akiko and Victora, Cesar and Oh, Juhwan and Gao, George F. and Agrawal, Anurag and Drosten, Christian and Söderberg-Naucler, Cecilia and López-Collazo, Eduardo and Pollock, Allyson M. and Viola, Antonella and Baker, Michael},
    journal = {{Med (NY)}},
    title = {The Global Response to the {COVID-19} Pandemic.},
    year = {2020},
    pages = {3--8},
    volume = {1},
    abstract = {Global approaches towards pandemic control range from strict lockdowns to minimal restrictions. We asked experts worldwide about the lessons learned from their countries' response. Their voices converge on the importance of scientifically guided interventions to limit the spread of SARS-CoV-2 and its impact on human health.},
    doi = {10.1016/j.medj.2020.12.003},
    issue = {1},
    pmid = {33363282},
    pubstate = {ppublish},
    }
  • [DOI] S. Peter, P. Dittrich, and B. Ibrahim, "Structure and hierarchy of SARS-CoV-2 infection dynamics models revealed by reaction network analysis.," Viruses, vol. 13, 2020.
    [Bibtex]
    @Article{Peter20,
    author = {Peter, Stephan and Dittrich, Peter and Ibrahim, Bashar},
    journal = {Viruses},
    title = {Structure and Hierarchy of {SARS-CoV-2} Infection Dynamics Models Revealed by Reaction Network Analysis.},
    year = {2020},
    volume = {13},
    abstract = {This work provides a mathematical technique for analyzing and comparing infection dynamics models with respect to their potential long-term behavior, resulting in a hierarchy integrating all models. We apply our technique to coupled ordinary and partial differential equation models of SARS-CoV-2 infection dynamics operating on different scales, that is, within a single organism and between several hosts. The structure of a model is assessed by the theory of chemical organizations, not requiring quantitative kinetic information. We present the Hasse diagrams of organizations for the twelve virus models analyzed within this study. For comparing models, each organization is characterized by the types of species it contains. For this, each species is mapped to one out of four types, representing uninfected, infected, immune system, and bacterial species, respectively. Subsequently, we can integrate these results with those of our former work on Influenza-A virus resulting in a single joint hierarchy of 24 models. It appears that the SARS-CoV-2 models are simpler with respect to their long term behavior and thus display a simpler hierarchy with little dependencies compared to the Influenza-A models. Our results can support further development towards more complex SARS-CoV-2 models targeting the higher levels of the hierarchy.},
    doi = {10.3390/v13010014},
    issue = {1},
    keywords = {COVID-19, virology; Host-Pathogen Interactions; Humans; Influenza A virus; Influenza, Human, virology; Models, Biological; Models, Theoretical; SARS-CoV-2; Covid-19; ODEs; PDEs; SARS-CoV-2; between hosts; chemical organization theory; corona; reaction networks analysis; virus dynamics modeling; within hosts},
    pmid = {33374824},
    pubstate = {epublish},
    }
  • [DOI] A. Strömer, R. Rose, M. Schäfer, F. Schön, A. Vollersen, T. Lorentz, H. Fickenscher, and A. Krumbholz, "Performance of a point-of-care test for the rapid detection of SARS-CoV-2 antigen.," Microorganisms, vol. 9, 2020.
    [Bibtex]
    @Article{Stroemer20,
    author = {Strömer, Annabelle and Rose, Ruben and Schäfer, Miriam and Schön, Frieda and Vollersen, Anna and Lorentz, Thomas and Fickenscher, Helmut and Krumbholz, Andi},
    journal = {Microorganisms},
    title = {Performance of a Point-of-Care Test for the Rapid Detection of {SARS-CoV-2} Antigen.},
    year = {2020},
    volume = {9},
    abstract = {The rapid detection of infections caused by the (SARS-CoV-2) is necessary in the ongoing pandemic. Antigen-specific point-of-care tests (POCT) may be useful for this purpose. Here, such a POCT (SARS-CoV-2 NADAL COVID-19 Ag) was compared to a laboratory-developed triplex real-time polymerase chain reaction (RT-PCR) designed for the detection of viral nucleoprotein gene and two control targets. This RT-PCR served as a reference to investigate POCT sensitivity by re-testing upper respiratory tract (URT) samples ( = 124) exhibiting different SARS-CoV-2 loads in terms of RT-PCR threshold cycle (Ct) values. The optical intensities of the antigen bands were compared to the Ct values of the RT-PCR. The infectivity of various virus loads was estimated by inoculating Vero cells with URT samples ( = 64, Ct 17-34). POCT sensitivity varied from 100% (Ct < 25) to 73.1% (Ct ≤ 30); higher SARS-CoV-2 loads correlated with higher band intensities. All samples with a Ct > 30 were negative; among SARS-CoV-2 free samples ( = 10) no false-positives were detected. A head-to-head comparison with another POCT (Abbott, Panbio™ COVID-19 Ag Rapid Test) yielded similar results. Isolation of SARS-CoV-2 in cell-culture was successful up to a Ct value of 29. The POCT reliably detects high SARS-CoV-2 loads and rapidly identifies infectious individuals.},
    doi = {10.3390/microorganisms9010058},
    issue = {1},
    keywords = {COVID-19; PCR; POCT; antigen; comparison; diagnostic},
    pmid = {33379279},
    pubstate = {epublish},
    }
  • [DOI] B. Morel, P. Barbera, L. Czech, B. Bettisworth, L. Hübner, S. Lutteropp, D. Serdari, E. Kostaki, I. Mamais, A. M. Kozlov, P. Pavlidis, D. Paraskevis, and A. Stamatakis, "Phylogenetic analysis of SARS-CoV-2 data is difficult," Mol Biol Evol, 2020.
    [Bibtex]
    @Article{Morel:20,
    author = {Benoit Morel and Pierre Barbera and Lucas Czech and Ben Bettisworth and Lukas Hübner and Sarah Lutteropp and Dora Serdari and Evangelia-Georgia Kostaki and Ioannis Mamais and Alexey M Kozlov and Pavlos Pavlidis and Dimitrios Paraskevis and Alexandros Stamatakis},
    title = {Phylogenetic analysis of {SARS}-{CoV}-2 data is difficult},
    journal = {{Mol Biol Evol}},
    year = {2020},
    doi = {10.1093/molbev/msaa314},
    editor = {Harmit Malik},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] K. P. Szillat, D. Höper, M. Beer, and P. König, "Full-genome sequencing of German rabbit haemorrhagic disease virus uncovers recombination between RHDV (GI.2) and EBHSV (GII.1)," Virus Evol, vol. 6, iss. 2, 2020.
    [Bibtex]
    @Article{Szillat:20,
    author = {Kevin P Szillat and Dirk Höper and Martin Beer and Patricia König},
    title = {Full-genome sequencing of {G}erman rabbit haemorrhagic disease virus uncovers recombination between {RHDV} ({GI}.2) and {EBHSV} ({GII}.1)},
    journal = {{Virus Evol}},
    year = {2020},
    volume = {6},
    number = {2},
    doi = {10.1093/ve/veaa080},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] C. P. Shannon, T. M. Blimkie, R. Ben-Othman, N. Gladish, N. Amenyogbe, S. Drissler, R. D. Edgar, Q. Chan, M. Krajden, L. J. Foster, M. S. Kobor, W. W. Mohn, R. R. Brinkman, K. L. Cao, R. H. Scheuermann, S. J. Tebbutt, R. E. W. Hancock, W. C. Koff, T. R. Kollmann, M. Sadarangani, and A. H. Lee, "Multi-omic data integration allows baseline immune signatures to predict hepatitis B vaccine response in a small cohort," Front Immunol, vol. 11, 2020.
    [Bibtex]
    @Article{Shannon:20b,
    author = {Casey P. Shannon and Travis M. Blimkie and Rym Ben-Othman and Nicole Gladish and Nelly Amenyogbe and Sibyl Drissler and Rachel D. Edgar and Queenie Chan and Mel Krajden and Leonard J. Foster and Michael S. Kobor and William W. Mohn and Ryan R. Brinkman and Kim-Anh Le Cao and Richard H. Scheuermann and Scott J. Tebbutt and Robert E.W. Hancock and Wayne C. Koff and Tobias R. Kollmann and Manish Sadarangani and Amy Huei-Yi Lee},
    title = {Multi-Omic Data Integration Allows Baseline Immune Signatures to Predict Hepatitis {B} Vaccine Response in a Small Cohort},
    journal = {{Front Immunol}},
    year = {2020},
    volume = {11},
    doi = {10.3389/fimmu.2020.578801},
    publisher = {Frontiers Media {SA}},
    }
  • [DOI] P. Simmonds, S. Williams, and H. Harvala, "Understanding the outcomes of COVID-19 – does the current model of an acute respiratory infection really fit?," J Gen Virol, 2020.
    [Bibtex]
    @Article{Simmonds:20,
    author = {Peter Simmonds and Sarah Williams and Heli Harvala},
    title = {Understanding the outcomes of {COVID}-19 {\textendash} does the current model of an acute respiratory infection really fit?},
    journal = {{J Gen Virol}},
    year = {2020},
    doi = {10.1099/jgv.0.001545},
    publisher = {Microbiology Society},
    }
  • [DOI] J. Wolff, S. A. E. Rahman, J. King, M. El-Beskawy, A. Pohlmann, M. Beer, and B. Hoffmann, "Establishment of a challenge model for sheeppox virus infection," Microorganisms, vol. 8, iss. 12, p. 2001, 2020.
    [Bibtex]
    @Article{Wolff:20,
    author = {Janika Wolff and Sahar Abd El Rahman and Jacqueline King and Mohamed El-Beskawy and Anne Pohlmann and Martin Beer and Bernd Hoffmann},
    title = {Establishment of a Challenge Model for Sheeppox Virus Infection},
    journal = {Microorganisms},
    year = {2020},
    volume = {8},
    number = {12},
    pages = {2001},
    doi = {10.3390/microorganisms8122001},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] A. S. da Filipe, J. G. Shepherd, T. Williams, J. Hughes, E. Aranday-Cortes, P. Asamaphan, S. Ashraf, C. Balcazar, K. Brunker, A. Campbell, S. Carmichael, C. Davis, R. Dewar, M. D. Gallagher, R. Gunson, V. Hill, A. Ho, B. Jackson, E. James, N. Jesudason, N. Johnson, C. M. E. Leitch, K. Li, A. MacLean, D. Mair, D. A. McAllister, J. T. McCrone, S. E. McDonald, M. P. McHugh, K. A. Morris, J. Nichols, M. Niebel, K. Nomikou, R. J. Orton, Á. O'Toole, M. Palmarini, B. J. Parcell, Y. A. Parr, A. Rambaut, S. Rooke, S. Shaaban, R. Shah, J. B. Singer, K. Smollett, I. Starinskij, L. Tong, V. B. Sreenu, E. Wastnedge, M. T. G. Holden, D. L. Robertson, K. Templeton, and E. C. Thomson, "Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland," Nat Microbiol, vol. 6, iss. 1, p. 112–122, 2020.
    [Bibtex]
    @Article{SilvaFilipe:20,
    author = {Ana da Silva Filipe and James G. Shepherd and Thomas Williams and Joseph Hughes and Elihu Aranday-Cortes and Patawee Asamaphan and Shirin Ashraf and Carlos Balcazar and Kirstyn Brunker and Alasdair Campbell and Stephen Carmichael and Chris Davis and Rebecca Dewar and Michael D. Gallagher and Rory Gunson and Verity Hill and Antonia Ho and Ben Jackson and Edward James and Natasha Jesudason and Natasha Johnson and E. Carol McWilliam Leitch and Kathy Li and Alasdair MacLean and Daniel Mair and David A. McAllister and John T. McCrone and Sarah E. McDonald and Martin P. McHugh and A. Keith Morris and Jenna Nichols and Marc Niebel and Kyriaki Nomikou and Richard J. Orton and {\'{A}}ine O'Toole and Massimo Palmarini and Benjamin J. Parcell and Yasmin A. Parr and Andrew Rambaut and Stefan Rooke and Sharif Shaaban and Rajiv Shah and Joshua B. Singer and Katherine Smollett and Igor Starinskij and Lily Tong and Vattipally B. Sreenu and Elizabeth Wastnedge and Matthew T. G. Holden and David L. Robertson and Kate Templeton and Emma C. Thomson},
    title = {Genomic epidemiology reveals multiple introductions of {SARS}-{CoV}-2 from mainland {E}urope into {S}cotland},
    journal = {{Nat Microbiol}},
    year = {2020},
    volume = {6},
    number = {1},
    pages = {112--122},
    doi = {10.1038/s41564-020-00838-z},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] N. Schmidt, C. A. Lareau, H. Keshishian, S. Ganskih, C. Schneider, T. Hennig, R. Melanson, S. Werner, Y. Wei, M. Zimmer, J. Ade, L. Kirschner, S. Zielinski, L. Dölken, E. S. Lander, N. Caliskan, U. Fischer, J. Vogel, S. A. Carr, J. Bodem, and M. Munschauer, "The SARS-CoV-2 RNA–protein interactome in infected human cells," Nat Microbiol, 2020.
    [Bibtex]
    @Article{Schmidt:20,
    author = {Nora Schmidt and Caleb A. Lareau and Hasmik Keshishian and Sabina Ganskih and Cornelius Schneider and Thomas Hennig and Randy Melanson and Simone Werner and Yuanjie Wei and Matthias Zimmer and Jens Ade and Luisa Kirschner and Sebastian Zielinski and Lars Dölken and Eric S. Lander and Neva Caliskan and Utz Fischer and Jörg Vogel and Steven A. Carr and Jochen Bodem and Mathias Munschauer},
    title = {The {SARS}-{CoV}-2 {RNA}{\textendash}protein interactome in infected human cells},
    journal = {{Nat Microbiol}},
    year = {2020},
    doi = {10.1038/s41564-020-00846-z},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] A. Michelitsch, D. Hoffmann, K. Wernike, and M. Beer, "Occurrence of antibodies against SARS-CoV-2 in the domestic cat population of Germany," Vaccines, vol. 8, iss. 4, p. 772, 2020.
    [Bibtex]
    @Article{Michelitsch:20,
    author = {Anna Michelitsch and Donata Hoffmann and Kerstin Wernike and Martin Beer},
    title = {Occurrence of Antibodies against {SARS}-{CoV}-2 in the Domestic Cat Population of {G}ermany},
    journal = {Vaccines},
    year = {2020},
    volume = {8},
    number = {4},
    pages = {772},
    doi = {10.3390/vaccines8040772},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] G. Nouailles, E. Wyler, P. Pennitz, D. Postmus, D. Vladimirova, J. Kazmierski, F. Pott, K. Dietert, M. Mülleder, V. Farztdinov, B. Obermayer, S. Wienhold, S. Andreotti, T. Höfler, B. Sawitzki, C. Drosten, L. E. Sander, N. Suttorp, M. Ralser, D. Beule, A. D. Gruber, C. Goffinet, M. Landthaler, J. Trimpert, and M. Witzenrath, "Longitudinal omics in Syrian hamsters integrated with human data unravel complexity of moderate immune responses to SARS-CoV-2," bioRxiv, 2020.
    [Bibtex]
    @Article{Nouailles:20,
    author = {Geraldine Nouailles and Emanuel Wyler and Peter Pennitz and Dylan Postmus and Daria Vladimirova and Julia Kazmierski and Fabian Pott and Kristina Dietert and Michael Mülleder and Vadim Farztdinov and Benedikt Obermayer and Sandra-Maria Wienhold and Sandro Andreotti and Thomas Höfler and Birgit Sawitzki and Christian Drosten and Leif Erik Sander and Norbert Suttorp and Markus Ralser and Dieter Beule and Achim Dieter Gruber and Christine Goffinet and Markus Landthaler and Jakob Trimpert and Martin Witzenrath},
    title = {Longitudinal omics in {S}yrian hamsters integrated with human data unravel complexity of moderate immune responses to {SARS}-{CoV}-2},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.12.18.423524},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] R. Weersma, R. Gacesa, A. Kurilshikov, A. V. Vila, T. Sinha, M. Klaassen, L. Bolte, S. Andreu-Sanchez, L. Chen, V. Collij, S. Hu, J. Dekens, V. Lenters, J. Björk, C. J. Swarte, M. Swertz, B. H. Jansen, J. Gelderloos-Arends, M. Hofker, R. Vermeuelen, S. Sanna, H. Harmsen, C. Wijmenga, J. Fu, and A. Zhernakova, "The Dutch Microbiome Project defines factors that shape the healthy gut microbiome," Research Square, 2020.
    [Bibtex]
    @Article{Weersma:20,
    author = {Rinse Weersma and Ranko Gacesa and Alexander Kurilshikov and Arnau Vich Vila and Trishla Sinha and Marjolein Klaassen and Laura Bolte and Sergio Andreu-Sanchez and Lianmin Chen and Valerie Collij and Shixian Hu and Jackie Dekens and Virissa Lenters and Johannes Björk and J. Casper Swarte and Morris Swertz and B. H. Jansen and Jody Gelderloos-Arends and Marten Hofker and Roel Vermeuelen and Serena Sanna and Hermie Harmsen and Cisca Wijmenga and Jingyuan Fu and Alexandra Zhernakova},
    title = {The {D}utch {M}icrobiome {P}roject defines factors that shape the healthy gut microbiome},
    journal = {{Research Square}},
    year = {2020},
    doi = {10.21203/rs.3.rs-117376/v1},
    publisher = {Research Square},
    }
  • [DOI] M. Kohls, M. Kircher, J. Krepel, P. Liebig, and K. Jung, "Estimating the distribution of viral taxa in next-generation sequencing data using artificial neural networks," Research Square, 2020.
    [Bibtex]
    @Article{Kohls:20,
    author = {Moritz Kohls and Magdalena Kircher and Jessica Krepel and Pamela Liebig and Klaus Jung},
    title = {Estimating the Distribution of Viral Taxa in Next-generation Sequencing data using Artificial Neural Networks},
    journal = {{Research Square}},
    year = {2020},
    doi = {10.21203/rs.3.rs-127809/v1},
    publisher = {Research Square},
    }
  • [DOI] E. Kostaki, S. Limnaios, S. Roussos, M. Psichogiou, G. K. Nikolopoulos, S. R. Friedman, A. Antoniadou, M. Chini, A. Hatzakis, V. Sypsa, G. Magiorkinis, C. Seguin-Devaux, and D. Paraskevis, "Validation of molecular clock inferred HIV infection ages: evidence for accurate estimation of infection dates," medRxiv, 2020.
    [Bibtex]
    @Article{Kostaki:20,
    author = {Evangelia-Georgia Kostaki and Stefanos Limnaios and Sotirios Roussos and Mina Psichogiou and Georgios K. Nikolopoulos and Samuel R. Friedman and Anastasia Antoniadou and Maria Chini and Angelos Hatzakis and Vana Sypsa and Gkikas Magiorkinis and Carole Seguin-Devaux and Dimitrios Paraskevis},
    title = {Validation of molecular clock inferred {HIV} infection ages: evidence for accurate estimation of infection dates},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.12.11.20247601},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] E. Karakike, E. J. Giamarellos-Bourboulis, M. Kyprianou, C. Fleischmann-Struzek, M. W. Pletz, M. G. Netea, K. Reinhart, and E. Kyriazopoulou, "COVID-19 as cause of viral sepsis: a systematic review and meta-analysis," medRxiv, 2020.
    [Bibtex]
    @Article{Karakike:20,
    author = {Eleni Karakike and Evangelos J. Giamarellos-Bourboulis and Miltiades Kyprianou and Carolin Fleischmann-Struzek and Mathias W. Pletz and Mihai G. Netea and Konrad Reinhart and Evdoxia Kyriazopoulou},
    title = {{COVID}-19 as cause of viral sepsis: A Systematic Review and Meta-Analysis},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.12.02.20242354},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. Zafferani, C. Haddad, L. Luo, J. Davila-Calderon, L. Yuan-Chiu, C. S. Mugisha, A. G. Monaghan, A. A. Kennedy, J. D. Yesselman, R. J. Gifford, A. W. Tai, S. B. Kutluay, M. Li, G. Brewer, B. S. Tolbert, and A. E. Hargrove, "Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures," bioRxiv, 2020.
    [Bibtex]
    @Article{Zafferani:20,
    author = {Martina Zafferani and Christina Haddad and Le Luo and Jesse Davila-Calderon and Liang Yuan-Chiu and Christian Shema Mugisha and Adeline G. Monaghan and Andrew A. Kennedy and Joseph D. Yesselman and Robert J. Gifford and Andrew W. Tai and Sebla B. Kutluay and Mei-Ling Li and Gary Brewer and Blanton S. Tolbert and Amanda E. Hargrove},
    journal = {{bioRxiv}},
    title = {Amilorides inhibit {SARS}-{CoV}-2 replication in vitro by targeting {RNA} structures},
    year = {2020},
    doi = {10.1101/2020.12.05.409821},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. Huber, P. W. Schreiber, T. Scheier, A. Audigé, R. Buonomano, A. Rudiger, D. L. Braun, G. Eich, D. Keller, B. Hasse, C. Berger, A. Manrique, H. F. Günthard, J. Böni, and A. Trkola, "Large parallel screen of saliva and nasopharyngeal swabs in a test center setting proofs utility of saliva as alternate specimen for SARS-CoV-2 detection by RT-PCR," medRxiv, 2020.
    [Bibtex]
    @Article{Huber:20,
    author = {Michael Huber and Peter W. Schreiber and Thomas Scheier and Annette Audig{\'{e}} and Roberto Buonomano and Alain Rudiger and Dominique L. Braun and Gerhard Eich and Dagmar Keller and Barbara Hasse and Christoph Berger and Amapola Manrique and Huldrych F. Günthard and Jürg Böni and Alexandra Trkola},
    title = {Large parallel screen of saliva and nasopharyngeal swabs in a test center setting proofs utility of saliva as alternate specimen for {SARS}-{CoV}-2 detection by {RT}-{PCR}},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.12.01.20241778},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] B. Bartolini, M. Rueca, C. E. M. Gruber, F. Messina, E. Giombini, G. Ippolito, M. R. Capobianchi, and A. D. Caro, "The newly introduced SARS-CoV-2 variant A222V is rapidly spreading in Lazio region, Italy," medRxiv, 2020.
    [Bibtex]
    @Article{Bartolini:20a,
    author = {Barbara Bartolini and Martina Rueca and Cesare Ernesto Maria Gruber and Francesco Messina and Emanuela Giombini and Giuseppe Ippolito and Maria Rosaria Capobianchi and Antonino Di Caro},
    title = {The newly introduced {SARS}-{CoV}-2 variant {A222V} is rapidly spreading in {L}azio region, {I}taly},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.11.28.20237016},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] J. S. Huisman, J. Scire, D. C. Angst, R. A. Neher, S. Bonhoeffer, and T. Stadler, "Estimation and worldwide monitoring of the effective reproductive number of SARS-CoV-2," medRxiv, 2020.
    [Bibtex]
    @Article{Huisman:20,
    author = {Jana S. Huisman and J{\'{e}}r{\'{e}}mie Scire and Daniel C. Angst and Richard A. Neher and Sebastian Bonhoeffer and Tanja Stadler},
    title = {Estimation and worldwide monitoring of the effective reproductive number of {SARS}-{CoV}-2},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.11.26.20239368},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] W. J. D. Ouwendijk, D. P. Depledge, L. Rajbhandari, T. L. Rovis, S. Jonjic, J. Breuer, A. Venkatesan, G. M. G. M. Verjans, and T. Sadaoka, "Varicella-zoster virus VLT-ORF63 fusion transcript induces broad viral gene expression during reactivation from neuronal latency," Nat Commun, vol. 11, iss. 1, 2020.
    [Bibtex]
    @Article{Ouwendijk:20,
    author = {Werner J. D. Ouwendijk and Daniel P. Depledge and Labchan Rajbhandari and Tihana Lenac Rovis and Stipan Jonjic and Judith Breuer and Arun Venkatesan and Georges M. G. M. Verjans and Tomohiko Sadaoka},
    title = {Varicella-zoster virus {VLT}-{ORF}63 fusion transcript induces broad viral gene expression during reactivation from neuronal latency},
    journal = {{Nat Commun}},
    year = {2020},
    volume = {11},
    number = {1},
    doi = {10.1038/s41467-020-20031-4},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] A. K. Lindner, O. Nikolai, F. Kausch, M. Wintel, F. Hommes, M. Gertler, L. J. Krüger, M. Gaeddert, F. Tobian, F. Lainati, L. Köppel, J. Seybold, V. M. Corman, C. Drosten, J. Hofmann, J. A. Sacks, F. P. Mockenhaupt, and C. M. Denkinger, "Head-to-head comparison of SARS-CoV-2 antigen-detecting rapid test with self-collected anterior nasal swab versus professional-collected nasopharyngeal swab.," Eur Respir J, 2020.
    [Bibtex]
    @Article{Lindner:20,
    author = {Lindner, Andreas K and Nikolai, Olga and Kausch, Franka and Wintel, Mia and Hommes, Franziska and Gertler, Maximilian and Krüger, Lisa J and Gaeddert, Mary and Tobian, Frank and Lainati, Federica and Köppel, Lisa and Seybold, Joachim and Corman, Victor M and Drosten, Christian and Hofmann, Jörg and Sacks, Jilian A and Mockenhaupt, Frank P and Denkinger, Claudia M},
    title = {Head-to-head comparison of {SARS-CoV-2} antigen-detecting rapid test with self-collected anterior nasal swab versus professional-collected nasopharyngeal swab.},
    journal = {{Eur Respir J}},
    year = {2020},
    doi = {10.1183/13993003.03961-2020},
    pmid = {33303544},
    }
  • [DOI] X. Chen and D. Li, "Sequencing facility and DNA source associated patterns of virus-mappable reads in whole-genome sequencing data," Genomics, 2020.
    [Bibtex]
    @Article{Chen:20,
    author = {Xun Chen and Dawei Li},
    title = {Sequencing facility and {DNA} source associated patterns of virus-mappable reads in whole-genome sequencing data},
    journal = {Genomics},
    year = {2020},
    doi = {10.1016/j.ygeno.2020.12.004},
    publisher = {Elsevier {BV}},
    }
  • [DOI] M. I. Andersson, C. V. Arancibia-Carcamo, K. Auckland, K. J. Baillie, E. Barnes, T. Beneke, S. Bibi, T. Brooks, M. Carroll, D. Crook, K. Dingle, C. Dold, L. O. Downs, L. Dunn, D. W. Eyre, J. G. Jaramillo, H. Harvala, S. Hoosdally, S. Ijaz, T. James, W. James, K. Jeffery, A. Justice, P. Klenerman, J. C. Knight, M. Knight, X. Liu, S. F. Lumley, P. C. Matthews, A. L. McNaughton, A. J. Mentzer, J. Mongkolsapaya, S. Oakley, M. S. Oliveira, T. Peto, R. J. Ploeg, J. Ratcliff, M. J. Robbins, D. J. Roberts, J. Rudkin, R. A. Russell, G. Screaton, M. G. Semple, D. Skelly, P. Simmonds, N. Stoesser, L. Turtle, S. Wareing, and M. Zambon, "SARS-CoV-2 RNA detected in blood products from patients with COVID-19 is not associated with infectious virus," Wellcome Open Res, vol. 5, p. 181, 2020.
    [Bibtex]
    @Article{Andersson:20,
    author = {Monique I. Andersson and Carolina V. Arancibia-Carcamo and Kathryn Auckland and J. Kenneth Baillie and Eleanor Barnes and Tom Beneke and Sagida Bibi and Tim Brooks and Miles Carroll and Derrick Crook and Kate Dingle and Christina Dold and Louise O. Downs and Laura Dunn and David W. Eyre and Javier Gilbert Jaramillo and Heli Harvala and Sarah Hoosdally and Samreen Ijaz and Tim James and William James and Katie Jeffery and Anita Justice and Paul Klenerman and Julian C. Knight and Michael Knight and Xu Liu and Sheila F. Lumley and Philippa C. Matthews and Anna L. McNaughton and Alexander J. Mentzer and Juthathip Mongkolsapaya and Sarah Oakley and Marta S. Oliveira and Timothy Peto and Rutger J. Ploeg and Jeremy Ratcliff and Melanie J. Robbins and David J. Roberts and Justine Rudkin and Rebecca A. Russell and Gavin Screaton and Malcolm G. Semple and Donal Skelly and Peter Simmonds and Nicole Stoesser and Lance Turtle and Susan Wareing and Maria Zambon},
    title = {{SARS}-{CoV}-2 {RNA} detected in blood products from patients with {COVID}-19 is not associated with infectious virus},
    journal = {{Wellcome Open Res}},
    year = {2020},
    volume = {5},
    pages = {181},
    doi = {10.12688/wellcomeopenres.16002.2},
    publisher = {F1000 Research Ltd},
    }
  • [DOI] F. Hufsky, N. Beerenwinkel, I. M. Meyer, S. Roux, G. M. Cook, C. M. Kinsella, K. Lamkiewicz, M. Marquet, D. F. Nieuwenhuijse, I. Olendraite, S. Paraskevopoulou, F. Young, R. Dijkman, B. Ibrahim, J. Kelly, P. Le Mercier, M. Marz, A. Ramette, and V. Thiel, "The International Virus Bioinformatics Meeting 2020.," Viruses, vol. 12, 2020.
    [Bibtex]
    @Article{Hufsky:20a,
    author = {Hufsky, Franziska and Beerenwinkel, Niko and Meyer, Irmtraud M and Roux, Simon and Cook, Georgia May and Kinsella, Cormac M and Lamkiewicz, Kevin and Marquet, Mike and Nieuwenhuijse, David F and Olendraite, Ingrida and Paraskevopoulou, Sofia and Young, Francesca and Dijkman, Ronald and Ibrahim, Bashar and Kelly, Jenna and Le Mercier, Philippe and Marz, Manja and Ramette, Alban and Thiel, Volker},
    title = {{T}he {I}nternational {V}irus {B}ioinformatics {M}eeting 2020.},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    abstract = {The International Virus Bioinformatics Meeting 2020 was originally planned to take place in Bern, Switzerland, in March 2020. However, the COVID-19 pandemic put a spoke in the wheel of almost all conferences to be held in 2020. After moving the conference to 8-9 October 2020, we got hit by the second wave and finally decided at short notice to go fully online. On the other hand, the pandemic has made us even more aware of the importance of accelerating research in viral bioinformatics. Advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks. The International Virus Bioinformatics Meeting 2020 has attracted approximately 120 experts in virology and bioinformatics from all over the world to join the two-day virtual meeting. Despite concerns being raised that virtual meetings lack possibilities for face-to-face discussion, the participants from this small community created a highly interactive scientific environment, engaging in lively and inspiring discussions and suggesting new research directions and questions. The meeting featured five invited and twelve contributed talks, on the four main topics: (1) proteome and RNAome of RNA viruses, (2) viral metagenomics and ecology, (3) virus evolution and classification and (4) viral infections and immunology. Further, the meeting featured 20 oral poster presentations, all of which focused on specific areas of virus bioinformatics. This report summarizes the main research findings and highlights presented at the meeting.},
    doi = {10.3390/v12121398},
    issue = {12},
    keywords = {COVID-19; genome evolution; identification; metagenomics; software; viral diversity; viral taxonomy; virology; virome; virus bioinformatics},
    pmid = {33291220},
    }
  • [DOI] A. Bahai, E. Asgari, M. R. K. Mofrad, A. Kloetgen, and A. C. McHardy, "EpitopeVec: linear epitope prediction using deep protein sequence embeddings," bioRxiv, 2020.
    [Bibtex]
    @Article{Bahai:20,
    author = {Akash Bahai and Ehsaneddin Asgari and Mohammad R.K. Mofrad and Andreas Kloetgen and Alice C. McHardy},
    title = {{EpitopeVec}: Linear Epitope Prediction Using Deep Protein Sequence Embeddings},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.11.26.395830},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] G. Cantelli, G. Cochrane, C. Brooksbank, E. McDonagh, P. Flicek, J. McEntyre, E. Birney, and R. Apweiler, "The European Bioinformatics Institute: empowering cooperation in response to a global health crisis," Nucleic Acids Res, 2020.
    [Bibtex]
    @Article{Cantelli:20,
    author = {Gaia Cantelli and Guy Cochrane and Cath Brooksbank and Ellen McDonagh and Paul Flicek and Johanna McEntyre and Ewan Birney and Rolf Apweiler},
    title = {The {E}uropean {B}ioinformatics {I}nstitute: empowering cooperation in response to a global health crisis},
    journal = {{Nucleic Acids Res}},
    year = {2020},
    doi = {10.1093/nar/gkaa1077},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] A. M. Price, K. E. Hayer, A. B. R. McIntyre, N. S. Gokhale, J. S. Abebe, A. D. N. Fera, C. E. Mason, S. M. Horner, A. C. Wilson, D. P. Depledge, and M. D. Weitzman, "Direct RNA sequencing reveals m6A modifications on adenovirus RNA are necessary for efficient splicing," Nat Commun, vol. 11, iss. 1, 2020.
    [Bibtex]
    @Article{Price:20,
    author = {Alexander M. Price and Katharina E. Hayer and Alexa B. R. McIntyre and Nandan S. Gokhale and Jonathan S. Abebe and Ashley N. Della Fera and Christopher E. Mason and Stacy M. Horner and Angus C. Wilson and Daniel P. Depledge and Matthew D. Weitzman},
    title = {Direct {RNA} sequencing reveals {m6A} modifications on adenovirus {RNA} are necessary for efficient splicing},
    journal = {{Nat Commun}},
    year = {2020},
    volume = {11},
    number = {1},
    doi = {10.1038/s41467-020-19787-6},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] C. Santos-Hövener, H. K. Neuhauser, A. S. Rosario, M. Busch, M. Schlaud, R. Hoffmann, A. Gößwald, C. Koschollek, J. Hoebel, J. Allen, A. Haack-Erdmann, S. Brockmann, T. Ziese, A. Nitsche, J. Michel, S. Haller, H. Wilking, O. Hamouda, V. M. Corman, C. Drosten, L. Schaade, L. H. Wieler, and T. L. and, "Serology- and PCR-based cumulative incidence of SARS-CoV-2 infection in adults in a successfully contained early hotspot (CoMoLo study), Germany, May to June 2020," Euro Surveill, vol. 25, iss. 47, 2020.
    [Bibtex]
    @Article{Santos-Hövener:20,
    author = {Claudia Santos-Hövener and Hannelore K Neuhauser and Angelika Schaffrath Rosario and Markus Busch and Martin Schlaud and Robert Hoffmann and Antje Gö{\ss}wald and Carmen Koschollek and Jens Hoebel and Jennifer Allen and Antje Haack-Erdmann and Stefan Brockmann and Thomas Ziese and Andreas Nitsche and Janine Michel and Sebastian Haller and Hendrik Wilking and Osamah Hamouda and Victor M Corman and Christian Drosten and Lars Schaade and Lothar H Wieler and Thomas Lampert and},
    title = {Serology- and {PCR}-based cumulative incidence of {SARS}-{CoV}-2 infection in adults in a successfully contained early hotspot ({CoMoLo} study), {G}ermany, {M}ay to {J}une 2020},
    journal = {{Euro Surveill}},
    year = {2020},
    volume = {25},
    number = {47},
    doi = {10.2807/1560-7917.es.2020.25.47.2001752},
    publisher = {European Centre for Disease Control and Prevention ({ECDC})},
    }
  • [DOI] F. Husain-Syed, I. Vadász, J. Wilhelm, H. Walmrath, W. Seeger, H. Birk, B. Jennert, H. Dietrich, S. Herold, J. Trauth, K. Tello, M. Sander, R. E. Morty, H. Slanina, C. G. Schüttler, J. Ziebuhr, S. Kassoumeh, C. Ronco, F. Ferrari, K. Warnatz, K. Stahl, B. Seeliger, M. M. Hoeper, T. Welte, and S. David, "Immunoglobulin deficiency as an indicator of disease severity in patients with COVID-19," Am J Physiol Lung Cell Mol Physiol, 2020.
    [Bibtex]
    @Article{Husain-Syed:20,
    author = {Faeq Husain-Syed and Istv{\'{a}}n Vad{\'{a}}sz and Jochen Wilhelm and Hans-Dieter Walmrath and Werner Seeger and Horst-Walter Birk and Birgit Jennert and Hartmut Dietrich and Susanne Herold and Janina Trauth and Khodr Tello and Michael Sander and Rory E. Morty and Heiko Slanina and Christian G. Schüttler and John Ziebuhr and Shadi Kassoumeh and Claudio Ronco and Fiorenza Ferrari and Klaus Warnatz and Klaus Stahl and Benjamin Seeliger and Marius M. Hoeper and Tobias Welte and Sascha David},
    title = {Immunoglobulin Deficiency as an Indicator of Disease Severity in Patients with {COVID}-19},
    journal = {{Am J Physiol Lung Cell Mol Physiol}},
    year = {2020},
    doi = {10.1152/ajplung.00359.2020},
    publisher = {American Physiological Society},
    }
  • [DOI] S. Duchene, L. Featherstone, M. Haritopoulou-Sinanidou, A. Rambaut, P. Lemey, and G. Baele, "Temporal signal and the phylodynamic threshold of SARS-CoV-2," Virus Evol, vol. 6, iss. 2, 2020.
    [Bibtex]
    @Article{Duchene:20,
    author = {Sebastian Duchene and Leo Featherstone and Melina Haritopoulou-Sinanidou and Andrew Rambaut and Philippe Lemey and Guy Baele},
    title = {Temporal signal and the phylodynamic threshold of {SARS}-{CoV}-2},
    journal = {{Virus Evol}},
    year = {2020},
    volume = {6},
    number = {2},
    doi = {10.1093/ve/veaa061},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] N. Alygizakis, A. N. Markou, N. I. Rousis, A. Galani, M. Avgeris, P. G. Adamopoulos, A. Scorilas, E. S. Lianidou, D. Paraskevis, S. Tsiodras, A. Tsakris, M. Dimopoulos, and N. S. Thomaidis, "Analytical methodologies for the detection of SARS-CoV-2 in wastewater: protocols and future perspectives," Trends Analyt Chem, p. 116125, 2020.
    [Bibtex]
    @Article{Alygizakis:20,
    author = {Nikiforos Alygizakis and Athina N. Markou and Nikolaos I. Rousis and Aikaterini Galani and Margaritis Avgeris and Panagiotis G. Adamopoulos and Andreas Scorilas and Evi S. Lianidou and Dimitrios Paraskevis and Sotirios Tsiodras and Athanassios Tsakris and Meletios-Athanasios Dimopoulos and Nikolaos S. Thomaidis},
    title = {Analytical methodologies for the detection of {SARS}-{CoV}-2 in wastewater: Protocols and future perspectives},
    journal = {{Trends Analyt Chem}},
    year = {2020},
    pages = {116125},
    doi = {10.1016/j.trac.2020.116125},
    publisher = {Elsevier {BV}},
    }
  • [DOI] T. Schlesinger, B. Weißbrich, F. Wedekink, Q. Notz, J. Herrmann, M. Krone, M. Sitter, B. Schmid, M. Kredel, J. Stumpner, L. Dölken, J. Wischhusen, P. Kranke, P. Meybohm, and C. Lotz, "Biodistribution and serologic response in SARS-CoV-2 induced ARDS: a cohort study," PLoS One, vol. 15, iss. 11, p. e0242917, 2020.
    [Bibtex]
    @Article{Schlesinger:20,
    author = {Tobias Schlesinger and Benedikt Wei{\ss}brich and Florian Wedekink and Quirin Notz and Johannes Herrmann and Manuel Krone and Magdalena Sitter and Benedikt Schmid and Markus Kredel and Jan Stumpner and Lars Dölken and Jörg Wischhusen and Peter Kranke and Patrick Meybohm and Christopher Lotz},
    title = {Biodistribution and serologic response in {SARS}-{CoV}-2 induced {ARDS}: A cohort study},
    journal = {{PLoS One}},
    year = {2020},
    volume = {15},
    number = {11},
    pages = {e0242917},
    doi = {10.1371/journal.pone.0242917},
    editor = {Francesco Di Gennaro},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] S. Gryseels, L. D. Bruyn, R. Gyselings, S. Calvignac-Spencer, F. H. Leendertz, and H. Leirs, "Risk of human-to-wildlife transmission of SARS-CoV-2," Mamm Rev, 2020.
    [Bibtex]
    @Article{Gryseels:20a,
    author = {Sophie Gryseels and Luc De Bruyn and Ralf Gyselings and S{\'{e}}bastien Calvignac-Spencer and Fabian H. Leendertz and Herwig Leirs},
    title = {Risk of human-to-wildlife transmission of {SARS}-{CoV}-2},
    journal = {{Mamm Rev}},
    year = {2020},
    doi = {10.1111/mam.12225},
    publisher = {Wiley},
    }
  • [DOI] A. Popa, J. Genger, M. D. Nicholson, T. Penz, D. Schmid, S. W. Aberle, B. Agerer, A. Lercher, L. Endler, H. Colaço, M. Smyth, M. Schuster, M. L. Grau, F. Martínez-Jiménez, O. Pich, W. Borena, E. Pawelka, Z. Keszei, M. Senekowitsch, J. Laine, J. H. Aberle, M. Redlberger-Fritz, M. Karolyi, A. Zoufaly, S. Maritschnik, M. Borkovec, P. Hufnagl, M. Nairz, G. Weiss, M. T. Wolfinger, D. von Laer, G. Superti-Furga, N. Lopez-Bigas, E. Puchhammer-Stöckl, F. Allerberger, F. Michor, C. Bock, and A. Bergthaler, "Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2," Sci Transl Med, p. eabe2555, 2020.
    [Bibtex]
    @Article{Popa:20,
    author = {Alexandra Popa and Jakob-Wendelin Genger and Michael D. Nicholson and Thomas Penz and Daniela Schmid and Stephan W. Aberle and Benedikt Agerer and Alexander Lercher and Lukas Endler and Henrique Cola{\c{c}}o and Mark Smyth and Michael Schuster and Miguel L. Grau and Francisco Mart{\'{\i}}nez-Jim{\'{e}}nez and Oriol Pich and Wegene Borena and Erich Pawelka and Zsofia Keszei and Martin Senekowitsch and Jan Laine and Judith H. Aberle and Monika Redlberger-Fritz and Mario Karolyi and Alexander Zoufaly and Sabine Maritschnik and Martin Borkovec and Peter Hufnagl and Manfred Nairz and Günter Weiss and Michael T. Wolfinger and Dorothee von Laer and Giulio Superti-Furga and Nuria Lopez-Bigas and Elisabeth Puchhammer-Stöckl and Franz Allerberger and Franziska Michor and Christoph Bock and Andreas Bergthaler},
    title = {Genomic epidemiology of superspreading events in {A}ustria reveals mutational dynamics and transmission properties of {SARS}-{CoV}-2},
    journal = {{Sci Transl Med}},
    year = {2020},
    pages = {eabe2555},
    doi = {10.1126/scitranslmed.abe2555},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
  • [DOI] V. Feuillet, B. Canard, and A. Trautmann, "Combining antivirals and immunomodulators to fight COVID-19," Trends Immunol, 2020.
    [Bibtex]
    @Article{Feuillet:20,
    author = {Vincent Feuillet and Bruno Canard and Alain Trautmann},
    title = {Combining Antivirals and Immunomodulators to Fight {COVID}-19},
    journal = {{Trends Immunol}},
    year = {2020},
    doi = {10.1016/j.it.2020.11.003},
    publisher = {Elsevier {BV}},
    }
  • [DOI] X. F. López-Labrador, J. R. Brown, N. Fischer, H. Harvala, S. V. Boheemen, O. Cinek, A. Sayiner, T. V. Madsen, E. Auvinen, V. Kufner, M. Huber, C. Rodriguez, M. Jonges, M. Hönemann, P. Susi, H. Sousa, P. E. Klapper, A. Pérez-Cataluña, M. Hernandez, R. Molenkamp, L. van der Hoek, R. Schuurman, N. Couto, K. Leuzinger, P. Simmonds, M. Beer, D. Höper, S. Kamminga, M. C. W. Feltkamp, J. Rodríguez-Díaz, E. Keyaerts, X. C. Nielsen, E. Puchhammer-Stöckl, A. C. M. Kroes, J. Buesa, J. Breuer, E. C. J. Claas, and J. J. C. de Vries, "Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: wet lab procedure," J Clin Virol, vol. 134, p. 104691, 2020.
    [Bibtex]
    @Article{Lopez-Labrador:20,
    author = {F. Xavier L{\'{o}}pez-Labrador and Julianne R. Brown and Nicole Fischer and Heli Harvala and Sander Van Boheemen and Ondrej Cinek and Arzu Sayiner and Tina Vasehus Madsen and Eeva Auvinen and Verena Kufner and Michael Huber and Christophe Rodriguez and Marcel Jonges and Mario Hönemann and Petri Susi and Hugo Sousa and Paul E. Klapper and Alba Pérez-Cataluña and Marta Hernandez and Richard Molenkamp and Lia van der Hoek and Rob Schuurman and Natacha Couto and Karoline Leuzinger and Peter Simmonds and Martin Beer and Dirk Höper and Sergio Kamminga and Mariet C.W. Feltkamp and Jes{\'{u}}s Rodr{\'{\i}}guez-D{\'{\i}}az and Els Keyaerts and Xiaohui Chen Nielsen and Elisabeth Puchhammer-Stöckl and Aloys C.M. Kroes and Javier Buesa and Judy Breuer and Eric C.J. Claas and Jutte J.C. de Vries},
    title = {Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part {I}: Wet lab procedure},
    journal = {{J Clin Virol}},
    year = {2020},
    volume = {134},
    pages = {104691},
    doi = {10.1016/j.jcv.2020.104691},
    publisher = {Elsevier {BV}},
    }
  • [DOI] A. Brinkmann, A. R. V. Souza, J. Esparza, A. Nitsche, and C. R. Damaso, "Re-assembly of nineteenth-century smallpox vaccine genomes reveals the contemporaneous use of horsepox and horsepox-related viruses in the USA," Genome Biol, vol. 21, iss. 1, 2020.
    [Bibtex]
    @Article{Brinkmann:20,
    author = {Annika Brinkmann and Aline R. V. Souza and Jos{\'{e}} Esparza and Andreas Nitsche and Clarissa R. Damaso},
    title = {Re-assembly of nineteenth-century smallpox vaccine genomes reveals the contemporaneous use of horsepox and horsepox-related viruses in the {USA}},
    journal = {{Genome Biol}},
    year = {2020},
    volume = {21},
    number = {1},
    doi = {10.1186/s13059-020-02202-0},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] E. Volz, V. Hill, J. T. McCrone, A. Price, D. Jorgensen, Á. O'Toole, J. Southgate, R. Johnson, B. Jackson, F. F. Nascimento, S. M. Rey, S. M. Nicholls, R. M. Colquhoun, A. S. da Filipe, J. Shepherd, D. J. Pascall, R. Shah, N. Jesudason, K. Li, R. Jarrett, N. Pacchiarini, M. Bull, L. Geidelberg, I. Siveroni, I. Goodfellow, N. J. Loman, O. G. Pybus, D. L. Robertson, E. C. Thomson, A. Rambaut, T. R. Connor, C. Koshy, E. Wise, N. Cortes, J. Lynch, S. Kidd, M. Mori, D. J. Fairley, T. Curran, J. P. McKenna, H. Adams, C. Fraser, T. Golubchik, D. Bonsall, C. Moore, S. L. Caddy, F. A. Khokhar, M. Wantoch, N. Reynolds, B. Warne, J. Maksimovic, K. Spellman, K. McCluggage, M. John, R. Beer, S. Afifi, S. Morgan, A. Marchbank, A. Price, C. Kitchen, H. Gulliver, I. Merrick, J. Southgate, M. Guest, R. Munn, T. Workman, T. R. Connor, W. Fuller, C. Bresner, L. B. Snell, T. Charalampous, G. Nebbia, R. Batra, J. Edgeworth, S. C. Robson, A. Beckett, K. F. Loveson, D. M. Aanensen, A. P. Underwood, C. A. Yeats, K. Abudahab, B. E. W. Taylor, M. Menegazzo, G. Clark, W. Smith, M. Khakh, V. M. Fleming, M. M. Lister, H. C. Howson-Wells, L. Berry, T. Boswell, A. Joseph, I. Willingham, P. Bird, T. Helmer, K. Fallon, C. Holmes, J. Tang, V. Raviprakash, S. Campbell, N. Sheriff, M. W. Loose, N. Holmes, C. Moore, M. Carlile, V. Wright, F. Sang, J. Debebe, F. Coll, A. W. Signell, G. Betancor, H. D. Wilson, T. Feltwell, C. J. Houldcroft, S. Eldirdiri, A. Kenyon, T. Davis, O. Pybus, L. du Plessis, A. Zarebski, J. Raghwani, M. Kraemer, S. Francois, S. Attwood, T. Vasylyeva, E. M. Torok, W. L. Hamilton, I. G. Goodfellow, G. Hall, A. S. Jahun, Y. Chaudhry, M. Hosmillo, M. L. Pinckert, I. Georgana, A. Yakovleva, L. W. Meredith, S. Moses, H. Lowe, F. Ryan, C. L. Fisher, A. R. Awan, J. Boyes, J. Breuer, K. A. Harris, J. R. Brown, D. Shah, L. Atkinson, J. C. D. Lee, A. Alcolea-Medina, N. Moore, N. Cortes, R. Williams, M. R. Chapman, L. J. Levett, J. Heaney, D. L. Smith, M. Bashton, G. R. Young, J. Allan, J. Loh, P. A. Randell, A. Cox, P. Madona, A. Holmes, F. Bolt, J. Price, S. Mookerjee, A. Rowan, G. P. Taylor, M. Ragonnet-Cronin, F. F. Nascimento, D. Jorgensen, I. Siveroni, R. Johnson, O. Boyd, L. Geidelberg, E. M. Volz, K. Brunker, K. L. Smollett, N. J. Loman, J. Quick, C. McMurray, J. Stockton, S. Nicholls, W. Rowe, R. Poplawski, R. T. Martinez-Nunez, J. Mason, T. I. Robinson, E. O. textquotesingle, J. Watts, C. Breen, A. Cowell, C. Ludden, G. Sluga, N. W. Machin, S. S. Y. Ahmad, R. P. George, F. Halstead, V. Sivaprakasam, E. C. Thomson, J. G. Shepherd, P. Asamaphan, M. O. Niebel, K. K. Li, R. N. Shah, N. G. Jesudason, Y. A. Parr, L. Tong, A. Broos, D. Mair, J. Nichols, S. N. Carmichael, K. Nomikou, E. Aranday-Cortes, N. Johnson, I. Starinskij, A. S. da Filipe, D. L. Robertson, R. J. Orton, J. Hughes, S. Vattipally, J. B. Singer, A. D. Hale, L. R. Macfarlane-Smith, K. L. Harper, Y. Taha, B. A. I. Payne, S. Burton-Fanning, S. Waugh, J. Collins, G. Eltringham, K. E. Templeton, M. P. McHugh, R. Dewar, E. Wastenge, S. Dervisevic, R. Stanley, R. Prakash, C. Stuart, N. Elumogo, D. K. Sethi, E. J. Meader, L. J. Coupland, W. Potter, C. Graham, E. Barton, D. Padgett, G. Scott, E. Swindells, J. Greenaway, A. Nelson, W. C. Yew, P. R. C. Silva, M. Andersson, R. Shaw, T. Peto, A. Justice, D. Eyre, D. Crooke, S. Hoosdally, T. J. Sloan, N. Duckworth, S. Walsh, A. J. Chauhan, S. Glaysher, K. Bicknell, S. Wyllie, E. Butcher, S. Elliott, A. Lloyd, R. Impey, N. Levene, L. Monaghan, D. T. Bradley, E. Allara, C. Pearson, P. Muir, I. B. Vipond, R. Hopes, H. M. Pymont, S. Hutchings, M. D. Curran, S. Parmar, A. Lackenby, T. Mbisa, S. Platt, S. Miah, D. Bibby, C. Manso, J. Hubb, M. Chand, G. Dabrera, M. Ramsay, D. Bradshaw, A. Thornton, R. Myers, U. Schaefer, N. Groves, E. Gallagher, D. Lee, D. Williams, N. Ellaby, I. Harrison, H. Hartman, N. Manesis, V. Patel, C. Bishop, V. Chalker, H. Osman, A. Bosworth, E. Robinson, M. T. G. Holden, S. Shaaban, A. Birchley, A. Adams, A. Davies, A. Gaskin, A. Plimmer, B. Gatica-Wilcox, C. McKerr, C. Moore, C. Williams, D. Heyburn, E. D. Lacy, E. Hilvers, F. Downing, G. Shankar, H. Jones, H. Asad, J. Coombes, J. Watkins, J. M. Evans, L. Fina, L. Gifford, L. Gilbert, L. Graham, M. Perry, M. Morgan, M. Bull, M. Cronin, N. Pacchiarini, N. Craine, R. Jones, R. Howe, S. Corden, S. Rey, S. Kumziene-Summerhayes, S. Taylor, S. Cottrell, S. Jones, S. Edwards, J. O'Grady, A. J. Page, J. Wain, M. A. Webber, A. E. Mather, D. J. Baker, S. Rudder, M. Yasir, N. M. Thomson, A. Aydin, A. P. Tedim, G. L. Kay, A. J. Trotter, R. A. J. Gilroy, N. Alikhan, L. O. de Martins, T. Le-Viet, L. Meadows, A. Kolyva, M. Diaz, A. Bell, A. V. Gutierrez, I. G. Charles, E. M. Adriaenssens, R. A. Kingsley, A. Casey, D. A. Simpson, Z. Molnar, T. Thompson, E. Acheson, J. A. H. Masoli, B. A. Knight, A. Hattersley, S. Ellard, C. Auckland, T. W. Mahungu, D. Irish-Tavares, T. Haque, Y. Bourgeois, G. P. Scarlett, D. G. Partridge, M. Raza, C. Evans, K. Johnson, S. Liggett, P. Baker, S. Essex, R. A. Lyons, L. G. Caller, S. Castellano, R. J. Williams, M. Kristiansen, S. Roy, C. A. Williams, P. L. Dyal, H. J. Tutill, Y. N. Panchbhaya, L. M. Forrest, P. Niola, J. Findlay, T. T. Brooks, A. Gavriil, L. Mestek-Boukhibar, S. Weeks, S. Pandey, L. Berry, K. Jones, A. Richter, A. Beggs, C. P. Smith, G. Bucca, A. R. Hesketh, E. M. Harrison, S. J. Peacock, S. Palmer, C. M. Churcher, K. L. Bellis, S. T. Girgis, P. Naydenova, B. Blane, S. Sridhar, C. Ruis, S. Forrest, C. Cormie, H. K. Gill, J. Dias, E. E. Higginson, M. Maes, J. Young, L. M. Kermack, N. F. Hadjirin, D. Aggarwal, L. Griffith, T. Swingler, R. K. Davidson, A. Rambaut, T. Williams, C. E. Balcazar, M. D. Gallagher, Á. O. textquotesingle, S. Rooke, B. Jackson, R. Colquhoun, J. Ashworth, V. Hill, J. T. McCrone, E. Scher, X. Yu, K. A. Williamson, T. D. Stanton, S. L. Michell, C. M. Bewshea, B. Temperton, M. L. Michelsen, J. Warwick-Dugdale, R. Manley, A. Farbos, J. W. Harrison, C. M. Sambles, D. J. Studholme, A. R. Jeffries, A. C. Darby, J. A. Hiscox, S. Paterson, M. Iturriza-Gomara, K. A. Jackson, A. O. Lucaci, E. E. Vamos, M. Hughes, L. Rainbow, R. Eccles, C. Nelson, M. Whitehead, L. Turtle, S. T. Haldenby, R. Gregory, M. Gemmell, D. Kwiatkowski, T. I. de Silva, N. Smith, A. Angyal, B. B. Lindsey, D. C. Groves, L. R. Green, D. Wang, T. M. Freeman, M. D. Parker, A. J. Keeley, P. J. Parsons, R. M. Tucker, R. Brown, M. Wyles, C. Constantinidou, M. Unnikrishnan, S. Ott, J. K. J. Cheng, H. E. Bridgewater, L. R. Frost, G. Taylor-Joyce, R. Stark, L. Baxter, M. T. Alam, P. E. Brown, P. C. McClure, J. G. Chappell, T. Tsoleridis, J. Ball, D. Gramatopoulos, D. Buck, J. A. Todd, A. Green, A. Trebes, G. MacIntyre-Cockett, M. de Cesare, C. Langford, A. Alderton, R. Amato, S. Goncalves, D. K. Jackson, I. Johnston, J. Sillitoe, S. Palmer, M. Lawniczak, M. Berriman, J. Danesh, R. Livett, L. Shirley, B. Farr, M. Quail, S. Thurston, N. Park, E. Betteridge, D. Weldon, S. Goodwin, R. Nelson, C. Beaver, L. Letchford, D. A. Jackson, L. Foulser, L. McMinn, L. Prestwood, S. Kay, L. Kane, M. J. Dorman, I. Martincorena, C. Puethe, J. Keatley, G. Tonkin-Hill, C. Smith, D. Jamrozy, M. A. Beale, M. Patel, C. Ariani, M. Spencer-Chapman, E. Drury, S. Lo, S. Rajatileka, C. Scott, K. James, S. K. Buddenborg, D. J. Berger, G. Patel, M. V. Garcia-Casado, T. Dibling, S. McGuigan, H. A. Rogers, A. D. Hunter, E. Souster, and A. S. Neaverson, "Evaluating the effects of SARS-CoV-2 spike mutation D614G on transmissibility and pathogenicity," Cell, 2020.
    [Bibtex]
    @Article{Volz:20,
    author = {Erik Volz and Verity Hill and John T. McCrone and Anna Price and David Jorgensen and {\'{A}}ine O'Toole and Joel Southgate and Robert Johnson and Ben Jackson and Fabricia F. Nascimento and Sara M. Rey and Samuel M. Nicholls and Rachel M. Colquhoun and Ana da Silva Filipe and James Shepherd and David J. Pascall and Rajiv Shah and Natasha Jesudason and Kathy Li and Ruth Jarrett and Nicole Pacchiarini and Matthew Bull and Lily Geidelberg and Igor Siveroni and Ian Goodfellow and Nicholas J. Loman and Oliver G. Pybus and David L. Robertson and Emma C. Thomson and Andrew Rambaut and Thomas R. Connor and Cherian Koshy and Emma Wise and Nick Cortes and Jessica Lynch and Stephen Kidd and Matilde Mori and Derek J. Fairley and Tanya Curran and James P. McKenna and Helen Adams and Christophe Fraser and Tanya Golubchik and David Bonsall and Catrin Moore and Sarah L. Caddy and Fahad A. Khokhar and Michelle Wantoch and Nicola Reynolds and Ben Warne and Joshua Maksimovic and Karla Spellman and Kathryn McCluggage and Michaela John and Robert Beer and Safiah Afifi and Sian Morgan and Angela Marchbank and Anna Price and Christine Kitchen and Huw Gulliver and Ian Merrick and Joel Southgate and Martyn Guest and Robert Munn and Trudy Workman and Thomas R. Connor and William Fuller and Catherine Bresner and Luke B. Snell and Themoula Charalampous and Gaia Nebbia and Rahul Batra and Jonathan Edgeworth and Samuel C. Robson and Angela Beckett and Katie F. Loveson and David M. Aanensen and Anthony P. Underwood and Corin A. Yeats and Khalil Abudahab and Ben E.W. Taylor and Mirko Menegazzo and Gemma Clark and Wendy Smith and Manjinder Khakh and Vicki M. Fleming and Michelle M. Lister and Hannah C. Howson-Wells and Louise Berry and Tim Boswell and Amelia Joseph and Iona Willingham and Paul Bird and Thomas Helmer and Karlie Fallon and Christopher Holmes and Julian Tang and Veena Raviprakash and Sharon Campbell and Nicola Sheriff and Matthew W. Loose and Nadine Holmes and Christopher Moore and Matthew Carlile and Victoria Wright and Fei Sang and Johnny Debebe and Francesc Coll and Adrian W. Signell and Gilberto Betancor and Harry D. Wilson and Theresa Feltwell and Charlotte J. Houldcroft and Sahar Eldirdiri and Anita Kenyon and Thomas Davis and Oliver Pybus and Louis du Plessis and Alex Zarebski and Jayna Raghwani and Moritz Kraemer and Sarah Francois and Stephen Attwood and Tetyana Vasylyeva and M. Estee Torok and William L. Hamilton and Ian G. Goodfellow and Grant Hall and Aminu S. Jahun and Yasmin Chaudhry and Myra Hosmillo and Malte L. Pinckert and Iliana Georgana and Anna Yakovleva and Luke W. Meredith and Samuel Moses and Hannah Lowe and Felicity Ryan and Chloe L. Fisher and Ali R. Awan and John Boyes and Judith Breuer and Kathryn Ann Harris and Julianne Rose Brown and Divya Shah and Laura Atkinson and Jack C.D. Lee and Adela Alcolea-Medina and Nathan Moore and Nicholas Cortes and Rebecca Williams and Michael R. Chapman and Lisa J. Levett and Judith Heaney and Darren L. Smith and Matthew Bashton and Gregory R. Young and John Allan and Joshua Loh and Paul A. Randell and Alison Cox and Pinglawathee Madona and Alison Holmes and Frances Bolt and James Price and Siddharth Mookerjee and Aileen Rowan and Graham P. Taylor and Manon Ragonnet-Cronin and Fabricia F. Nascimento and David Jorgensen and Igor Siveroni and Rob Johnson and Olivia Boyd and Lily Geidelberg and Erik M. Volz and Kirstyn Brunker and Katherine L. Smollett and Nicholas J. Loman and Joshua Quick and Claire McMurray and Joanne Stockton and Sam Nicholls and Will Rowe and Radoslaw Poplawski and Rocio T. Martinez-Nunez and Jenifer Mason and Trevor I. Robinson and Elaine O{\textquotesingle}Toole and Joanne Watts and Cassie Breen and Angela Cowell and Catherine Ludden and Graciela Sluga and Nicholas W. Machin and Shazaad S.Y. Ahmad and Ryan P. George and Fenella Halstead and Venkat Sivaprakasam and Emma C. Thomson and James G. Shepherd and Patawee Asamaphan and Marc O. Niebel and Kathy K. Li and Rajiv N. Shah and Natasha G. Jesudason and Yasmin A. Parr and Lily Tong and Alice Broos and Daniel Mair and Jenna Nichols and Stephen N. Carmichael and Kyriaki Nomikou and Elihu Aranday-Cortes and Natasha Johnson and Igor Starinskij and Ana da Silva Filipe and David L. Robertson and Richard J. Orton and Joseph Hughes and Sreenu Vattipally and Joshua B. Singer and Antony D. Hale and Louissa R. Macfarlane-Smith and Katherine L. Harper and Yusri Taha and Brendan A.I. Payne and Shirelle Burton-Fanning and Sheila Waugh and Jennifer Collins and Gary Eltringham and Kate E. Templeton and Martin P. McHugh and Rebecca Dewar and Elizabeth Wastenge and Samir Dervisevic and Rachael Stanley and Reenesh Prakash and Claire Stuart and Ngozi Elumogo and Dheeraj K. Sethi and Emma J. Meader and Lindsay J. Coupland and Will Potter and Clive Graham and Edward Barton and Debra Padgett and Garren Scott and Emma Swindells and Jane Greenaway and Andrew Nelson and Wen C. Yew and Paola C. Resende Silva and Monique Andersson and Robert Shaw and Timothy Peto and Anita Justice and David Eyre and Derrick Crooke and Sarah Hoosdally and Tim J. Sloan and Nichola Duckworth and Sarah Walsh and Anoop J. Chauhan and Sharon Glaysher and Kelly Bicknell and Sarah Wyllie and Ethan Butcher and Scott Elliott and Allyson Lloyd and Robert Impey and Nick Levene and Lynn Monaghan and Declan T. Bradley and Elias Allara and Clare Pearson and Peter Muir and Ian B. Vipond and Richard Hopes and Hannah M. Pymont and Stephanie Hutchings and Martin D. Curran and Surendra Parmar and Angie Lackenby and Tamyo Mbisa and Steven Platt and Shahjahan Miah and David Bibby and Carmen Manso and Jonathan Hubb and Meera Chand and Gavin Dabrera and Mary Ramsay and Daniel Bradshaw and Alicia Thornton and Richard Myers and Ulf Schaefer and Natalie Groves and Eileen Gallagher and David Lee and David Williams and Nicholas Ellaby and Ian Harrison and Hassan Hartman and Nikos Manesis and Vineet Patel and Chloe Bishop and Vicki Chalker and Husam Osman and Andrew Bosworth and Esther Robinson and Matthew T.G. Holden and Sharif Shaaban and Alec Birchley and Alexander Adams and Alisha Davies and Amy Gaskin and Amy Plimmer and Bree Gatica-Wilcox and Caoimhe McKerr and Catherine Moore and Chris Williams and David Heyburn and Elen De Lacy and Ember Hilvers and Fatima Downing and Giri Shankar and Hannah Jones and Hibo Asad and Jason Coombes and Joanne Watkins and Johnathan M. Evans and Laia Fina and Laura Gifford and Lauren Gilbert and Lee Graham and Malorie Perry and Mari Morgan and Matthew Bull and Michelle Cronin and Nicole Pacchiarini and Noel Craine and Rachel Jones and Robin Howe and Sally Corden and Sara Rey and Sara Kumziene-Summerhayes and Sarah Taylor and Simon Cottrell and Sophie Jones and Sue Edwards and Justin O'Grady and Andrew J. Page and John Wain and Mark A. Webber and Alison E. Mather and David J. Baker and Steven Rudder and Muhammad Yasir and Nicholas M. Thomson and Alp Aydin and Ana P. Tedim and Gemma L. Kay and Alexander J. Trotter and Rachel A.J. Gilroy and Nabil-Fareed Alikhan and Leonardo de Oliveira Martins and Thanh Le-Viet and Lizzie Meadows and Anastasia Kolyva and Maria Diaz and Andrew Bell and Ana Victoria Gutierrez and Ian G. Charles and Evelien M. Adriaenssens and Robert A. Kingsley and Anna Casey and David A. Simpson and Zoltan Molnar and Thomas Thompson and Erwan Acheson and Jane A.H. Masoli and Bridget A. Knight and Andrew Hattersley and Sian Ellard and Cressida Auckland and Tabitha W. Mahungu and Dianne Irish-Tavares and Tanzina Haque and Yann Bourgeois and Garry P. Scarlett and David G. Partridge and Mohammad Raza and Cariad Evans and Kate Johnson and Steven Liggett and Paul Baker and Sarah Essex and Ronan A. Lyons and Laura G. Caller and Sergi Castellano and Rachel J. Williams and Mark Kristiansen and Sunando Roy and Charlotte A. Williams and Patricia L. Dyal and Helena J. Tutill and Yasmin N. Panchbhaya and Leysa M. Forrest and Paola Niola and Jacqueline Findlay and Tony T. Brooks and Artemis Gavriil and Lamia Mestek-Boukhibar and Sam Weeks and Sarojini Pandey and Lisa Berry and Katie Jones and Alex Richter and Andrew Beggs and Colin P. Smith and Giselda Bucca and Andrew R. Hesketh and Ewan M. Harrison and Sharon J. Peacock and Sophie Palmer and Carol M. Churcher and Katherine L. Bellis and Sophia T. Girgis and Plamena Naydenova and Beth Blane and Sushmita Sridhar and Chris Ruis and Sally Forrest and Claire Cormie and Harmeet K. Gill and Joana Dias and Ellen E. Higginson and Mailis Maes and Jamie Young and Leanne M. Kermack and Nazreen F. Hadjirin and Dinesh Aggarwal and Luke Griffith and Tracey Swingler and Rose K. Davidson and Andrew Rambaut and Thomas Williams and Carlos E. Balcazar and Michael D. Gallagher and {\'{A}}ine O{\textquotesingle}Toole and Stefan Rooke and Ben Jackson and Rachel Colquhoun and Jordan Ashworth and Verity Hill and J.T. McCrone and Emily Scher and Xiaoyu Yu and Kathleen A. Williamson and Thomas D. Stanton and Stephen L. Michell and Claire M. Bewshea and Ben Temperton and Michelle L. Michelsen and Joanna Warwick-Dugdale and Robin Manley and Audrey Farbos and James W. Harrison and Christine M. Sambles and David J. Studholme and Aaron R. Jeffries and Alistair C. Darby and Julian A. Hiscox and Steve Paterson and Miren Iturriza-Gomara and Kathryn A. Jackson and Anita O. Lucaci and Edith E. Vamos and Margaret Hughes and Lucille Rainbow and Richard Eccles and Charlotte Nelson and Mark Whitehead and Lance Turtle and Sam T. Haldenby and Richard Gregory and Matthew Gemmell and Dominic Kwiatkowski and Thushan I. de Silva and Nikki Smith and Adrienn Angyal and Benjamin B. Lindsey and Danielle C. Groves and Luke R. Green and Dennis Wang and Timothy M. Freeman and Matthew D. Parker and Alexander J. Keeley and Paul J. Parsons and Rachel M. Tucker and Rebecca Brown and Matthew Wyles and Chrystala Constantinidou and Meera Unnikrishnan and Sascha Ott and Jeffrey K.J. Cheng and Hannah E. Bridgewater and Lucy R. Frost and Grace Taylor-Joyce and Richard Stark and Laura Baxter and Mohammad T. Alam and Paul E. Brown and Patrick C. McClure and Joseph G. Chappell and Theocharis Tsoleridis and Jonathan Ball and Dimitris Gramatopoulos and David Buck and John A. Todd and Angie Green and Amy Trebes and George MacIntyre-Cockett and Mariateresa de Cesare and Cordelia Langford and Alex Alderton and Roberto Amato and Sonia Goncalves and David K. Jackson and Ian Johnston and John Sillitoe and Steve Palmer and Mara Lawniczak and Matt Berriman and John Danesh and Rich Livett and Lesley Shirley and Ben Farr and Mike Quail and Scott Thurston and Naomi Park and Emma Betteridge and Danni Weldon and Scott Goodwin and Rachel Nelson and Charlotte Beaver and Laura Letchford and David A. Jackson and Luke Foulser and Liz McMinn and Liam Prestwood and Sally Kay and Leanne Kane and Matthew J. Dorman and Inigo Martincorena and Christoph Puethe and Jon-Paul Keatley and Gerry Tonkin-Hill and Christen Smith and Dorota Jamrozy and Mathew A. Beale and Minal Patel and Cristina Ariani and Michael Spencer-Chapman and Eleanor Drury and Stephanie Lo and Shavanthi Rajatileka and Carol Scott and Keith James and Sarah K. Buddenborg and Duncan J. Berger and Gaurang Patel and Maria V. Garcia-Casado and Thomas Dibling and Samantha McGuigan and Hazel A. Rogers and Adam D. Hunter and Emily Souster and Alexandra S. Neaverson},
    title = {Evaluating the Effects of {SARS}-{CoV}-2 Spike Mutation {D614G} on Transmissibility and Pathogenicity},
    journal = {Cell},
    year = {2020},
    doi = {10.1016/j.cell.2020.11.020},
    publisher = {Elsevier {BV}},
    }
  • [DOI] J. Trimpert, D. Vladimirova, K. Dietert, A. Abdelgawad, D. Kunec, S. Dökel, A. Voss, A. D. Gruber, L. D. Bertzbach, and N. Osterrieder, "The Roborovski dwarf hamster is a highly susceptible model for a rapid and fatal course of SARS-CoV-2 infection," Cell Rep, p. 108488, 2020.
    [Bibtex]
    @Article{Trimpert:20,
    author = {Jakob Trimpert and Daria Vladimirova and Kristina Dietert and Azza Abdelgawad and Dusan Kunec and Simon Dökel and Anne Voss and Achim D. Gruber and Luca D. Bertzbach and Nikolaus Osterrieder},
    title = {The {R}oborovski Dwarf Hamster Is A Highly Susceptible Model for a Rapid and Fatal Course of {SARS}-{CoV}-2 Infection},
    journal = {{Cell Rep}},
    year = {2020},
    pages = {108488},
    doi = {10.1016/j.celrep.2020.108488},
    publisher = {Elsevier {BV}},
    }
  • [DOI] E. Cuevas-Ferrando, A. Pérez-Cataluña, A. Allende, S. Guix, W. Randazzo, and G. Sánchez, "Recovering coronavirus from large volumes of water," Sci Total Environ, p. 143101, 2020.
    [Bibtex]
    @Article{Cuevas-Ferrando:20,
    author = {Enric Cuevas-Ferrando and Alba Pérez-Cataluña and Ana Allende and Susana Guix and Walter Randazzo and Gloria Sánchez},
    journal = {{Sci Total Environ}},
    title = {Recovering coronavirus from large volumes of water},
    year = {2020},
    pages = {143101},
    doi = {10.1016/j.scitotenv.2020.143101},
    publisher = {Elsevier {BV}},
    }
  • [DOI] D. Weissberg, J. Böni, S. K. Rampini, V. Kufner, M. Zaheri, P. W. Schreiber, I. A. Abela, M. Huber, H. Sax, and A. Wolfensberger, "Does respiratory co-infection facilitate dispersal of SARS-CoV-2? Investigation of a super-spreading event in an open-space office," Antimicrob Resist Infect Control, vol. 9, iss. 1, 2020.
    [Bibtex]
    @Article{Weissberg:20,
    author = {Dana Weissberg and Jürg Böni and Silvana K. Rampini and Verena Kufner and Maryam Zaheri and Peter W. Schreiber and Irene A. Abela and Michael Huber and Hugo Sax and Aline Wolfensberger},
    title = {Does respiratory co-infection facilitate dispersal of {SARS}-{CoV}-2? {I}nvestigation of a super-spreading event in an open-space office},
    journal = {{Antimicrob Resist Infect Control}},
    year = {2020},
    volume = {9},
    number = {1},
    doi = {10.1186/s13756-020-00861-z},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] M. Psichogiou, A. Karabinis, I. D. Pavlopoulou, D. Basoulis, K. Petsios, S. Roussos, M. Pratikaki, E. Jahaj, K. Protopapas, K. Leontis, V. Rapti, A. Kotanidou, A. Antoniadou, G. Poulakou, D. Paraskevis, V. Sypsa, and A. Hatzakis, "Antibodies against SARS-CoV-2 among health care workers in a country with low burden of COVID-19," PLoS One, vol. 15, iss. 12, p. e0243025, 2020.
    [Bibtex]
    @Article{Psichogiou:20,
    author = {Mina Psichogiou and Andreas Karabinis and Ioanna D. Pavlopoulou and Dimitrios Basoulis and Konstantinos Petsios and Sotirios Roussos and Maria Pratikaki and Edison Jahaj and Konstantinos Protopapas and Konstantinos Leontis and Vasiliki Rapti and Anastasia Kotanidou and Anastasia Antoniadou and Garyphallia Poulakou and Dimitrios Paraskevis and Vana Sypsa and Angelos Hatzakis},
    title = {Antibodies against {SARS}-{CoV}-2 among health care workers in a country with low burden of {COVID}-19},
    journal = {{PLoS One}},
    year = {2020},
    volume = {15},
    number = {12},
    pages = {e0243025},
    doi = {10.1371/journal.pone.0243025},
    editor = {Ronald Dijkman},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] M. Gasbarri, P. V'kovski, G. Torriani, V. Thiel, F. Stellacci, C. Tapparel, and V. Cagno, "SARS-CoV-2 inhibition by sulfonated compounds," Microorganisms, vol. 8, iss. 12, p. 1894, 2020.
    [Bibtex]
    @Article{Gasbarri:20,
    author = {Matteo Gasbarri and Philip V'kovski and Giulia Torriani and Volker Thiel and Francesco Stellacci and Caroline Tapparel and Valeria Cagno},
    title = {{SARS}-{CoV}-2 Inhibition by Sulfonated Compounds},
    journal = {Microorganisms},
    year = {2020},
    volume = {8},
    number = {12},
    pages = {1894},
    doi = {10.3390/microorganisms8121894},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] M. Rastogi, N. Pandey, A. Shukla, and S. K. Singh, "SARS coronavirus 2: from genome to infectome," Respir Res, vol. 21, iss. 1, 2020.
    [Bibtex]
    @Article{Rastogi:20,
    author = {Meghana Rastogi and Neha Pandey and Astha Shukla and Sunit K. Singh},
    title = {{SARS} coronavirus 2: from genome to infectome},
    journal = {{Respir Res}},
    year = {2020},
    volume = {21},
    number = {1},
    doi = {10.1186/s12931-020-01581-z},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] L. Sanchez-Felipe, T. Vercruysse, S. Sharma, J. Ma, V. Lemmens, D. V. Looveren, M. P. A. Javarappa, R. Boudewijns, B. Malengier-Devlies, L. Liesenborghs, S. J. F. Kaptein, C. D. Keyzer, L. Bervoets, S. Debaveye, M. Rasulova, L. Seldeslachts, L. Li, S. Jansen, M. B. Yakass, B. E. Verstrepen, K. P. Böszörményi, G. Kiemenyi-Kayere, N. van Driel, O. Quaye, X. Zhang, S. ter Horst, N. Mishra, W. Deboutte, J. Matthijnssens, L. Coelmont, C. Vandermeulen, E. Heylen, V. Vergote, D. Schols, Z. Wang, W. Bogers, T. Kuiken, E. Verschoor, C. Cawthorne, K. V. Laere, G. Opdenakker, G. V. Velde, B. Weynand, D. E. Teuwen, P. Matthys, J. Neyts, H. J. Thibaut, and K. Dallmeier, "A single-dose live-attenuated YF17D-vectored SARS-CoV-2 vaccine candidate," Nature, 2020.
    [Bibtex]
    @Article{Sanchez-Felipe:20,
    author = {Lorena Sanchez-Felipe and Thomas Vercruysse and Sapna Sharma and Ji Ma and Viktor Lemmens and Dominique Van Looveren and Mahadesh Prasad Arkalagud Javarappa and Robbert Boudewijns and Bert Malengier-Devlies and Laurens Liesenborghs and Suzanne J. F. Kaptein and Carolien De Keyzer and Lindsey Bervoets and Sarah Debaveye and Madina Rasulova and Laura Seldeslachts and Li-Hsin Li and Sander Jansen and Michael Bright Yakass and Babs E. Verstrepen and Kinga P. Böszörm{\'{e}}nyi and Gwendoline Kiemenyi-Kayere and Nikki van Driel and Osbourne Quaye and Xin Zhang and Sebastiaan ter Horst and Niraj Mishra and Ward Deboutte and Jelle Matthijnssens and Lotte Coelmont and Corinne Vandermeulen and Elisabeth Heylen and Valentijn Vergote and Dominique Schols and Zhongde Wang and Willy Bogers and Thijs Kuiken and Ernst Verschoor and Christopher Cawthorne and Koen Van Laere and Ghislain Opdenakker and Greetje Vande Velde and Birgit Weynand and Dirk E. Teuwen and Patrick Matthys and Johan Neyts and Hendrik Jan Thibaut and Kai Dallmeier},
    title = {A single-dose live-attenuated {YF17D}-vectored {SARS}-{CoV}-2 vaccine candidate},
    journal = {Nature},
    year = {2020},
    doi = {10.1038/s41586-020-3035-9},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] O. Ziv, J. Price, L. Shalamova, T. Kamenova, I. Goodfellow, F. Weber, and E. A. Miska, "The short- and long-range RNA-RNA interactome of SARS-CoV-2," Mol Cell, 2020.
    [Bibtex]
    @Article{Ziv:20,
    author = {Omer Ziv and Jonathan Price and Lyudmila Shalamova and Tsveta Kamenova and Ian Goodfellow and Friedemann Weber and Eric A. Miska},
    title = {The Short- and Long-Range {RNA}-{RNA} Interactome of {SARS}-{CoV}-2},
    journal = {{Mol Cell}},
    year = {2020},
    doi = {10.1016/j.molcel.2020.11.004},
    publisher = {Elsevier {BV}},
    }
  • [DOI] J. Meinhardt, J. Radke, C. Dittmayer, J. Franz, C. Thomas, R. Mothes, M. Laue, J. Schneider, S. Brünink, S. Greuel, M. Lehmann, O. Hassan, T. Aschman, E. Schumann, R. L. Chua, C. Conrad, R. Eils, W. Stenzel, M. Windgassen, L. Rößler, H. Goebel, H. R. Gelderblom, H. Martin, A. Nitsche, W. J. Schulz-Schaeffer, S. Hakroush, M. S. Winkler, B. Tampe, F. Scheibe, P. Körtvélyessy, D. Reinhold, B. Siegmund, A. A. Kühl, S. Elezkurtaj, D. Horst, L. Oesterhelweg, M. Tsokos, B. Ingold-Heppner, C. Stadelmann, C. Drosten, V. M. Corman, H. Radbruch, and F. L. Heppner, "Olfactory transmucosal SARS-CoV-2 invasion as a port of central nervous system entry in individuals with COVID-19," Nat Neurosci, 2020.
    [Bibtex]
    @Article{Meinhardt:20,
    author = {Jenny Meinhardt and Josefine Radke and Carsten Dittmayer and Jonas Franz and Carolina Thomas and Ronja Mothes and Michael Laue and Julia Schneider and Sebastian Brünink and Selina Greuel and Malte Lehmann and Olga Hassan and Tom Aschman and Elisa Schumann and Robert Lorenz Chua and Christian Conrad and Roland Eils and Werner Stenzel and Marc Windgassen and Larissa Rö{\ss}ler and Hans-Hilmar Goebel and Hans R. Gelderblom and Hubert Martin and Andreas Nitsche and Walter J. Schulz-Schaeffer and Samy Hakroush and Martin S. Winkler and Björn Tampe and Franziska Scheibe and P{\'{e}}ter Körtv{\'{e}}lyessy and Dirk Reinhold and Britta Siegmund and Anja A. Kühl and Sefer Elezkurtaj and David Horst and Lars Oesterhelweg and Michael Tsokos and Barbara Ingold-Heppner and Christine Stadelmann and Christian Drosten and Victor Max Corman and Helena Radbruch and Frank L. Heppner},
    title = {Olfactory transmucosal {SARS}-{CoV}-2 invasion as a port of central nervous system entry in individuals with {COVID}-19},
    journal = {{Nat Neurosci}},
    year = {2020},
    doi = {10.1038/s41593-020-00758-5},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] D. W. Hawman, G. Ahlén, S. K. Appelberg, K. Meade-White, P. W. Hanley, D. Scott, V. Monteil, S. Devignot, A. Okumura, F. Weber, H. Feldmann, M. Sällberg, and A. Mirazimi, "A DNA-based vaccine protects against Crimean-Congo haemorrhagic fever virus disease in a Cynomolgus macaque model," Nat Microbiol, 2020.
    [Bibtex]
    @Article{Hawman:20,
    author = {David W. Hawman and Gustaf Ahl{\'{e}}n and K. Sofia Appelberg and Kimberly Meade-White and Patrick W. Hanley and Dana Scott and Vanessa Monteil and Stephanie Devignot and Atsushi Okumura and Friedemann Weber and Heinz Feldmann and Matti Sällberg and Ali Mirazimi},
    title = {A {DNA}-based vaccine protects against {C}rimean-{C}ongo haemorrhagic fever virus disease in a {C}ynomolgus macaque model},
    journal = {{Nat Microbiol}},
    year = {2020},
    doi = {10.1038/s41564-020-00815-6},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] C. Hörner, C. Schürmann, A. Auste, A. Ebenig, S. Muraleedharan, K. H. Dinnon, T. Scholz, M. Herrmann, B. S. Schnierle, R. S. Baric, and M. D. Mühlebach, "A highly immunogenic and effective measles virus-based Th1-biased COVID-19 vaccine," Proc Natl Acad Sci USA, p. 202014468, 2020.
    [Bibtex]
    @Article{Hörner:20,
    author = {Cindy Hörner and Christoph Schürmann and Arne Auste and Aileen Ebenig and Samada Muraleedharan and Kenneth H. Dinnon and Tatjana Scholz and Maike Herrmann and Barbara S. Schnierle and Ralph S. Baric and Michael D. Mühlebach},
    title = {A highly immunogenic and effective measles virus-based {T}h1-biased {COVID}-19 vaccine},
    journal = {{Proc Natl Acad Sci USA}},
    year = {2020},
    pages = {202014468},
    doi = {10.1073/pnas.2014468117},
    publisher = {Proceedings of the National Academy of Sciences},
    }
  • [DOI] M. Holwerda, P. V'kovski, M. Wider, V. Thiel, and R. Dijkman, "Identification of an antiviral compound from the pandemic response box that efficiently inhibits SARS-CoV-2 infection in vitro," Microorganisms, vol. 8, iss. 12, p. 1872, 2020.
    [Bibtex]
    @Article{Holwerda:20,
    author = {Melle Holwerda and Philip V'kovski and Manon Wider and Volker Thiel and Ronald Dijkman},
    title = {Identification of an Antiviral Compound from the Pandemic Response Box that Efficiently Inhibits {SARS}-{CoV}-2 Infection In Vitro},
    journal = {Microorganisms},
    year = {2020},
    volume = {8},
    number = {12},
    pages = {1872},
    doi = {10.3390/microorganisms8121872},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] D. M. Brown, Y. Zhang, and R. H. Scheuermann, "Epidemiology and sequence-based evolutionary analysis of circulating non-polio enteroviruses," Microorganisms, vol. 8, iss. 12, p. 1856, 2020.
    [Bibtex]
    @Article{Brown:20,
    author = {David M. Brown and Yun Zhang and Richard H. Scheuermann},
    title = {Epidemiology and Sequence-Based Evolutionary Analysis of Circulating Non-Polio Enteroviruses},
    journal = {Microorganisms},
    year = {2020},
    volume = {8},
    number = {12},
    pages = {1856},
    doi = {10.3390/microorganisms8121856},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] R. Ben-Othman, B. Cai, A. C. Liu, N. Varankovich, D. He, T. M. Blimkie, A. H. Lee, E. E. Gill, M. Novotny, B. Aevermann, S. Drissler, C. P. Shannon, S. McCann, K. Marty, G. Bjornson, R. D. Edgar, D. T. S. Lin, N. Gladish, J. Maclsaac, N. Amenyogbe, Q. Chan, A. Llibre, J. Collin, E. Landais, K. Le, S. M. Reiss, W. C. Koff, C. Havenar-Daughton, M. Heran, B. Sangha, D. Walt, M. Krajden, S. Crotty, D. Sok, B. Briney, D. R. Burton, D. Duffy, L. J. Foster, W. W. Mohn, M. S. Kobor, S. J. Tebbutt, R. R. Brinkman, R. H. Scheuermann, R. E. W. Hancock, T. R. Kollmann, and M. Sadarangani, "Systems biology methods applied to blood and tissue for a comprehensive analysis of immune response to hepatitis B vaccine in adults," Frontiers in immunology, vol. 11, 2020.
    [Bibtex]
    @Article{Ben-Othman:20,
    author = {Rym Ben-Othman and Bing Cai and Aaron C. Liu and Natallia Varankovich and Daniel He and Travis M. Blimkie and Amy H. Lee and Erin E. Gill and Mark Novotny and Brian Aevermann and Sibyl Drissler and Casey P. Shannon and Sarah McCann and Kim Marty and Gordean Bjornson and Rachel D. Edgar and David Tse Shen Lin and Nicole Gladish and Julia Maclsaac and Nelly Amenyogbe and Queenie Chan and Alba Llibre and Joyce Collin and Elise Landais and Khoa Le and Samantha M. Reiss and Wayne C. Koff and Colin Havenar-Daughton and Manraj Heran and Bippan Sangha and David Walt and Mel Krajden and Shane Crotty and Devin Sok and Bryan Briney and Dennis R. Burton and Darragh Duffy and Leonard J. Foster and William W. Mohn and Michael S. Kobor and Scott J. Tebbutt and Ryan R. Brinkman and Richard H. Scheuermann and Robert E. W. Hancock and Tobias R. Kollmann and Manish Sadarangani},
    title = {Systems Biology Methods Applied to Blood and Tissue for a Comprehensive Analysis of Immune Response to Hepatitis {B} Vaccine in Adults},
    journal = {Frontiers in Immunology},
    year = {2020},
    volume = {11},
    doi = {10.3389/fimmu.2020.580373},
    publisher = {Frontiers Media {SA}},
    }
  • [DOI] F. L. Nobrega, H. Walinga, B. E. Dutilh, and S. J. J. Brouns, "Prophages are associated with extensive CRISPR–cas auto-immunity," Nucleic Acids Res, 2020.
    [Bibtex]
    @Article{Nobrega:20,
    author = {Franklin L Nobrega and Hielke Walinga and Bas E Dutilh and Stan J J Brouns},
    title = {Prophages are associated with extensive {CRISPR}{\textendash}Cas auto-immunity},
    journal = {{Nucleic Acids Res}},
    year = {2020},
    doi = {10.1093/nar/gkaa1071},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] S. Weis, A. Scherag, M. Baier, M. Kiehntopf, T. Kamradt, S. Kolanos, J. Ankert, S. Glöckner, O. Makarewicz, S. Hagel, C. Bahrs, A. Kimmig, H. Proquitté, J. Guerra, D. Rimek, B. Löffler, M. W. Pletz, T. Hotz, P. Enders, R. Koch, S. Mai, M. Ullrich, C. Richert, C. Eibner, B. Meinung, K. Stötzer, J. Köhler, H. Cipowicz, C. Pinkwart, M. Bauer, P. Dickmann, A. Licht, J. Scholz, W. Wetzker, A. Hartung, D. Weiss, L. Thieme, G. Hanf, C. Schnizer, J. Müller, J. Kosenkow, F. Röstel, N. Andreas, R. Marquardt, S. Deinhardt-Emmer, and S. Kuhn, "Antibody response using six different serological assays in a completely PCR-tested community after a COVID-19 outbreak - the CoNAN study," Clin Microbiol Infect, 2020.
    [Bibtex]
    @Article{Weis:20,
    author = {Sebastian Weis and Andr{\'{e}} Scherag and Michael Baier and Michael Kiehntopf and Thomas Kamradt and Steffi Kolanos and Juliane Ankert and Stefan Glöckner and Oliwia Makarewicz and Stefan Hagel and Christina Bahrs and Aurelia Kimmig and Hans Proquitt{\'{e}} and Joel Guerra and Dagmar Rimek and Bettina Löffler and Mathias W. Pletz and Thomas Hotz and Petra Enders and Renate Koch and Steffen Mai and Matthias Ullrich and Cora Richert and Cornelius Eibner and Bettina Meinung and Kay Stötzer and Julia Köhler and Hans Cipowicz and Christine Pinkwart and Michael Bauer and Petra Dickmann and Annika Licht and Juliane Scholz and Wibke Wetzker and Anita Hartung and Daniel Weiss and Lara Thieme and Gabi Hanf and Clara Schnizer and Jasmin Müller and Jennifer Kosenkow and Franziska Röstel and Nico Andreas and Raphaela Marquardt and Stefanie Deinhardt-Emmer and Sebastian Kuhn},
    title = {Antibody response using six different serological assays in a completely {PCR}-tested community after a {COVID}-19 outbreak - The {CoNAN} study},
    journal = {{Clin Microbiol Infect}},
    year = {2020},
    doi = {10.1016/j.cmi.2020.11.009},
    publisher = {Elsevier {BV}},
    }
  • [DOI] I. Kalvari, E. P. Nawrocki, N. Ontiveros-Palacios, J. Argasinska, K. Lamkiewicz, M. Marz, S. Griffiths-Jones, C. Toffano-Nioche, D. Gautheret, Z. Weinberg, E. Rivas, S. R. Eddy, R. Finn, A. Bateman, and A. I. Petrov, "Rfam 14: expanded coverage of metagenomic, viral and microRNA families," Nucleic Acids Res, 2020.
    [Bibtex]
    @Article{Kalvari:20,
    author = {Ioanna Kalvari and Eric P Nawrocki and Nancy Ontiveros-Palacios and Joanna Argasinska and Kevin Lamkiewicz and Manja Marz and Sam Griffiths-Jones and Claire Toffano-Nioche and Daniel Gautheret and Zasha Weinberg and Elena Rivas and Sean R Eddy and Robert~D Finn and Alex Bateman and Anton I Petrov},
    title = {Rfam 14: expanded coverage of metagenomic, viral and {microRNA} families},
    journal = {{Nucleic Acids Res}},
    year = {2020},
    doi = {10.1093/nar/gkaa1047},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] L. Novelli, F. Motta, A. Ceribelli, G. M. Guidelli, N. Luciano, N. Isailovic, M. Vecellio, M. Caprioli, N. Clementi, M. Clementi, N. Mancini, C. Selmi, and M. D. Santis, "A case of psoriatic arthritis triggered by SARS-CoV-2 infection," Rheumatology, 2020.
    [Bibtex]
    @Article{Novelli:20,
    author = {Lucia Novelli and Francesca Motta and Angela Ceribelli and Giacomo M Guidelli and Nicoletta Luciano and Natasa Isailovic and Matteo Vecellio and Marta Caprioli and Nicola Clementi and Massimo Clementi and Nicasio Mancini and Carlo Selmi and Maria De Santis},
    title = {A case of psoriatic arthritis triggered by {SARS}-{CoV}-2 infection},
    journal = {Rheumatology},
    year = {2020},
    doi = {10.1093/rheumatology/keaa691},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] P. A. Reuken, M. Wüst, B. Löffler, M. Bauer, and A. Stallmach, "Letter: SARS-CoV-2-induced gastrointestinal inflammation.," Aliment Pharmacol Ther, vol. 52, p. 1748–1749, 2020.
    [Bibtex]
    @Article{Reuken:20,
    author = {Reuken, Philipp A and Wüst, Michaela and Löffler, Bettina and Bauer, Michael and Stallmach, Andreas},
    title = {Letter: {SARS-CoV-2}-induced gastrointestinal inflammation.},
    journal = {{Aliment Pharmacol Ther}},
    year = {2020},
    volume = {52},
    pages = {1748--1749},
    doi = {10.1111/apt.16087},
    issue = {11-12},
    pmid = {33205881},
    }
  • [DOI] R. Boudewijns, H. J. Thibaut, S. J. F. Kaptein, R. Li, V. Vergote, L. Seldeslachts, J. Van Weyenbergh, C. De Keyzer, L. Bervoets, S. Sharma, L. Liesenborghs, J. Ma, S. Jansen, D. Van Looveren, T. Vercruysse, X. Wang, D. Jochmans, E. Martens, K. Roose, D. De Vlieger, B. Schepens, T. Van Buyten, S. Jacobs, Y. Liu, J. Martí-Carreras, B. Vanmechelen, T. Wawina-Bokalanga, L. Delang, J. Rocha-Pereira, L. Coelmont, W. Chiu, P. Leyssen, E. Heylen, D. Schols, L. Wang, L. Close, J. Matthijnssens, M. Van Ranst, V. Compernolle, G. Schramm, K. Van Laere, X. Saelens, N. Callewaert, G. Opdenakker, P. Maes, B. Weynand, C. Cawthorne, G. Vande Velde, Z. Wang, J. Neyts, and K. Dallmeier, "STAT2 signaling restricts viral dissemination but drives severe pneumonia in SARS-CoV-2 infected hamsters.," Nat Commun, vol. 11, p. 5838, 2020.
    [Bibtex]
    @Article{Boudewijns:20,
    author = {Boudewijns, Robbert and Thibaut, Hendrik Jan and Kaptein, Suzanne J F and Li, Rong and Vergote, Valentijn and Seldeslachts, Laura and Van Weyenbergh, Johan and De Keyzer, Carolien and Bervoets, Lindsey and Sharma, Sapna and Liesenborghs, Laurens and Ma, Ji and Jansen, Sander and Van Looveren, Dominique and Vercruysse, Thomas and Wang, Xinyu and Jochmans, Dirk and Martens, Erik and Roose, Kenny and De Vlieger, Dorien and Schepens, Bert and Van Buyten, Tina and Jacobs, Sofie and Liu, Yanan and Martí-Carreras, Joan and Vanmechelen, Bert and Wawina-Bokalanga, Tony and Delang, Leen and Rocha-Pereira, Joana and Coelmont, Lotte and Chiu, Winston and Leyssen, Pieter and Heylen, Elisabeth and Schols, Dominique and Wang, Lanjiao and Close, Lila and Matthijnssens, Jelle and Van Ranst, Marc and Compernolle, Veerle and Schramm, Georg and Van Laere, Koen and Saelens, Xavier and Callewaert, Nico and Opdenakker, Ghislain and Maes, Piet and Weynand, Birgit and Cawthorne, Christopher and Vande Velde, Greetje and Wang, Zhongde and Neyts, Johan and Dallmeier, Kai},
    title = {{STAT2} signaling restricts viral dissemination but drives severe pneumonia in {SARS-CoV-2} infected hamsters.},
    journal = {{Nat Commun}},
    year = {2020},
    volume = {11},
    pages = {5838},
    abstract = {Emergence of SARS-CoV-2 causing COVID-19 has resulted in hundreds of thousands of deaths. In search for key targets of effective therapeutics, robust animal models mimicking COVID-19 in humans are urgently needed. Here, we show that Syrian hamsters, in contrast to mice, are highly permissive to SARS-CoV-2 and develop bronchopneumonia and strong inflammatory responses in the lungs with neutrophil infiltration and edema, further confirmed as consolidations visualized by micro-CT alike in clinical practice. Moreover, we identify an exuberant innate immune response as key player in pathogenesis, in which STAT2 signaling plays a dual role, driving severe lung injury on the one hand, yet restricting systemic virus dissemination on the other. Our results reveal the importance of STAT2-dependent interferon responses in the pathogenesis and virus control during SARS-CoV-2 infection and may help rationalizing new strategies for the treatment of COVID-19 patients.},
    doi = {10.1038/s41467-020-19684-y},
    issue = {1},
    pmid = {33203860},
    }
  • [DOI] K. Wernike, A. Aebischer, A. Michelitsch, D. Hoffmann, C. Freuling, A. Balkema-Buschmann, A. Graaf, T. Müller, N. Osterrieder, M. Rissmann, D. Rubbenstroth, J. Schön, C. Schulz, J. Trimpert, L. Ulrich, A. Volz, T. C. Mettenleiter, and M. Beer, "Multi-species ELISA for the detection of antibodies against SARS-CoV-2 in animals," Transbound Emerg Dis, 2020.
    [Bibtex]
    @Article{Wernike:20b,
    author = {Kerstin Wernike and Andrea Aebischer and Anna Michelitsch and Donata Hoffmann and Conrad Freuling and Anne Balkema-Buschmann and Annika Graaf and Thomas Müller and Nikolaus Osterrieder and Melanie Rissmann and Dennis Rubbenstroth and Jacob Schön and Claudia Schulz and Jakob Trimpert and Lorenz Ulrich and Asisa Volz and Thomas C. Mettenleiter and Martin Beer},
    title = {Multi-species {ELISA} for the detection of antibodies against {SARS}-{CoV}-2 in animals},
    journal = {{Transbound Emerg Dis}},
    year = {2020},
    doi = {10.1111/tbed.13926},
    publisher = {Wiley},
    }
  • M. Gultom, M. Licheri, L. Laloli, M. Wider, M. Straessle, S. Steiner, A. Kratzel, T. T. N. Thao, H. Stalder, J. Portmann, and others, "Susceptibility of well-differentiated airway epithelial cell cultures from domestic and wildlife animals to SARS-CoV-2," bioRxiv, 2020.
    [Bibtex]
    @Article{Gultom:20,
    author = {Gultom, Mitra and Licheri, Matthias and Laloli, Laura and Wider, Manon and Straessle, Marina and Steiner, Silvio and Kratzel, Annika and Thao, Tran Thi Nhu and Stalder, Hanspeter and Portmann, Jasmine and others},
    title = {Susceptibility of well-differentiated airway epithelial cell cultures from domestic and wildlife animals to {SARS-CoV-2}},
    journal = {{bioRxiv}},
    year = {2020},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] S. Lytras, G. Arriagada, and R. J. Gifford, "Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes," bioRxiv, 2020.
    [Bibtex]
    @Article{Lytras:20a,
    author = {Spyros Lytras and Gloria Arriagada and Robert J. Gifford},
    title = {Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.11.02.364562},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] W. V. der Toorn, D. Oh, D. Bourquain, J. Michel, E. Krause, A. Nitsche, and M. V. K. and, "COVIDStrategyCalculator: a standalone software to assess testing- and quarantine strategies for incoming travelers, contact person management and de-isolation," medRxiv, 2020.
    [Bibtex]
    @Article{Toorn:20,
    author = {Wiep Van der Toorn and Djin-Ye Oh and Daniel Bourquain and Janine Michel and Eva Krause and Andreas Nitsche and Max Von Kleist and},
    title = {{COVIDStrategyCalculator}: A standalone software to assess testing- and quarantine strategies for incoming travelers, contact person management and de-isolation},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.11.18.20233825},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] A. C. Gregory, K. Gerhardt, Z. Zhong, B. Bolduc, B. Temperton, K. T. Konstantinidis, and M. B. Sullivan, "MetaPop: a pipeline for macro- and micro-diversity analyses and visualization of microbial and viral metagenome-derived populations," bioRxiv, 2020.
    [Bibtex]
    @Article{Gregory:20,
    author = {Ann C. Gregory and Kenji Gerhardt and Zhi-Ping Zhong and Benjamin Bolduc and Ben Temperton and Konstantinos T. Konstantinidis and Matthew B. Sullivan},
    title = {{MetaPop}: A pipeline for macro- and micro-diversity analyses and visualization of microbial and viral metagenome-derived populations},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.11.01.363960},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] P. Vetter, C. S. Eberhardt, B. Meyer, P. A. M. Murillo, G. Torriani, F. Pigny, S. Lemeille, S. Cordey, F. Laubscher, D. Vu, A. Calame, M. Schibler, F. Jacquerioz, G. Blanchard-Rohner, C. Siegrist, L. Kaiser, A. M. Didierlaurent, and I. Eckerle, "Daily viral kinetics and innate and adaptive immune response assessment in COVID-19: a case series," mSphere, vol. 5, iss. 6, 2020.
    [Bibtex]
    @Article{Vetter:20,
    author = {Pauline Vetter and Christiane S. Eberhardt and Benjamin Meyer and Paola Andrea Martinez Murillo and Giulia Torriani and Fiona Pigny and Sylvain Lemeille and Samuel Cordey and Florian Laubscher and Diem-Lan Vu and Adrien Calame and Manuel Schibler and Frederique Jacquerioz and G{\'{e}}raldine Blanchard-Rohner and Claire-Anne Siegrist and Laurent Kaiser and Arnaud M. Didierlaurent and Isabella Eckerle},
    title = {Daily Viral Kinetics and Innate and Adaptive Immune Response Assessment in {COVID}-19: a Case Series},
    journal = {{mSphere}},
    year = {2020},
    volume = {5},
    number = {6},
    doi = {10.1128/msphere.00827-20},
    editor = {Christina F. Spiropoulou},
    publisher = {American Society for Microbiology},
    }
  • [DOI] B. B. Oude Munnink, R. S. Sikkema, D. F. Nieuwenhuijse, R. J. Molenaar, E. Munger, R. Molenkamp, A. van der Spek, P. Tolsma, A. Rietveld, M. Brouwer, N. Bouwmeester-Vincken, F. Harders, R. H. der Honing, M. C. A. Wegdam-Blans, R. J. Bouwstra, C. GeurtsvanKessel, A. A. van der Eijk, F. C. Velkers, L. A. M. Smit, A. Stegeman, W. H. M. van der Poel, and M. P. G. Koopmans, "Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans," Science, p. eabe5901, 2020.
    [Bibtex]
    @Article{Munnink:20,
    author = {B. B. {Oude Munnink} and Reina S. Sikkema and David F. Nieuwenhuijse and Robert Jan Molenaar and Emmanuelle Munger and Richard Molenkamp and Arco van der Spek and Paulien Tolsma and Ariene Rietveld and Miranda Brouwer and Noortje Bouwmeester-Vincken and Frank Harders and Renate Hakze-van der Honing and Marjolein C. A. Wegdam-Blans and Ruth J. Bouwstra and Corine GeurtsvanKessel and Annemiek A. van der Eijk and Francisca C. Velkers and Lidwien A. M. Smit and Arjan Stegeman and Wim H. M. van der Poel and Marion P. G. Koopmans},
    title = {Transmission of {SARS}-{CoV}-2 on mink farms between humans and mink and back to humans},
    journal = {Science},
    year = {2020},
    pages = {eabe5901},
    doi = {10.1126/science.abe5901},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
  • [DOI] M. K. Mirzaei and L. Deng, "Sustainable microbiome: a symphony orchestrated by synthetic phages," Microb Biotechnol, 2020.
    [Bibtex]
    @Article{Mirzaei:20b,
    author = {Mohammadali Khan Mirzaei and Li Deng},
    title = {Sustainable Microbiome: a symphony orchestrated by synthetic phages},
    journal = {{Microb Biotechnol}},
    year = {2020},
    doi = {10.1111/1751-7915.13697},
    publisher = {Wiley},
    }
  • [DOI] I. Manfredonia, C. Nithin, A. Ponce-Salvatierra, P. Ghosh, T. K. Wirecki, T. Marinus, N. S. Ogando, E. Snijder, M. J. van~Hemert, J. M. Bujnicki, and D. Incarnato, "Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements," Nucleic Acids Res, 2020.
    [Bibtex]
    @Article{Manfredonia:20,
    author = {Ilaria Manfredonia and Chandran Nithin and Almudena Ponce-Salvatierra and Pritha Ghosh and Tomasz K Wirecki and Tycho Marinus and Natacha S Ogando and Eric~J Snijder and Martijn J van~Hemert and Janusz M Bujnicki and Danny Incarnato},
    title = {Genome-wide mapping of {SARS}-{CoV}-2 {RNA} structures identifies therapeutically-relevant elements},
    journal = {{Nucleic Acids Res}},
    year = {2020},
    doi = {10.1093/nar/gkaa1053},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] D. Glebe, N. Goldmann, C. Lauber, and S. Seitz, "HBV evolution and genetic variability: impact on prevention, treatment and development of antivirals," Antiviral Res, p. 104973, 2020.
    [Bibtex]
    @Article{Glebe:20,
    author = {Dieter Glebe and Nora Goldmann and Chris Lauber and Stefan Seitz},
    title = {{HBV} evolution and genetic variability: impact on prevention, treatment and development of antivirals},
    journal = {{Antiviral Res}},
    year = {2020},
    pages = {104973},
    doi = {10.1016/j.antiviral.2020.104973},
    publisher = {Elsevier {BV}},
    }
  • [DOI] B. Saremi, M. Kohls, P. Liebig, U. Siebert, and K. Jung, "Measuring reproducibility of virus meta-genomics analyses using bootstrap samples from FASTQ-files," Bioinformatics, 2020.
    [Bibtex]
    @Article{Saremi:20,
    author = {Babak Saremi and Moritz Kohls and Pamela Liebig and Ursula Siebert and Klaus Jung},
    title = {Measuring reproducibility of virus Meta-Genomics analyses using bootstrap samples from {FASTQ}-Files},
    journal = {Bioinformatics},
    year = {2020},
    doi = {10.1093/bioinformatics/btaa926},
    editor = {Lenore Cowen},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] K. L. Howe, P. Achuthan, J. Allen, J. Allen, J. Alvarez-Jarreta, R. M. Amode, I. M. Armean, A. G. Azov, R. Bennett, J. Bhai, K. Billis, S. Boddu, M. Charkhchi, C. Cummins, L. Da~Rin~Fioretto, C. Davidson, K. Dodiya, B. El~Houdaigui, R. Fatima, A. Gall, C. Garcia~Giron, T. Grego, C. Guijarro-Clarke, L. Haggerty, A. Hemrom, T. Hourlier, O. G. Izuogu, T. Juettemann, V. Kaikala, M. Kay, I. Lavidas, T. Le, D. Lemos, J. Gonzalez~Martinez, J. C. Marugán, T. Maurel, A. C. McMahon, S. Mohanan, B. Moore, M. Muffato, D. N. Oheh, D. Paraschas, A. Parker, A. Parton, I. Prosovetskaia, M. P. Sakthivel, A. Salam, B. M. Schmitt, H. Schuilenburg, D. Sheppard, E. Steed, M. Szpak, M. Szuba, K. Taylor, A. Thormann, G. Threadgold, B. Walts, A. Winterbottom, M. Chakiachvili, A. Chaubal, N. De~Silva, B. Flint, A. Frankish, S. E. Hunt, G. R. IIsley, N. Langridge, J. E. Loveland, F. J. Martin, J. M. Mudge, J. Morales, E. Perry, M. Ruffier, J. Tate, D. Thybert, S. J. Trevanion, F. Cunningham, A. D. Yates, D. R. Zerbino, and P. Flicek, "Ensembl 2021," Nucleic Acids Res, 2020.
    [Bibtex]
    @Article{Howe:20,
    author = {Kevin L Howe and Premanand Achuthan and James Allen and Jamie Allen and Jorge Alvarez-Jarreta and M Ridwan Amode and Irina M Armean and Andrey G Azov and Ruth Bennett and Jyothish Bhai and Konstantinos Billis and Sanjay Boddu and Mehrnaz Charkhchi and Carla Cummins and Luca Da~Rin~Fioretto and Claire Davidson and Kamalkumar Dodiya and Bilal El~Houdaigui and Reham Fatima and Astrid Gall and Carlos Garcia~Giron and Tiago Grego and Cristina Guijarro-Clarke and Leanne Haggerty and Anmol Hemrom and Thibaut Hourlier and Osagie G Izuogu and Thomas Juettemann and Vinay Kaikala and Mike Kay and Ilias Lavidas and Tuan Le and Diana Lemos and Jose Gonzalez~Martinez and Jos{\'{e}} Carlos Marug{\'{a}}n and Thomas Maurel and Aoife C McMahon and Shamika Mohanan and Benjamin Moore and Matthieu Muffato and Denye N Oheh and Dimitrios Paraschas and Anne Parker and Andrew Parton and Irina Prosovetskaia and Manoj P Sakthivel and Ahamed~I~Abdul Salam and Bianca M Schmitt and Helen Schuilenburg and Dan Sheppard and Emily Steed and Michal Szpak and Marek Szuba and Kieron Taylor and Anja Thormann and Glen Threadgold and Brandon Walts and Andrea Winterbottom and Marc Chakiachvili and Ameya Chaubal and Nishadi De~Silva and Bethany Flint and Adam Frankish and Sarah E Hunt and Garth R IIsley and Nick Langridge and Jane E Loveland and Fergal J Martin and Jonathan M Mudge and Joanella Morales and Emily Perry and Magali Ruffier and John Tate and David Thybert and Stephen J Trevanion and Fiona Cunningham and Andrew D Yates and Daniel R Zerbino and Paul Flicek},
    title = {Ensembl 2021},
    journal = {{Nucleic Acids Res}},
    year = {2020},
    doi = {10.1093/nar/gkaa942},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] A. Gleizes, F. Laubscher, N. Guex, C. Iseli, T. Junier, S. Cordey, J. Fellay, I. Xenarios, L. Kaiser, and P. Le Mercier, "Virosaurus a reference to explore and capture virus genetic diversity," Viruses, vol. 12, iss. 11, p. 1248, 2020.
    [Bibtex]
    @Article{Gleizes:20,
    author = {Anne Gleizes and Florian Laubscher and Nicolas Guex and Christian Iseli and Thomas Junier and Samuel Cordey and Jacques Fellay and Ioannis Xenarios and Laurent Kaiser and Philippe {Le Mercier}},
    title = {Virosaurus A Reference to Explore and Capture Virus Genetic Diversity},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    number = {11},
    pages = {1248},
    doi = {10.3390/v12111248},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] L. A. Carlisle, T. Turk, K. J. Metzner, H. A. Mbunkah, C. Shah, J. Böni, M. Huber, D. L. Braun, J. Fehr, L. Salazar-Vizcaya, A. Rauch, S. Yerly, A. Nguyen, M. Cavassini, M. Stoeckle, P. Vernazza, E. Bernasconi, H. F. Günthard, and R. D. Kouyos, "HCV genetic diversity can be used to infer infection recency and time since infection," Viruses, vol. 12, iss. 11, p. 1241, 2020.
    [Bibtex]
    @Article{Carlisle:20,
    author = {Louisa A. Carlisle and Teja Turk and Karin J. Metzner and Herbert A. Mbunkah and Cyril Shah and Jürg Böni and Michael Huber and Dominique L. Braun and Jan Fehr and Luisa Salazar-Vizcaya and Andri Rauch and Sabine Yerly and Aude Nguyen and Matthias Cavassini and Marcel Stoeckle and Pietro Vernazza and Enos Bernasconi and Huldrych F. Günthard and Roger D. Kouyos},
    title = {{HCV} Genetic Diversity Can Be Used to Infer Infection Recency and Time since Infection},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    number = {11},
    pages = {1241},
    doi = {10.3390/v12111241},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] D. Bojkova, M. Bechtel, K. McLaughlin, J. E. McGreig, K. Klann, C. Bellinghausen, G. Rohde, D. Jonigk, P. Braubach, S. Ciesek, C. Münch, M. N. Wass, M. Michaelis, and J. Cinatl, "Aprotinin inhibits SARS-CoV-2 replication," Cells, vol. 9, iss. 11, p. 2377, 2020.
    [Bibtex]
    @Article{Bojkova:20a,
    author = {Denisa Bojkova and Marco Bechtel and Katie-May McLaughlin and Jake E. McGreig and Kevin Klann and Carla Bellinghausen and Gernot Rohde and Danny Jonigk and Peter Braubach and Sandra Ciesek and Christian Münch and Mark N. Wass and Martin Michaelis and Jindrich Cinatl},
    title = {Aprotinin Inhibits {SARS}-{CoV}-2 Replication},
    journal = {Cells},
    year = {2020},
    volume = {9},
    number = {11},
    pages = {2377},
    doi = {10.3390/cells9112377},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] F. Hufsky, K. Lamkiewicz, A. Almeida, A. Aouacheria, C. Arighi, A. Bateman, J. Baumbach, N. Beerenwinkel, C. Brandt, M. Cacciabue, S. Chuguransky, O. Drechsel, R. D. Finn, A. Fritz, S. Fuchs, G. Hattab, A. Hauschild, D. Heider, M. Hoffmann, M. Hölzer, S. Hoops, L. Kaderali, I. Kalvari, M. von Kleist, R. Kmiecinski, D. Kühnert, G. Lasso, P. Libin, M. List, H. F. Löchel, M. J. Martin, R. Martin, J. Matschinske, A. C. McHardy, P. Mendes, J. Mistry, V. Navratil, E. P. Nawrocki, Á. N. O'Toole, N. Ontiveros-Palacios, A. I. Petrov, G. Rangel-Pineros, N. Redaschi, S. Reimering, K. Reinert, A. Reyes, L. Richardson, D. L. Robertson, S. Sadegh, J. B. Singer, K. Theys, C. Upton, M. Welzel, L. Williams, and M. Marz, "Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research," Briefings Bioinf, 2020.
    [Bibtex]
    @Article{Hufsky:20,
    author = {Franziska Hufsky and Kevin Lamkiewicz and Alexandre Almeida and Abdel Aouacheria and Cecilia Arighi and Alex Bateman and Jan Baumbach and Niko Beerenwinkel and Christian Brandt and Marco Cacciabue and Sara Chuguransky and Oliver Drechsel and Robert D Finn and Adrian Fritz and Stephan Fuchs and Georges Hattab and Anne-Christin Hauschild and Dominik Heider and Marie Hoffmann and Martin Hölzer and Stefan Hoops and Lars Kaderali and Ioanna Kalvari and Max von Kleist and Ren{\'{o}} Kmiecinski and Denise Kühnert and Gorka Lasso and Pieter Libin and Markus List and Hannah F Löchel and Maria J Martin and Roman Martin and Julian Matschinske and Alice C McHardy and Pedro Mendes and Jaina Mistry and Vincent Navratil and Eric P Nawrocki and {\'{A}}ine Niamh O'Toole and Nancy Ontiveros-Palacios and Anton I Petrov and Guillermo Rangel-Pineros and Nicole Redaschi and Susanne Reimering and Knut Reinert and Alejandro Reyes and Lorna Richardson and David L Robertson and Sepideh Sadegh and Joshua B Singer and Kristof Theys and Chris Upton and Marius Welzel and Lowri Williams and Manja Marz},
    title = {Computational strategies to combat {COVID}-19: useful tools to accelerate {SARS}-{CoV}-2 and coronavirus research},
    journal = {{Briefings Bioinf}},
    year = {2020},
    doi = {10.1093/bib/bbaa232},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] C. C. Friedel, A. W. Whisnant, L. Djakovic, A. J. Rutkowski, M. Friedl, M. Kluge, J. C. Williamson, S. Sai, R. O. Vidal, S. Sauer, T. Hennig, A. Grothey, A. Milić, B. K. Prusty, P. J. Lehner, N. J. Matheson, F. Erhard, and L. Dölken, "Dissecting herpes simplex virus 1-induced host shutoff at the RNA level," J Virol, 2020.
    [Bibtex]
    @Article{Friedel:20,
    author = {Caroline C. Friedel and Adam W. Whisnant and Lara Djakovic and Andrzej J. Rutkowski and Marie-Sophie Friedl and Michael Kluge and James C. Williamson and Somesh Sai and Ramon Oliveira Vidal and Sascha Sauer and Thomas Hennig and Arnhild Grothey and Andrea Mili{\'{c}} and Bhupesh K. Prusty and Paul J. Lehner and Nicholas J. Matheson and Florian Erhard and Lars Dölken},
    title = {Dissecting Herpes Simplex Virus 1-Induced Host Shutoff at the {RNA} Level},
    journal = {{J Virol}},
    year = {2020},
    doi = {10.1128/jvi.01399-20},
    publisher = {American Society for Microbiology},
    }
  • [DOI] K. Schlottau, D. Nobach, C. Herden, S. Finke, M. Beer, and D. Hoffmann, "First isolation, in vivo and genomic characterization of zoonotic variegated squirrel Bornavirus 1 (VSBV-1) isolates," Emerg Microbes Infect, p. 1–49, 2020.
    [Bibtex]
    @Article{Schlottau:20a,
    author = {Kore Schlottau and Daniel Nobach and Christiane Herden and Stefan Finke and Martin Beer and Donata Hoffmann},
    title = {First isolation, in vivo and genomic characterization of zoonotic variegated squirrel {B}ornavirus 1 ({VSBV}-1) isolates},
    journal = {{Emerg Microbes Infect}},
    year = {2020},
    pages = {1--49},
    doi = {10.1080/22221751.2020.1847604},
    publisher = {Informa {UK} Limited},
    }
  • [DOI] C. Zitzmann, L. Kaderali, and A. S. Perelson, "Mathematical modeling of hepatitis C RNA replication, exosome secretion and virus release," PLoS Comput Biol, vol. 16, iss. 11, p. e1008421, 2020.
    [Bibtex]
    @Article{Zitzmann:20a,
    author = {Carolin Zitzmann and Lars Kaderali and Alan S. Perelson},
    title = {Mathematical modeling of hepatitis {C} {RNA} replication, exosome secretion and virus release},
    journal = {{PLoS Comput Biol}},
    year = {2020},
    volume = {16},
    number = {11},
    pages = {e1008421},
    doi = {10.1371/journal.pcbi.1008421},
    editor = {Kathryn Miller-Jensen},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] S. H. Smith, A. G. Somsen, C. van Rijn, S. Kooij, L. van der Hoek, R. A. Bem, and D. Bonn, "Aerosol persistence in relation to possible transmission of SARS-CoV-2," Phys Fluids, vol. 32, iss. 10, p. 107108, 2020.
    [Bibtex]
    @Article{Smith:20,
    author = {Scott H. Smith and G. Aernout Somsen and Cees van Rijn and Stefan Kooij and Lia van der Hoek and Reinout A. Bem and Daniel Bonn},
    title = {Aerosol persistence in relation to possible transmission of {SARS}-{CoV}-2},
    journal = {{Phys Fluids}},
    year = {2020},
    volume = {32},
    number = {10},
    pages = {107108},
    doi = {10.1063/5.0027844},
    publisher = {{AIP} Publishing},
    }
  • [DOI] S. Dellicour, S. Lequime, B. Vrancken, M. S. Gill, P. Bastide, K. Gangavarapu, N. L. Matteson, Y. Tan, L. du Plessis, A. A. Fisher, M. I. Nelson, M. Gilbert, M. A. Suchard, K. G. Andersen, N. D. Grubaugh, O. G. Pybus, and P. Lemey, "Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework," Nat Commun, vol. 11, iss. 1, 2020.
    [Bibtex]
    @Article{Dellicour:20,
    author = {Simon Dellicour and Sebastian Lequime and Bram Vrancken and Mandev S. Gill and Paul Bastide and Karthik Gangavarapu and Nathaniel L. Matteson and Yi Tan and Louis du Plessis and Alexander A. Fisher and Martha I. Nelson and Marius Gilbert and Marc A. Suchard and Kristian G. Andersen and Nathan D. Grubaugh and Oliver G. Pybus and Philippe Lemey},
    title = {Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework},
    journal = {{Nat Commun}},
    year = {2020},
    volume = {11},
    number = {1},
    doi = {10.1038/s41467-020-19122-z},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] I. Schulien, J. Kemming, V. Oberhardt, K. Wild, L. M. Seidel, S. Killmer, Sagar, F. Daul, M. S. Lago, A. Decker, H. Luxenburger, B. Binder, D. Bettinger, O. Sogukpinar, S. Rieg, M. Panning, D. Huzly, M. Schwemmle, G. Kochs, C. F. Waller, A. Nieters, D. Duerschmied, F. Emmerich, H. E. Mei, A. R. Schulz, S. Llewellyn-Lacey, D. A. Price, T. Boettler, B. Bengsch, R. Thimme, M. Hofmann, and C. Neumann-Haefelin, "Characterization of pre-existing and induced SARS-CoV-2-specific CD8+ T cells," Nat Med, 2020.
    [Bibtex]
    @Article{Schulien:20,
    author = {Isabel Schulien and Janine Kemming and Valerie Oberhardt and Katharina Wild and Lea M. Seidel and Saskia Killmer and Sagar and Franziska Daul and Marilyn Salvat Lago and Annegrit Decker and Hendrik Luxenburger and Benedikt Binder and Dominik Bettinger and Oezlem Sogukpinar and Siegbert Rieg and Marcus Panning and Daniela Huzly and Martin Schwemmle and Georg Kochs and Cornelius F. Waller and Alexandra Nieters and Daniel Duerschmied and Florian Emmerich and Henrik E. Mei and Axel Ronald Schulz and Sian Llewellyn-Lacey and David A. Price and Tobias Boettler and Bertram Bengsch and Robert Thimme and Maike Hofmann and Christoph Neumann-Haefelin},
    title = {Characterization of pre-existing and induced {SARS}-{CoV}-2-specific {CD}8+ {T} cells},
    journal = {{Nat Med}},
    year = {2020},
    doi = {10.1038/s41591-020-01143-2},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] P. V'kovski, A. Kratzel, S. Steiner, H. Stalder, and V. Thiel, "Coronavirus biology and replication: implications for SARS-CoV-2," Nat Rev Microbiol, 2020.
    [Bibtex]
    @Article{V'kovski:20,
    author = {Philip V'kovski and Annika Kratzel and Silvio Steiner and Hanspeter Stalder and Volker Thiel},
    title = {Coronavirus biology and replication: implications for {SARS}-{CoV}-2},
    journal = {{Nat Rev Microbiol}},
    year = {2020},
    doi = {10.1038/s41579-020-00468-6},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] J. Wittmann, D. Turner, A. D. Millard, P. Mahadevan, A. M. Kropinski, and E. M. Adriaenssens, "From orphan phage to a proposed new family–the diversity of N4-like viruses," Antibiotics, vol. 9, iss. 10, p. 663, 2020.
    [Bibtex]
    @Article{Wittmann:20,
    author = {Johannes Wittmann and Dann Turner and Andrew D. Millard and Padmanabhan Mahadevan and Andrew M. Kropinski and Evelien M. Adriaenssens},
    title = {From Orphan Phage to a Proposed New Family{\textendash}The Diversity of {N4}-Like Viruses},
    journal = {Antibiotics},
    year = {2020},
    volume = {9},
    number = {10},
    pages = {663},
    doi = {10.3390/antibiotics9100663},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] C. Shi, L. Zhao, E. Atoni, W. Zeng, X. Hu, J. Matthijnssens, Z. Yuan, and H. Xia, "Stability of the virome in lab- and field-collected Aedes albopictus mosquitoes across different developmental stages and possible core viruses in the publicly available virome data of Aedes mosquitoes," mSystems, vol. 5, iss. 5, 2020.
    [Bibtex]
    @Article{Shi:20,
    author = {Chenyan Shi and Lu Zhao and Evans Atoni and Weifeng Zeng and Xiaomin Hu and Jelle Matthijnssens and Zhiming Yuan and Han Xia},
    title = {Stability of the Virome in Lab- and Field-Collected {A}edes albopictus Mosquitoes across Different Developmental Stages and Possible Core Viruses in the Publicly Available Virome Data of {A}edes Mosquitoes},
    journal = {{mSystems}},
    year = {2020},
    volume = {5},
    number = {5},
    doi = {10.1128/msystems.00640-20},
    editor = {Rup Lal},
    publisher = {American Society for Microbiology},
    }
  • [DOI] S. Hagel, A. Scherag, L. Schuierer, R. Hoffmann, C. Luyt, M. W. Pletz, M. Kesselmeier, and S. Weis, "Effect of antiviral therapy on the outcomes of mechanically ventilated patients with herpes simplex virus detected in the respiratory tract: a systematic review and meta-analysis," Crit Care, vol. 24, iss. 1, 2020.
    [Bibtex]
    @Article{Hagel:20,
    author = {Stefan Hagel and Andr{\'{e}} Scherag and Lukas Schuierer and Reinhard Hoffmann and Charles-Edouard Luyt and Mathias W. Pletz and Miriam Kesselmeier and Sebastian Weis},
    title = {Effect of antiviral therapy on the outcomes of mechanically ventilated patients with herpes simplex virus detected in the respiratory tract: a systematic review and meta-analysis},
    journal = {{Crit Care}},
    year = {2020},
    volume = {24},
    number = {1},
    doi = {10.1186/s13054-020-03296-5},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] R. Ancar, Y. Li, E. Kindler, D. A. Cooper, M. Ransom, V. Thiel, S. R. Weiss, J. R. Hesselberth, and D. J. Barton, "Physiologic RNA targets and refined sequence specificity of coronavirus EndoU," RNA, p. rna.076604.120, 2020.
    [Bibtex]
    @Article{Ancar:20,
    author = {Rachel Ancar and Yize Li and Eveline Kindler and Daphne A. Cooper and Monica Ransom and Volker Thiel and Susan R. Weiss and Jay R. Hesselberth and David J. Barton},
    title = {Physiologic {RNA} Targets and Refined Sequence Specificity of Coronavirus {EndoU}},
    journal = {{RNA}},
    year = {2020},
    pages = {rna.076604.120},
    doi = {10.1261/rna.076604.120},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] P. Lemey, S. L. Hong, V. Hill, G. Baele, C. Poletto, V. Colizza, Á. O'Toole, J. T. McCrone, K. G. Andersen, M. Worobey, M. I. Nelson, A. Rambaut, and M. A. Suchard, "Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2," Nat Commun, vol. 11, iss. 1, 2020.
    [Bibtex]
    @Article{Lemey:20a,
    author = {Philippe Lemey and Samuel L. Hong and Verity Hill and Guy Baele and Chiara Poletto and Vittoria Colizza and {\'{A}}ine O'Toole and John T. McCrone and Kristian G. Andersen and Michael Worobey and Martha I. Nelson and Andrew Rambaut and Marc A. Suchard},
    title = {Accommodating individual travel history and unsampled diversity in {B}ayesian phylogeographic inference of {SARS}-{CoV}-2},
    journal = {{Nat Commun}},
    year = {2020},
    volume = {11},
    number = {1},
    doi = {10.1038/s41467-020-18877-9},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] M. Sabatier, A. Bal, G. Destras, H. Regue, G. Quéromès, V. Cheynet, B. Lina, C. Bardel, K. Brengel-Pesce, V. Navratil, and L. Josset, "Comparison of nucleic acid extraction methods for a viral metagenomics analysis of respiratory viruses," Microorganisms, vol. 8, iss. 10, p. 1539, 2020.
    [Bibtex]
    @Article{Sabatier:20,
    author = {Marina Sabatier and Antonin Bal and Gr{\'{e}}gory Destras and Hadrien Regue and Gr{\'{e}}gory Qu{\'{e}}rom{\`{e}}s and Val{\'{e}}rie Cheynet and Bruno Lina and Claire Bardel and Karen Brengel-Pesce and Vincent Navratil and Laurence Josset},
    title = {Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses},
    journal = {Microorganisms},
    year = {2020},
    volume = {8},
    number = {10},
    pages = {1539},
    doi = {10.3390/microorganisms8101539},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] L. Ulrich, K. Wernike, D. Hoffmann, T. C. Mettenleiter, and M. Beer, "Experimental infection of cattle with SARS-CoV-2," Emerg Infect Dis, vol. 26, iss. 12, 2020.
    [Bibtex]
    @Article{Ulrich:20,
    author = {Lorenz Ulrich and Kerstin Wernike and Donata Hoffmann and Thomas C. Mettenleiter and Martin Beer},
    title = {Experimental Infection of Cattle with {SARS}-{CoV}-2},
    journal = {{Emerg Infect Dis}},
    year = {2020},
    volume = {26},
    number = {12},
    doi = {10.3201/eid2612.203799},
    publisher = {Centers for Disease Control and Prevention ({CDC})},
    }
  • [DOI] R. A. L. o, C. K. Lemvigh, M. V. T. Phan, P. T. L. C. Clausen, A. F. Florensa, M. P. G. Koopmans, O. Lund, and M. Cotten, "Automated download and clean-up of family specific databases for kmer-based virus identification," Bioinformatics, 2020.
    [Bibtex]
    @Article{Allesoe:20,
    author = {Rosa L Alles{\o}e and Camilla K Lemvigh and My V T Phan and Philip T L C Clausen and Alfred F Florensa and Marion P G Koopmans and Ole Lund and Matthew Cotten},
    title = {Automated download and clean-up of family specific databases for kmer-based virus identification},
    journal = {Bioinformatics},
    year = {2020},
    doi = {10.1093/bioinformatics/btaa857},
    editor = {Zhiyong Lu},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] A. J. Bennett, A. C. Paskey, A. Ebinger, F. Pfaff, G. Priemer, D. Höper, A. Breithaupt, E. Heuser, R. G. Ulrich, J. H. Kuhn, K. A. Bishop-Lilly, M. Beer, and T. L. Goldberg, "Relatives of rubella virus in diverse mammals," Nature, vol. 586, iss. 7829, p. 424–428, 2020.
    [Bibtex]
    @Article{Bennett:20,
    author = {Andrew J. Bennett and Adrian C. Paskey and Arnt Ebinger and Florian Pfaff and Grit Priemer and Dirk Höper and Angele Breithaupt and Elisa Heuser and Rainer G. Ulrich and Jens H. Kuhn and Kimberly A. Bishop-Lilly and Martin Beer and Tony L. Goldberg},
    title = {Relatives of rubella virus in diverse mammals},
    journal = {Nature},
    year = {2020},
    volume = {586},
    number = {7829},
    pages = {424--428},
    doi = {10.1038/s41586-020-2812-9},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] S. E. Braspenning, T. Sadaoka, J. Breuer, G. M. G. M. Verjans, W. J. D. Ouwendijk, and D. P. Depledge, "Decoding the architecture of the varicella-zoster virus transcriptome," mBio, vol. 11, iss. 5, 2020.
    [Bibtex]
    @Article{Braspenning:20,
    author = {Shirley E. Braspenning and Tomohiko Sadaoka and Judith Breuer and Georges M. G. M. Verjans and Werner J. D. Ouwendijk and Daniel P. Depledge},
    title = {Decoding the Architecture of the Varicella-Zoster Virus Transcriptome},
    journal = {{mBio}},
    year = {2020},
    volume = {11},
    number = {5},
    doi = {10.1128/mbio.01568-20},
    editor = {Thomas Shenk},
    publisher = {American Society for Microbiology},
    }
  • [DOI] C. Bai, S. H. Chotirmall, J. Rello, G. A. Alba, L. C. Ginns, J. A. Krishnan, R. Rogers, E. Bendstrup, P. Burgel, J. D. Chalmers, A. Chua, K. A. Crothers, A. Duggal, Y. W. Kim, J. G. Laffey, C. M. Luna, M. S. Niederman, G. Raghu, J. A. Ramirez, J. Riera, O. Roca, M. Tamae-Kakazu, A. Torres, R. R. Watkins, M. Barrecheguren, M. Belliato, H. A. Chami, R. Chen, G. A. Cortes-Puentes, C. Delacruz, M. M. Hayes, L. M. A. Heunks, S. R. Holets, C. L. Hough, S. Jagpal, K. Jeon, T. Johkoh, M. M. Lee, J. Liebler, G. N. McElvaney, A. Moskowitz, R. A. Oeckler, I. Ojanguren, A. O. textquotesingle, M. W. Pletz, C. K. Rhee, M. J. Schultz, E. Storti, C. Strange, C. C. Thomson, F. J. Torriani, X. Wang, W. Wuyts, T. Xu, D. Yang, Z. Zhang, and K. C. Wilson, "Updated guidance on the management of COVID-19: from an American Thoracic Society/European Respiratory Society coordinated International Task Force (29 July 2020)," Eur Respir Rev, vol. 29, iss. 157, p. 200287, 2020.
    [Bibtex]
    @Article{Bai:20,
    author = {Chunxue Bai and Sanjay H. Chotirmall and Jordi Rello and George A. Alba and Leo C. Ginns and Jerry A. Krishnan and Robert Rogers and Elisabeth Bendstrup and Pierre-Regis Burgel and James D. Chalmers and Abigail Chua and Kristina A. Crothers and Abhijit Duggal and Yeon Wook Kim and John G. Laffey and Carlos M. Luna and Michael S. Niederman and Ganesh Raghu and Julio A. Ramirez and Jordi Riera and Oriol Roca and Maximiliano Tamae-Kakazu and Antoni Torres and Richard R. Watkins and Miriam Barrecheguren and Mirko Belliato and Hassan A. Chami and Rongchang Chen and Gustavo A. Cortes-Puentes and Charles Delacruz and Margaret M. Hayes and Leo M.A. Heunks and Steven R. Holets and Catherine L. Hough and Sugeet Jagpal and Kyeongman Jeon and Takeshi Johkoh and May M. Lee and Janice Liebler and Gerry N. McElvaney and Ari Moskowitz and Richard A. Oeckler and I{\~{n}}igo Ojanguren and Anthony O{\textquotesingle}Regan and Mathias W. Pletz and Chin Kook Rhee and Marcus J. Schultz and Enrico Storti and Charlie Strange and Carey C. Thomson and Francesca J. Torriani and Xun Wang and Wim Wuyts and Tao Xu and Dawei Yang and Ziqiang Zhang and Kevin C. Wilson},
    title = {Updated guidance on the management of {COVID}-19: from an {A}merican {T}horacic {S}ociety/{E}uropean {R}espiratory {S}ociety coordinated {I}nternational {T}ask {F}orce (29 {J}uly 2020)},
    journal = {{Eur Respir Rev}},
    year = {2020},
    volume = {29},
    number = {157},
    pages = {200287},
    doi = {10.1183/16000617.0287-2020},
    publisher = {European Respiratory Society ({ERS})},
    }
  • [DOI] K. Ciminski, G. P. Chase, M. Beer, and M. Schwemmle, "Influenza A viruses: understanding human host determinants," Trends Mol Med, 2020.
    [Bibtex]
    @Article{Ciminski:20a,
    author = {Kevin Ciminski and Geoffrey P. Chase and Martin Beer and Martin Schwemmle},
    title = {Influenza {A} Viruses: Understanding Human Host Determinants},
    journal = {{Trends Mol Med}},
    year = {2020},
    doi = {10.1016/j.molmed.2020.09.014},
    publisher = {Elsevier {BV}},
    }
  • [DOI] S. R. Pallerla, D. Harms, R. Johne, D. Todt, E. Steinmann, M. Schemmerer, J. J. Wenzel, J. Hofmann, J. W. K. Shih, H. Wedemeyer, C. Bock, and T. P. Velavan, "Hepatitis E virus infection: circulation, molecular epidemiology, and impact on global health," Pathogens, vol. 9, iss. 10, p. 856, 2020.
    [Bibtex]
    @Article{Pallerla:20,
    author = {Srinivas Reddy Pallerla and Dominik Harms and Reimar Johne and Daniel Todt and Eike Steinmann and Mathias Schemmerer and Jürgen J. Wenzel and Jörg Hofmann and James Wai Kuo Shih and Heiner Wedemeyer and C.-Thomas Bock and Thirumalaisamy P. Velavan},
    title = {Hepatitis {E} Virus Infection: Circulation, Molecular Epidemiology, and Impact on Global Health},
    journal = {Pathogens},
    year = {2020},
    volume = {9},
    number = {10},
    pages = {856},
    doi = {10.3390/pathogens9100856},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] V. Deckert, T. Deckert-Gaudig, D. Cialla-May, J. Popp, R. Zell, S. Deinhard-Emmer, A. V. Sokolov, Z. Yi, and M. O. Scully, "Laser spectroscopic technique for direct identification of a single virus I: FASTER CARS," Proc Natl Acad Sci USA, p. 202013169, 2020.
    [Bibtex]
    @Article{Deckert:20,
    author = {Volker Deckert and Tanja Deckert-Gaudig and Dana Cialla-May and Jürgen Popp and Roland Zell and Stefanie Deinhard-Emmer and Alexei V. Sokolov and Zhenhuan Yi and Marlan O. Scully},
    title = {Laser spectroscopic technique for direct identification of a single virus {I}: {FASTER} {CARS}},
    journal = {{Proc Natl Acad Sci USA}},
    year = {2020},
    pages = {202013169},
    doi = {10.1073/pnas.2013169117},
    publisher = {Proceedings of the National Academy of Sciences},
    }
  • [DOI] M. Grossegesse, F. Hartkopf, A. Nitsche, L. Schaade, J. Doellinger, and T. Muth, "Perspective on proteomics for virus detection in clinical samples," Journal of proteome research, 2020.
    [Bibtex]
    @Article{Grossegesse:20,
    author = {Marica Grossegesse and Felix Hartkopf and Andreas Nitsche and Lars Schaade and Joerg Doellinger and Thilo Muth},
    title = {Perspective on Proteomics for Virus Detection in Clinical Samples},
    journal = {Journal of Proteome Research},
    year = {2020},
    doi = {10.1021/acs.jproteome.0c00674},
    publisher = {American Chemical Society ({ACS})},
    }
  • [DOI] C. M. Freuling, A. Breithaupt, T. Müller, J. Sehl, A. Balkema-Buschmann, M. Rissmann, A. Klein, C. Wylezich, D. Höper, K. Wernike, A. Aebischer, D. Hoffmann, V. Friedrichs, A. Dorhoi, M. H. Groschup, M. Beer, and T. C. Mettenleiter, "Susceptibility of raccoon dogs for experimental SARS-CoV-2 infection," Emerg Infect Dis, vol. 26, iss. 12, 2020.
    [Bibtex]
    @Article{Freuling:20,
    author = {Conrad M. Freuling and Angele Breithaupt and Thomas Müller and Julia Sehl and Anne Balkema-Buschmann and Melanie Rissmann and Antonia Klein and Claudia Wylezich and Dirk Höper and Kerstin Wernike and Andrea Aebischer and Donata Hoffmann and Virginia Friedrichs and Anca Dorhoi and Martin H. Groschup and Martin Beer and Thomas C. Mettenleiter},
    title = {Susceptibility of Raccoon Dogs for Experimental {SARS}-{CoV}-2 Infection},
    journal = {{Emerg Infect Dis}},
    year = {2020},
    volume = {26},
    number = {12},
    doi = {10.3201/eid2612.203733},
    publisher = {Centers for Disease Control and Prevention ({CDC})},
    }
  • [DOI] C. Conzelmann, R. Groß, T. L. Meister, D. Todt, A. Krawczyk, U. Dittmer, S. Stenger, J. Münch, E. Steinmann, J. A. Müller, and S. Pfaender, "Pasteurization inactivates SARS-CoV-2 spiked breast milk," Pediatrics, p. e2020031690, 2020.
    [Bibtex]
    @Article{Conzelmann:20,
    author = {Carina Conzelmann and Rüdiger Gro{\ss} and Toni Luise Meister and Daniel Todt and Adalbert Krawczyk and Ulf Dittmer and Steffen Stenger and Jan Münch and Eike Steinmann and Janis A Müller and Stephanie Pfaender},
    title = {Pasteurization Inactivates {SARS}-{CoV}-2 Spiked Breast Milk},
    journal = {Pediatrics},
    year = {2020},
    pages = {e2020031690},
    doi = {10.1542/peds.2020-031690},
    publisher = {American Academy of Pediatrics ({AAP})},
    }
  • [DOI] A. Flageul, P. Lucas, E. Hirchaud, F. Touzain, Y. Blanchard, N. Eterradossi, P. Brown, and B. Grasland, "Viral variant visualizer (VVV): a novel bioinformatic tool for rapid and simple visualization of viral genetic diversity," Virus Res, vol. 291, p. 198201, 2020.
    [Bibtex]
    @Article{Flageul:20,
    author = {Alexandre Flageul and Pierrick Lucas and Edouard Hirchaud and Fabrice Touzain and Yannick Blanchard and Nicolas Eterradossi and Paul Brown and B{\'{e}}atrice Grasland},
    title = {Viral variant visualizer ({VVV}): A novel bioinformatic tool for rapid and simple visualization of viral genetic diversity},
    journal = {{Virus Res}},
    year = {2020},
    volume = {291},
    pages = {198201},
    doi = {10.1016/j.virusres.2020.198201},
    publisher = {Elsevier {BV}},
    }
  • [DOI] A. J. Page, A. E. Mather, T. L. Viet, E. J. Meader, N. J. Alikhan, G. L. Kay, L. O. de Martins, A. Aydin, D. J. Baker, A. J. Trotter, S. Rudder, A. P. Tedim, A. Kolyva, R. Stanley, M. Diaz, W. Potter, C. Stuart, L. Meadows, A. Bell, A. V. Gutierrez, N. M. Thomson, E. M. Adriaenssens, T. Swingler, R. A. Gilroy, L. Griffith, D. K. Sethi, R. K. Davidson, R. A. Kingsley, L. Bedford, L. J. Coupland, I. G. Charles, N. Elumogo, J. Wain, R. Prakash, M. A. Webber, S. L. Smith, M. Chand, S. Dervisevic, J. O. textquotesingle, and The COVID-19 Genomics UK (COG-UK) consortium, "Large scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management," medRxiv, 2020.
    [Bibtex]
    @Article{Page:20,
    author = {Andrew J Page and Alison E Mather and Thanh Le Viet and Emma J Meader and Nabil-Fareed J Alikhan and Gemma L Kay and Leonardo de Oliveira Martins and Alp Aydin and David J Baker and Alexander J. Trotter and Steven Rudder and Ana P Tedim and Anastasia Kolyva and Rachael Stanley and Maria Diaz and Will Potter and Claire Stuart and Lizzie Meadows and Andrew Bell and Ana Victoria Gutierrez and Nicholas M Thomson and Evelien M Adriaenssens and Tracey Swingler and Rachel AJ Gilroy and Luke Griffith and Dheeraj K Sethi and Rose K Davidson and Robert A Kingsley and Luke Bedford and Lindsay J Coupland and Ian G Charles and Ngozi Elumogo and John Wain and Reenesh Prakash and Mark A Webber and SJ Louise Smith and Meera Chand and Samir Dervisevic and Justin O{\textquotesingle}Grady and {The COVID-19 Genomics UK (COG-UK) consortium}},
    title = {Large scale sequencing of {SARS}-{CoV}-2 genomes from one region allows detailed epidemiology and enables local outbreak management},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.09.28.20201475},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] J. Kuipers, A. A. Batavia, K. P. Jablonski, F. Bayer, N. Borgsmüller, A. Dondi, M. D. a}, P. Ferreira, K. Jahn, L. Lamberti, M. Pirkl, S. Posada-Céspedes, I. Topolsky, I. Nissen, N. Santacroce, E. Burcklen, T. Schär, V. Capece, C. Beckmann, O. Kobel, C. Noppen, M. Redondo, S. Nadeau, S. Seidel, N. S. de Souza, C. Beisel, T. Stadler, and N. Beerenwinkel, "Within-patient genetic diversity of SARS-CoV-2," bioRxiv, 2020.
    [Bibtex]
    @Article{Kuipers:20,
    author = {Jack Kuipers and Aashil A Batavia and Kim Philipp Jablonski and Fritz Bayer and Nico Borgsmüller and Arthur Dondi and Monica-Andreea Dr{\u{a}}gan and Pedro Ferreira and Katharina Jahn and Lisa Lamberti and Martin Pirkl and Susana Posada-C{\'{e}}spedes and Ivan Topolsky and Ina Nissen and Natascha Santacroce and Elodie Burcklen and Tobias Schär and Vincenzo Capece and Christiane Beckmann and Olivier Kobel and Christoph Noppen and Maurice Redondo and Sarah Nadeau and Sophie Seidel and Noemie Santamaria de Souza and Christian Beisel and Tanja Stadler and Niko Beerenwinkel},
    title = {Within-patient genetic diversity of {SARS}-{CoV}-2},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.10.12.335919},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. O. Pohl, I. Busnadiego, V. Kufner, S. Schmutz, M. Zaheri, I. Abela, A. Trkola, M. Huber, S. Stertz, and B. G. Hale, "Distinct phenotypes of SARS-CoV-2 isolates reveal viral traits critical for replication in primary human respiratory cells," bioRxiv, 2020.
    [Bibtex]
    @Article{Pohl:20,
    author = {Marie O. Pohl and Idoia Busnadiego and Verena Kufner and Stefan Schmutz and Maryam Zaheri and Irene Abela and Alexandra Trkola and Michael Huber and Silke Stertz and Benjamin G. Hale},
    title = {Distinct Phenotypes of {SARS}-{CoV}-2 Isolates Reveal Viral Traits Critical for Replication in Primary Human Respiratory Cells},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.10.22.350207},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. Cotten, D. L. Bugembe, P. Kaleebu, and M. V. T. Phan, "Alternate primers for whole-genome SARS-CoV-2 sequencing," bioRxiv, 2020.
    [Bibtex]
    @Article{Cotten:20,
    author = {Matthew Cotten and Dan Lule Bugembe and Pontiano Kaleebu and My V.T. Phan},
    title = {Alternate primers for whole-genome {SARS}-{CoV}-2 sequencing},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.10.12.335513},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] P. R. Bhatt, A. Scaiola, G. Loughran, M. Leibundgut, A. Kratzel, A. E. McMillan, K. M. O. textquotesingle, J. W. Bode, V. Thiel, J. F. Atkins, and N. Ban, "Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome," bioRxiv, 2020.
    [Bibtex]
    @Article{Bhatt:20,
    author = {Pramod R. Bhatt and Alain Scaiola and Gary Loughran and Marc Leibundgut and Annika Kratzel and Angus E. McMillan and Kate M. O{\textquotesingle}Connor and Jeffrey W. Bode and Volker Thiel and John F. Atkins and Nenad Ban},
    title = {Structural basis of ribosomal frameshifting during translation of the {SARS}-{CoV}-2 {RNA} genome},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.10.26.355099},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] K. M. Byrd, N. Huang, P. Perez, T. Kato, Y. Mikami, K. Okuda, R. C. Gilmore, C. D. Conde, B. Gasmi, S. Stein, M. Beach, E. Pelayo, J. Maldonado-Ortiz, B. LaFont, R. Padilla, V. Murrah, R. Maile, W. Lovell, S. Wallet, N. M. Bowman, S. L. Meinig, M. C. Wolfgang, S. N. Choudhury, M. Novotny, B. D. Aevermann, R. H. Scheuermann, G. Cannon, C. Anderson, J. Marchesan, M. Bush, M. Freire, A. Kimple, D. L. Herr, J. Rabin, A. Grazioli, B. N. French, T. J. Pranzatelli, J. A. Chiorini, D. E. Kleiner, S. Pittaluga, S. Hewitt, P. D. Burbelo, D. Chertow, K. M. Frank, J. Lee, R. B. C. C. Boucher, S. A. Teichmann, and B. M. Warner, "Integrated single-cell atlases reveal an oral SARS-CoV-2 infection and transmission axis," medRxiv, 2020.
    [Bibtex]
    @Article{Byrd:20,
    author = {Kevin M Byrd and Ni Huang and Paola Perez and Takafumi Kato and Yu Mikami and Kenichi Okuda and Rodney C. Gilmore and Cecilia Dominguez Conde and Billel Gasmi and Sydney Stein and Margaret Beach and Eileen Pelayo and Jose Maldonado-Ortiz and Bernard LaFont and Ricardo Padilla and Valerie Murrah and Robert Maile and Will Lovell and Shannon Wallet and Natalie M Bowman and Suzanne L Meinig and Matthew C Wolfgang and Saibyasachi N. Choudhury and Mark Novotny and Brian D Aevermann and Richard H. Scheuermann and Gabrielle Cannon and Carlton Anderson and Julie Marchesan and Mandy Bush and Marcelo Freire and Adam Kimple and Daniel L Herr and Joseph Rabin and Alison Grazioli and Benjamin N. French and Thomas JF Pranzatelli and John A. Chiorini and David E. Kleiner and Stefania Pittaluga and Stephen Hewitt and Peter D. Burbelo and Daniel Chertow and Karen M Frank and Janice Lee and Richard C. Boucher C. Boucher and Sarah A. Teichmann and Blake M Warner},
    title = {Integrated Single-Cell Atlases Reveal an Oral {SARS}-{CoV}-2 Infection and Transmission Axis},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.10.26.20219089},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] J. Schulte-Schrepping, N. Reusch, D. Paclik, K. Baßler, S. Schlickeiser, B. Zhang, B. Krämer, T. Krammer, S. Brumhard, L. Bonaguro, E. D. Domenico, D. Wendisch, M. Grasshoff, T. S. Kapellos, M. Beckstette, T. Pecht, A. Saglam, O. Dietrich, H. E. Mei, A. R. Schulz, C. Conrad, D. Kunkel, E. Vafadarnejad, C. Xu, A. Horne, M. Herbert, A. Drews, C. Thibeault, M. Pfeiffer, S. Hippenstiel, A. Hocke, H. Müller-Redetzky, K. Heim, F. Machleidt, A. Uhrig, L. B. de Jarcy, L. Jürgens, M. Stegemann, C. R. Glösenkamp, H. Volk, C. Goffinet, M. Landthaler, E. Wyler, P. Georg, M. Schneider, C. Dang-Heine, N. Neuwinger, K. Kappert, R. Tauber, V. Corman, J. Raabe, K. M. Kaiser, M. T. Vinh, G. Rieke, C. Meisel, T. Ulas, M. Becker, R. Geffers, M. Witzenrath, C. Drosten, N. Suttorp, C. von Kalle, F. Kurth, K. Händler, J. L. Schultze, A. C. Aschenbrenner, Y. Li, J. Nattermann, B. Sawitzki, A. Saliba, L. E. Sander, A. Angelov, R. Bals, A. Bartholomäus, A. Becker, D. Bezdan, E. Bonifacio, P. Bork, T. Clavel, M. Colome-Tatche, A. Diefenbach, A. Dilthey, N. Fischer, K. Förstner, J. Frick, J. Gagneur, A. Goesmann, T. Hain, M. Hummel, S. Janssen, J. Kalinowski, R. Kallies, B. Kehr, A. Keller, S. Kim-Hellmuth, C. Klein, O. Kohlbacher, J. O. Korbel, I. Kurth, M. Landthaler, Y. Li, K. Ludwig, O. Makarewicz, M. Marz, A. C. McHardy, C. Mertes, M. Nöthen, P. Nürnberg, U. Ohler, S. Ossowski, J. Overmann, S. Peter, K. Pfeffer, A. R. Poetsch, A. Pühler, N. Rajewsky, M. Ralser, O. Rieß, S. Ripke, U. N. da Rocha, P. Rosenstiel, A. Saliba, L. E. Sander, B. Sawitzki, P. Schiffer, E. Schulte, J. L. Schultze, A. Sczyrba, O. Stegle, J. Stoye, F. Theis, J. Vehreschild, J. Vogel, M. von Kleist, A. Walker, J. Walter, D. Wieczorek, and J. Ziebuhr, "Severe COVID-19 is marked by a dysregulated myeloid cell compartment," Cell, 2020.
    [Bibtex]
    @Article{Schulte-Schrepping:20,
    author = {Jonas Schulte-Schrepping and Nico Reusch and Daniela Paclik and Kevin Ba{\ss}ler and Stephan Schlickeiser and Bowen Zhang and Benjamin Krämer and Tobias Krammer and Sophia Brumhard and Lorenzo Bonaguro and Elena De Domenico and Daniel Wendisch and Martin Grasshoff and Theodore S. Kapellos and Michael Beckstette and Tal Pecht and Adem Saglam and Oliver Dietrich and Henrik E. Mei and Axel R. Schulz and Claudia Conrad and D{\'{e}}sir{\'{e}}e Kunkel and Ehsan Vafadarnejad and Cheng-Jian Xu and Arik Horne and Miriam Herbert and Anna Drews and Charlotte Thibeault and Moritz Pfeiffer and Stefan Hippenstiel and Andreas Hocke and Holger Müller-Redetzky and Katrin-Moira Heim and Felix Machleidt and Alexander Uhrig and Laure Bosquillon de Jarcy and Linda Jürgens and Miriam Stegemann and Christoph R. Glösenkamp and Hans-Dieter Volk and Christine Goffinet and Markus Landthaler and Emanuel Wyler and Philipp Georg and Maria Schneider and Chantip Dang-Heine and Nick Neuwinger and Kai Kappert and Rudolf Tauber and Victor Corman and Jan Raabe and Kim Melanie Kaiser and Michael To Vinh and Gereon Rieke and Christian Meisel and Thomas Ulas and Matthias Becker and Robert Geffers and Martin Witzenrath and Christian Drosten and Norbert Suttorp and Christof von Kalle and Florian Kurth and Kristian Händler and Joachim L. Schultze and Anna C. Aschenbrenner and Yang Li and Jacob Nattermann and Birgit Sawitzki and Antoine-Emmanuel Saliba and Leif Erik Sander and Angel Angelov and Robert Bals and Alexander Bartholomäus and Anke Becker and Daniela Bezdan and Ezio Bonifacio and Peer Bork and Thomas Clavel and Maria Colome-Tatche and Andreas Diefenbach and Alexander Dilthey and Nicole Fischer and Konrad Förstner and Julia-Stefanie Frick and Julien Gagneur and Alexander Goesmann and Torsten Hain and Michael Hummel and Stefan Janssen and Jörn Kalinowski and Ren{\'{e}} Kallies and Birte Kehr and Andreas Keller and Sarah Kim-Hellmuth and Christoph Klein and Oliver Kohlbacher and Jan O. Korbel and Ingo Kurth and Markus Landthaler and Yang Li and Kerstin Ludwig and Oliwia Makarewicz and Manja Marz and Alice C. McHardy and Christian Mertes and Markus Nöthen and Peter Nürnberg and Uwe Ohler and Stephan Ossowski and Jörg Overmann and Silke Peter and Klaus Pfeffer and Anna R. Poetsch and Alfred Pühler and Nikolaus Rajewsky and Markus Ralser and Olaf Rie{\ss} and Stephan Ripke and Ulisses Nunes da Rocha and Philip Rosenstiel and Antoine-Emmanuel Saliba and Leif Erik Sander and Birgit Sawitzki and Philipp Schiffer and Eva-Christina Schulte and Joachim L. Schultze and Alexander Sczyrba and Oliver Stegle and Jens Stoye and Fabian Theis and Janne Vehreschild and Jörg Vogel and Max von Kleist and Andreas Walker and Jörn Walter and Dagmar Wieczorek and John Ziebuhr},
    title = {Severe {COVID}-19 Is Marked by a Dysregulated Myeloid Cell Compartment},
    journal = {Cell},
    year = {2020},
    doi = {10.1016/j.cell.2020.08.001},
    publisher = {Elsevier {BV}},
    }
  • [DOI] P. J. Walker, S. G. Siddell, E. J. Lefkowitz, A. R. Mushegian, E. M. Adriaenssens, D. M. Dempsey, B. E. Dutilh, B. Harrach, R. L. Harrison, C. R. Hendrickson, S. Junglen, N. J. Knowles, A. M. Kropinski, M. Krupovic, J. H. Kuhn, M. Nibert, R. J. Orton, L. Rubino, S. Sabanadzovic, P. Simmonds, D. B. Smith, A. Varsani, F. M. Zerbini, and A. J. Davison, "Changes to virus taxonomy and the statutes ratified by the International Committee on Taxonomy of Viruses (2020)," Arch Virol, 2020.
    [Bibtex]
    @Article{Walker:20,
    author = {Peter J. Walker and Stuart G. Siddell and Elliot J. Lefkowitz and Arcady R. Mushegian and Evelien M. Adriaenssens and Donald M. Dempsey and Bas E. Dutilh and Bal{\'{a}}zs Harrach and Robert L. Harrison and R. Curtis Hendrickson and Sandra Junglen and Nick J. Knowles and Andrew M. Kropinski and Mart Krupovic and Jens H. Kuhn and Max Nibert and Richard J. Orton and Luisa Rubino and Sead Sabanadzovic and Peter Simmonds and Donald B. Smith and Arvind Varsani and Francisco Murilo Zerbini and Andrew J. Davison},
    title = {Changes to virus taxonomy and the Statutes ratified by the {I}nternational {C}ommittee on {T}axonomy of {V}iruses (2020)},
    journal = {{Arch Virol}},
    year = {2020},
    doi = {10.1007/s00705-020-04752-x},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] A. Jordan-Paiz, M. Nevot, K. Lamkiewicz, M. Lataretu, S. Franco, M. Marz, and M. A. Martinez, "HIV-1 lethality and loss of Env protein expression induced by single synonymous substitutions in the virus genome intronic splicing silencer," J Virol, 2020.
    [Bibtex]
    @Article{Jordan-Paiz:20,
    author = {Ana Jordan-Paiz and Maria Nevot and Kevin Lamkiewicz and Marie Lataretu and Sandra Franco and Manja Marz and Miguel Angel Martinez},
    title = {{HIV}-1 lethality and loss of {E}nv protein expression induced by single synonymous substitutions in the virus genome intronic splicing silencer},
    journal = {{J Virol}},
    year = {2020},
    doi = {10.1128/jvi.01108-20},
    publisher = {American Society for Microbiology},
    }
  • [DOI] O. A. MacLean, R. J. Orton, J. B. Singer, and D. L. Robertson, "No evidence for distinct types in the evolution of SARS-CoV-2," Virus Evol, vol. 6, iss. 1, 2020.
    [Bibtex]
    @Article{MacLean:20a,
    author = {Oscar A MacLean and Richard J Orton and Joshua B Singer and David L Robertson},
    title = {No evidence for distinct types in the evolution of {SARS}-{CoV}-2},
    journal = {{Virus Evol}},
    year = {2020},
    volume = {6},
    number = {1},
    doi = {10.1093/ve/veaa034},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] P. A. de Jonge, B. F. A. von Meijenfeldt, A. R. Costa, F. L. Nobrega, S. J. J. Brouns, and B. E. Dutilh, "Adsorption sequencing as a rapid method to link environmental bacteriophages to hosts," iScience, vol. 23, iss. 9, p. 101439, 2020.
    [Bibtex]
    @Article{Jonge:20,
    author = {Patrick A. de Jonge and F.A. Bastiaan von Meijenfeldt and Ana Rita Costa and Franklin L. Nobrega and Stan J.J. Brouns and Bas E. Dutilh},
    title = {Adsorption Sequencing as a Rapid Method to Link Environmental Bacteriophages to Hosts},
    journal = {{iScience}},
    year = {2020},
    volume = {23},
    number = {9},
    pages = {101439},
    doi = {10.1016/j.isci.2020.101439},
    publisher = {Elsevier {BV}},
    }
  • [DOI] M. Cacciabue, P. Aguilera, M. I. Gismondi, and O. Taboga, "Covidex: an ultrafast and accurate tool for virus subtyping," bioRxiv, 2020.
    [Bibtex]
    @Article{Cacciabue:20,
    author = {Marco Cacciabue and Pablo Aguilera and Mar{\'{\i}}a In{\'{e}}s Gismondi and Oscar Taboga},
    title = {Covidex: an ultrafast and accurate tool for virus subtyping},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.08.21.261347},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] N. Han, W. Hwang, K. Tzelepis, P. Schmerer, E. Yankova, M. MacMahon, W. Lei, N. M. Katritsis, A. Liu, A. Schuldt, R. Harris, K. Chapman, F. McCaughan, F. Weber, and T. Kouzarides, "Identification of SARS-CoV-2 induced pathways reveal drug repurposing strategies," bioRxiv, 2020.
    [Bibtex]
    @Article{Han:20,
    author = {Namshik Han and Woochang Hwang and Kostas Tzelepis and Patrick Schmerer and Eliza Yankova and Meabh MacMahon and Winnie Lei and Nicholas M Katritsis and Anika Liu and Alison Schuldt and Rebecca Harris and Kathryn Chapman and Frank McCaughan and Friedemann Weber and Tony Kouzarides},
    title = {Identification of {SARS}-{CoV}-2 induced pathways reveal drug repurposing strategies},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.08.24.265496},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. Rueca, B. Bartolini, C. E. M. Gruber, A. Piralla, F. Baldanti, E. Giombini, F. Messina, L. Marchioni, G. Ippolito, A. D. Caro, and M. R. Capobianchi, "Compartmentalized replication of SARS-Cov-2 in upper vs. lower respiratory tract assessed by whole genome quasispecies analysis," Microorganisms, vol. 8, iss. 9, p. 1302, 2020.
    [Bibtex]
    @Article{Rueca:20,
    author = {Martina Rueca and Barbara Bartolini and Cesare Ernesto Maria Gruber and Antonio Piralla and Fausto Baldanti and Emanuela Giombini and Francesco Messina and Luisa Marchioni and Giuseppe Ippolito and Antonino Di Caro and Maria Rosaria Capobianchi},
    title = {Compartmentalized Replication of {SARS}-{C}ov-2 in Upper vs. Lower Respiratory Tract Assessed by Whole Genome Quasispecies Analysis},
    journal = {Microorganisms},
    year = {2020},
    volume = {8},
    number = {9},
    pages = {1302},
    doi = {10.3390/microorganisms8091302},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] M. Zanella, S. Cordey, and L. Kaiser, "Beyond cytomegalovirus and epstein-barr virus: a review of viruses composing the blood virome of solid organ transplant and hematopoietic stem cell transplant recipients," Clin Microbiol Rev, vol. 33, iss. 4, 2020.
    [Bibtex]
    @Article{Zanella:20,
    author = {Marie-C{\'{e}}line Zanella and Samuel Cordey and Laurent Kaiser},
    title = {Beyond Cytomegalovirus and Epstein-Barr Virus: a Review of Viruses Composing the Blood Virome of Solid Organ Transplant and Hematopoietic Stem Cell Transplant Recipients},
    journal = {{Clin Microbiol Rev}},
    year = {2020},
    volume = {33},
    number = {4},
    doi = {10.1128/cmr.00027-20},
    publisher = {American Society for Microbiology},
    }
  • [DOI] U. Palatini, R. A. Masri, L. V. Cosme, S. Koren, F. Thibaud-Nissen, J. K. Biedler, F. Krsticevic, S. J. Johnston, R. Halbach, J. E. Crawford, I. Antoshechkin, A. Failloux, E. Pischedda, M. Marconcini, J. Ghurye, A. Rhie, A. Sharma, D. A. Karagodin, J. Jenrette, S. Gamez, P. Miesen, P. Masterson, A. Caccone, M. V. Sharakhova, Z. Tu, P. A. Papathanos, R. V. P. Rij, O. S. Akbari, J. Powell, A. M. Phillippy, and M. Bonizzoni, "Improved reference genome of the arboviral vector Aedes albopictus," Genome Biol, vol. 21, iss. 1, 2020.
    [Bibtex]
    @Article{Palatini:20,
    author = {Umberto Palatini and Reem A. Masri and Luciano V. Cosme and Sergey Koren and Fran{\c{c}}oise Thibaud-Nissen and James K. Biedler and Flavia Krsticevic and J. Spencer Johnston and Rebecca Halbach and Jacob E. Crawford and Igor Antoshechkin and Anna-Bella Failloux and Elisa Pischedda and Michele Marconcini and Jay Ghurye and Arang Rhie and Atashi Sharma and Dmitry A. Karagodin and Jeremy Jenrette and Stephanie Gamez and Pascal Miesen and Patrick Masterson and Adalgisa Caccone and Maria V. Sharakhova and Zhijian Tu and Philippos A. Papathanos and Ronald P. Van Rij and Omar S. Akbari and Jeffrey Powell and Adam M. Phillippy and Mariangela Bonizzoni},
    title = {Improved reference genome of the arboviral vector {A}edes albopictus},
    journal = {{Genome Biol}},
    year = {2020},
    volume = {21},
    number = {1},
    doi = {10.1186/s13059-020-02141-w},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] K. Schlottau, M. Rissmann, A. Graaf, J. Schön, J. Sehl, C. Wylezich, D. Höper, T. C. Mettenleiter, A. Balkema-Buschmann, T. Harder, C. Grund, D. Hoffmann, A. Breithaupt, and M. Beer, "SARS-CoV-2 in fruit bats, ferrets, pigs, and chickens: an experimental transmission study," Lancet Microbe, vol. 1, iss. 5, p. e218–e225, 2020.
    [Bibtex]
    @Article{Schlottau:20,
    author = {Kore Schlottau and Melanie Rissmann and Annika Graaf and Jacob Schön and Julia Sehl and Claudia Wylezich and Dirk Höper and Thomas C Mettenleiter and Anne Balkema-Buschmann and Timm Harder and Christian Grund and Donata Hoffmann and Angele Breithaupt and Martin Beer},
    title = {{SARS}-{CoV}-2 in fruit bats, ferrets, pigs, and chickens: an experimental transmission study},
    journal = {{Lancet Microbe}},
    year = {2020},
    volume = {1},
    number = {5},
    pages = {e218--e225},
    doi = {10.1016/s2666-5247(20)30089-6},
    publisher = {Elsevier {BV}},
    }
  • [DOI] K. Decock, K. Debackere, A. Vandamme, and B. V. Looy, "Scenario-driven forecasting: modeling peaks and paths. insights from the COVID-19 pandemic in Belgium," Scientometrics, vol. 124, iss. 3, p. 2703–2715, 2020.
    [Bibtex]
    @Article{Decock:20,
    author = {Kristof Decock and Koenraad Debackere and Anne-Mieke Vandamme and Bart Van Looy},
    title = {Scenario-driven forecasting: modeling peaks and paths. Insights from the {COVID}-19 pandemic in {B}elgium},
    journal = {Scientometrics},
    year = {2020},
    volume = {124},
    number = {3},
    pages = {2703--2715},
    doi = {10.1007/s11192-020-03591-6},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] P. V'kovski, S. Steiner, and V. Thiel, "Proximity labeling for the identification of Coronavirus-host protein interactions," in Coronaviruses, Springer US, 2020, p. 187–204.
    [Bibtex]
    @InCollection{Vkovski:20a,
    author = {Philip V'kovski and Silvio Steiner and Volker Thiel},
    title = {Proximity Labeling for the Identification of {C}oronavirus-Host Protein Interactions},
    booktitle = {Coronaviruses},
    publisher = {Springer {US}},
    year = {2020},
    pages = {187--204},
    doi = {10.1007/978-1-0716-0900-2_14},
    }
  • [DOI] T. T. N. Thao, F. Labroussaa, N. Ebert, J. Jores, and V. Thiel, "In-yeast assembly of coronavirus infectious cDNA clones using a synthetic genomics pipeline," in Coronaviruses, Springer US, 2020, p. 167–184.
    [Bibtex]
    @InCollection{Thao:20a,
    author = {Tran Thi Nhu Thao and Fabien Labroussaa and Nadine Ebert and Joerg Jores and Volker Thiel},
    title = {In-Yeast Assembly of Coronavirus Infectious {cDNA} Clones Using a Synthetic Genomics Pipeline},
    booktitle = {Coronaviruses},
    publisher = {Springer {US}},
    year = {2020},
    pages = {167--184},
    doi = {10.1007/978-1-0716-0900-2_13},
    }
  • [DOI] A. C. R. Hoste, A. Venteo, A. Fresco-Taboada, I. Tapia, A. Monedero, L. López, M. F. Jebbink, E. Pérez-Ramírez, M. A. Jimenez-Clavero, M. Almonacid, P. Muñoz, J. Guinea, C. Vela, L. van der Hoek, P. Rueda, and P. Sastre, "Two serological approaches for detection of antibodies to SARS-CoV-2 in different scenarios: a screening tool and a point-of-care test," Diagn Microbiol Infect Dis, vol. 98, iss. 4, p. 115167, 2020.
    [Bibtex]
    @Article{Hoste:20,
    author = {Alexis C.R. Hoste and Angel Venteo and Alba Fresco-Taboada and Istar Tapia and Alejandro Monedero and Lissette L{\'{o}}pez and Maarten F. Jebbink and Elisa P{\'{e}}rez-Ram{\'{\i}}rez and Miguel Angel Jimenez-Clavero and Mercedes Almonacid and Patricia Mu{\~{n}}oz and Jesus Guinea and Carmen Vela and Lia van der Hoek and Paloma Rueda and Patricia Sastre},
    title = {Two serological approaches for detection of antibodies to {SARS}-{CoV}-2 in different scenarios: a screening tool and a point-of-care test},
    journal = {{Diagn Microbiol Infect Dis}},
    year = {2020},
    volume = {98},
    number = {4},
    pages = {115167},
    doi = {10.1016/j.diagmicrobio.2020.115167},
    publisher = {Elsevier {BV}},
    }
  • [DOI] L. F. Ludwig-Begall, C. Wielick, L. Dams, H. J. Nauwynck, P-F. Demeuldre, A. Napp, J. Laperre, E. Haubruge, and E. Thiry, "The use of germicidal ultraviolet light, vaporized hydrogen peroxide and dry heat to decontaminate face masks and filtering respirators contaminated with a SARS-CoV-2 surrogate virus," J Hosp Infect, 2020.
    [Bibtex]
    @Article{Ludwig-Begall:20,
    author = {L.F. Ludwig-Begall and C. Wielick and L. Dams and H. J. Nauwynck and P-F. Demeuldre and A. Napp and J. Laperre and E. Haubruge and E. Thiry},
    title = {The use of germicidal ultraviolet light, vaporized hydrogen peroxide and dry heat to decontaminate face masks and filtering respirators contaminated with a {SARS}-{CoV}-2 surrogate virus},
    journal = {{J Hosp Infect}},
    year = {2020},
    doi = {10.1016/j.jhin.2020.08.025},
    publisher = {Elsevier {BV}},
    }
  • [DOI] J. King, T. Harder, M. Beer, and A. Pohlmann, "Rapid multiplex MinION nanopore sequencing workflow for influenza A viruses," BMC Infect Dis, vol. 20, iss. 1, 2020.
    [Bibtex]
    @Article{King:20,
    author = {Jacqueline King and Timm Harder and Martin Beer and Anne Pohlmann},
    title = {Rapid multiplex {MinION} nanopore sequencing workflow for Influenza {A} viruses},
    journal = {{BMC Infect Dis}},
    year = {2020},
    volume = {20},
    number = {1},
    doi = {10.1186/s12879-020-05367-y},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] S. Bach, J. Demper, N. Biedenkopf, S. Becker, and R. K. Hartmann, "RNA secondary structure at the transcription start site influences EBOV transcription initiation and replication in a length- and stability-dependent manner," RNA Biol, 2020.
    [Bibtex]
    @Article{Bach:20,
    author = {Simone Bach and Jana-Christin Demper and Nadine Biedenkopf and Stephan Becker and Roland K. Hartmann},
    title = {{RNA} secondary structure at the transcription start site influences {EBOV} transcription initiation and replication in a length- and stability-dependent manner},
    journal = {{RNA Biol}},
    year = {2020},
    doi = {10.1080/15476286.2020.1818459},
    publisher = {Informa {UK} Limited},
    }
  • [DOI] J. Abrantes, C. Droillard, A. M. Lopes, E. Lemaitre, P. Lucas, Y. Blanchard, S. Marchandeau, P. J. Esteves, and G. L. Gall-Reculé, "Recombination at the emergence of the pathogenic rabbit haemorrhagic disease virus lagovirus europaeus/GI.2," Scientific reports, vol. 10, iss. 1, 2020.
    [Bibtex]
    @Article{Abrantes:20,
    author = {Joana Abrantes and Cl{\'{e}}ment Droillard and Ana M. Lopes and Evelyne Lemaitre and Pierrick Lucas and Yannick Blanchard and St{\'{e}}phane Marchandeau and Pedro J. Esteves and Ghislaine Le Gall-Recul{\'{e}}},
    title = {Recombination at the emergence of the pathogenic rabbit haemorrhagic disease virus Lagovirus europaeus/{GI}.2},
    journal = {Scientific Reports},
    year = {2020},
    volume = {10},
    number = {1},
    doi = {10.1038/s41598-020-71303-4},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • A. Tehel, T. Streicher, S. Tragust, and R. J. Paxton, "Experimental infection of bumblebees with honeybee-associated viruses: no direct fitness costs but potential future threats to novel wild bee hosts," R Soc Open Sci, vol. 7, iss. 7, p. 200480, 2020.
    [Bibtex]
    @Article{Tehel:20,
    author = {Tehel, Anja and Streicher, Tabea and Tragust, Simon and Paxton, Robert J},
    title = {Experimental infection of bumblebees with honeybee-associated viruses: no direct fitness costs but potential future threats to novel wild bee hosts},
    journal = {{R Soc Open Sci}},
    year = {2020},
    volume = {7},
    number = {7},
    pages = {200480},
    publisher = {The Royal Society},
    }
  • [DOI] M. Balvert, X. Luo, E. Hauptfeld, A. Schönhuth, and B. E. Dutilh, "OGRE: Overlap Graph-based metagenomic Read clustEring," Bioinformatics, 2020.
    [Bibtex]
    @Article{Balvert:20,
    author = {Marleen Balvert and Xiao Luo and Ernestina Hauptfeld and Alexander Schönhuth and Bas E Dutilh},
    title = {{OGRE}: {O}verlap {G}raph-based metagenomic {R}ead clust{E}ring},
    journal = {Bioinformatics},
    year = {2020},
    doi = {10.1093/bioinformatics/btaa760},
    editor = {Pier Luigi Martelli},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] A. Mecate-Zambrano, S. Sukumar, G. Seebohm, K. Ciminski, A. Schreiber, D. Anhlan, L. Greune, L. Wixler, S. Grothe, N. C. Stein, A. M. Schmidt, K. Langer, M. Schwemmle, T. Shi, S. Ludwig, and Y. Boergeling, "Discrete spatio-temporal regulation of tyrosine phosphorylation directs influenza A virus M1 protein towards its function in virion assembly," PLoS Pathog, vol. 16, iss. 8, p. e1008775, 2020.
    [Bibtex]
    @Article{Mecate-Zambrano:20,
    author = {Angeles Mecate-Zambrano and Swathi Sukumar and Guiscard Seebohm and Kevin Ciminski and Andr{\'{e}} Schreiber and Darisuren Anhlan and Lilo Greune and Ludmilla Wixler and Stephanie Grothe and Nora Caroline Stein and M. Alexander Schmidt and Klaus Langer and Martin Schwemmle and Tianlai Shi and Stephan Ludwig and Yvonne Boergeling},
    title = {Discrete spatio-temporal regulation of tyrosine phosphorylation directs influenza {A} virus {M1} protein towards its function in virion assembly},
    journal = {{PLoS Pathog}},
    year = {2020},
    volume = {16},
    number = {8},
    pages = {e1008775},
    doi = {10.1371/journal.ppat.1008775},
    editor = {Beatriz M. Fontoura},
    publisher = {Public Library of Science ({PLoS})},
    }
  • K. Schubert, E. D. Karousis, A. Jomaa, A. Scaiola, B. Echeverria, L. Gurzeler, M. Leibundgut, V. Thiel, O. Mühlemann, and N. Ban, "SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation," Nat Struct Mol Biol, p. 1–8, 2020.
    [Bibtex]
    @Article{Schubert:20,
    author = {Schubert, Katharina and Karousis, Evangelos D and Jomaa, Ahmad and Scaiola, Alain and Echeverria, Blanca and Gurzeler, Lukas-Adrian and Leibundgut, Marc and Thiel, Volker and M{\"u}hlemann, Oliver and Ban, Nenad},
    title = {{SARS}-{CoV}-2 {Nsp1} binds the ribosomal {mRNA} channel to inhibit translation},
    journal = {{Nat Struct Mol Biol}},
    year = {2020},
    pages = {1--8},
    publisher = {Nature Publishing Group},
    }
  • [DOI] S. A. E. Rahman, B. Hoffmann, R. Karam, M. El-Beskawy, M. F. Hamed, L. F. Forth, D. Höper, and M. Eschbaumer, "Sequence analysis of Egyptian foot-and-mouth disease virus field and vaccine strains: intertypic recombination and evidence for accidental release of virulent virus," Viruses, vol. 12, iss. 9, p. 990, 2020.
    [Bibtex]
    @Article{Rahman:20,
    author = {Sahar Abd El Rahman and Bernd Hoffmann and Reham Karam and Mohamed El-Beskawy and Mohammed F. Hamed and Leonie F. Forth and Dirk Höper and Michael Eschbaumer},
    title = {Sequence Analysis of {E}gyptian Foot-and-Mouth Disease Virus Field and Vaccine Strains: Intertypic Recombination and Evidence for Accidental Release of Virulent Virus},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    number = {9},
    pages = {990},
    doi = {10.3390/v12090990},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] S. Duchene, P. Lemey, T. Stadler, S. Y. W. Ho, D. A. Duchene, V. Dhanasekaran, and G. Baele, "Bayesian evaluation of temporal signal in measurably evolving populations," Molecular biology and evolution, 2020.
    [Bibtex]
    @Article{Duchene:20a,
    author = {Sebastian Duchene and Philippe Lemey and Tanja Stadler and Simon Y W Ho and David A Duchene and Vijaykrishna Dhanasekaran and Guy Baele},
    title = {Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations},
    journal = {Molecular Biology and Evolution},
    year = {2020},
    doi = {10.1093/molbev/msaa163},
    editor = {Keith Crandall},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] A. Shannon, B. Selisko, N. Le, J. Huchting, F. Touret, G. Piorkowski, V. Fattorini, F. Ferron, E. Decroly, C. Meier, B. Coutard, O. Peersen, and B. Canard, "Rapid incorporation of Favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis," Nat Commun, vol. 11, iss. 1, 2020.
    [Bibtex]
    @Article{Shannon:20a,
    author = {Ashleigh Shannon and Barbara Selisko and Nhung-Thi-Tuyet Le and Johanna Huchting and Franck Touret and G{\'{e}}raldine Piorkowski and V{\'{e}}ronique Fattorini and Fran{\c{c}}ois Ferron and Etienne Decroly and Chris Meier and Bruno Coutard and Olve Peersen and Bruno Canard},
    title = {Rapid incorporation of {F}avipiravir by the fast and permissive viral {RNA} polymerase complex results in {SARS}-{CoV}-2 lethal mutagenesis},
    journal = {{Nat Commun}},
    year = {2020},
    volume = {11},
    number = {1},
    doi = {10.1038/s41467-020-18463-z},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] D. Polo, M. Quintela-Baluja, A. Corbishley, D. L. Jones, A. C. Singer, D. W. Graham, and J. L. Romalde, "Making waves: wastewater-based epidemiology for COVID-19 – approaches and challenges for surveillance and prediction," Water Res, vol. 186, p. 116404, 2020.
    [Bibtex]
    @Article{Polo:20,
    author = {David Polo and Marcos Quintela-Baluja and Alexander Corbishley and Davey L. Jones and Andrew C. Singer and David W. Graham and Jes{\'{u}}s L. Romalde},
    title = {Making waves: Wastewater-based epidemiology for {COVID}-19 -- approaches and challenges for surveillance and prediction},
    journal = {{Water Res}},
    year = {2020},
    volume = {186},
    pages = {116404},
    doi = {10.1016/j.watres.2020.116404},
    publisher = {Elsevier {BV}},
    }
  • [DOI] Y. Konno, I. Kimura, K. Uriu, M. Fukushi, T. Irie, Y. Koyanagi, D. Sauter, R. J. Gifford, S. Nakagawa, and K. Sato, "SARS-CoV-2 ORF3b is a potent interferon antagonist whose activity is increased by a naturally occurring elongation variant," Cell Rep, vol. 32, iss. 12, p. 108185, 2020.
    [Bibtex]
    @Article{Konno:20,
    author = {Yoriyuki Konno and Izumi Kimura and Keiya Uriu and Masaya Fukushi and Takashi Irie and Yoshio Koyanagi and Daniel Sauter and Robert J. Gifford and So Nakagawa and Kei Sato},
    title = {{SARS}-{CoV}-2 {ORF}3b Is a Potent Interferon Antagonist Whose Activity Is Increased by a Naturally Occurring Elongation Variant},
    journal = {{Cell Rep}},
    year = {2020},
    volume = {32},
    number = {12},
    pages = {108185},
    doi = {10.1016/j.celrep.2020.108185},
    publisher = {Elsevier {BV}},
    }
  • [DOI] C. M. Kinsella, A. Bart, M. Deijs, P. Broekhuizen, J. Kaczorowska, M. F. Jebbink, T. van Gool, M. Cotten, and L. van der Hoek, "Entamoeba and Giardia parasites implicated as hosts of CRESS viruses," Nat Commun, vol. 11, iss. 1, 2020.
    [Bibtex]
    @Article{Kinsella:20,
    author = {Cormac M. Kinsella and Aldert Bart and Martin Deijs and Patricia Broekhuizen and Joanna Kaczorowska and Maarten F. Jebbink and Tom van Gool and Matthew Cotten and Lia van der Hoek},
    title = {{E}ntamoeba and {G}iardia parasites implicated as hosts of {CRESS} viruses},
    journal = {{Nat Commun}},
    year = {2020},
    volume = {11},
    number = {1},
    doi = {10.1038/s41467-020-18474-w},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] A. Welker, C. Kersten, C. Müller, R. Madhugiri, C. Zimmer, P. Müller, R. A. Zimmermann, S. Hammerschmidt, H. Maus, J. Ziebuhr, C. Sotriffer, and T. Schirmeister, "SAR of novel benzamides and isoindolines, designed as SARS-CoV protease inhibitors – effective against SARS-CoV-2," ChemMedChem, 2020.
    [Bibtex]
    @Article{Welker:20,
    author = {Armin Welker and Christian Kersten and Christin Müller and Ramakanth Madhugiri and Collin Zimmer and Patrick Müller and Robert Alexander Zimmermann and Stefan Hammerschmidt and Hannah Maus and John Ziebuhr and Christoph Sotriffer and Tanja Schirmeister},
    title = {{SAR} of novel benzamides and isoindolines, designed as {SARS}-{CoV} protease inhibitors {\textendash} effective against {SARS}-{CoV}-2},
    journal = {{ChemMedChem}},
    year = {2020},
    doi = {10.1002/cmdc.202000548},
    publisher = {Wiley},
    }
  • [DOI] A. W. D. Edridge, J. Kaczorowska, A. C. R. Hoste, M. Bakker, M. Klein, K. Loens, M. F. Jebbink, A. Matser, C. M. Kinsella, P. Rueda, M. Ieven, H. Goossens, M. Prins, P. Sastre, M. Deijs, and L. van der Hoek, "Seasonal coronavirus protective immunity is short-lasting," Nat Med, 2020.
    [Bibtex]
    @Article{Edridge:20,
    author = {Arthur W. D. Edridge and Joanna Kaczorowska and Alexis C. R. Hoste and Margreet Bakker and Michelle Klein and Katherine Loens and Maarten F. Jebbink and Amy Matser and Cormac M. Kinsella and Paloma Rueda and Margareta Ieven and Herman Goossens and Maria Prins and Patricia Sastre and Martin Deijs and Lia van der Hoek},
    title = {Seasonal coronavirus protective immunity is short-lasting},
    journal = {{Nat Med}},
    year = {2020},
    doi = {10.1038/s41591-020-1083-1},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] E. M. L. Scerri, D. Kühnert, J. Blinkhorn, H. S. Groucutt, P. Roberts, K. Nicoll, A. Zerboni, E. A. Orijemie, H. Barton, I. Candy, S. T. Goldstein, J. Hawks, K. Niang, D. N'Dah, M. D. Petraglia, and N. C. Vella, "Field-based sciences must transform in response to COVID-19," Nat Ecol Evol, 2020.
    [Bibtex]
    @Article{Scerri:20,
    author = {Eleanor M. L. Scerri and Denise Kühnert and James Blinkhorn and Huw S. Groucutt and Patrick Roberts and Kathleen Nicoll and Andrea Zerboni and Emuobosa Akpo Orijemie and Huw Barton and Ian Candy and Steven T. Goldstein and John Hawks and Khady Niang and Didier N'Dah and Michael D. Petraglia and Nicholas C. Vella},
    title = {Field-based sciences must transform in response to {COVID}-19},
    journal = {{Nat Ecol Evol}},
    year = {2020},
    doi = {10.1038/s41559-020-01317-8},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] G. Baele, M. S. Gill, P. Lemey, and M. A. Suchard, "Hamiltonian Monte Carlo sampling to estimate past population dynamics using the skygrid coalescent model in a Bayesian phylogenetics framework," Wellcome Open Res, vol. 5, p. 53, 2020.
    [Bibtex]
    @Article{Baele:20,
    author = {Guy Baele and Mandev S. Gill and Philippe Lemey and Marc A. Suchard},
    title = {Hamiltonian {M}onte {C}arlo sampling to estimate past population dynamics using the skygrid coalescent model in a {B}ayesian phylogenetics framework},
    journal = {{Wellcome Open Res}},
    year = {2020},
    volume = {5},
    pages = {53},
    doi = {10.12688/wellcomeopenres.15770.1},
    publisher = {F1000 Research Ltd},
    }
  • [DOI] I. Almansour, "Mumps vaccines: current challenges and future prospects," Front Microbiol, vol. 11, 2020.
    [Bibtex]
    @Article{Almansour:20,
    author = {Iman Almansour},
    title = {Mumps Vaccines: Current Challenges and Future Prospects},
    journal = {{Front Microbiol}},
    year = {2020},
    volume = {11},
    doi = {10.3389/fmicb.2020.01999},
    publisher = {Frontiers Media {SA}},
    }
  • [DOI] C. Muñoz-Fontela, W. E. Dowling, S. G. P. Funnell, P. Gsell, X. R. Balta, R. A. Albrecht, H. Andersen, R. S. Baric, M. W. Carroll, M. Cavaleri, C. Qin, I. Crozier, K. Dallmeier, L. de Waal, E. de Wit, L. Delang, E. Dohm, P. W. Duprex, D. Falzarano, C. L. Finch, M. B. Frieman, B. S. Graham, L. Gralinski, K. Guilfoyle, B. L. Haagmans, G. A. Hamilton, A. L. Hartman, S. Herfst, S. J. F. Kaptein, W. Klimstra, I. Knezevic, P. R. Krause, J. H. Kuhn, R. L. Grand, M. Lewis, W. Liu, P. Maisonnasse, A. K. McElroy, V. Munster, N. Oreshkova, A. L. Rasmussen, J. Rocha-Pereira, B. Rockx, E. Rodríguez, T. Rogers, F. J. Salguero, M. Schotsaert, K. J. Stittelaar, H. J. Thibaut, C. Tseng, J. Vergara-Alert, M. Beer, T. Brasel, J. F. W. Chan, A. García-Sastre, J. Neyts, S. Perlman, D. S. Reed, J. A. Richt, C. J. Roy, J. Segalés, S. S. Vasan, A. M. Henao-Restrepo, and D. H. Barouch, "Animal models for COVID-19," Nature, 2020.
    [Bibtex]
    @Article{MunozFontela:20,
    author = {C{\'{e}}sar Mu{\~{n}}oz-Fontela and William E. Dowling and Simon G. P. Funnell and Pierre-S. Gsell and Ximena Riveros Balta and Randy A. Albrecht and Hanne Andersen and Ralph S. Baric and Miles W. Carroll and Marco Cavaleri and Chuan Qin and Ian Crozier and Kai Dallmeier and Leon de Waal and Emmie de Wit and Leen Delang and Erik Dohm and W. Paul Duprex and Darryl Falzarano and Courtney L. Finch and Matthew B. Frieman and Barney S. Graham and Lisa Gralinski and Kate Guilfoyle and Bart L. Haagmans and Geraldine A. Hamilton and Amy L. Hartman and Sander Herfst and Suzanne J. F. Kaptein and William Klimstra and Ivana Knezevic and Philip R. Krause and Jens H. Kuhn and Roger Le Grand and Mark Lewis and Wen-Chun Liu and Pauline Maisonnasse and Anita K. McElroy and Vincent Munster and Nadia Oreshkova and Angela L. Rasmussen and Joana Rocha-Pereira and Barry Rockx and Estefan{\'{\i}}a Rodr{\'{\i}}guez and Thomas Rogers and Francisco J. Salguero and Michael Schotsaert and Koert J. Stittelaar and Hendrik Jan Thibaut and Chien-Te Tseng and J{\'{u}}lia Vergara-Alert and Martin Beer and Trevor Brasel and Jasper F. W. Chan and Adolfo Garc{\'{\i}}a-Sastre and Johan Neyts and Stanley Perlman and Douglas S. Reed and Juergen A. Richt and Chad J. Roy and Joaquim Segal{\'{e}}s and Seshadri S. Vasan and Ana Mar{\'{\i}}a Henao-Restrepo and Dan H. Barouch},
    title = {Animal models for {COVID}-19},
    journal = {Nature},
    year = {2020},
    doi = {10.1038/s41586-020-2787-6},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] A. Rossi, L. Treu, S. Toppo, H. Zschach, S. Campanaro, and B. E. Dutilh, "Evolutionary study of the crAssphage virus at gene level," Viruses, vol. 12, iss. 9, p. 1035, 2020.
    [Bibtex]
    @Article{Rossi:20,
    author = {Alessandro Rossi and Laura Treu and Stefano Toppo and Henrike Zschach and Stefano Campanaro and Bas E. Dutilh},
    title = {Evolutionary Study of the cr{A}ssphage Virus at Gene Level},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    number = {9},
    pages = {1035},
    doi = {10.3390/v12091035},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] C. Tumescheit, A. E. Firth, and K. Brown, "CIAlign - a highly customisable command line tool to clean, interpret and visualise multiple sequence alignments," bioRxiv, 2020.
    [Bibtex]
    @Article{Tumescheit:20,
    author = {Charlotte Tumescheit and Andrew E. Firth and Katherine Brown},
    title = {{CIAlign} - A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.09.14.291484},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] V. Lulla, M. P. Wandel, K. J. Bandyra, T. Dendooven, X. Yang, N. Doyle, S. Oerum, S. O'Rourke, F. Randow, H. J. Maier, W. Scott, Y. Ding, A. E. Firth, K. Bloznelyte, and B. F. Luisi, "Antisense oligonucleotides target a nearly invariant structural element from the SARS-CoV-2 genome and drive RNA degradation," bioRxiv, 2020.
    [Bibtex]
    @Article{Lulla:20,
    author = {Valeria Lulla and Michal P. Wandel and Katarzyna J. Bandyra and Tom Dendooven and Xiaofei Yang and Nicole Doyle and Stephanie Oerum and Sara O'Rourke and Felix Randow and Helena J. Maier and William Scott and Yiliang Ding and Andrew E. Firth and Kotryna Bloznelyte and Ben F. Luisi},
    title = {Antisense oligonucleotides target a nearly invariant structural element from the {SARS}-{CoV}-2 genome and drive {RNA} degradation},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.09.18.304139},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. Ferrarini, A. Lal, R. Rebollo, A. Gruber, A. Guarracino, I. M. Gonzalez, T. Floyd, D. S. de Oliveira, J. Shanklin, E. Beausoleil, T. Pusa, B. E. Pickett, and V. Aguiar-Pulido, "Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis," Research Square, 2020.
    [Bibtex]
    @Article{Ferrarini:20a,
    author = {Mariana Ferrarini and Avantika Lal and Rita Rebollo and Andreas Gruber and Andrea Guarracino and Itziar Martinez Gonzalez and Taylor Floyd and Daniel Siqueira de Oliveira and Justin Shanklin and Ethan Beausoleil and Taneli Pusa and Brett E. Pickett and Vanessa Aguiar-Pulido},
    title = {Genome-wide bioinformatic analyses predict key host and viral factors in {SARS}-{CoV}-2 pathogenesis},
    journal = {{Research Square}},
    year = {2020},
    doi = {10.21203/rs.3.rs-63136/v1},
    publisher = {Research Square},
    }
  • [DOI] A. Ulyte, T. Radtke, I. A. Abela, S. H. Haile, J. Blankenberger, R. Jung, C. Capelli, C. Berger, A. Frei, M. Huber, M. Schanz, M. Schwarzmueller, A. Trkola, J. Fehr, M. A. Puhan, and S. Kriemler, "Variation in SARS-CoV-2 seroprevalence in school-children across districts, schools and classes," medRix, 2020.
    [Bibtex]
    @Article{Ulyte:20,
    author = {Agne Ulyte and Thomas Radtke and Irene A Abela and Sarah H Haile and Jacob Blankenberger and Ruedi Jung and Celine Capelli and Christoph Berger and Anja Frei and Michael Huber and Merle Schanz and Magdalena Schwarzmueller and Alexandra Trkola and Jan Fehr and Milo A Puhan and Susi Kriemler},
    title = {Variation in {SARS}-{CoV}-2 seroprevalence in school-children across districts, schools and classes},
    journal = {{medRix}},
    year = {2020},
    doi = {10.1101/2020.09.18.20191254},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. W. Pletz, A. Steiner, M. Kesselmeier, B. Loeffler, S. Trommer, S. Weis, J. Maschmann, and A. Stallmach, "Impact of universal masking in health care and community on SARS-CoV-2 spread," medRxiv, 2020.
    [Bibtex]
    @Article{Pletz:20,
    author = {Mathias W. Pletz and Andrea Steiner and Miriam Kesselmeier and Bettina Loeffler and Sabine Trommer and Sebastian Weis and Jens Maschmann and Andreas Stallmach},
    title = {Impact of universal masking in health care and community on {SARS}-{CoV}-2 spread},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.09.02.20187021},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. J. Hosie, I. Epifano, V. Herder, R. J. Orton, A. Stevenson, N. Johnson, E. MacDonald, D. Dunbar, M. McDonald, F. Howie, B. Tennant, D. Herrity, A. D. S. Filipe, D. G. Streicker, B. J. Willett, P. R. Murcia, R. F. Jarrett, D. L. Robertson, and W. W. and, "Respiratory disease in cats associated with human-to-cat transmission of SARS-CoV-2 in the UK," bioRxiv, 2020.
    [Bibtex]
    @Article{Hosie:20,
    author = {Margaret J Hosie and Ilaria Epifano and Vanessa Herder and Richard J Orton and Andrew Stevenson and Natasha Johnson and Emma MacDonald and Dawn Dunbar and Michael McDonald and Fiona Howie and Bryn Tennant and Darcy Herrity and Ana Da Silva Filipe and Daniel G Streicker and Brian J Willett and Pablo R Murcia and Ruth F Jarrett and David L Robertson and William Weir and},
    title = {Respiratory disease in cats associated with human-to-cat transmission of {SARS}-{CoV}-2 in the {UK}},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.09.23.309948},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] P. Nyasulu, J. Weyer, R. Tschopp, A. Mihret, A. Aseffa, S. V. Nuvor, L. Nyakarahuka, T. Balogun, J. L. Tamuzi, G. K. Helegbe, N. E. Ntinginya, M. T. Gebreyesus, S. Doumbia, L. Blumberg, R. Busse, and C. Drosten, "Rabies mortality and morbidity associated with animal bites in Africa: A case for Integrated Rabies Diseases Surveillance, Prevention and Control – A Scoping review," medRxiv, 2020.
    [Bibtex]
    @Article{Nyasulu:20,
    author = {Peter Nyasulu and Jacqueline Weyer and Rea Tschopp and Adane Mihret and Abraham Aseffa and Samuel Victor Nuvor and Luke Nyakarahuka and Tolulope Balogun and Jacques Lukenze Tamuzi and Gideon Kofi Helegbe and Nyanda Elias Ntinginya and Melaku Tefera Gebreyesus and Seydou Doumbia and Lucille Blumberg and Reinhard Busse and Christian Drosten},
    title = {Rabies mortality and morbidity associated with animal bites in {A}frica: {A} case for {I}ntegrated {R}abies {D}iseases {S}urveillance, {P}revention and {C}ontrol -- {A} {S}coping review},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.07.29.20164483},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. Seifert, S. C. Bera, P. van Nies, R. N. Kirchdoerfer, A. Shannon, T. Le, T. L. Grove, F. S. Papini, J. J. Arnold, S. C. Almo, B. Canard, M. Depken, C. E. Cameron, and D. Dulin, "Signatures and mechanisms of efficacious therapeutic ribonucleotides against SARS-CoV-2 revealed by analysis of its replicase using magnetic tweezers," bioRxiv, 2020.
    [Bibtex]
    @Article{Seifert:20,
    author = {Mona Seifert and Subhas Chandra Bera and Pauline van Nies and Robert N. Kirchdoerfer and Ashleigh Shannon and Thi-Tuyet-Nhung Le and Tyler L. Grove and Fl{\'{a}}via S. Papini and Jamie J. Arnold and Steven C. Almo and Bruno Canard and Martin Depken and Craig E. Cameron and David Dulin},
    title = {Signatures and mechanisms of efficacious therapeutic ribonucleotides against {SARS}-{CoV}-2 revealed by analysis of its replicase using magnetic tweezers},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.08.06.240325},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] C. Simsek, V. M. Corman, H. U. Everling, A. N. Lukashev, A. Rasche, G. D. Maganga, T. Binger, D. Jansen, L. Beller, W. Deboutte, F. Gloza-Rausch, A. Seebens-Hoyer, S. Yordanov, A. Sylverken, S. Oppong, Y. A. Sarkodie, P. Vallo, E. M. Leroy, M. Bourgarel, K. C. Yinda, M. V. Ranst, C. Drosten, J. F. Drexler, and J. Matthijnssens, "At least seven distinct rotavirus genotype constellations in bats with evidence of reassortment and zoonotic transmissions," bioRxiv, 2020.
    [Bibtex]
    @Article{Simsek:20,
    author = {Ceren Simsek and Victor Max Corman and Hermann Ulrich Everling and Alexander N. Lukashev and Andrea Rasche and Gael Darren Maganga and Tabea Binger and Daan Jansen and Leen Beller and Ward Deboutte and Florian Gloza-Rausch and Antje Seebens-Hoyer and Stoian Yordanov and Augustina Sylverken and Samuel Oppong and Yaw Adu Sarkodie and Peter Vallo and Eric M. Leroy and Mathieu Bourgarel and Kwe Claude Yinda and Marc Van Ranst and Christian Drosten and Jan Felix Drexler and Jelle Matthijnssens},
    title = {At least seven distinct rotavirus genotype constellations in bats with evidence of reassortment and zoonotic transmissions},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.08.13.250464},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] J. Kreye, M. S. Reincke, H. Kornau, E. Sánchez-Sendin, V. M. Corman, H. Liu, M. Yuan, N. C. Wu, X. Zhu, C. D. Lee, J. Trimpert, M. Höltje, K. Dietert, L. Stöffler, N. von Wardenburg, S. van Hoof, M. A. Homeyer, J. Hoffmann, A. Abdelgawad, A. D. Gruber, L. D. Bertzbach, D. Vladimirova, L. Y. Li, P. C. Barthel, K. Skriner, A. C. Hocke, S. Hippenstiel, M. Witzenrath, N. Suttorp, F. Kurth, C. Franke, M. Endres, D. Schmitz, L. M. Jeworowski, A. Richter, M. L. Schmidt, T. Schwarz, M. A. Müller, C. Drosten, D. Wendisch, L. E. Sander, N. Osterrieder, I. A. Wilson, and H. Prüss, "A SARS-CoV-2 neutralizing antibody protects from lung pathology in a COVID-19 hamster model," bioRxiv, 2020.
    [Bibtex]
    @Article{Kreye:20,
    author = {Jakob Kreye and S Momsen Reincke and Hans-Christian Kornau and Elisa S{\'{a}}nchez-Sendin and Victor Max Corman and Hejun Liu and Meng Yuan and Nicholas C. Wu and Xueyong Zhu and Chang-Chun D. Lee and Jakob Trimpert and Markus Höltje and Kristina Dietert and Laura Stöffler and Niels von Wardenburg and Scott van Hoof and Marie A Homeyer and Julius Hoffmann and Azza Abdelgawad and Achim D Gruber and Luca D Bertzbach and Daria Vladimirova and Lucie Y Li and Paula Charlotte Barthel and Karl Skriner and Andreas C Hocke and Stefan Hippenstiel and Martin Witzenrath and Norbert Suttorp and Florian Kurth and Christiana Franke and Matthias Endres and Dietmar Schmitz and Lara Maria Jeworowski and Anja Richter and Marie Luisa Schmidt and Tatjana Schwarz and Marcel Alexander Müller and Christian Drosten and Daniel Wendisch and Leif E Sander and Nikolaus Osterrieder and Ian A Wilson and Harald Prüss},
    title = {A {SARS}-{CoV}-2 neutralizing antibody protects from lung pathology in a {COVID}-19 hamster model},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.08.15.252320},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] R. Gilroy, A. Ravi, M. Getino, I. Pursley, D. Horton, N. Alikhan, D. Baker, K. Gharbi, N. Hall, M. Watson, E. M. Adriaenssens, E. Foster-Nyarko, S. Jarju, A. Secka, M. Antonio, A. Oren, R. Chaudhuri, F. Hildebrand, and M. Pallen, "A genomic blueprint of the chicken gut microbiome," Research Square, 2020.
    [Bibtex]
    @Article{Gilroy:20,
    author = {Rachel Gilroy and Anuradha Ravi and Maria Getino and Isabella Pursley and Daniel Horton and Nabil-Fareed Alikhan and David Baker and Karim Gharbi and Neil Hall and Mick Watson and Evelien M. Adriaenssens and Ebenezer Foster-Nyarko and Sheikh Jarju and Arss Secka and Martin Antonio and Aharon Oren and Roy Chaudhuri and Falk Hildebrand and Mark Pallen},
    title = {A Genomic Blueprint of the Chicken Gut Microbiome},
    journal = {{Research Square}},
    year = {2020},
    doi = {10.21203/rs.3.rs-56027/v1},
    publisher = {Research Square},
    }
  • [DOI] F. Meyer, T. Lesker, D. Koslicki, A. Fritz, A. Gurevich, A. E. Darling, A. Sczyrba, A. Bremges, and A. C. McHardy, "Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit," bioRxiv, 2020.
    [Bibtex]
    @Article{Meyer:20,
    author = {Fernando Meyer and Till-Robin Lesker and David Koslicki and Adrian Fritz and Alexey Gurevich and Aaron E. Darling and Alexander Sczyrba and Andreas Bremges and Alice C. McHardy},
    title = {Tutorial: Assessing metagenomics software with the {CAMI} benchmarking toolkit},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.08.11.245712},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. Hölzer and M. Marz, "PoSeiDon: a nextflow pipeline for the detection of evolutionary recombination events and positive selection," Bioinformatics, 2020.
    [Bibtex]
    @Article{Hölzer:20,
    author = {Martin Hölzer and Manja Marz},
    title = {{PoSeiDon}: a Nextflow pipeline for the detection of evolutionary recombination events and positive selection},
    journal = {Bioinformatics},
    year = {2020},
    doi = {10.1093/bioinformatics/btaa695},
    editor = {Alfonso Valencia},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] J. Braun, L. Loyal, M. Frentsch, D. Wendisch, P. Georg, F. Kurth, S. Hippenstiel, M. Dingeldey, B. Kruse, F. Fauchere, E. Baysal, M. Mangold, L. Henze, R. Lauster, M. A. Mall, K. Beyer, J. Röhmel, S. Voigt, J. Schmitz, S. Miltenyi, I. Demuth, M. A. Müller, A. Hocke, M. Witzenrath, N. Suttorp, F. Kern, U. Reimer, H. Wenschuh, C. Drosten, V. M. Corman, C. Giesecke-Thiel, L. E. Sander, and A. Thiel, "SARS-CoV-2-reactive T cells in healthy donors and patients with COVID-19," Nature, 2020.
    [Bibtex]
    @Article{Braun:20a,
    author = {Julian Braun and Lucie Loyal and Marco Frentsch and Daniel Wendisch and Philipp Georg and Florian Kurth and Stefan Hippenstiel and Manuela Dingeldey and Beate Kruse and Florent Fauchere and Emre Baysal and Maike Mangold and Larissa Henze and Roland Lauster and Marcus A. Mall and Kirsten Beyer and Jobst Röhmel and Sebastian Voigt and Jürgen Schmitz and Stefan Miltenyi and Ilja Demuth and Marcel A. Müller and Andreas Hocke and Martin Witzenrath and Norbert Suttorp and Florian Kern and Ulf Reimer and Holger Wenschuh and Christian Drosten and Victor M. Corman and Claudia Giesecke-Thiel and Leif Erik Sander and Andreas Thiel},
    title = {{SARS}-{CoV}-2-reactive {T} cells in healthy donors and patients with {COVID}-19},
    journal = {Nature},
    year = {2020},
    doi = {10.1038/s41586-020-2598-9},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] T. L. Meister, Y. Brüggemann, D. Todt, C. Conzelmann, J. A. Müller, R. Groß, J. Münch, A. Krawczyk, J. Steinmann, J. Steinmann, S. Pfaender, and E. Steinmann, "Virucidal efficacy of different oral rinses against SARS-CoV-2," J infect dis, 2020.
    [Bibtex]
    @Article{Meister:20,
    author = {Toni Luise Meister and Yannick Brüggemann and Daniel Todt and Carina Conzelmann and Janis A Müller and Rüdiger Gro{\ss} and Jan Münch and Adalbert Krawczyk and Jörg Steinmann and Jochen Steinmann and Stephanie Pfaender and Eike Steinmann},
    title = {Virucidal efficacy of different oral rinses against {SARS}-{CoV}-2},
    journal = {J Infect Dis},
    year = {2020},
    doi = {10.1093/infdis/jiaa471},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] M. F. Boni, P. Lemey, X. Jiang, T. T. Lam, B. W. Perry, T. A. Castoe, A. Rambaut, and D. L. Robertson, "Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic," Nat Microbiol, 2020.
    [Bibtex]
    @Article{Boni:20,
    author = {Maciej F. Boni and Philippe Lemey and Xiaowei Jiang and Tommy Tsan-Yuk Lam and Blair W. Perry and Todd A. Castoe and Andrew Rambaut and David L. Robertson},
    title = {Evolutionary origins of the {SARS}-{CoV}-2 sarbecovirus lineage responsible for the {COVID}-19 pandemic},
    journal = {{Nat Microbiol}},
    year = {2020},
    doi = {10.1038/s41564-020-0771-4},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] A. Lai, A. Bergna, S. Caucci, N. Clementi, I. Vicenti, F. Dragoni, A. M. Cattelan, S. Menzo, A. Pan, A. Callegaro, A. Tagliabracci, A. Caruso, F. Caccuri, S. Ronchiadin, C. Balotta, M. Zazzi, E. Vaccher, M. Clementi, M. Galli, and G. Zehender, "Molecular tracing of SARS-CoV-2 in Italy in the first three months of the epidemic," Viruses, vol. 12, iss. 8, p. 798, 2020.
    [Bibtex]
    @Article{Lai:20,
    author = {Alessia Lai and Annalisa Bergna and Sara Caucci and Nicola Clementi and Ilaria Vicenti and Filippo Dragoni and Anna Maria Cattelan and Stefano Menzo and Angelo Pan and Annapaola Callegaro and Adriano Tagliabracci and Arnaldo Caruso and Francesca Caccuri and Silvia Ronchiadin and Claudia Balotta and Maurizio Zazzi and Emanuela Vaccher and Massimo Clementi and Massimo Galli and Gianguglielmo Zehender},
    title = {Molecular Tracing of {SARS}-{CoV}-2 in {I}taly in the First Three Months of the Epidemic},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    number = {8},
    pages = {798},
    doi = {10.3390/v12080798},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] D. Henritzi, P. P. Petric, N. S. Lewis, A. Graaf, A. Pessia, E. Starick, A. Breithaupt, G. Strebelow, C. Luttermann, L. M. K. Parker, C. Schröder, B. Hammerschmidt, G. Herrler, E. große Beilage, D. Stadlbauer, V. Simon, F. Krammer, S. Wacheck, S. Pesch, M. Schwemmle, M. Beer, and T. C. Harder, "Surveillance of European domestic pig populations identifies an emerging reservoir of potentially zoonotic swine influenza A viruses," Cell Host Microbe, 2020.
    [Bibtex]
    @Article{Henritzi:20,
    author = {Dinah Henritzi and Philipp Peter Petric and Nicola Sarah Lewis and Annika Graaf and Alberto Pessia and Elke Starick and Angele Breithaupt and Günter Strebelow and Christine Luttermann and Larissa Mareike Kristin Parker and Charlotte Schröder and Bärbel Hammerschmidt and Georg Herrler and Elisabeth gro{\ss}e Beilage and Daniel Stadlbauer and Viviana Simon and Florian Krammer and Silke Wacheck and Stefan Pesch and Martin Schwemmle and Martin Beer and Timm Clemens Harder},
    title = {Surveillance of {E}uropean Domestic Pig Populations Identifies an Emerging Reservoir of Potentially Zoonotic Swine Influenza {A} Viruses},
    journal = {{Cell Host Microbe}},
    year = {2020},
    doi = {10.1016/j.chom.2020.07.006},
    publisher = {Elsevier {BV}},
    }
  • [DOI] P. Leonetti, P. Miesen, R. P. van Rij, and V. Pantaleo, "Viral and subviral derived small RNAs as pathogenic determinants in plants and insects," in Adv Virus Res, Elsevier, 2020, p. 1–36.
    [Bibtex]
    @InCollection{Leonetti:20,
    author = {Paola Leonetti and Pascal Miesen and Ronald P. van Rij and Vitantonio Pantaleo},
    title = {Viral and subviral derived small {RNAs} as pathogenic determinants in plants and insects},
    booktitle = {{Adv Virus Res}},
    publisher = {Elsevier},
    year = {2020},
    pages = {1--36},
    doi = {10.1016/bs.aivir.2020.04.001},
    }
  • [DOI] N. Papageorgiou, M. Spiliopoulou, T. V. Nguyen, A. Vaitsopoulou, E. Y. Laban, K. Alvarez, I. Margiolaki, B. Canard, and F. Ferron, "Brothers in arms: structure, assembly and function of Arenaviridae nucleoprotein," Viruses, vol. 12, iss. 7, p. 772, 2020.
    [Bibtex]
    @Article{Papageorgiou:20,
    author = {Nicolas Papageorgiou and Maria Spiliopoulou and Thi-Hong Van Nguyen and Afroditi Vaitsopoulou and Elsie Yekwa Laban and Karine Alvarez and Irene Margiolaki and Bruno Canard and Fran{\c{c}}ois Ferron},
    title = {Brothers in Arms: Structure, Assembly and Function of {A}renaviridae Nucleoprotein},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    number = {7},
    pages = {772},
    doi = {10.3390/v12070772},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] N. Zuckerman, R. Pando, E. Bucris, Y. Drori, Y. Lustig, O. Erster, O. Mor, E. Mendelson, and M. Mandelboim, "Comprehensive analyses of SARS-CoV-2 transmission in a public health virology laboratory," Viruses, vol. 12, iss. 8, p. 854, 2020.
    [Bibtex]
    @Article{Zuckerman:20,
    author = {Neta Zuckerman and Rakefet Pando and Efrat Bucris and Yaron Drori and Yaniv Lustig and Oran Erster and Orna Mor and Ella Mendelson and Michal Mandelboim},
    title = {Comprehensive Analyses of {SARS}-{CoV}-2 Transmission in a Public Health Virology Laboratory},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    number = {8},
    pages = {854},
    doi = {10.3390/v12080854},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] W. A. Overholt, M. Hölzer, P. Geesink, C. Diezel, M. Marz, and K. Küsel, "Inclusion of oxford nanopore long reads improves all microbial and viral metagenome-assembled genomes from a complex aquifer system," Environ Microbiol, 2020.
    [Bibtex]
    @Article{Overholt:20,
    author = {Will A. Overholt and Martin Hölzer and Patricia Geesink and Celia Diezel and Manja Marz and Kirsten Küsel},
    title = {Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome-assembled genomes from a complex aquifer system},
    journal = {{Environ Microbiol}},
    year = {2020},
    doi = {10.1111/1462-2920.15186},
    publisher = {Wiley},
    }
  • [DOI] S. Blome, K. Franzke, and M. Beer, "African swine fever – a review of current knowledge," Virus Res, vol. 287, p. 198099, 2020.
    [Bibtex]
    @Article{Blome:20,
    author = {Sandra Blome and Kati Franzke and Martin Beer},
    title = {African swine fever -- A review of current knowledge},
    journal = {{Virus Res}},
    year = {2020},
    volume = {287},
    pages = {198099},
    doi = {10.1016/j.virusres.2020.198099},
    publisher = {Elsevier {BV}},
    }
  • [DOI] N. Clementi, E. Criscuolo, R. A. Diotti, R. Ferrarese, M. Castelli, L. Dagna, R. Burioni, M. Clementi, and N. Mancini, "Combined prophylactic and therapeutic use maximizes hydroxychloroquine anti-SARS-CoV-2 effects in vitro," Front Microbiol, vol. 11, 2020.
    [Bibtex]
    @Article{Clementi:20,
    author = {Nicola Clementi and Elena Criscuolo and Roberta Antonia Diotti and Roberto Ferrarese and Matteo Castelli and Lorenzo Dagna and Roberto Burioni and Massimo Clementi and Nicasio Mancini},
    title = {Combined Prophylactic and Therapeutic Use Maximizes Hydroxychloroquine Anti-{SARS}-{CoV}-2 Effects in vitro},
    journal = {{Front Microbiol}},
    year = {2020},
    volume = {11},
    doi = {10.3389/fmicb.2020.01704},
    publisher = {Frontiers Media {SA}},
    }
  • [DOI] K. McLaughlin, M. Bechtel, D. Bojkova, C. Münch, S. Ciesek, M. N. Wass, M. Michaelis, and J. Cinatl, "COVID-19-related coagulopathy — Is transferrin a missing link?," Diagnostics, vol. 10, iss. 8, p. 539, 2020.
    [Bibtex]
    @Article{McLaughlin:20,
    author = {Katie-May McLaughlin and Marco Bechtel and Denisa Bojkova and Christian Münch and Sandra Ciesek and Mark N. Wass and Martin Michaelis and Jindrich Cinatl},
    title = {{COVID}-19-Related Coagulopathy {\textemdash} {Is} Transferrin a Missing Link?},
    journal = {Diagnostics},
    year = {2020},
    volume = {10},
    number = {8},
    pages = {539},
    doi = {10.3390/diagnostics10080539},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] C. Valle, B. Martin, F. Touret, A. Shannon, B. Canard, J. Guillemot, B. Coutard, and E. Decroly, "Drugs against SARS-CoV-2: What do we know about their mode of action?," Rev Med Virol, 2020.
    [Bibtex]
    @Article{Valle:20,
    author = {Coralie Valle and Baptiste Martin and Franck Touret and Ashleigh Shannon and Bruno Canard and Jean-Claude Guillemot and Bruno Coutard and Etienne Decroly},
    title = {Drugs against {SARS}-{CoV}-2: {What} do we know about their mode of action?},
    journal = {{Rev Med Virol}},
    year = {2020},
    doi = {10.1002/rmv.2143},
    publisher = {Wiley},
    }
  • [DOI] F. Mock, A. Viehweger, E. Barth, and M. Marz, "VIDHOP, viral host prediction with deep learning," Bioinformatics, 2020.
    [Bibtex]
    @Article{Mock:20,
    author = {Florian Mock and Adrian Viehweger and Emanuel Barth and Manja Marz},
    title = {{VIDHOP}, viral host prediction with Deep Learning},
    journal = {Bioinformatics},
    year = {2020},
    doi = {10.1093/bioinformatics/btaa705},
    editor = {Jinbo Xu},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] S. J. Lycett, A. Pohlmann, C. Staubach, V. Caliendo, M. Woolhouse, M. Beer, and T. K. and, "Genesis and spread of multiple reassortants during the 2016/2017 H5 avian influenza epidemic in Eurasia," Proc Natl Acad Sci USA, p. 202001813, 2020.
    [Bibtex]
    @Article{Lycett:20,
    author = {Samantha J. Lycett and Anne Pohlmann and Christoph Staubach and Valentina Caliendo and Mark Woolhouse and Martin Beer and Thijs Kuiken and},
    title = {Genesis and spread of multiple reassortants during the 2016/2017 {H5} avian influenza epidemic in {E}urasia},
    journal = {{Proc Natl Acad Sci USA}},
    year = {2020},
    pages = {202001813},
    doi = {10.1073/pnas.2001813117},
    publisher = {Proceedings of the National Academy of Sciences},
    }
  • [DOI] D. A. Hofmänner, P. W. D. Garcia, B. Duvnjak, B. Chakrakodi, J. D. Maier, M. Huber, J. Huder, A. Wolfensberger, P. W. Schreiber, R. A. Schüpbach, A. S. Zinkernagel, P. K. Bühler, and S. D. Brugger, "Bacterial but no SARS-CoV-2 contamination after terminal disinfection of tertiary care intensive care units treating COVID-19 patients," Research Square, 2020.
    [Bibtex]
    @Article{Hofmänner:20,
    author = {Daniel A Hofmänner and Pedro D Wendel Garcia and Branko Duvnjak and Bhavya Chakrakodi and Julian D Maier and Michael Huber and Jon Huder and Aline Wolfensberger and Peter W Schreiber and Reto A. Schüpbach and Annelies S Zinkernagel and Philipp K Bühler and Silvio D Brugger},
    title = {Bacterial but no {SARS}-{CoV}-2 contamination after terminal disinfection of tertiary care intensive care units treating {COVID}-19 patients},
    journal = {{Research Square}},
    year = {2020},
    doi = {10.21203/rs.3.rs-47872/v1},
    publisher = {Research Square},
    }
  • [DOI] M. G. Ferrarini, A. Lal, R. Rebollo, A. Gruber, A. Guarracino, I. M. Gonzalez, T. Floyd, D. S. de Oliveira, J. Shanklin, E. Beausoleil, T. Pusa, B. E. Pickett, and V. Aguiar-Pulido, "Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis," bioRxiv, 2020.
    [Bibtex]
    @Article{Ferrarini:20,
    author = {Mariana G. Ferrarini and Avantika Lal and Rita Rebollo and Andreas Gruber and Andrea Guarracino and Itziar Martinez Gonzalez and Taylor Floyd and Daniel Siqueira de Oliveira and Justin Shanklin and Ethan Beausoleil and Taneli Pusa and Brett E. Pickett and Vanessa Aguiar-Pulido},
    title = {Genome-wide bioinformatic analyses predict key host and viral factors in {SARS}-{CoV}-2 pathogenesis},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.07.28.225581},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] H. Loessner, I. Schlattmeier, M. Anders-Maurer, I. Bekeredjian-Ding, C. Rohde, J. Wittmann, C. Pokalyuk, O. Krut, and C. Kamp, "Kinetic fingerprinting links bacteria-phage interactions with emergent dynamics: rapid depletion of Klebsiella pneumoniae indicates phage synergy," Antibiotics, vol. 9, iss. 7, p. 408, 2020.
    [Bibtex]
    @Article{Loessner:20,
    author = {Holger Loessner and Insea Schlattmeier and Marie Anders-Maurer and Isabelle Bekeredjian-Ding and Christine Rohde and Johannes Wittmann and Cornelia Pokalyuk and Oleg Krut and Christel Kamp},
    title = {Kinetic Fingerprinting Links Bacteria-Phage Interactions with Emergent Dynamics: Rapid Depletion of {K}lebsiella pneumoniae Indicates Phage Synergy},
    journal = {Antibiotics},
    year = {2020},
    volume = {9},
    number = {7},
    pages = {408},
    doi = {10.3390/antibiotics9070408},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] P. M. Folegatti, K. J. Ewer, P. K. Aley, B. Angus, S. Becker, S. Belij-Rammerstorfer, D. Bellamy, S. Bibi, M. Bittaye, E. A. Clutterbuck, C. Dold, S. N. Faust, A. Finn, A. L. Flaxman, B. Hallis, P. Heath, D. Jenkin, R. Lazarus, R. Makinson, A. M. Minassian, K. M. Pollock, M. Ramasamy, H. Robinson, M. Snape, R. Tarrant, M. Voysey, C. Green, A. D. Douglas, A. V. S. Hill, T. Lambe, S. C. Gilbert, A. J. Pollard, J. Aboagye, K. Adams, A. Ali, E. Allen, J. L. Allison, R. Anslow, E. H. Arbe-Barnes, G. Babbage, K. Baillie, M. Baker, P. Baker, I. Baleanu, J. Ballaminut, E. Barnes, J. Barrett, L. Bates, A. Batten, K. Beadon, R. Beckley, E. Berrie, L. Berry, A. Beveridge, K. R. Bewley, E. M. Bijker, T. Bingham, L. Blackwell, C. L. Blundell, E. Bolam, E. Boland, N. Borthwick, T. Bower, A. Boyd, T. Brenner, P. D. Bright, C. B. textquotesingle, E. Brunt, J. Burbage, S. Burge, K. R. Buttigieg, N. Byard, I. C. Puig, A. Calvert, S. Camara, M. Cao, F. Cappuccini, M. Carr, M. W. Carroll, V. Carter, K. Cathie, R. J. Challis, I. Chelysheva, J. Cho, P. Cicconi, L. Cifuentes, H. Clark, E. Clark, T. Cole, R. Colin-Jones, C. P. Conlon, A. Cook, N. S. Coombes, R. Cooper, C. A. Cosgrove, K. Coy, W. E. M. Crocker, C. J. Cunningham, B. E. Damratoski, L. Dando, M. S. Datoo, H. Davies, H. D. Graaf, T. Demissie, C. D. Maso, I. Dietrich, T. Dong, F. R. Donnellan, N. Douglas, C. Downing, J. Drake, R. Drake-Brockman, R. E. Drury, S. J. Dunachie, N. J. Edwards, F. D. L. Edwards, C. J. Edwards, S. C. Elias, M. J. Elmore, K. R. W. Emary, M. R. English, S. Fagerbrink, S. Felle, S. Feng, S. Field, C. Fixmer, C. Fletcher, K. J. Ford, J. Fowler, P. Fox, E. Francis, J. Frater, J. Furze, M. Fuskova, E. Galiza, D. Gbesemete, C. Gilbride, G. Gorini, L. Goulston, C. Grabau, L. Gracie, Z. Gray, L. B. Guthrie, M. Hackett, S. Halwe, E. Hamilton, J. Hamlyn, B. Hanumunthadu, I. Harding, S. A. Harris, A. Harris, D. Harrison, C. Harrison, T. C. Hart, L. Haskell, S. Hawkins, I. Head, J. A. Henry, J. Hill, S. H. C. Hodgson, M. M. Hou, E. Howe, N. Howell, C. Hutlin, S. Ikram, C. Isitt, P. Iveson, S. Jackson, F. Jackson, S. W. James, M. Jenkins, E. Jones, K. Jones, C. E. Jones, B. Jones, R. Kailath, K. Karampatsas, J. Keen, S. Kelly, D. Kelly, D. Kerr, S. Kerridge, L. Khan, U. Khan, A. Killen, J. Kinch, T. B. King, L. King, J. King, L. Kingham-Page, P. Klenerman, F. Knapper, J. C. Knight, S. Koleva, A. Kupke, C. W. Larkworthy, J. P. J. Larwood, A. Laskey, A. M. Lawrie, A. Lee, K. Y. N. Lee, E. A. Lee, H. Legge, A. Lelliott, N. Lemm, A. M. Lias, A. Linder, S. Lipworth, X. Liu, S. Liu, R. L. Ramon, M. Lwin, F. Mabesa, M. Madhavan, G. Mallett, K. Mansatta, I. e}, S. Marinou, E. Marlow, J. L. Marshall, J. Martin, J. McEwan, G. Meddaugh, A. J. Mentzer, N. Mirtorabi, M. Moore, E. Moran, E. Morey, V. Morgan, S. J. Morris, H. Morrison, G. Morshead, R. Morter, Y. F. Mujadidi, J. Muller, T. Munera-Huertas, C. Munro, A. Munro, S. Murphy, V. J. Muster, P. Mweu, A. Noé, F. L. Nugent, E. Nugent, K. O. textquotesingle, D. O. textquotesingle, B. Oguti, J. L. Oliver, C. Oliveira, P. J. O. textquotesingle, M. Osborn, P. Osborne, C. Owen, D. Owens, N. Owino, M. Pacurar, K. Parker, H. Parracho, M. Patrick-Smith, V. Payne, J. Pearce, Y. Peng, M. P. P. Alvarez, J. Perring, K. Pfafferott, D. Pipini, E. Plested, H. Pluess-Hall, K. Pollock, I. Poulton, L. Presland, S. Provstgaard-Morys, D. Pulido, K. Radia, F. R. Lopez, J. Rand, H. Ratcliffe, T. Rawlinson, S. Rhead, A. Riddell, A. J. Ritchie, H. Roberts, J. Robson, S. Roche, C. Rohde, C. S. Rollier, R. Romani, I. Rudiansyah, S. Saich, S. Sajjad, S. Salvador, L. S. Riera, H. Sanders, K. Sanders, S. Sapaun, C. Sayce, E. Schofield, G. Screaton, B. Selby, C. Semple, H. R. Sharpe, A. Shea, H. Shelton, S. Silk, L. Silva-Reyes, D. T. Skelly, H. Smee, C. C. Smith, D. J. Smith, R. Song, A. J. Spencer, E. Stafford, A. Steele, E. Stefanova, L. Stockdale, A. Szigeti, A. Tahiri-Alaoui, M. Tait, H. Talbot, R. Tanner, I. J. Taylor, V. Taylor, R. T. W. Naude, N. Thakur, Y. Themistocleous, A. Themistocleous, M. Thomas, T. M. Thomas, A. Thompson, S. Thomson-Hill, J. Tomlins, S. Tonks, J. Towner, N. Tran, J. A. Tree, A. Truby, K. Turkentine, C. Turner, N. Turner, S. Turner, T. Tuthill, M. Ulaszewska, R. Varughese, N. V. Doremalen, K. Veighey, M. K. Verheul, I. Vichos, E. Vitale, L. Walker, M. E. E. Watson, B. Welham, J. Wheat, C. White, R. White, A. T. Worth, D. Wright, S. Wright, X. L. Yao, and Y. Yau, "Safety and immunogenicity of the ChAdOx1 nCoV-19 vaccine against SARS-CoV-2: a preliminary report of a phase 1/2, single-blind, randomised controlled trial," Lancet, 2020.
    [Bibtex]
    @Article{Folegatti:20a,
    author = {Pedro M Folegatti and Katie J Ewer and Parvinder K Aley and Brian Angus and Stephan Becker and Sandra Belij-Rammerstorfer and Duncan Bellamy and Sagida Bibi and Mustapha Bittaye and Elizabeth A Clutterbuck and Christina Dold and Saul N Faust and Adam Finn and Amy L Flaxman and Bassam Hallis and Paul Heath and Daniel Jenkin and Rajeka Lazarus and Rebecca Makinson and Angela M Minassian and Katrina M Pollock and Maheshi Ramasamy and Hannah Robinson and Matthew Snape and Richard Tarrant and Merryn Voysey and Catherine Green and Alexander D Douglas and Adrian V S Hill and Teresa Lambe and Sarah C Gilbert and Andrew J Pollard and Jeremy Aboagye and Kelly Adams and Aabidah Ali and Elizabeth Allen and Jennifer L. Allison and Rachel Anslow and Edward H. Arbe-Barnes and Gavin Babbage and Kenneth Baillie and Megan Baker and Philip Baker and Ioana Baleanu and Juliana Ballaminut and Eleanor Barnes and Jordan Barrett and Louise Bates and Alexander Batten and Kirsten Beadon and Rebecca Beckley and Eleanor Berrie and Lisa Berry and Amy Beveridge and Kevin R. Bewley and Else Margreet Bijker and Tracey Bingham and Luke Blackwell and Caitlin L. Blundell and Emma Bolam and Elena Boland and Nicola Borthwick and Thomas Bower and Amy Boyd and Tanja Brenner and Philip D. Bright and Charlie Brown-O{\textquotesingle}Sullivan and Emily Brunt and Jamie Burbage and Sharon Burge and Karen R. Buttigieg and Nicholas Byard and Ingrid Cabera Puig and Anna Calvert and Susana Camara and Michelangelo Cao and Federica Cappuccini and Melanie Carr and Miles W. Carroll and Victoria Carter and Katrina Cathie and Ruth J. Challis and Irina Chelysheva and Jee-Sun Cho and Paola Cicconi and Liliana Cifuentes and Helen Clark and Elizabeth Clark and Tom Cole and Rachel Colin-Jones and Christopher P. Conlon and Aislinn Cook and Naomi S. Coombes and Rachel Cooper and Catherine A. Cosgrove and Karen Coy and Wendy E.M. Crocker and Christina J. Cunningham and Brad E. Damratoski and Lynne Dando and Mehreen S. Datoo and Hannah Davies and Hans De Graaf and Tesfaye Demissie and Claudio Di Maso and Isabelle Dietrich and Tao Dong and Francesca R. Donnellan and Naomi Douglas and Charlotte Downing and Jonathan Drake and Rachael Drake-Brockman and Ruth Elizabeth Drury and Susanna Jane Dunachie and Nick J. Edwards and Frances D.L. Edwards and Chris J. Edwards and Sean C. Elias and Michael J. Elmore and Katherine R.W. Emary and Marcus Rex English and Susanne Fagerbrink and Sally Felle and Shuo Feng and Samantha Field and Carine Fixmer and Clare Fletcher and Karen J. Ford and Jamie Fowler and Polly Fox and Emma Francis and John Frater and Julie Furze and Michelle Fuskova and Eva Galiza and Diane Gbesemete and Ciaran Gilbride and Giacomo Gorini and Lyndsey Goulston and Caroline Grabau and Lara Gracie and Zoe Gray and Lucy Belle Guthrie and Mark Hackett and Sandro Halwe and Elizabeth Hamilton and Joseph Hamlyn and Brama Hanumunthadu and Irasha Harding and Stephanie A. Harris and Andrew Harris and Daisy Harrison and Clare Harrison and Thomas C. Hart and Louise Haskell and Sophia Hawkins and Ian Head and John Aaron Henry and Jennifer Hill and Susanne H.C. Hodgson and Mimi M. Hou and Elizabeth Howe and Nicola Howell and Cecilia Hutlin and Sabina Ikram and Catherine Isitt and Poppy Iveson and Susan Jackson and Frederic Jackson and Sir William James and Megan Jenkins and Elizabeth Jones and Kathryn Jones and Christine E. Jones and Bryony Jones and Reshma Kailath and Konstantinos Karampatsas and Jade Keen and Sarah Kelly and Dearbhla Kelly and David Kerr and Simon Kerridge and Liaquat Khan and Uzma Khan and Annabel Killen and Jasmin Kinch and Thomas B. King and Lloyd King and Jade King and Lucy Kingham-Page and Paul Klenerman and Francesca Knapper and Julian C. Knight and Stanislava Koleva and Alexandra Kupke and Colin W. Larkworthy and Jessica P.J. Larwood and Anna Laskey and Alison M. Lawrie and Arlene Lee and Kim Yee Ngan Lee and Emily A. Lee and Helen Legge and Alice Lelliott and Nana-Marie Lemm and Amelia M. Lias and Aline Linder and Samuel Lipworth and Xinxue Liu and Shuchang Liu and Raquel Lopez Ramon and May Lwin and Francesca Mabesa and Meera Madhavan and Gary Mallett and Kushal Mansatta and In{\={e}}s Marcal and Spyridoula Marinou and Emma Marlow and Julia L. Marshall and Jane Martin and Joanne McEwan and Gretchen Meddaugh and Alexander J. Mentzer and Neginsadat Mirtorabi and Maria Moore and Edward Moran and Ella Morey and Victoria Morgan and Susan Jane Morris and Hazel Morrison and Gertraud Morshead and Richard Morter and Yama F. Mujadidi and Jilly Muller and Tatiana Munera-Huertas and Claire Munro and Alasdair Munro and Sarah Murphy and Vincent J. Muster and Philomena Mweu and Andr{\'{e}}s No{\'{e}} and Fay L. Nugent and Elizabeth Nugent and Katie O{\textquotesingle}Brien and Daniel O{\textquotesingle}Connor and Blanch{\'{e}} Oguti and Jennifer L. Oliver and Catarina Oliveira and Peter John O{\textquotesingle}Reilly and Mairead Osborn and Piper Osborne and Cathy Owen and Daniel Owens and Nelly Owino and Mihaela Pacurar and Kaye Parker and Helena Parracho and Maia Patrick-Smith and Victoria Payne and Jennifer Pearce and Yanchun Peng and Marco Polo Peralta Alvarez and James Perring and Katja Pfafferott and Dimitra Pipini and Emma Plested and Helen Pluess-Hall and Katrina Pollock and Ian Poulton and Laura Presland and Samuel Provstgaard-Morys and David Pulido and Kajal Radia and Fernando Ramos Lopez and Jade Rand and Helen Ratcliffe and Thomas Rawlinson and Sarah Rhead and Amy Riddell and Adam John Ritchie and Hannah Roberts and Joanna Robson and Sophie Roche and Cornelius Rohde and Christine S. Rollier and Rosanna Romani and Indra Rudiansyah and Stephen Saich and Sara Sajjad and Stephannie Salvador and Lidia Sanchez Riera and Helen Sanders and Katherine Sanders and Shari Sapaun and Chloe Sayce and Ella Schofield and Gavin Screaton and Beatrice Selby and Calum Semple and Hannah R. Sharpe and Adam Shea and Holly Shelton and Sarah Silk and Laura Silva-Reyes and Donal T. Skelly and Heather Smee and Catherine C. Smith and David J. Smith and Rinn Song and Alexandra J. Spencer and Elizabeth Stafford and Amy Steele and Elena Stefanova and Lisa Stockdale and Anna Szigeti and Abdessamad Tahiri-Alaoui and Moira Tait and Helen Talbot and Rachel Tanner and Iona Jennifer Taylor and Victoria Taylor and Rebecca Te Water Naude and Nazia Thakur and Yrene Themistocleous and Andreas Themistocleous and Merin Thomas and Tonia M. Thomas and Amber Thompson and Samantha Thomson-Hill and Jennifer Tomlins and Susan Tonks and James Towner and Nguyen Tran and Julia A. Tree and Adam Truby and Kate Turkentine and Cheryl Turner and Nicola Turner and Sally Turner and Toby Tuthill and Marta Ulaszewska and Rachel Varughese and Neeltje Van Doremalen and Kristin Veighey and Marije K. Verheul and Iason Vichos and Elia Vitale and Laura Walker and Marion E.E. Watson and Benjamin Welham and Julie Wheat and Caroline White and Rachel White and Andrew T. Worth and Danny Wright and Suzie Wright and Xin Li Yao and Yasmine Yau},
    title = {Safety and immunogenicity of the {ChAdOx}1 {nCoV}-19 vaccine against {SARS}-{CoV}-2: a preliminary report of a phase 1/2, single-blind, randomised controlled trial},
    journal = {Lancet},
    year = {2020},
    doi = {10.1016/s0140-6736(20)31604-4},
    publisher = {Elsevier {BV}},
    }
  • [DOI] N. Osterrieder, L. D. Bertzbach, K. Dietert, A. Abdelgawad, D. Vladimirova, D. Kunec, D. Hoffmann, M. Beer, A. D. Gruber, and J. Trimpert, "Age-dependent progression of SARS-CoV-2 infection in Syrian hamsters," Viruses, vol. 12, iss. 7, p. 779, 2020.
    [Bibtex]
    @Article{Osterrieder:20,
    author = {Nikolaus Osterrieder and Luca D. Bertzbach and Kristina Dietert and Azza Abdelgawad and Daria Vladimirova and Dusan Kunec and Donata Hoffmann and Martin Beer and Achim D. Gruber and Jakob Trimpert},
    title = {Age-Dependent Progression of {SARS}-{CoV}-2 Infection in {S}yrian Hamsters},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    number = {7},
    pages = {779},
    doi = {10.3390/v12070779},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] M. Hoffmann, K. Mösbauer, H. Hofmann-Winkler, A. Kaul, H. Kleine-Weber, N. Krüger, N. C. Gassen, M. A. Müller, C. Drosten, and S. Pöhlmann, "Chloroquine does not inhibit infection of human lung cells with SARS-CoV-2," Nature, 2020.
    [Bibtex]
    @Article{Hoffmann:20d,
    author = {Markus Hoffmann and Kirstin Mösbauer and Heike Hofmann-Winkler and Artur Kaul and Hannah Kleine-Weber and Nadine Krüger and Nils C. Gassen and Marcel A. Müller and Christian Drosten and Stefan Pöhlmann},
    title = {Chloroquine does not inhibit infection of human lung cells with {SARS}-{CoV}-2},
    journal = {Nature},
    year = {2020},
    doi = {10.1038/s41586-020-2575-3},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] A. A. Fisher, X. Ji, Z. Zhang, P. Lemey, and M. A. Suchard, "Relaxed random walks at scale," Syst Biol, 2020.
    [Bibtex]
    @Article{Fisher:20,
    author = {Alexander A Fisher and Xiang Ji and Zhenyu Zhang and Philippe Lemey and Marc A Suchard},
    title = {Relaxed Random Walks at Scale},
    journal = {{Syst Biol}},
    year = {2020},
    doi = {10.1093/sysbio/syaa056},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] M. Marquet, M. Hölzer, M. W. Pletz, A. Viehweger, O. Makarewicz, R. Ehricht, and C. Brandt, "What the Phage: a scalable workflow for the identification and analysis of phage sequences," bioRxiv, 2020.
    [Bibtex]
    @Article{Marquet:20,
    author = {Mike Marquet and Martin Hölzer and Mathias W. Pletz and Adrian Viehweger and Oliwia Makarewicz and Ralf Ehricht and Christian Brandt},
    title = {What the {P}hage: A scalable workflow for the identification and analysis of phage sequences},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.07.24.219899},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] D. Bonn, S. H. Smith, A. Somsen, C. van Rijn, S. Kooij, L. van der Hoek, and R. A. Bem, "Probability of aerosol transmission of SARS-CoV-2," medRxiv, 2020.
    [Bibtex]
    @Article{Bonn:20,
    author = {Daniel Bonn and Scott Howard Smith and Aernout Somsen and Cees van Rijn and Stefan Kooij and Lia van der Hoek and Reinout A Bem},
    title = {Probability of aerosol transmission of {SARS}-{CoV}-2},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.07.16.20155572},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] F. Zettl, T. L. Meister, T. Vollmer, B. Fischer, J. Steinmann, A. Krawczyk, P. V'kovski, D. Todt, E. Steinmann, S. Pfaender, and G. Zimmer, "Rapid quantification of SARS-CoV-2-neutralizing antibodies using propagation-defective vesicular stomatitis virus pseudotypes," Vaccines, vol. 8, iss. 3, p. 386, 2020.
    [Bibtex]
    @Article{Zettl:20,
    author = {Ferdinand Zettl and Toni Luise Meister and Tanja Vollmer and Bastian Fischer and Jörg Steinmann and Adalbert Krawczyk and Philip V'kovski and Daniel Todt and Eike Steinmann and Stephanie Pfaender and Gert Zimmer},
    title = {Rapid Quantification of {SARS}-{CoV}-2-Neutralizing Antibodies Using Propagation-Defective Vesicular Stomatitis Virus Pseudotypes},
    journal = {Vaccines},
    year = {2020},
    volume = {8},
    number = {3},
    pages = {386},
    doi = {10.3390/vaccines8030386},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] B. B. Oude Munnink, D. F. Nieuwenhuijse, M. Stein, Á. O'Toole, M. Haverkate, M. Mollers, S. K. Kamga, C. Schapendonk, M. Pronk, P. Lexmond, A. van der Linden, T. Bestebroer, I. Chestakova, R. J. Overmars, S. van Nieuwkoop, R. Molenkamp, A. A. van der Eijk, C. GeurtsvanKessel, H. Vennema, A. Meijer, A. Rambaut, J. van Dissel, R. S. Sikkema, A. Timen, and M. Koopmans, "Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands," Nat Med, 2020.
    [Bibtex]
    @Article{OudeMunnink:20,
    author = {Bas B. {Oude Munnink} and David F. Nieuwenhuijse and Mart Stein and {\'{A}}ine O'Toole and Manon Haverkate and Madelief Mollers and Sandra K. Kamga and Claudia Schapendonk and Mark Pronk and Pascal Lexmond and Anne van der Linden and Theo Bestebroer and Irina Chestakova and Ronald J. Overmars and Stefan van Nieuwkoop and Richard Molenkamp and Annemiek A. van der Eijk and Corine GeurtsvanKessel and Harry Vennema and Adam Meijer and Andrew Rambaut and Jaap van Dissel and Reina S. Sikkema and Aura Timen and Marion Koopmans},
    title = {Rapid {SARS}-{CoV}-2 whole-genome sequencing and analysis for informed public health decision-making in the {N}etherlands},
    journal = {{Nat Med}},
    year = {2020},
    doi = {10.1038/s41591-020-0997-y},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] C. Kreer, M. Zehner, T. Weber, M. S. Ercanoglu, L. Gieselmann, C. Rohde, S. Halwe, M. Korenkov, P. Schommers, K. Vanshylla, V. D. Cristanziano, H. Janicki, R. Brinker, A. Ashurov, V. Krähling, A. Kupke, H. Cohen-Dvashi, M. Koch, J. M. Eckert, S. Lederer, N. Pfeifer, T. Wolf, M. J. G. T. Vehreschild, C. Wendtner, R. Diskin, H. Gruell, S. Becker, and F. Klein, "Longitudinal isolation of potent near-germline SARS-CoV-2-neutralizing antibodies from COVID-19 patients," Cell, 2020.
    [Bibtex]
    @Article{Kreer:20a,
    author = {Christoph Kreer and Matthias Zehner and Timm Weber and Meryem S. Ercanoglu and Lutz Gieselmann and Cornelius Rohde and Sandro Halwe and Michael Korenkov and Philipp Schommers and Kanika Vanshylla and Veronica Di Cristanziano and Hanna Janicki and Reinhild Brinker and Artem Ashurov and Verena Krähling and Alexandra Kupke and Hadas Cohen-Dvashi and Manuel Koch and Jan Mathis Eckert and Simone Lederer and Nico Pfeifer and Timo Wolf and Maria J.G.T. Vehreschild and Clemens Wendtner and Ron Diskin and Henning Gruell and Stephan Becker and Florian Klein},
    title = {Longitudinal Isolation of Potent Near-Germline {SARS}-{CoV}-2-Neutralizing Antibodies from {COVID}-19 Patients},
    journal = {Cell},
    year = {2020},
    doi = {10.1016/j.cell.2020.06.044},
    publisher = {Elsevier {BV}},
    }
  • [DOI] V. Matheeussen, V. M. Corman, O. D. Mantke, E. McCulloch, C. Lammens, H. Goossens, D. Niemeyer, P. S. Wallace, P. Klapper, H. G. Niesters, C. Drosten, and M. I. and, "International external quality assessment for SARS-CoV-2 molecular detection and survey on clinical laboratory preparedness during the COVID-19 pandemic, April/May 2020," Euro Surveill, vol. 25, iss. 27, 2020.
    [Bibtex]
    @Article{Matheeussen:20,
    author = {Veerle Matheeussen and Victor M Corman and Oliver Donoso Mantke and Elaine McCulloch and Christine Lammens and Herman Goossens and Daniela Niemeyer and Paul S Wallace and Paul Klapper and Hubert GM Niesters and Christian Drosten and Margareta Ieven and},
    title = {International external quality assessment for {SARS}-{CoV}-2 molecular detection and survey on clinical laboratory preparedness during the {COVID}-19 pandemic, {A}pril/{M}ay 2020},
    journal = {{Euro Surveill}},
    year = {2020},
    volume = {25},
    number = {27},
    doi = {10.2807/1560-7917.es.2020.25.27.2001223},
    publisher = {European Centre for Disease Control and Prevention ({ECDC})},
    }
  • [DOI] A. E. Firth, "A putative new SARS-CoV protein, 3c, encoded in an ORF overlapping ORF3a," J Gen Virol, 2020.
    [Bibtex]
    @Article{Firth:20,
    author = {Andrew E. Firth},
    title = {A putative new {SARS}-{CoV} protein, 3c, encoded in an {ORF} overlapping {ORF}3a},
    journal = {{J Gen Virol}},
    year = {2020},
    doi = {10.1099/jgv.0.001469},
    publisher = {Microbiology Society},
    }
  • [DOI] V. Caputo, R. A. Diotti, E. Boeri, H. Hasson, M. Sampaolo, E. Criscuolo, S. Bagaglio, E. Messina, C. Uberti-Foppa, M. Castelli, R. Burioni, N. Mancini, M. Clementi, and N. Clementi, "Detection of low-level HCV variants in DAA treated patients: comparison amongst three different NGS data analysis protocols," Virol J, vol. 17, iss. 1, 2020.
    [Bibtex]
    @Article{Caputo:20,
    author = {Valeria Caputo and Roberta Antonia Diotti and Enzo Boeri and Hamid Hasson and Michela Sampaolo and Elena Criscuolo and Sabrina Bagaglio and Emanuela Messina and Caterina Uberti-Foppa and Matteo Castelli and Roberto Burioni and Nicasio Mancini and Massimo Clementi and Nicola Clementi},
    title = {Detection of low-level {HCV} variants in {DAA} treated patients: comparison amongst three different {NGS} data analysis protocols},
    journal = {{Virol J}},
    year = {2020},
    volume = {17},
    number = {1},
    doi = {10.1186/s12985-020-01381-3},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] D. D. Pollock, T. A. Castoe, B. W. Perry, S. Lytras, K. J. Wade, D. L. Robertson, E. C. Holmes, M. F. Boni, S. K. L. Pond, R. Parry, E. J. Carlton, J. L. N. Wood, P. S. Pennings, and R. A. Goldstein, "Viral CpG deficiency provides no evidence that dogs were intermediate hosts for SARS-CoV-2," Mol Biol Evol, 2020.
    [Bibtex]
    @Article{Pollock:20,
    author = {David D Pollock and Todd A Castoe and Blair W Perry and Spyros Lytras and Kristen J Wade and David L Robertson and Edward C Holmes and Maciej F Boni and Sergei L Kosakovsky Pond and Rhys Parry and Elizabeth J Carlton and James L N Wood and Pleuni S Pennings and Richard A Goldstein},
    title = {Viral {CpG} deficiency provides no evidence that dogs were intermediate hosts for {SARS}-{CoV}-2},
    journal = {{Mol Biol Evol}},
    year = {2020},
    doi = {10.1093/molbev/msaa178},
    editor = {Thomas Leitner},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] Y. Suzuki, A. Baidaliuk, P. Miesen, L. Frangeul, A. B. Crist, S. H. Merkling, A. Fontaine, S. Lequime, I. Moltini-Conclois, H. Blanc, R. P. van Rij, L. Lambrechts, and M. Saleh, "Non-retroviral endogenous viral element limits cognate virus replication in Aedes aegypti ovaries," Curr Biol, 2020.
    [Bibtex]
    @Article{Suzuki:20,
    author = {Yasutsugu Suzuki and Artem Baidaliuk and Pascal Miesen and Lionel Frangeul and Anna B. Crist and Sarah H. Merkling and Albin Fontaine and Sebastian Lequime and Isabelle Moltini-Conclois and Herv{\'{e}} Blanc and Ronald P. van Rij and Louis Lambrechts and Maria-Carla Saleh},
    title = {Non-retroviral Endogenous Viral Element Limits Cognate Virus Replication in {Aedes} aegypti Ovaries},
    journal = {{Curr Biol}},
    year = {2020},
    doi = {10.1016/j.cub.2020.06.057},
    publisher = {Elsevier {BV}},
    }
  • [DOI] V. C. Piro, T. H. Dadi, E. Seiler, K. Reinert, and B. Y. Renard, "ganon: precise metagenomics classification against large and up-to-date sets of reference sequences," Bioinformatics, vol. 36, iss. Supplement_1, p. i12–i20, 2020.
    [Bibtex]
    @Article{Piro:20,
    author = {Vitor C Piro and Temesgen H Dadi and Enrico Seiler and Knut Reinert and Bernhard Y Renard},
    title = {{ganon}: precise metagenomics classification against large and up-to-date sets of reference sequences},
    journal = {Bioinformatics},
    year = {2020},
    volume = {36},
    number = {Supplement\_1},
    pages = {i12--i20},
    doi = {10.1093/bioinformatics/btaa458},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] C. Wylezich, S. Calvelage, K. Schlottau, U. Ziegler, A. Pohlmann, D. Höper, and M. Beer, "Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including SARS-CoV-2," bioRxiv, 2020.
    [Bibtex]
    @Article{Wylezich:20,
    author = {Claudia Wylezich and Sten Calvelage and Kore Schlottau and Ute Ziegler and Anne Pohlmann and Dirk Höper and Martin Beer},
    title = {Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including {SARS}-{CoV}-2},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.06.30.181446},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. Foglierini, L. Pappas, A. Lanzavecchia, D. Corti, and L. Perez, "AncesTree: an interactive immunoglobulin lineage tree visualizer," PLoS Comput Biol, vol. 16, iss. 7, p. e1007731, 2020.
    [Bibtex]
    @Article{Foglierini:20,
    author = {Mathilde Foglierini and Leontios Pappas and Antonio Lanzavecchia and Davide Corti and Laurent Perez},
    title = {{AncesTree}: An interactive immunoglobulin lineage tree visualizer},
    journal = {{PLoS Comput Biol}},
    year = {2020},
    volume = {16},
    number = {7},
    pages = {e1007731},
    doi = {10.1371/journal.pcbi.1007731},
    editor = {Mihaela Pertea},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] M. K. Mirzaei, J. Xue, R. Costa, J. Ru, S. Schulz, Z. E. Taranu, and L. Deng, "Challenges of studying the human virome – relevant emerging technologies," Trends Microbiol, 2020.
    [Bibtex]
    @Article{Mirzaei:20a,
    author = {Mohammadali Khan Mirzaei and Jinling Xue and Rita Costa and Jinlong Ru and Sarah Schulz and Zofia E. Taranu and Li Deng},
    title = {Challenges of Studying the Human Virome {\textendash} Relevant Emerging Technologies},
    journal = {{Trends Microbiol}},
    year = {2020},
    doi = {10.1016/j.tim.2020.05.021},
    publisher = {Elsevier {BV}},
    }
  • [DOI] R. S. Sikkema, S. D. Pas, D. F. Nieuwenhuijse, Á. O'Toole, J. Verweij, A. van der Linden, I. Chestakova, C. Schapendonk, M. Pronk, P. Lexmond, T. Bestebroer, R. J. Overmars, S. van Nieuwkoop, W. van den Bijllaardt, R. G. Bentvelsen, M. M. L. van Rijen, A. G. M. Buiting, A. J. G. van Oudheusden, B. M. Diederen, A. M. C. Bergmans, A. van der Eijk, R. Molenkamp, A. Rambaut, A. Timen, J. A. J. W. Kluytmans, B. B. Oude Munnink, M. K. F. Q. van den Bergh, and M. P. G. Koopmans, "COVID-19 in health-care workers in three hospitals in the south of the Netherlands: a cross-sectional study," Lancet Infect Dis, 2020.
    [Bibtex]
    @Article{Sikkema:20,
    author = {Reina S Sikkema and Suzan D Pas and David F Nieuwenhuijse and {\'{A}}ine O'Toole and Jaco Verweij and Anne van der Linden and Irina Chestakova and Claudia Schapendonk and Mark Pronk and Pascal Lexmond and Theo Bestebroer and Ronald J Overmars and Stefan van Nieuwkoop and Wouter van den Bijllaardt and Robbert G Bentvelsen and Miranda M L van Rijen and Anton G M Buiting and Anne J G van Oudheusden and Bram M Diederen and Anneke M C Bergmans and Annemiek van der Eijk and Richard Molenkamp and Andrew Rambaut and Aura Timen and Jan A J W Kluytmans and Bas B {Oude Munnink} and Marjolein F Q Kluytmans van den Bergh and Marion P G Koopmans},
    title = {{COVID}-19 in health-care workers in three hospitals in the south of the {N}etherlands: a cross-sectional study},
    journal = {{Lancet Infect Dis}},
    year = {2020},
    doi = {10.1016/s1473-3099(20)30527-2},
    publisher = {Elsevier {BV}},
    }
  • [DOI] M. Panning, J. and Wiener, K. Rothe, J. Schneider, M. W. Pletz, G. Rohde, J. Rupp, M. Witzenrath, and C. D. Spinner, "No SARS-CoV-2 detection in the german CAPNETZ cohort of community acquired pneumonia before COVID-19 peak in March 2020," Infection, 2020.
    [Bibtex]
    @Article{Panning:20,
    author = {Marcus Panning and and Julius Wiener and Kathrin Rothe and Jochen Schneider and Mathias W. Pletz and Gernot Rohde and Jan Rupp and Martin Witzenrath and Christoph D. Spinner},
    title = {No {SARS}-{CoV}-2 detection in the German {CAPNETZ} cohort of community acquired pneumonia before {COVID}-19 peak in {M}arch 2020},
    journal = {Infection},
    year = {2020},
    doi = {10.1007/s15010-020-01471-y},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] C. B. Messner, V. Demichev, D. Wendisch, L. Michalick, M. White, A. Freiwald, K. Textoris-Taube, S. I. Vernardis, A. Egger, M. Kreidl, D. Ludwig, C. Kilian, F. Agostini, A. Zelezniak, C. Thibeault, M. Pfeiffer, S. Hippenstiel, A. Hocke, C. von Kalle, A. Campbell, C. Hayward, D. J. Porteous, R. E. Marioni, C. Langenberg, K. S. Lilley, W. M. Kuebler, M. Mülleder, C. Drosten, N. Suttorp, M. Witzenrath, F. Kurth, L. E. Sander, and M. Ralser, "Ultra-high-throughput clinical proteomics reveals classifiers of COVID-19 infection," Cell Syst, 2020.
    [Bibtex]
    @Article{Messner:20,
    author = {Christoph B. Messner and Vadim Demichev and Daniel Wendisch and Laura Michalick and Matthew White and Anja Freiwald and Kathrin Textoris-Taube and Spyros I. Vernardis and Anna-Sophia Egger and Marco Kreidl and Daniela Ludwig and Christiane Kilian and Federica Agostini and Aleksej Zelezniak and Charlotte Thibeault and Moritz Pfeiffer and Stefan Hippenstiel and Andreas Hocke and Christof von Kalle and Archie Campbell and Caroline Hayward and David J. Porteous and Riccardo E. Marioni and Claudia Langenberg and Kathryn S. Lilley and Wolfgang M. Kuebler and Michael Mülleder and Christian Drosten and Norbert Suttorp and Martin Witzenrath and Florian Kurth and Leif Erik Sander and Markus Ralser},
    title = {Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of {COVID}-19 Infection},
    journal = {{Cell Syst}},
    year = {2020},
    doi = {10.1016/j.cels.2020.05.012},
    publisher = {Elsevier {BV}},
    }
  • [DOI] D. L. Bugembe, J. Kayiwa, M. V. T. Phan, P. Tushabe, S. Balinandi, B. Dhaala, J. Lexow, H. Mwebesa, J. Aceng, H. Kyobe, D. Ssemwanga, J. Lutwama, P. Kaleebu, and M. Cotten, "Main routes of entry and genomic diversity of SARS-CoV-2, Uganda," Emerg Infect Dis, vol. 26, iss. 10, 2020.
    [Bibtex]
    @Article{Bugembe:20,
    author = {Daniel Lule Bugembe and John Kayiwa and My V.T. Phan and Phiona Tushabe and Stephen Balinandi and Beatrice Dhaala and Jonas Lexow and Henry Mwebesa and Jane Aceng and Henry Kyobe and Deogratius Ssemwanga and Julius Lutwama and Pontiano Kaleebu and Matthew Cotten},
    title = {Main Routes of Entry and Genomic Diversity of {SARS}-{CoV}-2, {U}ganda},
    journal = {{Emerg Infect Dis}},
    year = {2020},
    volume = {26},
    number = {10},
    doi = {10.3201/eid2610.202575},
    publisher = {Centers for Disease Control and Prevention ({CDC})},
    }
  • [DOI] M. Beer, M. Doherr, K. Osterrieder, D. Pfeiffer, and J. Trimpert, "SARS-CoV-2 vaccination—a plea for fast and coordinated action," Zoonoses Public Health, 2020.
    [Bibtex]
    @Article{Beer:20,
    author = {Martin Beer and Marcus Doherr and Klaus Osterrieder and Dirk Pfeiffer and Jakob Trimpert},
    title = {{SARS}-{CoV}-2 vaccination{\textemdash}A plea for fast and coordinated action},
    journal = {{Zoonoses Public Health}},
    year = {2020},
    doi = {10.1111/zph.12740},
    publisher = {Wiley},
    }
  • [DOI] N. Clementi, R. Ferrarese, M. Tonelli, V. Amato, S. Racca, M. Locatelli, G. Lippi, G. Silvestri, M. Clementi, and N. Mancini, "Lower nasopharyngeal viral load during the latest phase of COVID-19 pandemic in a Northern Italy University Hospital," Clin Chem Lab Med, 2020.
    [Bibtex]
    @Article{Clementi:20b,
    author = {Nicola Clementi and Roberto Ferrarese and Marco Tonelli and Virginia Amato and Sara Racca and Massimo Locatelli and Giuseppe Lippi and Guido Silvestri and Massimo Clementi and Nicasio Mancini},
    title = {Lower nasopharyngeal viral load during the latest phase of {COVID}-19 pandemic in a {N}orthern {I}taly {U}niversity {H}ospital},
    journal = {{Clin Chem Lab Med}},
    year = {2020},
    volume = {0},
    number = {0},
    doi = {10.1515/cclm-2020-0815},
    publisher = {Walter de Gruyter {GmbH}},
    }
  • [DOI] U. Felgenhauer, A. Schoen, H. H. Gad, R. Hartmann, A. R. Schaubmar, K. Failing, C. Drosten, and F. Weber, "Inhibition of SARS-CoV-2 by type I and type III interferons," J Biol Chem, p. jbc.AC120.013788, 2020.
    [Bibtex]
    @Article{Felgenhauer:20,
    author = {Ulrike Felgenhauer and Andreas Schoen and Hans Henrik Gad and Rune Hartmann and Andreas R Schaubmar and Klaus Failing and Christian Drosten and Friedemann Weber},
    title = {Inhibition of {SARS}-{CoV}-2 by type {I} and type {III} interferons},
    journal = {{J Biol Chem}},
    year = {2020},
    pages = {jbc.AC120.013788},
    doi = {10.1074/jbc.ac120.013788},
    publisher = {American Society for Biochemistry {\&} Molecular Biology ({ASBMB})},
    }
  • [DOI] A. Torneri, P. Libin, J. Vanderlocht, A. Vandamme, J. Neyts, and N. Hens, "A prospect on the use of antiviral drugs to control local outbreaks of COVID-19," BMC Med, vol. 18, p. 191, 2020.
    [Bibtex]
    @Article{Torneri:20,
    author = {Andrea Torneri and Pieter Libin and Joris Vanderlocht and Anne-Mieke Vandamme and Johan Neyts and Niel Hens},
    title = {A prospect on the use of antiviral drugs to control local outbreaks of {COVID}-19},
    journal = {{BMC Med}},
    year = {2020},
    volume = {18},
    pages = {191},
    doi = {10.1186/s12916-020-01636-4},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] M. Muenchhoff, H. Mairhofer, H. Nitschko, N. Grzimek-Koschewa, D. Hoffmann, A. Berger, H. Rabenau, M. Widera, N. Ackermann, R. Konrad, S. Zange, A. Graf, S. Krebs, H. Blum, A. Sing, B. Liebl, R. Wölfel, S. Ciesek, C. Drosten, U. Protzer, S. Boehm, and O. T. Keppler, "Multicentre comparison of quantitative PCR-based assays to detect SARS-CoV-2, Germany, March 2020," Euro Surveill, vol. 25, iss. 24, p. 2001057, 2020.
    [Bibtex]
    @Article{Muenchhoff:20,
    author = {Maximilian Muenchhoff and Helga Mairhofer and Hans Nitschko and Natascha Grzimek-Koschewa and Dieter Hoffmann and Annemarie Berger and Holger Rabenau and Marek Widera and Nikolaus Ackermann and Regina Konrad and Sabine Zange and Alexander Graf and Stefan Krebs and Helmut Blum and Andreas Sing and Bernhard Liebl and Roman Wölfel and Sandra Ciesek and Christian Drosten and Ulrike Protzer and Stephan Boehm and Oliver T Keppler},
    title = {Multicentre comparison of quantitative {PCR}-based assays to detect {SARS}-{CoV}-2, {G}ermany, {M}arch 2020},
    journal = {{Euro Surveill}},
    year = {2020},
    volume = {25},
    number = {24},
    pages = {2001057},
    doi = {10.2807/1560-7917.es.2020.25.24.2001057},
    publisher = {European Centre for Disease Control and Prevention ({ECDC})},
    }
  • [DOI] P. Lemey, S. Hong, V. Hill, G. Baele, C. Poletto, V. Colizza, Á. O'Toole, J. T. McCrone, K. G. Andersen, M. Worobey, M. I. Nelson, A. Rambaut, and M. A. Suchard, "Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study," bioRxiv, 2020.
    [Bibtex]
    @Article{Lemey:20,
    author = {Philippe Lemey and Samuel Hong and Verity Hill and Guy Baele and Chiara Poletto and Vittoria Colizza and {\'{A}}ine O'Toole and John T. McCrone and Kristian G. Andersen and Michael Worobey and Martha I. Nelson and Andrew Rambaut and Marc A. Suchard},
    title = {Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a {SARS}-{CoV}-2 case study},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.06.22.165464},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] F. Kurth, M. Roennefarth, C. Thibeault, V. M. Corman, H. Müller-Redetzky, M. Mittermaier, C. Ruwwe-Glösenkamp, K. M. Heim, A. Krannich, S. Zvorc, S. Schmidt, L. Kretzler, C. Dang-Heine, M. Rose, M. Hummel, A. Hocke, R. H. Hübner, B. Opitz, M. A. Mall, J. Röhmel, U. Landmesser, B. Pieske, S. Knauss, M. Endres, J. Spranger, F. P. Mockenhaupt, F. Tacke, S. Treskatsch, S. Angermair, B. Siegmund, C. Spies, S. Weber-Carstens, K. Eckardt, D. Schürmann, A. Uhrig, M. S. Stegemann, T. Zoller, C. Drosten, N. Suttorp, M. Witzenrath, S. Hippenstiel, C. von Kalle, and L. E. Sander, "Studying the pathophysiology of coronavirus disease 2019: a protocol for the Berlin prospective COVID-19 patient cohort (Pa-COVID-19)," Infection, 2020.
    [Bibtex]
    @Article{Kurth:20,
    author = {Florian Kurth and Maria Roennefarth and Charlotte Thibeault and Victor M. Corman and Holger Müller-Redetzky and Mirja Mittermaier and Christoph Ruwwe-Glösenkamp and Katrin M. Heim and Alexander Krannich and Saskia Zvorc and Sein Schmidt and Lucie Kretzler and Chantip Dang-Heine and Matthias Rose and Michael Hummel and Andreas Hocke and Ralf H. Hübner and Bastian Opitz and Marcus A. Mall and Jobst Röhmel and Ulf Landmesser and Burkert Pieske and Samuel Knauss and Matthias Endres and Joachim Spranger and Frank P. Mockenhaupt and Frank Tacke and Sascha Treskatsch and Stefan Angermair and Britta Siegmund and Claudia Spies and Steffen Weber-Carstens and Kai-Uwe Eckardt and Dirk Schürmann and Alexander Uhrig and Miriam S. Stegemann and Thomas Zoller and Christian Drosten and Norbert Suttorp and Martin Witzenrath and Stefan Hippenstiel and Christof von Kalle and Leif Erik Sander},
    title = {Studying the pathophysiology of coronavirus disease 2019: a protocol for the {B}erlin prospective {COVID}-19 patient cohort ({Pa}-{COVID}-19)},
    journal = {Infection},
    year = {2020},
    doi = {10.1007/s15010-020-01464-x},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] J. J. Pénzes, M. Söderlund-Venermo, M. Canuti, A. M. Eis-Hübinger, J. Hughes, S. F. Cotmore, and B. Harrach, "Reorganizing the family Parvoviridae: a revised taxonomy independent of the canonical approach based on host association," Arch Virol, 2020.
    [Bibtex]
    @Article{Penzes:20,
    author = {Judit J. P{\'{e}}nzes and Maria Söderlund-Venermo and Marta Canuti and Anna Maria Eis-Hübinger and Joseph Hughes and Susan F. Cotmore and Bal{\'{a}}zs Harrach},
    title = {Reorganizing the family {P}arvoviridae: a revised taxonomy independent of the canonical approach based on host association},
    journal = {{Arch Virol}},
    year = {2020},
    doi = {10.1007/s00705-020-04632-4},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] A. Broggi, S. Ghosh, B. Sposito, R. Spreafico, F. Balzarini, A. L. Cascio, N. Clementi, M. D. Santis, N. Mancini, F. Granucci, and I. Zanoni, "Type III interferons disrupt the lung epithelial barrier upon viral recognition," Science, p. eabc3545, 2020.
    [Bibtex]
    @Article{Broggi:20,
    author = {Achille Broggi and Sreya Ghosh and Benedetta Sposito and Roberto Spreafico and Fabio Balzarini and Antonino Lo Cascio and Nicola Clementi and Maria De Santis and Nicasio Mancini and Francesca Granucci and Ivan Zanoni},
    title = {Type {III} interferons disrupt the lung epithelial barrier upon viral recognition},
    journal = {Science},
    year = {2020},
    pages = {eabc3545},
    doi = {10.1126/science.abc3545},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
  • [DOI] P. Pérot, F. Bielle, T. Bigot, V. Foulongne, K. Bolloré, D. Chrétien, P. Gil, S. Gutiérrez, G. L'Ambert, K. Mokhtari, J. Hellert, M. Flamand, C. Tamietti, M. Coulpier, A. H. de Verneuil, S. Temmam, T. Couderc, E. D. S. Cunha, S. Boluda, I. Plu, M. B. Delisle, F. Bonneville, D. Brassat, C. Fieschi, M. Malphettes, C. Duyckaerts, B. Mathon, S. Demeret, D. Seilhean, and M. Eloit, "Identification of Umbre orthobunyavirus as a novel zoonotic virus responsible for lethal encephalitis in 2 French patients with hypogammaglobulinemia," Clin Infect Dis, p. ciaa308, 2020.
    [Bibtex]
    @Article{Perot:20,
    author = {Philippe P{\'{e}}rot and Franck Bielle and Thomas Bigot and Vincent Foulongne and Karine Bollor{\'{e}} and Delphine Chr{\'{e}}tien and Patricia Gil and Seraf{\'{\i}}n Guti{\'{e}}rrez and Gr{\'{e}}gory L'Ambert and Karima Mokhtari and Jan Hellert and Marie Flamand and Carole Tamietti and Muriel Coulpier and Anne Huard de Verneuil and Sarah Temmam and Th{\'{e}}r{\`{e}}se Couderc and Edouard De Sousa Cunha and Susana Boluda and Isabelle Plu and Marie Bernadette Delisle and Fabrice Bonneville and David Brassat and Claire Fieschi and Marion Malphettes and Charles Duyckaerts and Bertrand Mathon and Sophie Demeret and Danielle Seilhean and Marc Eloit},
    title = {Identification of {Umbre} Orthobunyavirus as a Novel Zoonotic Virus Responsible for Lethal Encephalitis in 2 {French} Patients with Hypogammaglobulinemia},
    journal = {{Clin Infect Dis}},
    year = {2020},
    pages = {ciaa308},
    doi = {10.1093/cid/ciaa308},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] D. S. da Candido, I. M. Claro, J. G. de Jesus, W. M. de Souza, F. R. R. Moreira, S. Dellicour, T. A. Mellan, L. du Plessis, R. H. M. Pereira, F. C. S. da Sales, E. R. Manuli, J. Theze, L. Almeida, M. T. de Menezes, C. M. Voloch, M. J. Fumagalli, T. M. de Coletti, C. A. M. Silva, M. S. Ramundo, M. R. Amorim, H. Hoeltgebaum, S. Mishra, M. Gill, L. M. Carvalho, L. F. Buss, C. A. Prete, J. Ashworth, H. Nakaya, P. S. da Peixoto, O. J. Brady, S. M. Nicholls, A. Tanuri, A. D. Rossi, C. K. V. Braga, A. L. Gerber, A. P. Guimaraes, N. Gaburo, C. S. Alencar, A. C. S. de Ferreira, C. X. Lima, J. E. Levi, C. Granato, G. M. Ferreira, R. S. da Francisco, F. Granja, M. T. Garcia, M. L. Moretti, M. W. Perroud, T. M. P. P. Castineiras, C. D. S. Lazari, S. C. Hill, A. A. S. de Santos, C. L. Simeoni, J. Forato, A. C. Sposito, A. Z. Schreiber, M. N. N. Santos, C. Z. Sa, R. P. Souza, L. C. R. Moreira, M. M. Teixeira, J. Hubner, P. A. F. Leme, R. G. Moreira, M. L. Nogueira, N. Ferguson, S. F. Costa, J. L. Proenca-Modena, A. T. Vasconcelos, S. Bhatt, P. Lemey, C. Wu, A. Rambaut, N. J. Loman, R. S. Aguiar, O. G. Pybus, E. C. Sabino, and N. R. Faria, "Evolution and epidemic spread of SARS-CoV-2 in Brazil," medRxiv, 2020.
    [Bibtex]
    @Article{SilvaCandido:20,
    author = {Darlan da Silva Candido and Ingra Morales Claro and Jaqueline Goes de Jesus and William Marciel de Souza and Filipe Romero Rebello Moreira and Simon Dellicour and Thomas A. Mellan and Louis du Plessis and Rafael Henrique Moraes Pereira and Flavia Cristina da Silva Sales and Erika Regina Manuli and Julien Theze and Luis Almeida and Mariane Talon de Menezes and Carolina Moreira Voloch and Marcilio Jorge Fumagalli and Thais de Moura Coletti and Camila Alves Maia Silva and Mariana Severo Ramundo and Mariene Ribeiro Amorim and Henrique Hoeltgebaum and Swapnil Mishra and Mandev Gill and Luiz Max Carvalho and Lewis Fletcher Buss and Carlos Augusto Prete and Jordan Ashworth and Helder Nakaya and Pedro da Silva Peixoto and Oliver J Brady and Samuel M. Nicholls and Amilcar Tanuri and Atila Duque Rossi and Carlos Kaue Vieira Braga and Alexandra Lehmkuhl Gerber and Ana Paula Guimaraes and Nelson Gaburo and Cecilia Salete Alencar and Alessandro Clayton de Souza Ferreira and Cristiano Xavier Lima and Jose Eduardo Levi and Celso Granato and Giula Magalhaes Ferreira and Ronaldo da Silva Francisco and Fabiana Granja and Marcia Teixeira Garcia and Maria Luiza Moretti and Mauricio Wesley Perroud and Terezinha Marta Pereira Pinto Castineiras and Carolina Dos Santos Lazari and Sarah C Hill and Andreza Aruska de Souza Santos and Camila Lopes Simeoni and Julia Forato and Andrei Carvalho Sposito and Angelica Zaninelli Schreiber and Magnun Nueldo Nunes Santos and Camila Zolini Sa and Renan Pedra Souza and Luciana Cunha Resende Moreira and Mauro Martins Teixeira and Josy Hubner and Patricia Asfora Falabella Leme and Rennan Garcias Moreira and Mauricio Lacerda Nogueira and Neil Ferguson and Silvia Figueiredo Costa and Jose Luiz Proenca-Modena and Ana Tereza Vasconcelos and Samir Bhatt and Philippe Lemey and Chieh-Hsi Wu and Andrew Rambaut and Nick J Loman and Renato Santana Aguiar and Oliver G Pybus and Ester Cerdeira Sabino and Nuno Rodrigues Faria},
    title = {Evolution and epidemic spread of {SARS}-{CoV}-2 in {Brazil}},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.06.11.20128249},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] J. Singer, R. J. Gifford, M. Cotten, and D. L. Robertson, "CoV-GLUE: a web application for tracking SARS-CoV-2 genomic variation," Preprints, 2020.
    [Bibtex]
    @Article{Singer:20,
    author = {Joshua Singer and Robert J. Gifford and Matthew Cotten and David L. Robertson},
    title = {{CoV}-{GLUE}: A Web Application for Tracking {SARS}-{CoV}-2 Genomic Variation},
    journal = {Preprints},
    year = {2020},
    doi = {10.20944/preprints202006.0225.v1},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] R. Martin, H. F. Löchel, M. Welzel, G. Hattab, A. Hauschild, and D. Heider, "CORDITE: the curated CORona drug InTERactions database for SARS-CoV-2," iScience, vol. 23, iss. 7, p. 101297, 2020.
    [Bibtex]
    @Article{Martin:20,
    author = {Roman Martin and Hannah F. Löchel and Marius Welzel and Georges Hattab and Anne-Christin Hauschild and Dominik Heider},
    title = {{CORDITE}: The Curated {CORona} Drug {InTERactions} Database for {SARS}-{CoV}-2},
    journal = {{iScience}},
    year = {2020},
    volume = {23},
    number = {7},
    pages = {101297},
    doi = {10.1016/j.isci.2020.101297},
    publisher = {Elsevier {BV}},
    }
  • [DOI] J. S. Y. Ho, M. Angel, Y. Ma, E. Sloan, G. Wang, C. Martinez-Romero, M. Alenquer, V. Roudko, L. Chung, S. Zheng, M. Chang, Y. Fstkchyan, S. Clohisey, A. M. Dinan, J. Gibbs, R. J. Gifford, R. Shen, Q. Gu, N. Irigoyen, L. Campisi, C. Huang, N. Zhao, J. D. Jones, I. van Knippenberg, Z. Zhu, N. Moshkina, Léa. Meyer, J. Noel, Z. Peralta, V. Rezelj, R. Kaake, B. Rosenberg, B. Wang, J. Wei, S. Paessler, H. M. Wise, J. Johnson, A. Vannini, M. J. Amorim, K. J. Baillie, E. R. Miraldi, C. Benner, I. Brierley, P. Digard, M. L, A. E. Firth, N. Krogan, B. D. Greenbaum, M. K. MacLeod, H. van Bakel, A. Garcìa-Sastre, J. W. Yewdell, E. Hutchinson, and I. Marazzi, "Hybrid gene origination creates human-virus chimeric proteins during infection," Cell, vol. 181, p. 1502–1517, 2020.
    [Bibtex]
    @Article{Ho:20,
    author = {Jessica Sook Yuin Ho and Matthew Angel and Yixuan Ma and Elizabeth Sloan and Guojun Wang and Carles Martinez-Romero and Marta Alenquer and Vladimir Roudko and Liliane Chung and Simin Zheng and Max Chang and Yesai Fstkchyan and Sara Clohisey and Adam M. Dinan and James Gibbs and Robert J. Gifford and Rong Shen and Quan Gu and Nerea Irigoyen and Laura Campisi and Cheng Huang and Nan Zhao and Joshua D. Jones and Ingeborg van Knippenberg and Zeyu Zhu and Natasha Moshkina and L{\'{e}}a Meyer and Justine Noel and Zuleyma Peralta and Veronica Rezelj and Robyn Kaake and Brad Rosenberg and Bo Wang and Jiajie Wei and Slobodan Paessler and Helen M. Wise and Jeffrey Johnson and Alessandro Vannini and Maria Jo{\~{a}}o Amorim and J. Kenneth Baillie and Emily R. Miraldi and Christopher Benner and Ian Brierley and Paul Digard and Marta {\L}uksza and Andrew E. Firth and Nevan Krogan and Benjamin D. Greenbaum and Megan K. MacLeod and Harm van Bakel and Adolfo Garc{\`{\i}}a-Sastre and Jonathan W. Yewdell and Edward Hutchinson and Ivan Marazzi},
    title = {Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection},
    journal = {Cell},
    year = {2020},
    volume = {181},
    pages = {1502--1517},
    doi = {10.1016/j.cell.2020.05.035},
    publisher = {Elsevier {BV}},
    }
  • [DOI] N. Clementi, R. Ferrarese, E. Criscuolo, R. A. Diotti, M. Castelli, C. Scagnolari, R. Burioni, G. Antonelli, M. Clementi, and N. Mancini, "Interferon-$\upbeta$ 1a inhibits SARS-CoV-2 in vitro when administered after virus infection," J Infect Dis, p. jiaa350, 2020.
    [Bibtex]
    @Article{Clementi:20a,
    author = {Nicola Clementi and Roberto Ferrarese and Elena Criscuolo and Roberta Antonia Diotti and Matteo Castelli and Carolina Scagnolari and Roberto Burioni and Guido Antonelli and Massimo Clementi and Nicasio Mancini},
    title = {Interferon-$\upbeta$ 1a inhibits {SARS}-{CoV}-2 in vitro when administered after virus infection},
    journal = {{J Infect Dis}},
    year = {2020},
    pages = {jiaa350},
    doi = {10.1093/infdis/jiaa350},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] A. Düx, S. Lequime, L. V. Patrono, B. Vrancken, S. Boral, J. F. Gogarten, A. Hilbig, D. Horst, K. Merkel, B. Prepoint, S. Santibanez, J. Schlotterbeck, M. A. Suchard, M. Ulrich, N. Widulin, A. Mankertz, F. H. Leendertz, K. Harper, T. Schnalke, P. Lemey, and S. Calvignac-Spencer, "Measles virus and rinderpest virus divergence dated to the sixth century BCE," Science, vol. 368, iss. 6497, p. 1367–1370, 2020.
    [Bibtex]
    @Article{Duex:20,
    author = {Ariane Düx and Sebastian Lequime and Livia Victoria Patrono and Bram Vrancken and Sengül Boral and Jan F. Gogarten and Antonia Hilbig and David Horst and Kevin Merkel and Baptiste Prepoint and Sabine Santibanez and Jasmin Schlotterbeck and Marc A. Suchard and Markus Ulrich and Navena Widulin and Annette Mankertz and Fabian H. Leendertz and Kyle Harper and Thomas Schnalke and Philippe Lemey and S{\'{e}}bastien Calvignac-Spencer},
    title = {Measles virus and rinderpest virus divergence dated to the sixth century {BCE}},
    journal = {Science},
    year = {2020},
    volume = {368},
    number = {6497},
    pages = {1367--1370},
    doi = {10.1126/science.aba9411},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
  • [DOI] R. Capina, K. Li, L. Kearney, A. Vandamme, R. P. Harrigan, and K. V. Laethem, "Quality control of next-generation sequencing-based HIV-1 drug resistance data in clinical laboratory information systems framework," Viruses, vol. 12, iss. 6, p. 645, 2020.
    [Bibtex]
    @Article{Capina:20,
    author = {Rupert Capina and Katherine Li and Levon Kearney and Anne-Mieke Vandamme and P. Richard Harrigan and Kristel Van Laethem},
    title = {Quality Control of Next-Generation Sequencing-Based {HIV}-1 Drug Resistance Data in Clinical Laboratory Information Systems Framework},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    number = {6},
    pages = {645},
    doi = {10.3390/v12060645},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] K. Wernike, M. Keller, F. J. Conraths, T. C. Mettenleiter, M. H. Groschup, and M. Beer, "Pitfalls in SARS-CoV-2 PCR diagnostics," Transbound Emerg Dis, 2020.
    [Bibtex]
    @Article{Wernike:20a,
    author = {Kerstin Wernike and Markus Keller and Franz J. Conraths and Thomas C. Mettenleiter and Martin H. Groschup and Martin Beer},
    title = {Pitfalls in {SARS}-{CoV}-2 {PCR} diagnostics},
    journal = {{Transbound Emerg Dis}},
    year = {2020},
    doi = {10.1111/tbed.13684},
    }
  • [DOI] A. A. Guzmán-Solís, D. Blanco-Melo, V. Villa-Islas, M. J. Bravo-López, M. Sandoval-Velasco, J. K. Wesp, J. A. Gómez-Valdés, M. L. de la Moreno-Cabrera, A. Meraz-Moreno, G. Solís-Pichardo, P. Schaaf, B. R. tenOever, and M. C. Ávila-Arcos, "Ancient viral genomes reveal introduction of HBV and B19V to Mexico during the transatlantic slave trade," bioRxiv, 2020.
    [Bibtex]
    @Article{Guzman-Solis:20,
    author = {Axel A. Guzm{\'{a}}n-Sol{\'{\i}}s and Daniel Blanco-Melo and Viridiana Villa-Islas and Miriam J. Bravo-L{\'{o}}pez and Marcela Sandoval-Velasco and Julie K. Wesp and Jorge A. G{\'{o}}mez-Vald{\'{e}}s and Mar{\'{\i}}a de la Luz Moreno-Cabrera and Alejandro Meraz-Moreno and Gabriela Sol{\'{\i}}s-Pichardo and Peter Schaaf and Benjamin R. tenOever and Mar{\'{\i}}a C. {\'{A}}vila-Arcos},
    title = {Ancient viral genomes reveal introduction of {HBV} and {B19V} to {M}exico during the transatlantic slave trade},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.06.05.137083},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] T. C. Jones, B. Mühlemann, T. Veith, G. Biele, M. Zuchowski, J. Hoffmann, A. Stein, A. Edelmann, V. M. Corman, and C. Drosten, "An analysis of SARS-CoV-2 viral load by patient age," medRxiv, 2020.
    [Bibtex]
    @Article{Jones:20,
    author = {Terry C Jones and Barbara Mühlemann and Talitha Veith and Guido Biele and Marta Zuchowski and Jörg Hoffmann and Angela Stein and Anke Edelmann and Victor Max Corman and Christian Drosten},
    title = {An analysis of {SARS}-{CoV}-2 viral load by patient age},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.06.08.20125484},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] S. Posada-Cespedes, D. Seifert, I. Topolsky, K. J. Metzner, and N. Beerenwinkel, "V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput sequencing data," bioRxiv, 2020.
    [Bibtex]
    @Article{Cespedes:20,
    author = {Susana Posada-Cespedes and David Seifert and Ivan Topolsky and Karin J Metzner and Niko Beerenwinkel},
    journal = {{bioRxiv}},
    title = {V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput sequencing data},
    year = {2020},
    doi = {10.1101/2020.06.09.142919},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] A. D. S. Filipe, J. Shepherd, T. Williams, J. Hughes, E. Aranday-Cortes, P. Asamaphan, C. Balcazar, K. Brunker, S. Carmichael, R. Dewar, M. D. Gallagher, R. Gunson, A. Ho, N. Jesudason, N. Johnson, C. M. E. Leitch, K. Li, A. MacLean, D. Mair, S. E. McDonald, M. McHugh, J. Nichols, M. Niebel, K. Nomikou, R. J. Orton, A. O'Toole, M. Palmarini, Y. A. Parr, A. Rambaut, S. Rooke, S. Shaaban, R. Shah, J. B. Singer, K. Smollett, I. Starinskij, L. Tong, V. B. Sreenu, E. Wastnedge, D. L. Robertson, M. T. G. Holden, K. Templeton, and E. C. Thomson, "Genomic epidemiology of SARS-CoV-2 spread in Scotland highlights the role of European travel in COVID-19 emergence," medRxiv, 2020.
    [Bibtex]
    @Article{Filipe:20,
    author = {Ana Da Silva Filipe and James Shepherd and Thomas Williams and Joseph Hughes and Elihu Aranday-Cortes and Patawee Asamaphan and Carlos Balcazar and Kirstyn Brunker and Stephen Carmichael and Rebecca Dewar and Michael D Gallagher and Rory Gunson and Antonia Ho and Natasha Jesudason and Natasha Johnson and E. Carol McWilliam Leitch and Kathy Li and Alasdair MacLean and Daniel Mair and Sarah E. McDonald and Martin McHugh and Jenna Nichols and Marc Niebel and Kyriaki Nomikou and Richard J. Orton and Aine O'Toole and Massimo Palmarini and Yasmin A. Parr and Andrew Rambaut and Stefan Rooke and Sharif Shaaban and Rajiv Shah and Joshua B. Singer and Katherine Smollett and Igor Starinskij and Lily Tong and Vattipally B. Sreenu and Elizabeth Wastnedge and David L. Robertson and Matthew T.G. Holden and Kate Templeton and Emma C. Thomson},
    title = {Genomic epidemiology of {SARS}-{CoV}-2 spread in {S}cotland highlights the role of {E}uropean travel in {COVID}-19 emergence},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.06.08.20124834},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] P. Murcia, D. Streiker, A. D. S. Philipe, D. L. Robertson, R. Jarrett, B. Willett, M. Hosie, R. Biek, K. Allan, and W. Weir, "Send cat and dog samples to test for SARS-CoV-2," Vet Rec, vol. 186, p. 571, 2020.
    [Bibtex]
    @Article{Murcia:20,
    author = {Pablo Murcia and Daniel Streiker and Ana Da Silva Philipe and David L. Robertson and Ruth Jarrett and Brian Willett and Margaret Hosie and Roman Biek and Kathryn Allan and William Weir},
    title = {Send cat and dog samples to test for {SARS}-{CoV}-2},
    journal = {{Vet Rec}},
    year = {2020},
    volume = {186},
    pages = {571},
    doi = {10.1136/vr.m2019},
    publisher = {{BMJ}},
    }
  • [DOI] F. Young, S. Rogers, and D. L. Robertson, "Predicting host taxonomic information from viral genomes: a comparison of feature representations," PLoS Comput Biol, vol. 16, iss. 5, p. e1007894, 2020.
    [Bibtex]
    @Article{Young:20,
    author = {Francesca Young and Simon Rogers and David L. Robertson},
    title = {Predicting host taxonomic information from viral genomes: A comparison of feature representations},
    journal = {{PLoS Comput Biol}},
    year = {2020},
    volume = {16},
    number = {5},
    pages = {e1007894},
    doi = {10.1371/journal.pcbi.1007894},
    editor = {Morgan Langille},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] J. M. Eizenga, A. M. Novak, J. A. Sibbesen, S. Heumos, A. Ghaffaari, G. Hickey, X. Chang, J. D. Seaman, R. Rounthwaite, J. Ebler, M. Rautiainen, S. Garg, B. Paten, T. Marschall, J. Sirén, and E. Garrison, "Pangenome graphs," Annu Rev Genomics Hum Genet, vol. 21, iss. 1, 2020.
    [Bibtex]
    @Article{Eizenga:20,
    author = {Jordan M. Eizenga and Adam M. Novak and Jonas A. Sibbesen and Simon Heumos and Ali Ghaffaari and Glenn Hickey and Xian Chang and Josiah D. Seaman and Robin Rounthwaite and Jana Ebler and Mikko Rautiainen and Shilpa Garg and Benedict Paten and Tobias Marschall and Jouni Sir{\'{e}}n and Erik Garrison},
    title = {Pangenome Graphs},
    journal = {{Annu Rev Genomics Hum Genet}},
    year = {2020},
    volume = {21},
    number = {1},
    doi = {10.1146/annurev-genom-120219-080406},
    publisher = {Annual Reviews},
    }
  • [DOI] A. Vandamme and T. Nguyen, "Belgium – concerns about coronavirus contact-tracing apps," Nature, vol. 581, p. 384, 2020.
    [Bibtex]
    @Article{Vandamme:20,
    author = {Anne-Mieke Vandamme and ToTran Nguyen},
    title = {{B}elgium -- concerns about coronavirus contact-tracing apps},
    journal = {Nature},
    year = {2020},
    volume = {581},
    pages = {384},
    doi = {10.1038/d41586-020-01552-w},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] X. Ji, Z. Zhang, A. Holbrook, A. Nishimura, G. Baele, A. Rambaut, P. Lemey, and M. A. Suchard, "Gradients do grow on trees: a linear-time $\mathcal{O}$(N)-dimensional gradient for statistical phylogenetics," Mol Biol Evol, p. msaa130, 2020.
    [Bibtex]
    @Article{Ji:20,
    author = {Xiang Ji and Zhenyu Zhang and Andrew Holbrook and Akihiko Nishimura and Guy Baele and Andrew Rambaut and Philippe Lemey and Marc A Suchard},
    title = {Gradients do grow on trees: a linear-time $\mathcal{O}$({N})-dimensional gradient for statistical phylogenetics},
    journal = {{Mol Biol Evol}},
    year = {2020},
    pages = {msaa130},
    doi = {10.1093/molbev/msaa130},
    editor = {Jeffrey Townsend},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] B. Bartolini, M. Rueca, C. E. M. Gruber, F. Messina, F. Carletti, E. Giombini, E. Lalle, L. Bordi, G. Matusali, F. Colavita, C. Castilletti, F. Vairo, G. Ippolito, M. R. Capobianchi, and A. D. Caro, "SARS-CoV-2 phylogenetic analysis, Lazio region, Italy, February–March 2020," Emerg Infect Dis, vol. 26, iss. 8, 2020.
    [Bibtex]
    @Article{Bartolini:20,
    author = {Barbara Bartolini and Martina Rueca and Cesare Ernesto Maria Gruber and Francesco Messina and Fabrizio Carletti and Emanuela Giombini and Eleonora Lalle and Licia Bordi and Giulia Matusali and Francesca Colavita and Concetta Castilletti and Francesco Vairo and Giuseppe Ippolito and Maria Rosaria Capobianchi and Antonino Di Caro},
    title = {{SARS}-{CoV}-2 Phylogenetic Analysis, {L}azio Region, {I}taly, {F}ebruary--{M}arch 2020},
    journal = {{Emerg Infect Dis}},
    year = {2020},
    volume = {26},
    number = {8},
    doi = {10.3201/eid2608.201525},
    publisher = {Centers for Disease Control and Prevention ({CDC})},
    }
  • [DOI] W. Randazzo and G. Sánchez, "Hepatitis A infections from food," J Appl Microbiol, 2020.
    [Bibtex]
    @Article{Randazzo:20a,
    author = {Walter Randazzo and Gloria Sánchez},
    journal = {{J Appl Microbiol}},
    title = {Hepatitis {A} infections from food},
    year = {2020},
    doi = {10.1111/jam.14727},
    publisher = {Wiley},
    }
  • [DOI] A. Kratzel, S. Steiner, D. Todt, P. V'Kovski, Y. Brueggemann, J. Steinmann, E. Steinmann, V. Thiel, and S. Pfaender, "Temperature-dependent surface stability of SARS-CoV-2," J Infect, 2020.
    [Bibtex]
    @Article{Kratzel:20a,
    author = {Annika Kratzel and Silvio Steiner and Daniel Todt and Philip V'Kovski and Yannick Brueggemann and Joerg Steinmann and Eike Steinmann and Volker Thiel and Stephanie Pfaender},
    title = {Temperature-dependent surface stability of {SARS}-{CoV}-2},
    journal = {{J Infect}},
    year = {2020},
    doi = {10.1016/j.jinf.2020.05.074},
    publisher = {Elsevier {BV}},
    }
  • [DOI] K. Kitsou, A. Kotanidou, D. Paraskevis, T. Karamitros, A. Katzourakis, R. Tedder, T. Hurst, S. Sapounas, A. Kotsinas, V. Gorgoulis, V. Spoulou, S. Tsiodras, P. Lagiou, and G. Magiorkinis, "Upregulation of human endogenous retroviruses in bronchoalveolar lavage fluid of COVID-19 patients," medRxiv, 2020.
    [Bibtex]
    @Article{Kitsou:20,
    author = {Konstantina Kitsou and Anastasia Kotanidou and Dimitrios Paraskevis and Timokratis Karamitros and Aris Katzourakis and Richard Tedder and Tara Hurst and Spyros Sapounas and Athanassios Kotsinas and Vassilis Gorgoulis and Vana Spoulou and Sotirios Tsiodras and Pagona Lagiou and Gkikas Magiorkinis},
    title = {Upregulation of Human Endogenous Retroviruses in Bronchoalveolar Lavage Fluid of {COVID}-19 Patients},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.05.10.20096958},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] V. Sypsa, S. Roussos, D. Paraskevis, T. Lytras, S. Tsiodras, and A. Hatzakis, "Modelling the SARS-CoV-2 first epidemic wave in Greece: social contact patterns for impact assessment and an exit strategy from social distancing measures," medRxiv, 2020.
    [Bibtex]
    @Article{Sypsa:20,
    author = {Vana Sypsa and Sotirios Roussos and Dimitrios Paraskevis and Theodore Lytras and Sotirios Tsiodras and Angelos Hatzakis},
    title = {Modelling the {SARS}-{CoV}-2 first epidemic wave in {G}reece: social contact patterns for impact assessment and an exit strategy from social distancing measures},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.05.27.20114017},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] G. Kemenesi, S. Zeghbib, B. A. Somogyi, G. E. Tóth, K. Bányai, N. Solymosi, P. M. Szabo, I. Szabó, Ádám. Bálint, P. Urbán, R. Herczeg, A. Gyenesei, Á. Nagy, C. I. Pereszlényi, G. C. Babinszky, G. Dudás, G. Terhes, V. Zöldi, R. Lovas, S. Tenczer, L. Kornya, and F. Jakab, "Multiple SARS-CoV-2 introductions shaped the early outbreak in Central Eastern Europe: comparing Hungarian data to a worldwide sequence data-matrix," bioRxiv, 2020.
    [Bibtex]
    @Article{Kemenesi:20a,
    author = {G{\'{a}}bor Kemenesi and Safia Zeghbib and Bal{\'{a}}zs A Somogyi and G{\'{a}}bor Endre T{\'{o}}th and Kriszti{\'{a}}n B{\'{a}}nyai and Norbert Solymosi and Peter M Szabo and Istv{\'{a}}n Szab{\'{o}} and {\'{A}}d{\'{a}}m B{\'{a}}lint and P{\'{e}}ter Urb{\'{a}}n and R{\'{o}}bert Herczeg and Attila Gyenesei and {\'{A}}gnes Nagy and Csaba Istv{\'{a}}n Pereszl{\'{e}}nyi and Gergely Csaba Babinszky and G{\'{a}}bor Dud{\'{a}}s and Gabriella Terhes and Viktor Zöldi and R{\'{o}}bert Lovas and Szabolcs Tenczer and L{\'{a}}szl{\'{o}} Kornya and Ferenc Jakab},
    title = {Multiple {SARS}-{CoV}-2 introductions shaped the early outbreak in {C}entral {E}astern {E}urope: comparing {H}ungarian data to a worldwide sequence data-matrix},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.05.06.080119},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. Collatz, F. Mock, M. Hölzer, E. Barth, K. Sachse, and M. Marz, "EpiDope: A Deep neural network for linear B-cell epitope prediction," bioRxiv, 2020.
    [Bibtex]
    @Article{Collatz:20,
    author = {Maximilian Collatz and Florian Mock and Martin Hölzer and Emanuel Barth and Konrad Sachse and Manja Marz},
    title = {{EpiDope}: {A Deep} neural network for linear {B}-cell epitope prediction},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.05.12.090019},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] S. Pach, T. N. Nguyen, J. Trimpert, D. Kunec, N. Osterrieder, and G. Wolber, "ACE2-variants indicate potential SARS-CoV-2-susceptibility in animals: an extensive molecular dynamics study," bioRxiv, 2020.
    [Bibtex]
    @Article{Pach:20,
    author = {Szymon Pach and Trung Ngoc Nguyen and Jakob Trimpert and Dusan Kunec and Nikolaus Osterrieder and Gerhard Wolber},
    title = {{ACE}2-Variants Indicate Potential {SARS}-{CoV}-2-Susceptibility in Animals: An Extensive Molecular Dynamics Study},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.05.14.092767},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. Worobey, J. Pekar, B. B. Larsen, M. I. Nelson, V. Hill, J. B. Joy, A. Rambaut, M. A. Suchard, J. O. Wertheim, and P. Lemey, "The emergence of SARS-CoV-2 in Europe and the US," bioRxiv, 2020.
    [Bibtex]
    @Article{Worobey:20,
    author = {Michael Worobey and Jonathan Pekar and Brendan B. Larsen and Martha I. Nelson and Verity Hill and Jeffrey B. Joy and Andrew Rambaut and Marc A. Suchard and Joel O. Wertheim and Philippe Lemey},
    title = {The emergence of {SARS}-{CoV}-2 in {Europe} and the {US}},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.05.21.109322},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] O. A. MacLean, S. Lytras, J. B. Singer, S. Weaver, S. K. L. Pond, and D. L. Robertson, "Evidence of significant natural selection in the evolution of SARS-CoV-2 in bats, not humans," bioRxiv, 2020.
    [Bibtex]
    @Article{MacLean:20,
    author = {Oscar A. MacLean and Spyros Lytras and Joshua B. Singer and Steven Weaver and Sergei L. Kosakovsky Pond and David L. Robertson},
    title = {Evidence of significant natural selection in the evolution of {SARS}-{CoV}-2 in bats, not humans},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.05.28.122366},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] H. E. Grant, E. B. Hodcroft, D. Ssemwanga, J. M. Kitayimbwa, G. Yebra, L. R. E. Gomez, D. Frampton, A. Gall, P. Kellam, T. de Oliveira, N. Bbosa, R. N. Nsubuga, F. Kibengo, T. H. Kwan, S. Lycett, R. Kao, D. L. Robertson, O. Ratmann, C. Fraser, D. Pillay, P. Kaleebu, and A. L. J. Brown, "Pervasive and non-random recombination in near full-length HIV genomes from Uganda," Virus Evol, vol. 6, iss. 1, p. veaa004, 2020.
    [Bibtex]
    @Article{Grant:20,
    author = {Heather E Grant and Emma B Hodcroft and Deogratius Ssemwanga and John M Kitayimbwa and Gonzalo Yebra and Luis Roger Esquivel Gomez and Dan Frampton and Astrid Gall and Paul Kellam and Tulio de Oliveira and Nicholas Bbosa and Rebecca N Nsubuga and Freddie Kibengo and Tsz Ho Kwan and Samantha Lycett and Rowland Kao and David L Robertson and Oliver Ratmann and Christophe Fraser and Deenan Pillay and Pontiano Kaleebu and Andrew J Leigh Brown},
    title = {Pervasive and non-random recombination in near full-length {HIV} genomes from {U}ganda},
    journal = {{Virus Evol}},
    year = {2020},
    volume = {6},
    number = {1},
    pages = {veaa004},
    doi = {10.1093/ve/veaa004},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] O. Faye, M. L. de Monteiro, B. Vrancken, M. Prot, S. Lequime, M. Diarra, O. Ndiaye, T. Valdez, S. Tavarez, J. Ramos, S. V. da Leal, C. Pires, A. Moreira, M. F. Tavares, L. Fernandes, J. N. Barreto, M. Céu. do Teixeira, M. L. L. da de Mendonça, C. C. S. L. da Gomes, M. S. Castellon, L. Ma, F. Lemoine, F. Gámbaro-Roglia, D. Delaune, G. Fall, I. S. Fall, M. Diop, A. Sakuntabhai, C. Loucoubar, P. Lemey, E. C. Holmes, O. Faye, A. A. Sall, and E. Simon-Loriere, "Genomic epidemiology of 2015–2016 Zika virus outbreak in Cape Verde," Emerg. Infect. Dis., vol. 26, iss. 6, p. 1084–1090, 2020.
    [Bibtex]
    @Article{Faye:20,
    author = {Oumar Faye and Maria de Lourdes Monteiro and Bram Vrancken and Matthieu Prot and Sebastian Lequime and Maryam Diarra and Oumar Ndiaye and Tomas Valdez and Sandra Tavarez and Jessica Ramos and Silv{\^{a}}nia da Veiga Leal and Cecilio Pires and Antonio Moreira and Maria Filomena Tavares and Linete Fernandes and Jorge Noel Barreto and Maria do C{\'{e}}u Teixeira and Maria da Luz de Lima Mendon{\c{c}}a and Carolina Cardoso da Silva Leite Gomes and Mariano Salazar Castellon and Laurence Ma and Fr{\'{e}}d{\'{e}}ric Lemoine and Fabiana G{\'{a}}mbaro-Roglia and D{\'{e}}borah Delaune and Gamou Fall and Ibrahima Soc{\'{e}} Fall and Mamadou Diop and Anavaj Sakuntabhai and Cheikh Loucoubar and Philippe Lemey and Edward C. Holmes and Ousmane Faye and Amadou Alpha Sall and Etienne Simon-Loriere},
    title = {Genomic Epidemiology of 2015{\textendash}2016 {Zika} Virus Outbreak in {Cape} {Verde}},
    journal = {{Emerg. Infect. Dis.}},
    year = {2020},
    volume = {26},
    number = {6},
    pages = {1084--1090},
    doi = {10.3201/eid2606.190928},
    publisher = {Centers for Disease Control and Prevention ({CDC})},
    }
  • [DOI] S. Gryseels, T. D. Watts, J. K. Mpolesha, B. B. Larsen, P. Lemey, J. Muyembe-Tamfum, D. E. Teuwen, and M. Worobey, "A near full-length HIV-1 genome from 1966 recovered from formalin-fixed paraffin-embedded tissue," Proc Natl Acad Sci USA, vol. 117, iss. 22, p. 12222–12229, 2020.
    [Bibtex]
    @Article{Gryseels:20,
    author = {Sophie Gryseels and Thomas D. Watts and Jean-Marie Kabongo Mpolesha and Brendan B. Larsen and Philippe Lemey and Jean-Jacques Muyembe-Tamfum and Dirk E. Teuwen and Michael Worobey},
    title = {A near full-length {HIV}-1 genome from 1966 recovered from formalin-fixed paraffin-embedded tissue},
    journal = {{Proc Natl Acad Sci USA}},
    year = {2020},
    volume = {117},
    number = {22},
    pages = {12222--12229},
    doi = {10.1073/pnas.1913682117},
    publisher = {Proceedings of the National Academy of Sciences},
    }
  • [DOI] G. Kemenesi, L. Kornya, G. E. Tóth, K. Kurucz, S. Zeghbib, B. A. Somogyi, V. Zöldi, P. Urbán, R. Herczeg, and F. Jakab, "Nursing homes and the elderly regarding the COVID-19 pandemic: situation report from Hungary," GeroScience, 2020.
    [Bibtex]
    @Article{Kemenesi:20,
    author = {G{\'{a}}bor Kemenesi and L{\'{a}}szl{\'{o}} Kornya and G{\'{a}}bor Endre T{\'{o}}th and Korn{\'{e}}lia Kurucz and Safia Zeghbib and Bal{\'{a}}zs A. Somogyi and Viktor Zöldi and P{\'{e}}ter Urb{\'{a}}n and R{\'{o}}bert Herczeg and Ferenc Jakab},
    title = {Nursing homes and the elderly regarding the {COVID}-19 pandemic: situation report from {H}ungary},
    journal = {{GeroScience}},
    year = {2020},
    doi = {10.1007/s11357-020-00195-z},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] W. Randazzo, P. Truchado, E. Cuevas-Ferrando, P. Simón, A. Allende, and G. Sánchez, "SARS-CoV-2 RNA in wastewater anticipated COVID-19 occurrence in a low prevalence area," Water Res, vol. 181, p. 115942, 2020.
    [Bibtex]
    @Article{Randazzo:20,
    author = {Walter Randazzo and Pilar Truchado and Enric Cuevas-Ferrando and Pedro Sim{\'{o}}n and Ana Allende and Gloria Sánchez},
    journal = {{Water Res}},
    title = {{SARS}-{CoV}-2 {RNA} in wastewater anticipated {COVID}-19 occurrence in a low prevalence area},
    year = {2020},
    pages = {115942},
    volume = {181},
    doi = {10.1016/j.watres.2020.115942},
    publisher = {Elsevier {BV}},
    }
  • [DOI] M. M. Böhmer, U. Buchholz, V. M. Corman, M. Hoch, K. Katz, D. V. Marosevic, S. Böhm, T. Woudenberg, N. Ackermann, R. Konrad, U. Eberle, B. Treis, A. Dangel, K. Bengs, V. Fingerle, A. Berger, S. Hörmansdorfer, S. Ippisch, B. Wicklein, A. Grahl, K. Pörtner, N. Muller, N. Zeitlmann, S. T. Boender, W. Cai, A. Reich, M. an der Heiden, U. Rexroth, O. Hamouda, J. Schneider, T. Veith, B. Mühlemann, R. Wölfel, M. Antwerpen, M. Walter, U. Protzer, B. Liebl, W. Haas, A. Sing, C. Drosten, and A. Zapf, "Investigation of a COVID-19 outbreak in Germany resulting from a single travel-associated primary case: a case series," Lancet Infect Dis, 2020.
    [Bibtex]
    @Article{Böhmer:20,
    author = {Merle M Böhmer and Udo Buchholz and Victor M Corman and Martin Hoch and Katharina Katz and Durdica V Marosevic and Stefanie Böhm and Tom Woudenberg and Nikolaus Ackermann and Regina Konrad and Ute Eberle and Bianca Treis and Alexandra Dangel and Katja Bengs and Volker Fingerle and Anja Berger and Stefan Hörmansdorfer and Siegfried Ippisch and Bernd Wicklein and Andreas Grahl and Kirsten Pörtner and Nadine Muller and Nadine Zeitlmann and T Sonia Boender and Wei Cai and Andreas Reich and Maria an der Heiden and Ute Rexroth and Osamah Hamouda and Julia Schneider and Talitha Veith and Barbara Mühlemann and Roman Wölfel and Markus Antwerpen and Mathias Walter and Ulrike Protzer and Bernhard Liebl and Walter Haas and Andreas Sing and Christian Drosten and Andreas Zapf},
    title = {Investigation of a {COVID}-19 outbreak in {G}ermany resulting from a single travel-associated primary case: a case series},
    journal = {{Lancet Infect Dis}},
    year = {2020},
    doi = {10.1016/s1473-3099(20)30314-5},
    publisher = {Elsevier {BV}},
    }
  • [DOI] K. Farkas, D. I. Walker, E. M. Adriaenssens, J. E. McDonald, L. S. Hillary, S. K. Malham, and D. L. Jones, "Viral indicators for tracking domestic wastewater contamination in the aquatic environment," Water Res, vol. 181, p. 115926, 2020.
    [Bibtex]
    @Article{Farkas:20,
    author = {Kata Farkas and David I. Walker and Evelien M. Adriaenssens and James E. McDonald and Luke S. Hillary and Shelagh K. Malham and Davey L. Jones},
    title = {Viral indicators for tracking domestic wastewater contamination in the aquatic environment},
    journal = {{Water Res}},
    year = {2020},
    volume = {181},
    pages = {115926},
    doi = {10.1016/j.watres.2020.115926},
    publisher = {Elsevier {BV}},
    }
  • [DOI] C. Zitzmann, B. Schmid, A. Ruggieri, A. S. Perelson, M. Binder, R. Bartenschlager, and L. Kaderali, "A coupled mathematical model of the intracellular replication of dengue virus and the host cell immune response to infection," Front Microbiol, vol. 11, p. 725, 2020.
    [Bibtex]
    @Article{Zitzmann:20,
    author = {Carolin Zitzmann and Bianca Schmid and Alessia Ruggieri and Alan S. Perelson and Marco Binder and Ralf Bartenschlager and Lars Kaderali},
    title = {A Coupled Mathematical Model of the Intracellular Replication of Dengue Virus and the Host Cell Immune Response to Infection},
    journal = {{Front Microbiol}},
    year = {2020},
    volume = {11},
    pages = {725},
    doi = {10.3389/fmicb.2020.00725},
    publisher = {Frontiers Media {SA}},
    }
  • [DOI] W. He, X. Ji, W. He, S. Dellicour, S. Wang, G. Li, L. Zhang, M. Gilbert, H. Zhu, G. Xing, M. Veit, Z. Huang, G. Han, Y. Huang, M. A. Suchard, G. Baele, P. Lemey, and S. Su, "Genomic epidemiology, evolution, and transmission dynamics of porcine deltacoronavirus," Mol Biol Evol, p. msaa117, 2020.
    [Bibtex]
    @Article{He:20,
    author = {Wan-Ting He and Xiang Ji and Wei He and Simon Dellicour and Shilei Wang and Gairu Li and Letian Zhang and Marius Gilbert and Henan Zhu and Gang Xing and Michael Veit and Zhen Huang and Guan-Zhu Han and Yaowei Huang and Marc A Suchard and Guy Baele and Philippe Lemey and Shuo Su},
    title = {Genomic epidemiology, evolution, and transmission dynamics of porcine deltacoronavirus},
    journal = {{Mol Biol Evol}},
    year = {2020},
    pages = {msaa117},
    doi = {10.1093/molbev/msaa117},
    editor = {Sergei Kosakovsky Pond},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] G. D. Maganga, A. Pinto, I. M. Mombo, M. Madjitobaye, A. M. M. Beyeme, L. Boundenga, M. A. Gouilh, N. N'Dilimabaka, J. F. Drexler, C. Drosten, and E. M. Leroy, "Genetic diversity and ecology of coronaviruses hosted by cave-dwelling bats in Gabon," Sci Rep, vol. 10, p. 7314, 2020.
    [Bibtex]
    @Article{Maganga:20,
    author = {Gael Darren Maganga and Anaïs Pinto and Illich Manfred Mombo and Mankomra Madjitobaye and Antoine Mitte Mbeang Beyeme and Larson Boundenga and Meriadeg Ar Gouilh and Nadine N'Dilimabaka and Jan Felix Drexler and Christian Drosten and Eric Maurice Leroy},
    title = {Genetic diversity and ecology of coronaviruses hosted by cave-dwelling bats in {G}abon},
    journal = {{Sci Rep}},
    year = {2020},
    volume = {10},
    pages = {7314},
    doi = {10.1038/s41598-020-64159-1},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] N. Groenke, J. Trimpert, S. Merz, A. M. Conradie, E. Wyler, H. Zhang, O. Hazapis, S. Rausch, M. Landthaler, N. Osterrieder, and D. Kunec, "Mechanism of virus attenuation by codon pair deoptimization," Cell Rep, vol. 31, iss. 4, p. 107586, 2020.
    [Bibtex]
    @Article{Groenke:20,
    author = {Nicole Groenke and Jakob Trimpert and Sophie Merz and Andel{\'{e}} M. Conradie and Emanuel Wyler and Hongwei Zhang and Orsalia-Georgia Hazapis and Sebastian Rausch and Markus Landthaler and Nikolaus Osterrieder and Dusan Kunec},
    title = {Mechanism of Virus Attenuation by Codon Pair Deoptimization},
    journal = {{Cell Rep}},
    year = {2020},
    volume = {31},
    number = {4},
    pages = {107586},
    doi = {10.1016/j.celrep.2020.107586},
    publisher = {Elsevier {BV}},
    }
  • [DOI] D. J. Pascall, K. Nomikou, E. Bréard, S. Zientara, A. S. da Filipe, B. Hoffmann, M. Jacquot, J. B. Singer, K. D. Clercq, A. B. o, C. Sailleau, C. Viarouge, C. Batten, G. Puggioni, C. Ligios, G. Savini, P. A. van Rijn, P. P. C. Mertens, R. Biek, and M. Palmarini, ""Frozen evolution" of an RNA virus suggests accidental release as a potential cause of arbovirus re-emergence," PLoS Biol, vol. 18, iss. 4, p. e3000673, 2020.
    [Bibtex]
    @Article{Pascall:20,
    author = {David J. Pascall and Kyriaki Nomikou and Emmanuel Br{\'{e}}ard and Stephan Zientara and Ana da Silva Filipe and Bernd Hoffmann and Maude Jacquot and Joshua B. Singer and Kris De Clercq and Anette B{\o}tner and Corinne Sailleau and Cyril Viarouge and Carrie Batten and Giantonella Puggioni and Ciriaco Ligios and Giovanni Savini and Piet A. van Rijn and Peter P. C. Mertens and Roman Biek and Massimo Palmarini},
    title = {"{F}rozen evolution" of an {RNA} virus suggests accidental release as a potential cause of arbovirus re-emergence},
    journal = {{PLoS Biol}},
    year = {2020},
    volume = {18},
    number = {4},
    pages = {e3000673},
    doi = {10.1371/journal.pbio.3000673},
    editor = {Andrew Fraser Read},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] L. V. Patrono, K. Pléh, L. Samuni, M. Ulrich, C. Röthemeier, A. Sachse, S. Muschter, A. Nitsche, E. Couacy-Hymann, C. Boesch, R. M. Wittig, S. Calvignac-Spencer, and F. H. Leendertz, "Monkeypox virus emergence in wild chimpanzees reveals distinct clinical outcomes and viral diversity," Nat Microbiol, vol. 5, p. 955–965, 2020.
    [Bibtex]
    @Article{Patrono:20,
    author = {Livia V. Patrono and Kamilla Pl{\'{e}}h and Liran Samuni and Markus Ulrich and Caroline Röthemeier and Andreas Sachse and Silvia Muschter and Andreas Nitsche and Emmanuel Couacy-Hymann and Christophe Boesch and Roman M. Wittig and S{\'{e}}bastien Calvignac-Spencer and Fabian H. Leendertz},
    title = {Monkeypox virus emergence in wild chimpanzees reveals distinct clinical outcomes and viral diversity},
    journal = {{Nat Microbiol}},
    year = {2020},
    volume = {5},
    pages = {955--965},
    doi = {10.1038/s41564-020-0706-0},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] A. W. Whisnant, C. S. Jürges, T. Hennig, E. Wyler, B. Prusty, A. J. Rutkowski, A. L'hernault, L. Djakovic, M. Göbel, K. Döring, J. Menegatti, R. Antrobus, N. J. Matheson, F. W. H. Künzig, G. Mastrobuoni, C. Bielow, S. Kempa, C. Liang, T. Dandekar, R. Zimmer, M. Landthaler, F. Grässer, P. J. Lehner, C. C. Friedel, F. Erhard, and L. Dölken, "Integrative functional genomics decodes herpes simplex virus 1," Nat Commun, vol. 11, p. 2038, 2020.
    [Bibtex]
    @Article{Whisnant:20,
    author = {Adam W. Whisnant and Christopher S. Jürges and Thomas Hennig and Emanuel Wyler and Bhupesh Prusty and Andrzej J. Rutkowski and Anne L'hernault and Lara Djakovic and Margarete Göbel and Kristina Döring and Jennifer Menegatti and Robin Antrobus and Nicholas J. Matheson and Florian W. H. Künzig and Guido Mastrobuoni and Chris Bielow and Stefan Kempa and Chunguang Liang and Thomas Dandekar and Ralf Zimmer and Markus Landthaler and Friedrich Grässer and Paul J. Lehner and Caroline C. Friedel and Florian Erhard and Lars Dölken},
    title = {Integrative functional genomics decodes herpes simplex virus 1},
    journal = {{Nat Commun}},
    year = {2020},
    volume = {11},
    pages = {2038},
    doi = {10.1038/s41467-020-15992-5},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] C. Mavian, S. K. Pond, S. Marini, B. R. Magalis, A. Vandamme, S. Dellicour, S. V. Scarpino, C. Houldcroft, J. Villabona-Arenas, T. K. Paisie, N. S. Trovão, C. Boucher, Y. Zhang, R. H. Scheuermann, O. Gascuel, T. T. Lam, M. A. Suchard, A. B. Abecasis, E. Wilkinson, T. de Oliveira, A. I. Bento, H. A. Schmidt, D. Martin, J. Hadfield, N. Faria, N. D. Grubaugh, R. A. Neher, G. Baele, P. Lemey, T. Stadler, J. Albert, K. A. Crandall, T. Leitner, A. Stamatakis, M. Prosperi, and M. Salemi, "Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable," Proc Natl Acad Sci USA, vol. 117, iss. 23, p. 12522–12523, 2020.
    [Bibtex]
    @Article{Mavian:20,
    author = {Carla Mavian and Sergei Kosakovsky Pond and Simone Marini and Brittany Rife Magalis and Anne-Mieke Vandamme and Simon Dellicour and Samuel V. Scarpino and Charlotte Houldcroft and Julian Villabona-Arenas and Taylor K. Paisie and N{\'{\i}}dia S. Trov{\~{a}}o and Christina Boucher and Yun Zhang and Richard H. Scheuermann and Olivier Gascuel and Tommy Tsan-Yuk Lam and Marc A. Suchard and Ana B. Abecasis and Eduan Wilkinson and Tulio de Oliveira and Ana I. Bento and Heiko A. Schmidt and Darren Martin and James Hadfield and Nuno Faria and Nathan D. Grubaugh and Richard A. Neher and Guy Baele and Philippe Lemey and Tanja Stadler and Jan Albert and Keith A. Crandall and Thomas Leitner and Alexandros Stamatakis and Mattia Prosperi and Marco Salemi},
    title = {Sampling bias and incorrect rooting make phylogenetic network tracing of {SARS}-{COV}-2 infections unreliable},
    journal = {{Proc Natl Acad Sci USA}},
    year = {2020},
    volume = {117},
    number = {23},
    pages = {12522--12523},
    doi = {10.1073/pnas.2007295117},
    publisher = {Proceedings of the National Academy of Sciences},
    }
  • [DOI] O. K. I. Bezuidt, P. H. Lebre, R. Pierneef, C. León-Sobrino, E. M. Adriaenssens, D. A. Cowan, Y. V. de Peer, and T. P. Makhalanyane, "Phages actively challenge niche communities in Antarctic soils," mSystems, vol. 5, iss. 3, p. e00234-20, 2020.
    [Bibtex]
    @Article{Bezuidt:20,
    author = {Oliver K. I. Bezuidt and Pedro Humberto Lebre and Rian Pierneef and Carlos Le{\'{o}}n-Sobrino and Evelien M. Adriaenssens and Don A. Cowan and Yves Van de Peer and Thulani P. Makhalanyane},
    title = {Phages Actively Challenge Niche Communities in {Antarctic} Soils},
    journal = {{mSystems}},
    year = {2020},
    volume = {5},
    number = {3},
    pages = {e00234-20},
    doi = {10.1128/msystems.00234-20},
    editor = {Theodore M. Flynn},
    publisher = {American Society for Microbiology},
    }
  • [DOI] T. T. N. Thao, F. Labroussaa, N. Ebert, P. V'Kovski, H. Stalder, J. Portmann, J. Kelly, S. Steiner, M. Holwerda, A. Kratzel, M. Gultom, K. Schmied, L. Laloli, L. Hüsser, M. Wider, S. Pfaender, D. Hirt, V. Cippà, S. Crespo-Pomar, S. Schröder, D. Muth, D. Niemeyer, V. Corman, M. A. Müller, C. Drosten, R. Dijkman, J. Jores, and V. Thiel, "Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform," Nature, vol. 582, p. 561–565, 2020.
    [Bibtex]
    @Article{Thao:20,
    author = {Tran Thi Nhu Thao and Fabien Labroussaa and Nadine Ebert and Philip V'Kovski and Hanspeter Stalder and Jasmine Portmann and Jenna Kelly and Silvio Steiner and Melle Holwerda and Annika Kratzel and Mitra Gultom and Kimberly Schmied and Laura Laloli and Linda Hüsser and Manon Wider and Stephanie Pfaender and Dagny Hirt and Valentina Cipp{\`{a}} and Silvia Crespo-Pomar and Simon Schröder and Doreen Muth and Daniela Niemeyer and Victor Corman and Marcel A. Müller and Christian Drosten and Ronald Dijkman and Joerg Jores and Volker Thiel},
    title = {Rapid reconstruction of {SARS}-{CoV}-2 using a synthetic genomics platform},
    journal = {Nature},
    year = {2020},
    volume = {582},
    pages = {561--565},
    doi = {10.1038/s41586-020-2294-9},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] M. Kuhring, J. Doellinger, A. Nitsche, T. Muth, and B. Y. Renard, "TaxIt: an iterative computational pipeline for untargeted strain-level identification using MS/MS spectra from pathogenic single-organism samples," J Proteome Res, vol. 19, iss. 6, p. 2501–2510, 2020.
    [Bibtex]
    @Article{Kuhring:20,
    author = {Mathias Kuhring and Joerg Doellinger and Andreas Nitsche and Thilo Muth and Bernhard Y. Renard},
    title = {{TaxIt}: An iterative computational pipeline for untargeted strain-level identification using {MS}/{MS} spectra from pathogenic single-organism samples},
    journal = {{J Proteome Res}},
    year = {2020},
    volume = {19},
    number = {6},
    pages = {2501--2510},
    doi = {10.1021/acs.jproteome.9b00714},
    publisher = {American Chemical Society ({ACS})},
    }
  • [DOI] R. L. Chua, S. Lukassen, S. Trump, B. P. Hennig, D. Wendisch, F. Pott, O. Debnath, L. Thürmann, F. Kurth, J. Kazmierski, B. Timmermann, S. Twardziok, S. Schneider, F. Machleidt, H. Müller-Redetzky, A. Krannich, S. Schmidt, F. Balzer, J. Liebig, J. Loske, J. Eils, N. Ishaque, C. von Kalle, A. Hocke, M. Witzenrath, C. Goffinet, C. Drosten, S. Laudi, I. Lehmann, C. Conrad, L. Sander, and R. Eils, "Cross-talk between the airway epithelium and activated immune cells defines severity in COVID-19," medRxiv, 2020.
    [Bibtex]
    @Article{Chua:20,
    author = {Robert Lorenz Chua and Soeren Lukassen and Saskia Trump and Bianca P Hennig and Daniel Wendisch and Fabian Pott and Olivia Debnath and Loreen Thürmann and Florian Kurth and Julia Kazmierski and Bernd Timmermann and Sven Twardziok and Stefan Schneider and Felix Machleidt and Holger Müller-Redetzky and Alexander Krannich and Sein Schmidt and Felix Balzer and Johannes Liebig and Jennifer Loske and Jürgen Eils and Naveed Ishaque and Christof von Kalle and Andreas Hocke and Martin Witzenrath and Christine Goffinet and Christian Drosten and Sven Laudi and Irina Lehmann and Christian Conrad and Leif-Erik Sander and Roland Eils},
    title = {Cross-talk between the airway epithelium and activated immune cells defines severity in {COVID}-19},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.04.29.20084327},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] W. Deboutte, L. Beller, C. K. Yinda, P. Maes, D. C. de Graaf, and J. Matthijnssens, "Honey-bee–associated prokaryotic viral communities reveal wide viral diversity and a profound metabolic coding potential," Proc Natl Acad Sci USA, vol. 117, iss. 19, p. 10511–10519, 2020.
    [Bibtex]
    @Article{Deboutte:20,
    author = {Ward Deboutte and Leen Beller and Claude Kwe Yinda and Piet Maes and Dirk C. de Graaf and Jelle Matthijnssens},
    title = {Honey-bee{\textendash}associated prokaryotic viral communities reveal wide viral diversity and a profound metabolic coding potential},
    journal = {{Proc Natl Acad Sci USA}},
    year = {2020},
    volume = {117},
    number = {19},
    pages = {10511--10519},
    doi = {10.1073/pnas.1921859117},
    publisher = {Proceedings of the National Academy of Sciences},
    }
  • [DOI] A. Baidaliuk, S. Lequime, I. Moltini-Conclois, S. Dabo, L. B. Dickson, M. Prot, V. Duong, P. Dussart, S. Boyer, C. Shi, J. Matthijnssens, J. Guglielmini, A. Gloria-Soria, E. Simon-Lorière, and L. Lambrechts, "Novel genome sequences of cell-fusing agent virus allow comparison of virus phylogeny with the genetic structure of Aedes aegypti populations," Virus Evol, vol. 6, iss. 1, p. veaa018, 2020.
    [Bibtex]
    @Article{Baidaliuk:20,
    author = {Artem Baidaliuk and S{\'{e}}bastian Lequime and Isabelle Moltini-Conclois and St{\'{e}}phanie Dabo and Laura B Dickson and Matthieu Prot and Veasna Duong and Philippe Dussart and S{\'{e}}bastien Boyer and Chenyan Shi and Jelle Matthijnssens and Julien Guglielmini and Andrea Gloria-Soria and Etienne Simon-Lori{\`{e}}re and Louis Lambrechts},
    title = {Novel genome sequences of cell-fusing agent virus allow comparison of virus phylogeny with the genetic structure of {Aedes} aegypti populations},
    journal = {{Virus Evol}},
    year = {2020},
    volume = {6},
    number = {1},
    pages = {veaa018},
    doi = {10.1093/ve/veaa018},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] A. E. Gorbalenya, M. Krupovic, A. Mushegian, A. M. Kropinski, S. G. Siddell, A. Varsani, M. J. Adams, A. J. Davison, B. E. Dutilh, B. Harrach, R. L. Harrison, S. Junglen, A. M. Q. King, N. J. Knowles, E. J. Lefkowitz, M. L. Nibert, L. Rubino, S. Sabanadzovic, H. Sanfaçon, P. Simmonds, P. J. Walker, M. F. Zerbini, J. H. Kuhn, and International Committee on Taxonomy of Viruses Executive Committee, "The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks," Nat Microbiol, vol. 5, iss. 5, p. 668–674, 2020.
    [Bibtex]
    @Article{Gorbalenya:20b,
    author = {Gorbalenya, Alexander E. and Krupovic, Mart and Mushegian, Arcady and Kropinski, Andrew M. and Siddell, Stuart G. and Varsani, Arvind and Adams, Michael J. and Davison, Andrew J. and Dutilh, Bas E. and Harrach, Balázs and Harrison, Robert L. and Junglen, Sandra and King, Andrew M. Q. and Knowles, Nick J. and Lefkowitz, Elliot J. and Nibert, Max L. and Rubino, Luisa and Sabanadzovic, Sead and Sanfaçon, Hélène and Simmonds, Peter and Walker, Peter J. and Zerbini, F. Murilo and Kuhn, Jens H. and {International Committee on Taxonomy of Viruses Executive Committee}},
    title = {The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks},
    journal = {{Nat Microbiol}},
    year = {2020},
    volume = {5},
    number = {5},
    pages = {668--674},
    doi = {10.1038/s41564-020-0709-x},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] B. Rockx, T. Kuiken, S. Herfst, T. Bestebroer, M. M. Lamers, B. B. Oude Munnink, D. de Meulder, G. van Amerongen, J. van den Brand, N. M. A. Okba, D. Schipper, P. van Run, L. Leijten, R. Sikkema, E. Verschoor, B. Verstrepen, W. Bogers, J. Langermans, C. Drosten, M. F. van Vlissingen, R. Fouchier, R. de Swart, M. Koopmans, and B. L. Haagmans, "Comparative pathogenesis of COVID-19, MERS, and SARS in a nonhuman primate model," Science, vol. 368, iss. 6494, p. 1012–1015, 2020.
    [Bibtex]
    @Article{Rockx:20,
    author = {Barry Rockx and Thijs Kuiken and Sander Herfst and Theo Bestebroer and Mart M. Lamers and Bas B. {Oude Munnink} and Dennis de Meulder and Geert van Amerongen and Judith van den Brand and Nisreen M. A. Okba and Debby Schipper and Peter van Run and Lonneke Leijten and Reina Sikkema and Ernst Verschoor and Babs Verstrepen and Willy Bogers and Jan Langermans and Christian Drosten and Martje Fentener van Vlissingen and Ron Fouchier and Rik de Swart and Marion Koopmans and Bart L. Haagmans},
    title = {Comparative pathogenesis of {COVID}-19, {MERS}, and {SARS} in a nonhuman primate model},
    journal = {Science},
    year = {2020},
    volume = {368},
    number = {6494},
    pages = {1012--1015},
    doi = {10.1126/science.abb7314},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
  • [DOI] K. Bačnik, D. Kutnjak, A. Pecman, N. Mehle, M. T. Žnidarič, I. G. Aguirre, and M. Ravnikar, "Viromics and infectivity analysis reveal the release of infective plant viruses from wastewater into the environment," Water Res, vol. 177, p. 115628, 2020.
    [Bibtex]
    @Article{Bacnik:20,
    author = {Katarina Ba{\v{c}}nik and Denis Kutnjak and Anja Pecman and Nata{\v{s}}a Mehle and Magda Tu{\v{s}}ek {\v{Z}}nidari{\v{c}} and Ion Guti{\'{e}}rrez Aguirre and Maja Ravnikar},
    title = {Viromics and infectivity analysis reveal the release of infective plant viruses from wastewater into the environment},
    journal = {{Water Res}},
    year = {2020},
    volume = {177},
    pages = {115628},
    doi = {10.1016/j.watres.2020.115628},
    publisher = {Elsevier {BV}},
    }
  • [DOI] K. Ciminski, F. Pfaff, M. Beer, and M. Schwemmle, "Bats reveal the true power of influenza A virus adaptability," PLoS Pathog, vol. 16, iss. 4, p. e1008384, 2020.
    [Bibtex]
    @Article{Ciminski:20,
    author = {Kevin Ciminski and Florian Pfaff and Martin Beer and Martin Schwemmle},
    title = {Bats reveal the true power of influenza {A} virus adaptability},
    journal = {{PLoS Pathog}},
    year = {2020},
    volume = {16},
    number = {4},
    pages = {e1008384},
    doi = {10.1371/journal.ppat.1008384},
    editor = {Andrew Mehle},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] N. F. Mostajo, M. Lataretu, S. Krautwurst, F. Mock, D. Desirò, K. Lamkiewicz, M. Collatz, A. Schoen, F. Weber, M. Marz, and M. Hölzer, "A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes," NAR Genom Bioinform, vol. 2, iss. 1, 2020.
    [Bibtex]
    @Article{Mostajo:20,
    author = {Nelly F Mostajo and Marie Lataretu and Sebastian Krautwurst and Florian Mock and Daniel Desir{\`{o}} and Kevin Lamkiewicz and Maximilian Collatz and Andreas Schoen and Friedemann Weber and Manja Marz and Martin Hölzer},
    title = {A comprehensive annotation and differential expression analysis of short and long non-coding {RNAs} in 16 bat genomes},
    journal = {{NAR Genom Bioinform}},
    year = {2020},
    volume = {2},
    number = {1},
    doi = {10.1093/nargab/lqz006},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] A. Kratzel, D. Todt, P. V'Kovski, S. Steiner, M. Gultom, T. T. N. Thao, N. Ebert, M. Holwerda, J. Steinmann, D. Niemeyer, R. Dijkman, G. Kampf, C. Drosten, E. Steinmann, V. Thiel, and S. Pfaender, "Inactivation of severe acute respiratory syndrome coronavirus 2 by WHO-recommended hand rub formulations and alcohols," Emerg Infect Dis, vol. 26, iss. 7, p. 1592–1595, 2020.
    [Bibtex]
    @Article{Kratzel:20,
    author = {Annika Kratzel and Daniel Todt and Philip V'Kovski and Silvio Steiner and Mitra Gultom and Tran Thi Nhu Thao and Nadine Ebert and Melle Holwerda and Jörg Steinmann and Daniela Niemeyer and Ronald Dijkman and Günter Kampf and Christian Drosten and Eike Steinmann and Volker Thiel and Stephanie Pfaender},
    title = {Inactivation of Severe Acute Respiratory Syndrome Coronavirus 2 by {WHO}-Recommended Hand Rub Formulations and Alcohols},
    journal = {{Emerg Infect Dis}},
    year = {2020},
    volume = {26},
    number = {7},
    pages = {1592--1595},
    doi = {10.3201/eid2607.200915},
    publisher = {Centers for Disease Control and Prevention ({CDC})},
    }
  • [DOI] A. Shannon, N. T. Le, B. Selisko, C. Eydoux, K. Alvarez, J. Guillemot, E. Decroly, O. Peersen, F. Ferron, and B. Canard, "Remdesivir and SARS-CoV-2: Structural requirements at both nsp12 RdRp and nsp14 Exonuclease active-sites," Antiviral Res, vol. 178, p. 104793, 2020.
    [Bibtex]
    @Article{Shannon:20,
    author = {Ashleigh Shannon and Nhung Thi-Tuyet Le and Barbara Selisko and Cecilia Eydoux and Karine Alvarez and Jean-Claude Guillemot and Etienne Decroly and Olve Peersen and Francois Ferron and Bruno Canard},
    title = {Remdesivir and {SARS}-{CoV}-2: {Structural} requirements at both nsp12 {RdRp} and nsp14 {Exonuclease} active-sites},
    journal = {{Antiviral Res}},
    year = {2020},
    volume = {178},
    pages = {104793},
    doi = {10.1016/j.antiviral.2020.104793},
    publisher = {Elsevier {BV}},
    }
  • [DOI] S. Lytras and J. Hughes, "Synonymous dinucleotide usage: a codon-aware metric for quantifying dinucleotide representation in viruses," Viruses, vol. 12, iss. 4, p. 462, 2020.
    [Bibtex]
    @Article{Lytras:20,
    author = {Spyros Lytras and Joseph Hughes},
    title = {Synonymous Dinucleotide Usage: A Codon-Aware Metric for Quantifying Dinucleotide Representation in Viruses},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    number = {4},
    pages = {462},
    doi = {10.3390/v12040462},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] N. C. Gassen, J. Papies, T. Bajaj, F. Dethloff, J. Emanuel, K. Weckmann, D. E. Heinz, N. Heinemann, M. Lennarz, A. Richter, D. Niemeyer, V. M. Corman, P. Giavalisco, C. Drosten, and M. A. Müller, "Analysis of SARS-CoV-2-controlled autophagy reveals spermidine, MK-2206, and niclosamide as putative antiviral therapeutics," bioRxiv, 2020.
    [Bibtex]
    @Article{Gassen:20,
    author = {Nils C. Gassen and Jan Papies and Thomas Bajaj and Frederik Dethloff and Jackson Emanuel and Katja Weckmann and Daniel E. Heinz and Nicolas Heinemann and Martina Lennarz and Anja Richter and Daniela Niemeyer and Victor M. Corman and Patrick Giavalisco and Christian Drosten and Marcel A. Müller},
    title = {Analysis of {SARS}-{CoV}-2-controlled autophagy reveals spermidine, {MK}-2206, and niclosamide as putative antiviral therapeutics},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.04.15.997254},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] D. Bestle, M. R. Heindl, H. Limburg, T. V. L. van, O. Pilgram, H. Moulton, D. A. Stein, K. Hardes, M. Eickmann, O. Dolnik, C. Rohde, S. Becker, H. Klenk, W. Garten, T. Steinmetzer, and E. Böttcher-Friebertshäuser, "TMPRSS2 and furin are both essential for proteolytic activation and spread of SARS-CoV-2 in human airway epithelial cells and provide promising drug targets," bioRxiv, 2020.
    [Bibtex]
    @Article{Bestle:20,
    author = {Dorothea Bestle and Miriam Ruth Heindl and Hannah Limburg and Thuy Van Lam van and Oliver Pilgram and Hong Moulton and David A. Stein and Kornelia Hardes and Markus Eickmann and Olga Dolnik and Cornelius Rohde and Stephan Becker and Hans-Dieter Klenk and Wolfgang Garten and Torsten Steinmetzer and Eva Böttcher-Friebertshäuser},
    title = {{TMPRSS}2 and furin are both essential for proteolytic activation and spread of {SARS}-{CoV}-2 in human airway epithelial cells and provide promising drug targets},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.04.15.042085},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] J. A. Hayward, M. Tachedjian, A. Johnson, T. B. Gordon, J. Cui, G. A. Marsh, M. L. Baker, L. Wang, and G. Tachedjian, "Bats possess unique variants of the antiviral restriction factor tetherin," bioRxiv, 2020.
    [Bibtex]
    @Article{Hayward:20,
    author = {Joshua A. Hayward and Mary Tachedjian and Adam Johnson and Tamsin B. Gordon and Jie Cui and Glenn A. Marsh and Michelle L. Baker and Lin-Fa Wang and Gilda Tachedjian},
    title = {Bats Possess Unique Variants of the Antiviral Restriction Factor Tetherin},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.04.08.031203},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] J. F. Gogarten, M. Rühlemann, E. Archie, J. Tung, C. Akoua-Koffi, C. Bang, T. Deschner, J. Muyembe-Tamfun, M. M. Robbins, G. Schubert, M. Surbeck, R. M. Wittig, K. Zuberbühler, J. F. Baines, A. Franke, F. H. Leendertz, and S. Calvignac-Spencer, "Primate phageomes are structured by superhost phylogeny and environment," bioRxiv, 2020.
    [Bibtex]
    @Article{Gogarten:20,
    author = {Jan F. Gogarten and Malte Rühlemann and Elizabeth Archie and Jenny Tung and Chantal Akoua-Koffi and Corinna Bang and Tobias Deschner and Jean-Jacques Muyembe-Tamfun and Martha M. Robbins and Grit Schubert and Martin Surbeck and Roman M. Wittig and Klaus Zuberbühler and John F. Baines and Andre Franke and Fabian H. Leendertz and S{\'{e}}bastien Calvignac-Spencer},
    title = {Primate phageomes are structured by superhost phylogeny and environment},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.04.06.011684},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] V. Navratil, L. Lionnard, S. Longhi, M. Hardwick, C. Combet, and A. Aouacheria, "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) envelope (E) protein harbors a conserved BH3-like sequence," bioRxiv, 2020.
    [Bibtex]
    @Article{Navratil:20,
    author = {Vincent Navratil and Loic Lionnard and Sonia Longhi and Marie Hardwick and Christophe Combet and Abdel Aouacheria},
    title = {The severe acute respiratory syndrome coronavirus 2 ({SARS}-{CoV}-2) envelope ({E}) protein harbors a conserved {BH}3-like sequence},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.04.09.033522},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. Hoffmann, M. T. Monaghan, and K. Reinert, "PriSeT: efficient de novo primer discovery," bioRxiv, 2020.
    [Bibtex]
    @Article{Hoffmann:20b,
    author = {Marie Hoffmann and Michael T. Monaghan and Knut Reinert},
    title = {{PriSeT}: Efficient De Novo Primer Discovery},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.04.06.027961},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] T. I. Vasylyeva, A. Zarebski, P. Smyrnov, L. D. Williams, A. Korobchuk, M. Liulchuk, V. Zadorozhna, G. Nikolopoulos, D. Paraskevis, J. Schneider, B. Skaathun, A. Hatzakis, O. G. Pybus, and S. R. Friedman, "Phylodynamics helps to evaluate the impact of an HIV prevention intervention," Viruses, vol. 12, iss. 4, p. 469, 2020.
    [Bibtex]
    @Article{Vasylyeva:20,
    author = {Tetyana I. Vasylyeva and Alexander Zarebski and Pavlo Smyrnov and Leslie D. Williams and Ania Korobchuk and Mariia Liulchuk and Viktoriia Zadorozhna and Georgios Nikolopoulos and Dimitrios Paraskevis and John Schneider and Britt Skaathun and Angelos Hatzakis and Oliver G. Pybus and Samuel R. Friedman},
    title = {Phylodynamics Helps to Evaluate the Impact of an {HIV} Prevention Intervention},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    number = {4},
    pages = {469},
    doi = {10.3390/v12040469},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] T. Koch, C. Dahlke, A. Fathi, A. Kupke, V. Krähling, N. M. A. Okba, S. Halwe, C. Rohde, M. Eickmann, A. Volz, T. Hesterkamp, A. Jambrecina, S. Borregaard, M. L. Ly, M. E. Zinser, E. Bartels, J. S. H. Poetsch, R. Neumann, R. Fux, S. Schmiedel, A. W. Lohse, B. L. Haagmans, G. Sutter, S. Becker, and M. M. Addo, "Safety and immunogenicity of a modified vaccinia virus Ankara vector vaccine candidate for Middle East respiratory syndrome: an open-label, phase 1 trial," Lancet Infect Dis, vol. 20, iss. 7, p. 827–838, 2020.
    [Bibtex]
    @Article{Koch:20,
    author = {Till Koch and Christine Dahlke and Anahita Fathi and Alexandra Kupke and Verena Krähling and Nisreen M A Okba and Sandro Halwe and Cornelius Rohde and Markus Eickmann and Asisa Volz and Thomas Hesterkamp and Alen Jambrecina and Saskia Borregaard and My L Ly and Madeleine E Zinser and Etienne Bartels and Joseph S H Poetsch and Reza Neumann and Robert Fux and Stefan Schmiedel and Ansgar W Lohse and Bart L Haagmans and Gerd Sutter and Stephan Becker and Marylyn M Addo},
    title = {Safety and immunogenicity of a modified vaccinia virus {Ankara} vector vaccine candidate for {Middle East} respiratory syndrome: an open-label, phase 1 trial},
    journal = {{Lancet Infect Dis}},
    year = {2020},
    volume = {20},
    number = {7},
    pages = {827--838},
    doi = {10.1016/s1473-3099(20)30248-6},
    publisher = {Elsevier {BV}},
    }
  • [DOI] P. M. Folegatti, M. Bittaye, A. Flaxman, F. R. Lopez, D. Bellamy, A. Kupke, C. Mair, R. Makinson, J. Sheridan, C. Rohde, S. Halwe, Y. Jeong, Y. Park, J. Kim, M. Song, A. Boyd, N. Tran, D. Silman, I. Poulton, M. Datoo, J. Marshal, Y. Themistocleous, A. Lawrie, R. Roberts, E. Berrie, S. Becker, T. Lambe, A. Hill, K. Ewer, and S. Gilbert, "Safety and immunogenicity of a candidate Middle East respiratory syndrome coronavirus viral-vectored vaccine: a dose-escalation, open-label, non-randomised, uncontrolled, phase 1 trial," Lancet Infect Dis, vol. 20, iss. 7, p. 816–826, 2020.
    [Bibtex]
    @Article{Folegatti:20,
    author = {Pedro M Folegatti and Mustapha Bittaye and Amy Flaxman and Fernando Ramos Lopez and Duncan Bellamy and Alexandra Kupke and Catherine Mair and Rebecca Makinson and Jonathan Sheridan and Cornelius Rohde and Sandro Halwe and Yuji Jeong and Young-Shin Park and Jae-Ouk Kim and Manki Song and Amy Boyd and Nguyen Tran and Daniel Silman and Ian Poulton and Mehreen Datoo and Julia Marshal and Yrene Themistocleous and Alison Lawrie and Rachel Roberts and Eleanor Berrie and Stephan Becker and Teresa Lambe and Adrian Hill and Katie Ewer and Sarah Gilbert},
    title = {Safety and immunogenicity of a candidate {Middle East} respiratory syndrome coronavirus viral-vectored vaccine: a dose-escalation, open-label, non-randomised, uncontrolled, phase 1 trial},
    journal = {{Lancet Infect Dis}},
    year = {2020},
    volume = {20},
    number = {7},
    pages = {816--826},
    doi = {10.1016/s1473-3099(20)30160-2},
    publisher = {Elsevier {BV}},
    }
  • [DOI] K. Wernike and M. Beer, "Re-circulation of Schmallenberg virus, Germany, 2019," Transbound Emerg Dis, 2020.
    [Bibtex]
    @Article{Wernike:20,
    author = {Kerstin Wernike and Martin Beer},
    title = {Re-circulation of {S}chmallenberg virus, {G}ermany, 2019},
    journal = {{Transbound Emerg Dis}},
    year = {2020},
    doi = {10.1111/tbed.13592},
    publisher = {Wiley},
    }
  • [DOI] M. Hoffmann, S. Schroeder, H. Kleine-Weber, M. A. Müller, C. Drosten, and S. Pöhlmann, "Nafamostat mesylate blocks activation of SARS-CoV-2: new treatment option for COVID-19," Antimicrob Agents Chemother, vol. 64, p. e00754-20, 2020.
    [Bibtex]
    @Article{Hoffmann:20c,
    author = {Markus Hoffmann and Simon Schroeder and Hannah Kleine-Weber and Marcel A. Müller and Christian Drosten and Stefan Pöhlmann},
    title = {Nafamostat mesylate blocks activation of {SARS}-{CoV}-2: New treatment option for {COVID}-19},
    journal = {{Antimicrob Agents Chemother}},
    year = {2020},
    volume = {64},
    pages = {e00754-20},
    doi = {10.1128/aac.00754-20},
    publisher = {American Society for Microbiology},
    }
  • [DOI] P. V'Kovski, S. Steiner, M. Gultom, J. N. Kelly, J. Russeil, B. Mangeat, E. Cora, J. Pezoldt, M. Holwerda, A. Kratzel, L. Laloli, M. Wider, J. Portmann, T. T. N. Thao, N. Ebert, H. Stalder, R. Hartmann, V. Gardeux, D. Alpern, B. Deplancke, V. Thiel, and R. Dijkman, "Disparate temperature-dependent virus - host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epithelium," bioRxiv, 2020.
    [Bibtex]
    @Article{Vkovski:20,
    author = {Philip V'Kovski and Silvio Steiner and Mitra Gultom and Jenna N Kelly and Julie Russeil and Bastien Mangeat and Elisa Cora and Joern Pezoldt and Melle Holwerda and Annika Kratzel and Laura Laloli and Manon Wider and Jasmine Portmann and Tran Thi Nhu Thao and Nadine Ebert and Hanspeter Stalder and Rune Hartmann and Vincent Gardeux and Daniel Alpern and Bart Deplancke and Volker Thiel and Ronald Dijkman},
    title = {Disparate temperature-dependent virus - host dynamics for {SARS}-{CoV}-2 and {SARS}-{CoV} in the human respiratory epithelium},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.04.27.062315},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] H. Anzt, F. Bach, S. Druskat, F. Löffler, A. Loewe, B. Y. Renard, G. Seemann, A. Struck, E. Achhammer, P. Aggarwal, F. Appel, M. Bader, L. Brusch, C. Busse, G. Chourdakis, P. W. Dabrowski, P. Ebert, B. Flemisch, S. Friedl, B. Fritzsch, M. D. Funk, V. Gast, F. Goth, J. Grad, S. Hermann, F. Hohmann, S. Janosch, D. Kutra, J. Linxweiler, T. Muth, W. Peters-Kottig, F. Rack, F. H. C. Raters, S. Rave, G. Reina, M. Reißig, T. Ropinski, J. Schaarschmidt, H. Seibold, J. P. Thiele, B. Uekerman, S. Unger, and R. Weeber, "An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action," F1000Res, vol. 9, p. 295, 2020.
    [Bibtex]
    @Article{Anzt:20,
    author = {Hartwig Anzt and Felix Bach and Stephan Druskat and Frank Löffler and Axel Loewe and Bernhard Y. Renard and Gunnar Seemann and Alexander Struck and Elke Achhammer and Piush Aggarwal and Franziska Appel and Michael Bader and Lutz Brusch and Christian Busse and Gerasimos Chourdakis and Piotr Wojciech Dabrowski and Peter Ebert and Bernd Flemisch and Sven Friedl and Bernadette Fritzsch and Maximilian D. Funk and Volker Gast and Florian Goth and Jean-Noël Grad and Sibylle Hermann and Florian Hohmann and Stephan Janosch and Dominik Kutra and Jan Linxweiler and Thilo Muth and Wolfgang Peters-Kottig and Fabian Rack and Fabian H.C. Raters and Stephan Rave and Guido Reina and Malte Rei{\ss}ig and Timo Ropinski and Joerg Schaarschmidt and Heidi Seibold and Jan P. Thiele and Benjamin Uekerman and Stefan Unger and Rudolf Weeber},
    title = {An environment for sustainable research software in {G}ermany and beyond: current state, open challenges, and call for action},
    journal = {{F1000Res}},
    year = {2020},
    volume = {9},
    pages = {295},
    doi = {10.12688/f1000research.23224.1},
    publisher = {F1000 Research Ltd},
    }
  • [DOI] P. J. Hotez, M. E. Bottazzi, S. K. Singh, P. J. Brindley, and S. Kamhawi, "Will COVID-19 become the next neglected tropical disease?," PLoS Negl Trop Dis, vol. 14, iss. 4, p. e0008271, 2020.
    [Bibtex]
    @Article{Hotez:20,
    author = {Peter J. Hotez and Maria E. Bottazzi and Sunit K. Singh and Paul J. Brindley and Shaden Kamhawi},
    title = {Will {COVID}-19 become the next neglected tropical disease?},
    journal = {{PLoS Negl Trop Dis}},
    year = {2020},
    volume = {14},
    number = {4},
    pages = {e0008271},
    doi = {10.1371/journal.pntd.0008271},
    editor = {Sara Lustigman},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] N. M. A. Okba, M. A. Müller, W. Li, C. Wang, C. H. GeurtsvanKessel, V. M. Corman, M. M. Lamers, R. S. Sikkema, E. de Bruin, F. D. Chandler, Y. Yazdanpanah, Q. L. Hingrat, D. Descamps, N. Houhou-Fidouh, C. B. E. M. Reusken, B. Bosch, C. Drosten, M. P. G. Koopmans, and B. L. Haagmans, "Severe acute respiratory syndrome coronavirus 2-specific antibody responses in coronavirus disease 2019 patients," Emerg Infect Dis, vol. 26, iss. 7, p. 1478–1488, 2020.
    [Bibtex]
    @Article{Okba:20,
    author = {Nisreen M.A. Okba and Marcel A. Müller and Wentao Li and Chunyan Wang and Corine H. GeurtsvanKessel and Victor M. Corman and Mart M. Lamers and Reina S. Sikkema and Erwin de Bruin and Felicity D. Chandler and Yazdan Yazdanpanah and Quentin Le Hingrat and Diane Descamps and Nadhira Houhou-Fidouh and Chantal B.E.M. Reusken and Berend-Jan Bosch and Christian Drosten and Marion P.G. Koopmans and Bart L. Haagmans},
    title = {Severe Acute Respiratory Syndrome Coronavirus 2-Specific Antibody Responses in Coronavirus Disease 2019 Patients},
    journal = {{Emerg Infect Dis}},
    year = {2020},
    volume = {26},
    number = {7},
    pages = {1478--1488},
    doi = {10.3201/eid2607.200841},
    publisher = {Centers for Disease Control and Prevention ({CDC})},
    }
  • [DOI] G. Venturi, S. W. Aberle, T. Avšič-Županc, L. Barzon, C. Batejat, E. Burdino, F. Carletti, R. Charrel, I. Christova, J. Connell, V. M. Corman, M. Emmanouil, A. J. Jääskeläinen, I. Kurolt, Y. Lustig, M. J. Martinez, M. Koopmans, O. Nagy, T. Nguyen, A. Papa, M. Pérez-Ruiz, M. Pfeffer, J. Protic, J. Reimerink, G. Rossini, M. P. S. Fariñas, J. Schmidt-Chanasit, S. Söderholm, B. Sudre, M. V. Esbroeck, and C. R. B. and, "Specialist laboratory networks as preparedness and response tool - the Emerging Viral Diseases-Expert Laboratory Network and the Chikungunya outbreak, Thailand, 2019," Euro Surveill, vol. 25, iss. 13, p. 1900438, 2020.
    [Bibtex]
    @Article{Venturi:20,
    author = {Giulietta Venturi and Stephan W Aberle and Tatjana Av{\v{s}}i{\v{c}}-{\v{Z}}upanc and Luisa Barzon and Christoph Batejat and Elisa Burdino and Fabrizio Carletti and R{\'{e}}mi Charrel and Iva Christova and Jeff Connell and Victor Max Corman and Mary Emmanouil and Anne J Jääskeläinen and Ivan Kurolt and Yaniv Lustig and Miguel J Martinez and Marion Koopmans and Orsolya Nagy and Trung Nguyen and Anna Papa and Mercedes P{\'{e}}rez-Ruiz and Martin Pfeffer and Jelena Protic and Johan Reimerink and Giada Rossini and Mar{\'{\i}}a Paz S{\'{a}}nchez-Seco Fari{\~{n}}as and Jonas Schmidt-Chanasit and Sandra Söderholm and Bertrand Sudre and Marjan Van Esbroeck and Chantal B Reusken and},
    title = {Specialist laboratory networks as preparedness and response tool - the {E}merging {V}iral {D}iseases-{E}xpert {L}aboratory {N}etwork and the {C}hikungunya outbreak, {T}hailand, 2019},
    journal = {{Euro Surveill}},
    year = {2020},
    volume = {25},
    number = {13},
    pages = {1900438},
    doi = {10.2807/1560-7917.es.2020.25.13.1900438},
    publisher = {European Centre for Disease Control and Prevention ({ECDC})},
    }
  • [DOI] D. P. Depledge and A. C. Wilson, "Using direct RNA nanopore sequencing to deconvolute viral transcriptomes," Curr Protoc Microbiol, vol. 57, iss. 1, 2020.
    [Bibtex]
    @Article{Depledge:20,
    author = {Daniel P. Depledge and Angus C. Wilson},
    title = {Using Direct {RNA} Nanopore Sequencing to Deconvolute Viral Transcriptomes},
    journal = {{Curr Protoc Microbiol}},
    year = {2020},
    volume = {57},
    number = {1},
    doi = {10.1002/cpmc.99},
    publisher = {Wiley},
    }
  • [DOI] R. Wölfel, V. M. Corman, W. Guggemos, M. Seilmaier, S. Zange, M. A. Müller, D. Niemeyer, T. C. Jones, P. Vollmar, C. Rothe, M. Hoelscher, T. Bleicker, S. Brünink, J. Schneider, R. Ehmann, K. Zwirglmaier, C. Drosten, and C. Wendtner, "Virological assessment of hospitalized patients with COVID-2019," Nature, vol. 581, p. 465–469, 2020.
    [Bibtex]
    @Article{Wölfel:20,
    author = {Roman Wölfel and Victor M. Corman and Wolfgang Guggemos and Michael Seilmaier and Sabine Zange and Marcel A. Müller and Daniela Niemeyer and Terry C. Jones and Patrick Vollmar and Camilla Rothe and Michael Hoelscher and Tobias Bleicker and Sebastian Brünink and Julia Schneider and Rosina Ehmann and Katrin Zwirglmaier and Christian Drosten and Clemens Wendtner},
    title = {Virological assessment of hospitalized patients with {COVID}-2019},
    journal = {Nature},
    year = {2020},
    volume = {581},
    pages = {465--469},
    doi = {10.1038/s41586-020-2196-x},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] H. F. Löchel and D. Heider, "Comparative analyses of error handling strategies for next-generation sequencing in precision medicine," Sci Rep, vol. 10, p. 5750, 2020.
    [Bibtex]
    @Article{Löchel:20,
    author = {Hannah F. Löchel and Dominik Heider},
    title = {Comparative analyses of error handling strategies for next-generation sequencing in precision medicine},
    journal = {{Sci Rep}},
    year = {2020},
    volume = {10},
    pages = {5750},
    doi = {10.1038/s41598-020-62675-8},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] J. N. Kelly, L. Laloli, P. V'Kovski, M. Holwerda, J. Portmann, V. Thiel, and R. Dijkman, "Comprehensive single cell analysis of pandemic influenza A virus infection in the human airways uncovers cell-type specific host transcriptional signatures relevant for disease progression and pathogenesis.," bioRxiv, 2020.
    [Bibtex]
    @Article{Kelly:20,
    author = {Jenna N Kelly and Laura Laloli and Philip V'Kovski and Melle Holwerda and Jasmine Portmann and Volker Thiel and Ronald Dijkman},
    title = {Comprehensive single cell analysis of pandemic influenza {A} virus infection in the human airways uncovers cell-type specific host transcriptional signatures relevant for disease progression and pathogenesis.},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.04.03.014282},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] D. Bojkova, J. E. McGreig, K. McLaughlin, S. G. Masterson, M. Widera, V. Kraehling, S. Ciesek, M. N. Wass, M. Michaelis, and J. N. Cinatl, "SARS-CoV-2 and SARS-CoV differ in their cell tropism and drug sensitivity profiles," bioRxiv, 2020.
    [Bibtex]
    @Article{Bojkova:20,
    author = {Denisa Bojkova and Jake E McGreig and Katie-May McLaughlin and Stuart G Masterson and Marek Widera and Verena Kraehling and Sandra Ciesek and Mark N Wass and Martin Michaelis and Jindrich N Cinatl},
    title = {{SARS}-{CoV}-2 and {SARS}-{CoV} differ in their cell tropism and drug sensitivity profiles},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.04.03.024257},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] É. Leal, C. R. Arrais, M. Barreiros, J. K. F. Rodrigues, N. P. S. Sousa, D. D. Costa, F. D. R. P. Santos, A. D. Silva, A. I. S. e Viana, A. K. Barros, and K. O. de Lima, "Characterization of HIV-1 genetic diversity and antiretroviral resistance in the state of Maranhão, Northeast Brazil," PLoS One, vol. 15, iss. 3, p. e0230878, 2020.
    [Bibtex]
    @Article{Leal:20,
    author = {{\'{E}}lcio Leal and Claudia Regina Arrais and Marta Barreiros and Jessyca Kalynne Farias Rodrigues and Nilviane Pires Silva Sousa and Daniel Duarte Costa and Francisco Dimitre Rodrigo Pereira Santos and Antonio Dantas Silva and Antonia Iracilda e Silva Viana and Allan Kardec Barros and Kledoaldo Oliveira de Lima},
    title = {Characterization of {HIV}-1 genetic diversity and antiretroviral resistance in the state of {M}aranh{\~{a}}o, {Northeast Brazil}},
    journal = {{PLoS One}},
    year = {2020},
    volume = {15},
    number = {3},
    pages = {e0230878},
    doi = {10.1371/journal.pone.0230878},
    editor = {Luis Men{\'{e}}ndez-Arias},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] M. R. Capobianchi, M. Rueca, F. Messina, E. Giombini, F. Carletti, F. Colavita, C. Castilletti, E. Lalle, L. Bordi, F. Vairo, E. Nicastri, G. Ippolito, C. E. M. Gruber, and B. Bartolini, "Molecular characterization of SARS-CoV-2 from the first case of COVID-19 in Italy," Clin Microbiol Infect, vol. 26, iss. 7, p. 954–956, 2020.
    [Bibtex]
    @Article{Capobianchi:20,
    author = {M.R. Capobianchi and M. Rueca and F. Messina and E. Giombini and F. Carletti and F. Colavita and C. Castilletti and E. Lalle and L. Bordi and F. Vairo and E. Nicastri and G. Ippolito and C.E.M. Gruber and B. Bartolini},
    title = {Molecular characterization of {SARS}-{CoV}-2 from the first case of {COVID}-19 in {Italy}},
    journal = {{Clin Microbiol Infect}},
    year = {2020},
    volume = {26},
    number = {7},
    pages = {954--956},
    doi = {10.1016/j.cmi.2020.03.025},
    publisher = {Elsevier {BV}},
    }
  • [DOI] D. Blanco-Melo, B. E. Nilsson-Payant, W. Liu, S. Uhl, D. Hoagland, R. M. o, T. X. Jordan, K. Oishi, M. Panis, D. Sachs, T. T. Wang, R. E. Schwartz, J. K. Lim, R. A. Albrecht, and B. R. tenOever, "Imbalanced host response to SARS-CoV-2 drives development of COVID-19," Cell, vol. 181, iss. 5, p. 1036–1045.e9, 2020.
    [Bibtex]
    @Article{Blanco-Melo:20a,
    author = {Daniel Blanco-Melo and Benjamin E. Nilsson-Payant and Wen-Chun Liu and Skyler Uhl and Daisy Hoagland and Rasmus M{\o}ller and Tristan X. Jordan and Kohei Oishi and Maryline Panis and David Sachs and Taia T. Wang and Robert E. Schwartz and Jean K. Lim and Randy A. Albrecht and Benjamin R. tenOever},
    title = {Imbalanced host response to {SARS}-{CoV}-2 drives development of {COVID}-19},
    journal = {{Cell}},
    year = {2020},
    volume = {181},
    number = {5},
    pages = {1036--1045.e9},
    doi = {10.1016/j.cell.2020.04.026},
    publisher = {Elsevier {BV}},
    }
  • [DOI] V. M. Corman, H. F. Rabenau, O. Adams, D. Oberle, M. B. Funk, B. Keller-Stanislawski, J. Timm, C. Drosten, and S. Ciesek, "SARS-CoV-2 asymptomatic and symptomatic patients and risk for transfusion transmission," Transfusion, vol. 60, iss. 6, p. 1119–1122, 2020.
    [Bibtex]
    @Article{Corman:20a,
    author = {Victor M Corman and Holger F Rabenau and Ortwin Adams and Doris Oberle and Markus B Funk and Brigitte Keller-Stanislawski and Joerg Timm and Christian Drosten and Sandra Ciesek},
    title = {{SARS}-{CoV}-2 asymptomatic and symptomatic patients and risk for transfusion transmission},
    journal = {{Transfusion}},
    year = {2020},
    volume = {60},
    number = {6},
    pages = {1119--1122},
    doi = {10.1111/trf.15841},
    publisher = {Wiley},
    }
  • [DOI] V. Thiel, "Viral RNA in an m6A disguise," Nat Microbiol, vol. 5, iss. 4, p. 531–532, 2020.
    [Bibtex]
    @Article{Thiel:20,
    author = {Volker Thiel},
    title = {Viral {RNA} in an m6{A} disguise},
    journal = {{Nat Microbiol}},
    year = {2020},
    volume = {5},
    number = {4},
    pages = {531--532},
    doi = {10.1038/s41564-020-0689-x},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] M. Pingarilho, V. F. Pimentel, I. Diogo, S. Fernandes, M. Miranda, A. Pineda-Pena, P. Libin, K. Theys, R. O. M. Martins, A. Vandamme, P. Gomes, and A. B. Abecasis, "Increasing prevalence of HIV-1 Transmitted Drug Resistance in Portugal: implications for first line treatment recommendations," medRxiv, 2020.
    [Bibtex]
    @Article{Pingarilho:20,
    author = {Marta Pingarilho and Victor F Pimentel and Isabel Diogo and Sandra Fernandes and Mafalda Miranda and Andrea Pineda-Pena and Pieter Libin and Kristof Theys and M. Rosario Oliveira Martins and Annemieke Vandamme and Perpetua Gomes and Ana B. Abecasis},
    title = {Increasing prevalence of {HIV}-1 {Transmitted Drug Resistance} in {Portugal}: implications for first line treatment recommendations},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.03.17.20033092},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] D. Paraskevis, E. Kostaki, G. Magiorkinis, G. Panayiotakopoulos, G. Sourvinos, and S. Tsiodras, "Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event," Infect Genet Evol, vol. 79, p. 104212, 2020.
    [Bibtex]
    @Article{Paraskevis:20,
    author = {D. Paraskevis and E. Kostaki and G. Magiorkinis and G. Panayiotakopoulos and G. Sourvinos and S. Tsiodras},
    title = {Full-genome evolutionary analysis of the novel corona virus (2019-{nCoV}) rejects the hypothesis of emergence as a result of a recent recombination event},
    journal = {{Infect Genet Evol}},
    year = {2020},
    volume = {79},
    pages = {104212},
    doi = {10.1016/j.meegid.2020.104212},
    publisher = {Elsevier {BV}},
    }
  • [DOI] A. Grifoni, J. Sidney, Y. Zhang, R. H. Scheuermann, B. Peters, and A. Sette, "A sequence homology and bioinformatic approach can predict candidate targets for immune responses to SARS-CoV-2," Cell Host Microbe, vol. 27, iss. 4, p. 671–680.e2, 2020.
    [Bibtex]
    @Article{Grifoni:20a,
    author = {Alba Grifoni and John Sidney and Yun Zhang and Richard H. Scheuermann and Bjoern Peters and Alessandro Sette},
    title = {A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to {SARS}-{CoV}-2},
    journal = {{Cell Host Microbe}},
    year = {2020},
    volume = {27},
    number = {4},
    pages = {671--680.e2},
    doi = {10.1016/j.chom.2020.03.002},
    publisher = {Elsevier {BV}},
    }
  • [DOI] J. Kaczorowska and L. van der Hoek, "Human Anelloviruses: diverse, omnipresent and commensal members of the virome," FEMS Microbiol Rev, vol. 44, iss. 3, p. 305–313, 2020.
    [Bibtex]
    @Article{Kaczorowska:20,
    author = {Joanna Kaczorowska and Lia van der Hoek},
    title = {Human {A}nelloviruses: diverse, omnipresent and commensal members of the virome},
    journal = {{FEMS Microbiol Rev}},
    year = {2020},
    volume = {44},
    number = {3},
    pages = {305--313},
    doi = {10.1093/femsre/fuaa007},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] L. Zhang, D. Lin, X. Sun, U. Curth, C. Drosten, L. Sauerhering, S. Becker, K. Rox, and R. Hilgenfeld, "Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved $\alpha$-ketoamide inhibitors," Science, vol. 368, iss. 6489, p. eabb3405, 2020.
    [Bibtex]
    @Article{Zhang:20,
    author = {Linlin Zhang and Daizong Lin and Xinyuanyuan Sun and Ute Curth and Christian Drosten and Lucie Sauerhering and Stephan Becker and Katharina Rox and Rolf Hilgenfeld},
    title = {Crystal structure of {SARS}-{CoV}-2 main protease provides a basis for design of improved $\alpha$-ketoamide inhibitors},
    journal = {Science},
    year = {2020},
    volume = {368},
    number = {6489},
    pages = {409--412},
    pages = {eabb3405},
    doi = {10.1126/science.abb3405},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
  • [DOI] E. M. Adriaenssens, M. B. Sullivan, P. Knezevic, L. J. van Zyl, B. L. Sarkar, B. E. Dutilh, P. Alfenas-Zerbini, M. L, Y. Tong, J. R. Brister, A. M. I. Switt, J. Klumpp, R. K. Aziz, J. Barylski, J. Uchiyama, R. A. Edwards, A. M. Kropinski, N. K. Petty, M. R. J. Clokie, A. I. Kushkina, V. V. Morozova, S. Duffy, A. Gillis, J. Rumnieks, I. Kurtböke, N. Chanishvili, L. Goodridge, J. Wittmann, R. Lavigne, H. B. Jang, D. Prangishvili, F. Enault, D. Turner, M. M. Poranen, H. M. Oksanen, and M. Krupovic, "Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee," Arch Virol, vol. 165, p. 1253–1260, 2020.
    [Bibtex]
    @Article{Adriaenssens:20,
    author = {Evelien M. Adriaenssens and Matthew B. Sullivan and Petar Knezevic and Leonardo J. van Zyl and B. L. Sarkar and Bas E. Dutilh and Poliane Alfenas-Zerbini and Ma{\l}gorzata {\L}obocka and Yigang Tong and James Rodney Brister and Andrea I. Moreno Switt and Jochen Klumpp and Ramy Karam Aziz and Jakub Barylski and Jumpei Uchiyama and Rob A. Edwards and Andrew M. Kropinski and Nicola K. Petty and Martha R. J. Clokie and Alla I. Kushkina and Vera V. Morozova and Siobain Duffy and Annika Gillis and Janis Rumnieks and Ipek Kurtböke and Nina Chanishvili and Lawrence Goodridge and Johannes Wittmann and Rob Lavigne and Ho Bin Jang and David Prangishvili and Francois Enault and Dann Turner and Minna M. Poranen and Hanna M. Oksanen and Mart Krupovic},
    title = {Taxonomy of prokaryotic viruses: 2018-2019 update from the {ICTV} {Bacterial} and {Archaeal Viruses Subcommittee}},
    journal = {{Arch Virol}},
    year = {2020},
    volume = {165},
    pages = {1253--1260},
    doi = {10.1007/s00705-020-04577-8},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] D. Blanco-Melo, B. E. Nilsson-Payant, S. Uhl, B. Escudero, S. Olschewski, P. Thibault, M. Panis, M. Rosenthal, C. Munoz-Fontela, B. Lee, and B. tenOever, "An inability to maintain the ribonucleoprotein genomic structure is responsible for host detection of negative-sense RNA viruses," bioRxiv, 2020.
    [Bibtex]
    @Article{Blanco-Melo:20,
    author = {Daniel Blanco-Melo and Benjamin E. Nilsson-Payant and Skyler Uhl and Beatriz Escudero and Silke Olschewski and Patricia Thibault and Maryline Panis and Maria Rosenthal and Cesar Munoz-Fontela and Benhur Lee and Benjamin tenOever},
    title = {An inability to maintain the ribonucleoprotein genomic structure is responsible for host detection of negative-sense {RNA} viruses},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.03.12.989319},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. Hoffmann, H. Kleine-Weber, S. Schroeder, N. Krüger, T. Herrler, S. Erichsen, T. S. Schiergens, G. Herrler, N. Wu, A. Nitsche, M. A. Müller, C. Drosten, and S. Pöhlmann, "SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor," Cell, vol. 181, iss. 2, p. 271–280.e8, 2020.
    [Bibtex]
    @Article{Hoffmann:20a,
    author = {Markus Hoffmann and Hannah Kleine-Weber and Simon Schroeder and Nadine Krüger and Tanja Herrler and Sandra Erichsen and Tobias S. Schiergens and Georg Herrler and Nai-Huei Wu and Andreas Nitsche and Marcel A. Müller and Christian Drosten and Stefan Pöhlmann},
    title = {{SARS}-{CoV}-2 Cell Entry Depends on {ACE}2 and {TMPRSS}2 and Is Blocked by a Clinically Proven Protease Inhibitor},
    journal = {Cell},
    year = {2020},
    volume = {181},
    number = {2},
    pages = {271--280.e8},
    doi = {10.1016/j.cell.2020.02.052},
    publisher = {Elsevier {BV}},
    }
  • [DOI] S. Pfaender, K. B. Mar, E. Michailidis, A. Kratzel, D. Hirt, P. V'Kovski, W. Fan, N. Ebert, H. Stalder, H. Kleine-Weber, M. Hoffmann, H. H. Hoffmann, M. Saeed, R. Dijkman, E. Steinmann, M. Wight-Carter, N. W. Hanners, S. Pohlmann, T. Gallagher, D. Todt, G. Zimmer, C. M. Rice, J. W. Schoggins, and V. Thiel, "LY6E impairs coronavirus fusion and confers immune control of viral disease," bioRxiv, 2020.
    [Bibtex]
    @Article{Pfaender:20,
    author = {Stephanie Pfaender and Katrina B Mar and Eleftherios Michailidis and Annika Kratzel and Dagny Hirt and Philip V'Kovski and Wenchun Fan and Nadine Ebert and Hanspeter Stalder and Hannah Kleine-Weber and Markus Hoffmann and H. Heinrich Hoffmann and Mohsan Saeed and Ronald Dijkman and Eike Steinmann and Mary Wight-Carter and Natasha W Hanners and Stefan Pohlmann and Tom Gallagher and Daniel Todt and Gert Zimmer and Charles M Rice and John W Schoggins and Volker Thiel},
    title = {{LY}6{E} impairs coronavirus fusion and confers immune control of viral disease},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.03.05.979260},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] J. H. Forth, L. F. Forth, S. J. Lycett, L. Bell-Sakyi, G. M. Keil, S. Blome, S. Calvignac-Spencer, A. Wissgott, J. Krause, D. Hoeper, H. Kampen, and M. Beer, "African swine fever virus-like integrated elements in a soft tick genome – an ancient virus vector arms race?," bioRxiv, 2020.
    [Bibtex]
    @Article{Forth:20,
    author = {Jan Hendrik Forth and Leonie Franziska Forth and Samantha J Lycett and Lesley Bell-Sakyi and Guenther Michael Keil and Sandra Blome and Sebastien Calvignac-Spencer and Antje Wissgott and Johannes Krause and Dirk Hoeper and Helge Kampen and Martin Beer},
    title = {African swine fever virus-like integrated elements in a soft tick genome {\textendash} an ancient virus vector arms race?},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.03.08.978106},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] R. Woelfel, V. M. Corman, W. Guggemos, M. Seilmaier, S. Zange, M. A. Mueller, D. Niemeyer, P. Vollmar, C. Rothe, M. Hoelscher, T. Bleicker, S. Bruenink, J. Schneider, R. Ehmann, K. Zwirglmaier, C. Drosten, and C. Wendtner, "Clinical presentation and virological assessment of hospitalized cases of coronavirus disease 2019 in a travel-associated transmission cluster," medRxiv, 2020.
    [Bibtex]
    @Article{Woelfel:20,
    author = {Roman Woelfel and Victor Max Corman and Wolfgang Guggemos and Michael Seilmaier and Sabine Zange and Marcel A Mueller and Daniela Niemeyer and Patrick Vollmar and Camilla Rothe and Michael Hoelscher and Tobias Bleicker and Sebastian Bruenink and Julia Schneider and Rosina Ehmann and Katrin Zwirglmaier and Christian Drosten and Clemens Wendtner},
    title = {Clinical presentation and virological assessment of hospitalized cases of coronavirus disease 2019 in a travel-associated transmission cluster},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.03.05.20030502},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] S. Lequime, P. Bastide, S. Dellicour, P. Lemey, and G. Baele, "nosoi: A stochastic agent-based transmission chain simulation framework in R," Methods Ecol Evol, 2020.
    [Bibtex]
    @Article{Lequime:20,
    author = {Sebastian Lequime and Paul Bastide and Simon Dellicour and Philippe Lemey and Guy Baele},
    title = {{nosoi}: {A} stochastic agent-based transmission chain simulation framework in {R}},
    journal = {{Methods Ecol Evol}},
    year = {2020},
    doi = {10.1111/2041-210X.13422},
    publisher = {Wiley},
    }
  • [DOI] C. Claus, M. Jung, and J. M. Hübschen, "Pluripotent stem cell-based models: a peephole into virus infections during early pregnancy," Cells, vol. 9, iss. 3, p. 542, 2020.
    [Bibtex]
    @Article{Claus:20,
    author = {Claudia Claus and Matthias Jung and Judith M. Hübschen},
    title = {Pluripotent Stem Cell-Based Models: A Peephole into Virus Infections during Early Pregnancy},
    journal = {{Cells}},
    year = {2020},
    volume = {9},
    number = {3},
    pages = {542},
    doi = {10.3390/cells9030542},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] M. S. Gill, P. Lemey, M. A. Suchard, A. Rambaut, and G. Baele, "Online Bayesian phylodynamic inference in BEAST with application to epidemic reconstruction," Mol Biol Evol, vol. 37, iss. 6, p. 1832–1842, 2020.
    [Bibtex]
    @Article{Gill:20,
    author = {Mandev S Gill and Philippe Lemey and Marc A Suchard and Andrew Rambaut and Guy Baele},
    title = {Online {Bayesian} phylodynamic inference in {BEAST} with application to epidemic reconstruction},
    journal = {{Mol Biol Evol}},
    year = {2020},
    volume = {37},
    number = {6},
    pages = {1832--1842},
    doi = {10.1093/molbev/msaa047},
    editor = {Michael Rosenberg},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] A. Tomazatos, R. E. Marschang, I. Maranda, H. Baum, A. Bialonski, M. Spînu, R. Lühken, J. Schmidt-Chanasit, and D. Cadar, "Letea virus: comparative genomics and phylogenetic analysis of a novel reassortant orbivirus discovered in grass snakes (Natrix natrix)," Viruses, vol. 12, iss. 2, p. 243, 2020.
    [Bibtex]
    @Article{Tomazatos:20,
    author = {Alexandru Tomazatos and Rachel E. Marschang and Iulia Maranda and Heike Baum and Alexandra Bialonski and Marina Sp{\^{\i}}nu and Renke Lühken and Jonas Schmidt-Chanasit and Daniel Cadar},
    title = {Letea Virus: Comparative Genomics and Phylogenetic Analysis of a Novel Reassortant Orbivirus Discovered in Grass Snakes ({N}atrix natrix)},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    number = {2},
    pages = {243},
    doi = {10.3390/v12020243},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] K. Brunker, G. Jaswant, S. M. Thumbi, K. Lushasi, A. Lugelo, A. M. Czupryna, F. Ade, G. Wambura, V. Chuchu, R. Steenson, C. Ngeleja, C. Bautista, D. L. Manalo, M. R. R. Gomez, M. Y. J. V. Chu, M. E. Miranda, M. Kamat, K. Rysava, J. Espineda, E. A. V. Silo, A. M. Aringo, R. P. Bernales, F. F. Adonay, M. J. Tildesley, D. A. Marston, D. L. Jennings, A. R. Fooks, W. Zhu, L. W. Meredith, S. C. Hill, R. Poplawski, R. J. Gifford, J. B. Singer, M. Maturi, A. Mwatondo, R. Biek, and K. Hampson, "Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes," Wellcome Open Res, vol. 5, p. 3, 2020.
    [Bibtex]
    @Article{Brunker:20,
    author = {Kirstyn Brunker and Gurdeep Jaswant and S.M. Thumbi and Kennedy Lushasi and Ahmed Lugelo and Anna M. Czupryna and Fred Ade and Gati Wambura and Veronicah Chuchu and Rachel Steenson and Chanasa Ngeleja and Criselda Bautista and Daria L. Manalo and Ma. Ricci R. Gomez and Maria Yna Joyce V. Chu and Mary Elizabeth Miranda and Maya Kamat and Kristyna Rysava and Jason Espineda and Eva Angelica V. Silo and Ariane Mae Aringo and Rona P. Bernales and Florencio F. Adonay and Michael J. Tildesley and Denise A. Marston and Daisy L. Jennings and Anthony R. Fooks and Wenlong Zhu and Luke W. Meredith and Sarah C. Hill and Radoslaw Poplawski and Robert J. Gifford and Joshua B. Singer and Mathew Maturi and Athman Mwatondo and Roman Biek and Katie Hampson},
    title = {Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes},
    journal = {{Wellcome Open Res}},
    year = {2020},
    volume = {5},
    pages = {3},
    doi = {10.12688/wellcomeopenres.15518.1},
    publisher = {Faculty of 1000 Ltd},
    }
  • [DOI] R. Zell, A. E. Gorbalenya, N. J. Knowles, P. Simmonds, and T. Skern, "How to recognise and deal with dubious virus sequences?," Infect Genet Evol, vol. 81, p. 104242, 2020.
    [Bibtex]
    @Article{Zell:20,
    author = {Roland Zell and Alexander E. Gorbalenya and Nick J. Knowles and Peter Simmonds and Tim Skern},
    title = {How to recognise and deal with dubious virus sequences?},
    journal = {{Infect Genet Evol}},
    year = {2020},
    volume = {81},
    pages = {104242},
    doi = {10.1016/j.meegid.2020.104242},
    publisher = {Elsevier {BV}},
    }
  • [DOI] A. M. Dinan, N. I. Lukhovitskaya, I. Olendraite, and A. E. Firth, "A case for a negative-strand coding sequence in a group of positive-sense RNA viruses.," Virus Evol, vol. 6, iss. 1, p. veaa007, 2020.
    [Bibtex]
    @Article{Dinan:20,
    author = {Dinan, Adam M and Lukhovitskaya, Nina I and Olendraite, Ingrida and Firth, Andrew E},
    title = {A case for a negative-strand coding sequence in a group of positive-sense {RNA} viruses.},
    journal = {{Virus Evol}},
    year = {2020},
    volume = {6},
    number = {1},
    pages = {veaa007},
    abstract = {Positive-sense single-stranded RNA viruses form the largest and most diverse group of eukaryote-infecting viruses. Their genomes comprise one or more segments of coding-sense RNA that function directly as messenger RNAs upon release into the cytoplasm of infected cells. Positive-sense RNA viruses are generally accepted to encode proteins solely on the positive strand. However, we previously identified a surprisingly long (∼1,000-codon) open reading frame (ORF) on the negative strand of some members of the family which, together with RNA bacteriophages of the family , form a sister group to all other positive-sense RNA viruses. Here, we completed the genomes of three mosquito-associated narnaviruses, all of which have the long reverse-frame ORF. We systematically identified narnaviral sequences in public data sets from a wide range of sources, including arthropod, fungal, and plant transcriptomic data sets. Long reverse-frame ORFs are widespread in one clade of narnaviruses, where they frequently occupy >95 per cent of the genome. The reverse-frame ORFs correspond to a specific avoidance of CUA, UUA, and UCA codons (i.e. stop codon reverse complements) in the forward-frame RNA-dependent RNA polymerase ORF. However, absence of these codons cannot be explained by other factors such as inability to decode these codons or GC3 bias. Together with other analyses, we provide the strongest evidence yet of coding capacity on the negative strand of a positive-sense RNA virus. As these ORFs comprise some of the longest known overlapping genes, their study may be of broad relevance to understanding overlapping gene evolution and origin of genes.},
    doi = {10.1093/ve/veaa007},
    issue = {1},
    keywords = {RNA virus; overlapping genes},
    pmid = {32064120},
    }
  • [DOI] B. B. Oude Munnink, E. Münger, D. F. Nieuwenhuijse, R. Kohl, A. van der Linden, C. M. E. Schapendonk, H. van der Jeugd, M. Kik, J. M. Rijks, C. B. E. M. Reusken, and M. Koopmans, "Genomic monitoring to understand the emergence and spread of Usutu virus in the Netherlands, 2016-2018.," Sci Rep, vol. 10, p. 2798, 2020.
    [Bibtex]
    @Article{OudeMunnink:20a,
    author = {Oude Munnink, Bas B and Münger, E and Nieuwenhuijse, D F and Kohl, R and van der Linden, A and Schapendonk, C M E and van der Jeugd, H and Kik, M and Rijks, J M and Reusken, C B E M and Koopmans, M},
    title = {Genomic monitoring to understand the emergence and spread of {U}sutu virus in the {N}etherlands, 2016-2018.},
    journal = {{Sci Rep}},
    year = {2020},
    volume = {10},
    pages = {2798},
    abstract = {Usutu virus (USUV) is a mosquito-borne flavivirus circulating in Western Europe that causes die-offs of mainly common blackbirds (Turdus merula). In the Netherlands, USUV was first detected in 2016, when it was identified as the likely cause of an outbreak in birds. In this study, dead blackbirds were collected, screened for the presence of USUV and submitted to Nanopore-based sequencing. Genomic sequences of 112 USUV were obtained and phylogenetic analysis showed that most viruses identified belonged to the USUV Africa 3 lineage, and molecular clock analysis evaluated their most recent common ancestor to 10 to 4 years before first detection of USUV in the Netherlands. USUV Europe 3 lineage, commonly found in Germany, was less frequently detected. This analyses further suggest some extent of circulation of USUV between the Netherlands, Germany and Belgium, as well as likely overwintering of USUV in the Netherlands.},
    doi = {10.1038/s41598-020-59692-y},
    issue = {1},
    pmid = {32071379},
    }
  • [DOI] M. J. Poen, A. Pohlmann, C. Amid, T. M. Bestebroer, S. M. Brookes, I. H. Brown, H. Everett, C. M. E. Schapendonk, R. D. Scheuer, S. L. Smits, M. Beer, R. A. M. Fouchier, and R. J. Ellis, "Comparison of sequencing methods and data processing pipelines for whole genome sequencing and minority single nucleotide variant (mSNV) analysis during an influenza A/H5N8 outbreak.," PLoS One, vol. 15, iss. 2, p. e0229326, 2020.
    [Bibtex]
    @Article{Poen:20,
    author = {Poen, Marjolein J and Pohlmann, Anne and Amid, Clara and Bestebroer, Theo M and Brookes, Sharon M and Brown, Ian H and Everett, Helen and Schapendonk, Claudia M E and Scheuer, Rachel D and Smits, Saskia L and Beer, Martin and Fouchier, Ron A M and Ellis, Richard J},
    title = {Comparison of sequencing methods and data processing pipelines for whole genome sequencing and minority single nucleotide variant (m{SNV}) analysis during an influenza {A/H5N8} outbreak.},
    journal = {{PLoS One}},
    year = {2020},
    volume = {15},
    number = {2},
    pages = {e0229326},
    abstract = {As high-throughput sequencing technologies are becoming more widely adopted for analysing pathogens in disease outbreaks there needs to be assurance that the different sequencing technologies and approaches to data analysis will yield reliable and comparable results. Conversely, understanding where agreement cannot be achieved provides insight into the limitations of these approaches and also allows efforts to be focused on areas of the process that need improvement. This manuscript describes the next-generation sequencing of three closely related viruses, each analysed using different sequencing strategies, sequencing instruments and data processing pipelines. In order to determine the comparability of consensus sequences and minority (sub-consensus) single nucleotide variant (mSNV) identification, the biological samples, the sequence data from 3 sequencing platforms and the *.bam quality-trimmed alignment files of raw data of 3 influenza A/H5N8 viruses were shared. This analysis demonstrated that variation in the final result could be attributed to all stages in the process, but the most critical were the well-known homopolymer errors introduced by 454 sequencing, and the alignment processes in the different data processing pipelines which affected the consistency of mSNV detection. However, homopolymer errors aside, there was generally a good agreement between consensus sequences that were obtained for all combinations of sequencing platforms and data processing pipelines. Nevertheless, minority variant analysis will need a different level of careful standardization and awareness about the possible limitations, as shown in this study.},
    doi = {10.1371/journal.pone.0229326},
    issue = {2},
    pmid = {32078666},
    }
  • [DOI] A. Grifoni, J. Sidney, Y. Zhang, R. H. Scheuermann, B. Peters, and A. Sette, "Candidate targets for immune responses to 2019-Novel Coronavirus (nCoV): sequence homology- and bioinformatic-based predictions," bioRxiv, 2020.
    [Bibtex]
    @Article{Grifoni:20,
    author = {Alba Grifoni and John Sidney and Yun Zhang and Richard H Scheuermann and Bjoern Peters and Alessandro Sette},
    title = {Candidate targets for immune responses to 2019-{N}ovel {C}oronavirus ({nCoV}): sequence homology- and bioinformatic-based predictions},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.02.12.946087},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] R. V. Damme, M. Hölzer, A. Viehweger, B. Müller, E. Bongcam-Rudloff, and C. Brandt, "Metagenomics workflow for hybrid assembly, differential coverage binning, transcriptomics and pathway analysis (MUFFIN)," bioRxiv, 2020.
    [Bibtex]
    @Article{Damme:20,
    author = {Renaud Van Damme and Martin Hölzer and Adrian Viehweger and Bettina Müller and Erik Bongcam-Rudloff and Christian Brandt},
    title = {Metagenomics workflow for hybrid assembly, differential coverage binning, transcriptomics and pathway analysis ({MUFFIN})},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.02.08.939843},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. Hoffmann, H. Kleine-Weber, N. Krüger, M. Müller, C. Drosten, and S. Pöhlmann, "The novel coronavirus 2019 (2019-nCoV) uses the SARS-coronavirus receptor ACE2 and the cellular protease TMPRSS2 for entry into target cells," bioRxiv, 2020.
    [Bibtex]
    @Article{Hoffmann:20,
    author = {Markus Hoffmann and Hannah Kleine-Weber and Nadine Krüger and Marcel Müller and Christian Drosten and Stefan Pöhlmann},
    title = {The novel coronavirus 2019 (2019-{nCoV}) uses the {SARS}-coronavirus receptor {ACE}2 and the cellular protease {TMPRSS}2 for entry into target cells},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.01.31.929042},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] G. Kampf, D. Todt, S. Pfaender, and E. Steinmann, "Persistence of coronaviruses on inanimate surfaces and its inactivation with biocidal agents," J Hosp Infect, vol. 104, iss. 3, p. 246–251, 2020.
    [Bibtex]
    @Article{Kampf:20,
    author = {Günter Kampf and Daniel Todt and Stephanie Pfaender and Eike Steinmann},
    title = {Persistence of coronaviruses on inanimate surfaces and its inactivation with biocidal agents},
    journal = {{J Hosp Infect}},
    year = {2020},
    volume = {104},
    number = {3},
    pages = {246--251},
    doi = {10.1016/j.jhin.2020.01.022},
    publisher = {Elsevier {BV}},
    }
  • [DOI] S. L. Hong, S. Dellicour, B. Vrancken, M. A. Suchard, M. T. Pyne, D. R. Hillyard, P. Lemey, and G. Baele, "In search of covariates of HIV-1 subtype B spread in the United States – A cautionary tale of large-scale bayesian phylogeography," Viruses, vol. 12, iss. 2, p. 182, 2020.
    [Bibtex]
    @Article{Hong:20,
    author = {Samuel L. Hong and Simon Dellicour and Bram Vrancken and Marc A. Suchard and Michael T. Pyne and David R. Hillyard and Philippe Lemey and Guy Baele},
    title = {In Search of Covariates of {HIV}-1 Subtype {B} Spread in the {United States} -- {A} Cautionary Tale of Large-Scale Bayesian Phylogeography},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    number = {2},
    pages = {182},
    doi = {10.3390/v12020182},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] S. Reimering, S. Muñoz, and A. C. McHardy, "Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic," PLoS Comput Biol, vol. 16, iss. 2, p. e1007101, 2020.
    [Bibtex]
    @Article{Reimering:20,
    author = {Susanne Reimering and Sebastian Mu{\~{n}}oz and Alice C. McHardy},
    title = {Phylogeographic reconstruction using air transportation data and its application to the 2009 {H1N1} influenza {A} pandemic},
    journal = {{PLoS Comput Biol}},
    year = {2020},
    volume = {16},
    number = {2},
    pages = {e1007101},
    doi = {10.1371/journal.pcbi.1007101},
    editor = {Cecile Viboud},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] C. E. Brook, M. Boots, K. Chandran, A. P. Dobson, C. Drosten, A. L. Graham, B. T. Grenfell, M. A. Müller, M. Ng, L. Wang, and A. van Leeuwen, "Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence," eLife, vol. 9, p. e48401, 2020.
    [Bibtex]
    @Article{Brook:20,
    author = {Cara E Brook and Mike Boots and Kartik Chandran and Andrew P Dobson and Christian Drosten and Andrea L Graham and Bryan T Grenfell and Marcel A Müller and Melinda Ng and Lin-Fa Wang and Anieke van Leeuwen},
    title = {Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence},
    journal = {{eLife}},
    year = {2020},
    volume = {9},
    pages = {e48401},
    doi = {10.7554/elife.48401},
    publisher = {{eLife} Sciences Publications, Ltd},
    }
  • [DOI] M. K. Mirzaei, M. A. A. Khan, P. Ghosh, Z. E. Taranu, M. Taguer, J. Ru, R. Chowdhury, M. M. Kabir, L. Deng, D. Mondal, and C. F. Maurice, "Bacteriophages isolated from stunted children can regulate gut bacterial communities in an age-specific manner," Cell Host Microbe, vol. 27, iss. 2, p. 199–212.e5, 2020.
    [Bibtex]
    @Article{Mirzaei:20,
    author = {Mohammadali Khan Mirzaei and Md. Anik Ashfaq Khan and Prakash Ghosh and Zofia E. Taranu and Mariia Taguer and Jinlong Ru and Rajashree Chowdhury and Md. Mamun Kabir and Li Deng and Dinesh Mondal and Corinne F. Maurice},
    title = {Bacteriophages Isolated from Stunted Children Can Regulate Gut Bacterial Communities in an Age-Specific Manner},
    journal = {{Cell Host Microbe}},
    year = {2020},
    volume = {27},
    number = {2},
    pages = {199--212.e5},
    doi = {10.1016/j.chom.2020.01.004},
    publisher = {Elsevier {BV}},
    }
  • [DOI] C. B. E. M. Reusken, E. K. Broberg, B. Haagmans, A. Meijer, V. M. Corman, A. Papa, R. Charrel, C. Drosten, M. Koopmans, and K. L. and, "Laboratory readiness and response for novel coronavirus (2019-nCoV) in expert laboratories in 30 EU/EEA countries, January 2020," Euro Surveill, vol. 25, iss. 6, p. 2000082, 2020.
    [Bibtex]
    @Article{Reusken:20,
    author = {Chantal B.E.M. Reusken and Eeva K. Broberg and Bart Haagmans and Adam Meijer and Victor M. Corman and Anna Papa and Remi Charrel and Christian Drosten and Marion Koopmans and Katrin Leitmeyer and},
    title = {Laboratory readiness and response for novel coronavirus (2019-{nCoV}) in expert laboratories in 30 {EU}/{EEA} countries, {J}anuary 2020},
    journal = {{Euro Surveill}},
    year = {2020},
    volume = {25},
    number = {6},
    pages = {2000082},
    doi = {10.2807/1560-7917.es.2020.25.6.2000082},
    publisher = {European Centre for Disease Control and Prevention ({ECDC})},
    }
  • [DOI] S. Dirmeier, C. Dächert, M. van Hemert, A. Tas, N. S. Ogando, F. van Kuppeveld, R. Bartenschlager, L. Kaderali, M. Binder, and N. Beerenwinkel, "Host factor prioritization for pan-viral genetic perturbation screens using random intercept models and network propagation," PLoS Comput Biol, vol. 16, iss. 2, p. e1007587, 2020.
    [Bibtex]
    @Article{Dirmeier:20,
    author = {Simon Dirmeier and Christopher Dächert and Martijn van Hemert and Ali Tas and Natacha S. Ogando and Frank van Kuppeveld and Ralf Bartenschlager and Lars Kaderali and Marco Binder and Niko Beerenwinkel},
    title = {Host factor prioritization for pan-viral genetic perturbation screens using random intercept models and network propagation},
    journal = {{PLoS Comput Biol}},
    year = {2020},
    volume = {16},
    number = {2},
    pages = {e1007587},
    doi = {10.1371/journal.pcbi.1007587},
    editor = {Natalia L. Komarova},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] A. A. Gulyaeva, A. I. Sigorskih, E. S. Ocheredko, D. V. Samborskiy, and A. E. Gorbalenya, "LAMPA, LArge Multidomain Protein Annotator, and its application to RNA virus polyproteins," Bioinformatics, vol. 36, iss. 9, p. 2731–2739, 2020.
    [Bibtex]
    @Article{Gulyaeva:20,
    author = {Anastasia A Gulyaeva and Andrey I Sigorskih and Elena S Ocheredko and Dmitry V Samborskiy and Alexander E Gorbalenya},
    title = {{LAMPA}, {LArge} {Multidomain Protein Annotator}, and its application to {RNA} virus polyproteins},
    journal = {Bioinformatics},
    year = {2020},
    volume = {36},
    number = {9},
    pages = {2731--2739},
    doi = {10.1093/bioinformatics/btaa065},
    editor = {Yann Ponty},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] C. Rothe, M. Schunk, P. Sothmann, G. Bretzel, G. Froeschl, C. Wallrauch, T. Zimmer, V. Thiel, C. Janke, W. Guggemos, M. Seilmaier, C. Drosten, P. Vollmar, K. Zwirglmaier, S. Zange, R. Wölfel, and M. Hoelscher, "Transmission of 2019-nCoV infection from an asymptomatic contact in Germany," N Engl J Med, vol. 382, p. 970–971, 2020.
    [Bibtex]
    @Article{Rothe:20,
    author = {Camilla Rothe and Mirjam Schunk and Peter Sothmann and Gisela Bretzel and Guenter Froeschl and Claudia Wallrauch and Thorbjörn Zimmer and Verena Thiel and Christian Janke and Wolfgang Guggemos and Michael Seilmaier and Christian Drosten and Patrick Vollmar and Katrin Zwirglmaier and Sabine Zange and Roman Wölfel and Michael Hoelscher},
    title = {Transmission of 2019-{nCoV} Infection from an Asymptomatic Contact in {G}ermany},
    journal = {{N Engl J Med}},
    year = {2020},
    volume = {382},
    pages = {970--971},
    doi = {10.1056/nejmc2001468},
    publisher = {Massachusetts Medical Society},
    }
  • [DOI] R. J. Paxton, "A microbiome silver bullet for honey bees," Science, vol. 367, iss. 6477, p. 504–506, 2020.
    [Bibtex]
    @Article{Paxton:20,
    author = {Robert J. Paxton},
    title = {A microbiome silver bullet for honey bees},
    journal = {Science},
    year = {2020},
    volume = {367},
    number = {6477},
    pages = {504--506},
    doi = {10.1126/science.aba6135},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
  • [DOI] V. M. Corman, O. Landt, M. Kaiser, R. Molenkamp, A. Meijer, D. K. Chu, T. Bleicker, S. Brünink, J. Schneider, M. L. Schmidt, D. G. Mulders, B. L. Haagmans, B. van der Veer, S. van den Brink, L. Wijsman, G. Goderski, J. Romette, J. Ellis, M. Zambon, M. Peiris, H. Goossens, C. Reusken, M. P. Koopmans, and C. Drosten, "Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR," Euro Surveill, vol. 25, iss. 3, p. 2000045, 2020.
    [Bibtex]
    @Article{Corman:20,
    author = {Victor M Corman and Olfert Landt and Marco Kaiser and Richard Molenkamp and Adam Meijer and Daniel KW Chu and Tobias Bleicker and Sebastian Brünink and Julia Schneider and Marie Luisa Schmidt and Daphne GJC Mulders and Bart L Haagmans and Bas van der Veer and Sharon van den Brink and Lisa Wijsman and Gabriel Goderski and Jean-Louis Romette and Joanna Ellis and Maria Zambon and Malik Peiris and Herman Goossens and Chantal Reusken and Marion PG Koopmans and Christian Drosten},
    title = {Detection of 2019 novel coronavirus (2019-{nCoV}) by real-time {RT}-{PCR}},
    journal = {{Euro Surveill}},
    year = {2020},
    volume = {25},
    number = {3},
    pages = {2000045},
    doi = {10.2807/1560-7917.es.2020.25.3.2000045},
    publisher = {European Centre for Disease Control and Prevention ({ECDC})},
    }
  • [DOI] C. Kreer, M. Döring, N. Lehnen, M. S. Ercanoglu, L. Gieselmann, D. Luca, K. Jain, P. Schommers, N. Pfeifer, and F. Klein, "openPrimeR for multiplex amplification of highly diverse templates," J Immunol Methods, vol. 480, p. 112752, 2020.
    [Bibtex]
    @Article{Kreer:20,
    author = {Christoph Kreer and Matthias Döring and Nathalie Lehnen and Meryem S. Ercanoglu and Lutz Gieselmann and Domnica Luca and Kanika Jain and Philipp Schommers and Nico Pfeifer and Florian Klein},
    title = {{openPrimeR} for multiplex amplification of highly diverse templates},
    journal = {{J Immunol Methods}},
    year = {2020},
    volume = {480},
    pages = {112752},
    doi = {10.1016/j.jim.2020.112752},
    publisher = {Elsevier {BV}},
    }
  • [DOI] K. T. T. Kwok, D. F. Nieuwenhuijse, M. V. T. Phan, and M. P. G. Koopmans, "Virus metagenomics in farm animals: a systematic review," Viruses, vol. 12, iss. 1, p. 107, 2020.
    [Bibtex]
    @Article{Kwok:20,
    author = {Kirsty T. T. Kwok and David F. Nieuwenhuijse and My V. T. Phan and Marion P. G. Koopmans},
    title = {Virus Metagenomics in Farm Animals: A Systematic Review},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    number = {1},
    pages = {107},
    doi = {10.3390/v12010107},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] H. Kleine-Weber, S. Schroeder, N. Krüger, A. Prokscha, H. Y. Naim, M. A. Müller, C. Drosten, S. Pöhlmann, and M. Hoffmann, "Polymorphisms in dipeptidyl peptidase 4 reduce host cell entry of Middle East respiratory syndrome coronavirus," Emerg Microbes Infect, vol. 9, iss. 1, p. 155–168, 2020.
    [Bibtex]
    @Article{Kleine-Weber:20,
    author = {Hannah Kleine-Weber and Simon Schroeder and Nadine Krüger and Alexander Prokscha and Hassan Y. Naim and Marcel A. Müller and Christian Drosten and Stefan Pöhlmann and Markus Hoffmann},
    title = {Polymorphisms in dipeptidyl peptidase 4 reduce host cell entry of {Middle East} respiratory syndrome coronavirus},
    journal = {{Emerg Microbes Infect}},
    year = {2020},
    volume = {9},
    number = {1},
    pages = {155--168},
    doi = {10.1080/22221751.2020.1713705},
    publisher = {Informa {UK} Limited},
    }
  • [DOI] A. O. Abdelkareem, M. I. Khalil, A. H. Elbehery, and H. M. Abbas, "Viral sequence identification in metagenomes using natural language processing techniques," bioRxiv, 2020.
    [Bibtex]
    @Article{Abdelkareem:20,
    author = {Aly O. Abdelkareem and Mahmoud I. Khalil and Ali H. Elbehery and Hazem M. Abbas},
    title = {Viral Sequence Identification in Metagenomes using Natural Language Processing Techniques},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.01.10.892158},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] C. Masembe, M. V. T. Phan, D. L. Robertson, and M. Cotten, "Increased resolution of African Swine Fever Virus genome patterns based on profile HMM protein domains," Virus Evolution, p. veaa044, 2020.
    [Bibtex]
    @Article{Masembe:20,
    author = {Charles Masembe and My V.T. Phan and David L. Robertson and Matthew Cotten},
    title = {Increased resolution of {African Swine Fever Virus} genome patterns based on profile {HMM} protein domains},
    journal = {{Virus Evolution}},
    year = {2020},
    pages = {veaa044},
    doi = {10.1093/ve/veaa044},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] J. Scire, J. Barido-Sottani, D. Kühnert, T. G. Vaughan, and T. Stadler, "Improved multi-type birth-death phylodynamic inference in BEAST 2," bioRxiv, 2020.
    [Bibtex]
    @Article{Scire:20,
    author = {J{\'{e}}r{\'{e}}mie Scire and Joëlle Barido-Sottani and Denise Kühnert and Timothy G. Vaughan and Tanja Stadler},
    title = {Improved multi-type birth-death phylodynamic inference in {BEAST} 2},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.01.06.895532},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] D. Todt, M. Friesland, N. Moeller, D. Praditya, V. Kinast, Y. Brüggemann, L. Knegendorf, T. Burkard, J. Steinmann, R. Burm, L. Verhoye, A. Wahid, T. L. Meister, M. Engelmann, V. M. Pfankuche, C. Puff, F. W. R. Vondran, W. Baumgärtner, P. Meuleman, P. Behrendt, and E. Steinmann, "Robust hepatitis E virus infection and transcriptional response in human hepatocytes," Proc Natl Acad Sci USA, vol. 117, iss. 3, p. 1731–1741, 2020.
    [Bibtex]
    @Article{Todt:20,
    author = {Daniel Todt and Martina Friesland and Nora Moeller and Dimas Praditya and Volker Kinast and Yannick Brüggemann and Leonard Knegendorf and Thomas Burkard and Joerg Steinmann and Rani Burm and Lieven Verhoye and Avista Wahid and Toni Luise Meister and Michael Engelmann and Vanessa M. Pfankuche and Christina Puff and Florian W. R. Vondran and Wolfgang Baumgärtner and Philip Meuleman and Patrick Behrendt and Eike Steinmann},
    title = {Robust hepatitis {E} virus infection and transcriptional response in human hepatocytes},
    journal = {{Proc Natl Acad Sci USA}},
    year = {2020},
    volume = {117},
    number = {3},
    pages = {1731--1741},
    doi = {10.1073/pnas.1912307117},
    publisher = {Proceedings of the National Academy of Sciences},
    }
  • [DOI] E. Hietanen and P. Susi, "Recombination events and conserved nature of receptor binding motifs in coxsackievirus A9 isolates," Viruses, vol. 12, iss. 1, p. 68, 2020.
    [Bibtex]
    @Article{Hietanen:20,
    author = {Eero Hietanen and Petri Susi},
    title = {Recombination Events and Conserved Nature of Receptor Binding Motifs in Coxsackievirus {A9} Isolates},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    number = {1},
    pages = {68},
    doi = {10.3390/v12010068},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] H. H. Niller, K. Angstwurm, D. Rubbenstroth, K. Schlottau, A. Ebinger, S. Giese, S. Wunderlich, B. Banas, L. F. Forth, D. Hoffmann, D. Höper, M. Schwemmle, D. Tappe, J. Schmidt-Chanasit, D. Nobach, C. Herden, C. Brochhausen, N. Velez-Char, A. Mamilos, K. Utpatel, M. Evert, S. Zoubaa, M. J. Riemenschneider, V. Ruf, J. Herms, G. Rieder, M. Errath, K. Matiasek, J. Schlegel, F. Liesche-Starnecker, B. Neumann, K. Fuchs, R. A. Linker, B. Salzberger, T. Freilinger, L. Gartner, J. J. Wenzel, U. Reischl, W. Jilg, A. Gessner, J. Jantsch, M. Beer, and B. Schmidt, "Zoonotic spillover infections with Borna disease virus 1 leading to fatal human encephalitis, 1999-2019: an epidemiological investigation.," Lancet Infect Dis, vol. 20, iss. 4, p. 467–477, 2020.
    [Bibtex]
    @Article{Niller:20,
    author = {Niller, Hans Helmut and Angstwurm, Klemens and Rubbenstroth, Dennis and Schlottau, Kore and Ebinger, Arnt and Giese, Sebastian and Wunderlich, Silke and Banas, Bernhard and Forth, Leonie F and Hoffmann, Donata and Höper, Dirk and Schwemmle, Martin and Tappe, Dennis and Schmidt-Chanasit, Jonas and Nobach, Daniel and Herden, Christiane and Brochhausen, Christoph and Velez-Char, Natalia and Mamilos, Andreas and Utpatel, Kirsten and Evert, Matthias and Zoubaa, Saida and Riemenschneider, Markus J and Ruf, Viktoria and Herms, Jochen and Rieder, Georg and Errath, Mario and Matiasek, Kaspar and Schlegel, Jürgen and Liesche-Starnecker, Friederike and Neumann, Bernhard and Fuchs, Kornelius and Linker, Ralf A and Salzberger, Bernd and Freilinger, Tobias and Gartner, Lisa and Wenzel, Jürgen J and Reischl, Udo and Jilg, Wolfgang and Gessner, André and Jantsch, Jonathan and Beer, Martin and Schmidt, Barbara},
    title = {Zoonotic spillover infections with {B}orna disease virus 1 leading to fatal human encephalitis, 1999-2019: an epidemiological investigation.},
    journal = {{Lancet Infect Dis}},
    year = {2020},
    volume = {20},
    number = {4},
    pages = {467--477},
    abstract = {In 2018-19, Borna disease virus 1 (BoDV-1), the causative agent of Borna disease in horses, sheep, and other domestic mammals, was reported in five human patients with severe to fatal encephalitis in Germany. However, information on case frequencies, clinical courses, and detailed epidemiological analyses are still lacking. We report the occurrence of BoDV-1-associated encephalitis in cases submitted to the Institute of Clinical Microbiology and Hygiene, Regensburg University Hospital, Regensburg, Germany, and provide a detailed description of newly identified cases of BoDV-1-induced encephalitis. All brain tissues from 56 encephalitis cases from Bavaria, Germany, of putative viral origin (1999-2019), which had been submitted for virological testing upon request of the attending clinician and stored for stepwise diagnostic procedure, were systematically screened for BoDV-1 RNA. Two additional BoDV-1-positive cases were contributed by other diagnostic centres. Positive results were confirmed by deep sequencing, antigen detection, and determination of BoDV-1-reactive antibodies in serum and cerebrospinal fluid. Clinical and epidemiological data from infected patients were collected and analysed. BoDV-1 RNA and bornavirus-reactive antibodies were detected in eight newly analysed encephalitis cases and the first human BoDV-1 isolate was obtained from an unequivocally confirmed human BoDV-1 infection from the endemic area. Six of the eight BoDV-1-positive patients had no record of immunosuppression before the onset of fatal disease, whereas two were immunocompromised after solid organ transplantation. Typical initial symptoms were headache, fever, and confusion, followed by various neurological signs, deep coma, and severe brainstem involvement. Seven of nine patients with fatal encephalitis of unclear cause were BoDV-1 positive within one diagnostic centre. BoDV-1 sequence information and epidemiological analyses indicated independent spillover transmissions most likely from the local wild animal reservoir. BoDV-1 infection has to be considered as a potentially lethal zoonosis in endemic regions with reported spillover infections in horses and sheep. BoDV-1 infection can result in fatal encephalitis in immunocompromised and apparently healthy people. Consequently, all severe encephalitis cases of unclear cause should be tested for bornaviruses especially in endemic regions. German Federal Ministry of Education and Research.},
    doi = {10.1016/S1473-3099(19)30546-8},
    pmid = {31924550},
    }
  • [DOI] O. Ratmann, J. Kagaayi, M. Hall, T. Golubchick, G. Kigozi, X. Xi, C. Wymant, G. Nakigozi, L. Abeler-Dörner, D. Bonsall, A. Gall, A. Hoppe, P. Kellam, J. Bazaale, S. Kalibbala, O. Laeyendecker, J. Lessler, F. Nalugoda, L. W. Chang, T. de Oliveira, D. Pillay, T. C. Quinn, S. J. Reynolds, S. E. F. Spencer, R. Ssekubugu, D. Serwadda, M. J. Wawer, R. H. Gray, C. Fraser, K. M. Grabowski, Rakai Health Sciences Program, and the Pangea HIV Consortium, "Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda.," Lancet HIV, vol. 7, iss. 3, p. e173–e183, 2020.
    [Bibtex]
    @Article{Ratmann:20,
    author = {Ratmann, Oliver and Kagaayi, Joseph and Hall, Matthew and Golubchick, Tanya and Kigozi, Godfrey and Xi, Xiaoyue and Wymant, Chris and Nakigozi, Gertrude and Abeler-Dörner, Lucie and Bonsall, David and Gall, Astrid and Hoppe, Anne and Kellam, Paul and Bazaale, Jeremiah and Kalibbala, Sarah and Laeyendecker, Oliver and Lessler, Justin and Nalugoda, Fred and Chang, Larry W and de Oliveira, Tulio and Pillay, Deenan and Quinn, Thomas C and Reynolds, Steven J and Spencer, Simon E F and Ssekubugu, Robert and Serwadda, David and Wawer, Maria J and Gray, Ronald H and Fraser, Christophe and Grabowski, M Kate and {Rakai Health Sciences Program} and {the Pangea HIV Consortium}},
    title = {Quantifying {HIV} transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in {R}akai, {U}ganda.},
    journal = {{Lancet HIV}},
    year = {2020},
    volume = {7},
    number = {3},
    pages = {e173--e183},
    abstract = {International and global organisations advocate targeting interventions to areas of high HIV prevalence (ie, hotspots). To better understand the potential benefits of geo-targeted control, we assessed the extent to which HIV hotspots along Lake Victoria sustain transmission in neighbouring populations in south-central Uganda. We did a population-based survey in Rakai, Uganda, using data from the Rakai Community Cohort Study. The study surveyed all individuals aged 15-49 years in four high-prevalence Lake Victoria fishing communities and 36 neighbouring inland communities. Viral RNA was deep sequenced from participants infected with HIV who were antiretroviral therapy-naive during the observation period. Phylogenetic analysis was used to infer partial HIV transmission networks, including direction of transmission. Reconstructed networks were interpreted through data for current residence and migration history. HIV transmission flows within and between high-prevalence and low-prevalence areas were quantified adjusting for incomplete sampling of the population. Between Aug 10, 2011, and Jan 30, 2015, data were collected for the Rakai Community Cohort Study. 25 882 individuals participated, including an estimated 75·7% of the lakeside population and 16·2% of the inland population in the Rakai region of Uganda. 5142 participants were HIV-positive (2703 [13·7%] in inland and 2439 [40·1%] in fishing communities). 3878 (75·4%) people who were HIV-positive did not report antiretroviral therapy use, of whom 2652 (68·4%) had virus deep-sequenced at sufficient quality for phylogenetic analysis. 446 transmission networks were reconstructed, including 293 linked pairs with inferred direction of transmission. Adjusting for incomplete sampling, an estimated 5·7% (95% credibility interval 4·4-7·3) of transmissions occurred within lakeside areas, 89·2% (86·0-91·8) within inland areas, 1·3% (0·6-2·6) from lakeside to inland areas, and 3·7% (2·3-5·8) from inland to lakeside areas. Cross-community HIV transmissions between Lake Victoria hotspots and surrounding inland populations are infrequent and when they occur, virus more commonly flows into rather than out of hotspots. This result suggests that targeted interventions to these hotspots will not alone control the epidemic in inland populations, where most transmissions occur. Thus, geographical targeting of high prevalence areas might not be effective for broader epidemic control depending on underlying epidemic dynamics. The Bill & Melinda Gates Foundation, the National Institute of Allergy and Infectious Diseases, the National Institute of Mental Health, the National Institute of Child Health and Development, the Division of Intramural Research of the National Institute for Allergy and Infectious Diseases, the World Bank, the Doris Duke Charitable Foundation, the Johns Hopkins University Center for AIDS Research, and the President's Emergency Plan for AIDS Relief through the Centers for Disease Control and Prevention.},
    doi = {10.1016/S2352-3018(19)30378-9},
    investigator = {Ayles, Helen and Bowden, Rory and Calvez, Vincent and Cohen, Myron and Dennis, Anne and Essex, Max and Fidler, Sarah and Frampton, Dan and Hayes, Richard and Herbeck, Josh and Kaleebu, Pontiano and Kityo, Cissy and Lingappa, Jairam and Novitsky, Vladimir and Paton, Nick and Rambaut, Andrew and Seeley, Janet and Ssemwanga, Deogratius and Tanser, Frank and Lutalo, Tom and Galiwango, Ronald and Makumbi, Fred and Sewankambo, Nelson K and Nabukalu, Dorean and Ndyanabo, Anthony and Ssekasanvu, Joseph and Nakawooya, Hadijja and Nakukumba, Jessica and Kigozi, Grace N and Nantume, Betty S and Resty, Nampijja and Kambasu, Jedidah and Nalugemwa, Margaret and Nakabuye, Regina and Ssebanobe, Lawrence and Nankinga, Justine and Kayiira, Adrian and Nanfuka, Gorreth and Ahimbisibwe, Ruth and Tomusange, Stephen and Galiwango, Ronald M and Nakalanzi, Margaret and Otobi, Joseph O and Ankunda, Denis and Ssembatya, Joseph L and Ssemanda, John B and Kato, Emmanuel and Kairania, Robert and Kisakye, Alice and Batte, James and Ludigo, James and Nampijja, Abisagi and Watya, Steven and Nehemia, Kighoma and Anyokot, Sr Margaret and Mwinike, Joshua and Kibumba, George and Ssebowa, Paschal and Mondo, George and Wasswa, Francis and Nantongo, Agnes and Kakembo, Rebecca and Galiwango, Josephine and Ssemango, Geoffrey and Redd, Andrew D and Santelli, John and Kennedy, Caitlin E and Wagman, Jennifer and Tobian, Aaron},
    pmid = {31953184},
    }
  • [DOI] A. L. Monjane, S. Dellicour, P. Hartnady, K. A. Oyeniran, B. E. Owor, M. Bezeidenhout, D. Linderme, R. A. Syed, L. Donaldson, S. Murray, E. P. Rybicki, A. Kvarnheden, E. Yazdkhasti, P. Lefeuvre, R. Froissart, P. Roumagnac, D. N. Shepherd, G. W. Harkins, M. A. Suchard, P. Lemey, A. Varsani, and D. P. Martin, "Symptom evolution following the emergence of maize streak virus.," eLife, vol. 9, p. e51984, 2020.
    [Bibtex]
    @Article{Monjane:20,
    author = {Monjane, Adérito L and Dellicour, Simon and Hartnady, Penelope and Oyeniran, Kehinde A and Owor, Betty E and Bezeidenhout, Marion and Linderme, Daphne and Syed, Rizwan A and Donaldson, Lara and Murray, Shane and Rybicki, Edward P and Kvarnheden, Anders and Yazdkhasti, Elhman and Lefeuvre, Pierre and Froissart, Rémy and Roumagnac, Philippe and Shepherd, Dionne N and Harkins, Gordon W and Suchard, Marc A and Lemey, Philippe and Varsani, Arvind and Martin, Darren P},
    title = {Symptom evolution following the emergence of maize streak virus.},
    journal = {{eLife}},
    year = {2020},
    volume = {9},
    pages = {e51984},
    abstract = {For pathogens infecting single host species evolutionary trade-offs have previously been demonstrated between pathogen-induced mortality rates and transmission rates. It remains unclear, however, how such trade-offs impact sub-lethal pathogen-inflicted damage, and whether these trade-offs even occur in broad host-range pathogens. Here, we examine changes over the past 110 years in symptoms induced in maize by the broad host-range pathogen, maize streak virus (MSV). Specifically, we use the quantified symptom intensities of cloned MSV isolates in differentially resistant maize genotypes to phylogenetically infer ancestral symptom intensities and check for phylogenetic signal associated with these symptom intensities. We show that whereas symptoms reflecting harm to the host have remained constant or decreased, there has been an increase in how extensively MSV colonizes the cells upon which transmission vectors feed. This demonstrates an evolutionary trade-off between amounts of pathogen-inflicted harm and how effectively viruses position themselves within plants to enable onward transmission.},
    doi = {10.7554/eLife.51984},
    keywords = {evolutionary biology; maize; viruses},
    pmid = {31939738},
    }
  • [DOI] X. Wang, T. Hennig, A. W. Whisnant, F. Erhard, B. K. Prusty, C. C. Friedel, E. Forouzmand, W. Hu, L. Erber, Y. Chen, R. M. Sandri-Goldin, L. Dölken, and Y. Shi, "Herpes simplex virus blocks host transcription termination via the bimodal activities of ICP27.," Nat Commun, vol. 11, p. 293, 2020.
    [Bibtex]
    @Article{Wang:20,
    author = {Wang, Xiuye and Hennig, Thomas and Whisnant, Adam W and Erhard, Florian and Prusty, Bhupesh K and Friedel, Caroline C and Forouzmand, Elmira and Hu, William and Erber, Luke and Chen, Yue and Sandri-Goldin, Rozanne M and Dölken, Lars and Shi, Yongsheng},
    title = {Herpes simplex virus blocks host transcription termination via the bimodal activities of {ICP27}.},
    journal = {{Nat Commun}},
    year = {2020},
    volume = {11},
    pages = {293},
    abstract = {Infection by viruses, including herpes simplex virus-1 (HSV-1), and cellular stresses cause widespread disruption of transcription termination (DoTT) of RNA polymerase II (RNAPII) in host genes. However, the underlying mechanisms remain unclear. Here, we demonstrate that the HSV-1 immediate early protein ICP27 induces DoTT by directly binding to the essential mRNA 3' processing factor CPSF. It thereby induces the assembly of a dead-end 3' processing complex, blocking mRNA 3' cleavage. Remarkably, ICP27 also acts as a sequence-dependent activator of mRNA 3' processing for viral and a subset of host transcripts. Our results unravel a bimodal activity of ICP27 that plays a key role in HSV-1-induced host shutoff and identify CPSF as an important factor that mediates regulation of transcription termination. These findings have broad implications for understanding the regulation of transcription termination by other viruses, cellular stress and cancer.},
    doi = {10.1038/s41467-019-14109-x},
    issue = {1},
    pmid = {31941886},
    }
  • [DOI] A. Mathieu, M. Dion, L. Deng, D. Tremblay, E. Moncaut, S. A. Shah, J. Stokholm, K. A. Krogfelt, S. Schjørring, H. Bisgaard, D. S. Nielsen, S. Moineau, and M. A. Petit, "Virulent coliphages in 1-year-old children fecal samples are fewer, but more infectious than temperate coliphages.," Nat Commun, vol. 11, p. 378, 2020.
    [Bibtex]
    @Article{Mathieu:20,
    author = {Mathieu, Aurélie and Dion, Moïra and Deng, Ling and Tremblay, Denise and Moncaut, Elisabeth and Shah, Shiraz A and Stokholm, Jakob and Krogfelt, Karen A and Schjørring, Susanne and Bisgaard, Hans and Nielsen, Dennis S and Moineau, Sylvain and Petit, Marie Agnès},
    title = {Virulent coliphages in 1-year-old children fecal samples are fewer, but more infectious than temperate coliphages.},
    journal = {{Nat Commun}},
    year = {2020},
    volume = {11},
    pages = {378},
    abstract = {Bacteriophages constitute an important part of the human gut microbiota, but their impact on this community is largely unknown. Here, we cultivate temperate phages produced by 900 E. coli strains isolated from 648 fecal samples from 1-year-old children and obtain coliphages directly from the viral fraction of the same fecal samples. We find that 63% of strains hosted phages, while 24% of the viromes contain phages targeting E. coli. 150 of these phages, half recovered from strain supernatants, half from virome (73% temperate and 27% virulent) were tested for their host range on 75 E. coli strains isolated from the same cohort. Temperate phages barely infected the gut strains, whereas virulent phages killed up to 68% of them. We conclude that in fecal samples from children, temperate coliphages dominate, while virulent ones have greater infectivity and broader host range, likely playing a role in gut microbiota dynamics.},
    doi = {10.1038/s41467-019-14042-z},
    issue = {1},
    pmid = {31953385},
    }
  • [DOI] E. Dugat-Bony, J. Lossouarn, M. De Paepe, A. Sarthou, Y. Fedala, M. A. Petit, and S. Chaillou, "Viral metagenomic analysis of the cheese surface: a comparative study of rapid procedures for extracting viral particles.," Food Microbiol, vol. 85, p. 103278, 2020.
    [Bibtex]
    @Article{Dugat-Bony:20,
    author = {Dugat-Bony, Eric and Lossouarn, Julien and De Paepe, Marianne and Sarthou, Anne-Sophie and Fedala, Yasmina and Petit, Marie Agnès and Chaillou, Stéphane},
    title = {Viral metagenomic analysis of the cheese surface: A comparative study of rapid procedures for extracting viral particles.},
    journal = {{Food Microbiol}},
    year = {2020},
    volume = {85},
    pages = {103278},
    abstract = {The structure and functioning of microbial communities from fermented foods, including cheese, have been extensively studied during the past decade. However, there is still a lack of information about both the occurrence and the role of viruses in modulating the function of this type of spatially structured and solid ecosystems. Viral metagenomics was recently applied to a wide variety of environmental samples and standardized procedures for recovering viral particles from different type of materials has emerged. In this study, we adapted a procedure originally developed to extract viruses from fecal samples, in order to enable efficient virome analysis of cheese surface. We tested and validated the positive impact of both addition of a filtration step prior to virus concentration and substitution of purification by density gradient ultracentrifugation by a simple chloroform treatment to eliminate membrane vesicles. Viral DNA extracted from the several procedures, as well as a vesicle sample, were sequenced using Illumina paired-end MiSeq technology and the subsequent clusters assembled from the virome were analyzed to assess those belonging to putative phages, plasmid-derived DNA, or even from bacterial chromosomal DNA. The best procedure was then chosen, and used to describe the first cheese surface virome, using Epoisses cheese as example. This study provides the basis of future investigations regarding the ecological importance of viruses in cheese microbial ecosystems.},
    doi = {10.1016/j.fm.2019.103278},
    keywords = {Cheese rind; Viral metagenomic; Viral particles extraction procedure},
    pmid = {31500705},
    }

2019

  • [DOI] A. Cecil, I. Gentschev, M. Adelfinger, T. Dandekar, and A. A. Szalay, "Vaccinia virus injected human tumors: oncolytic virus efficiency predicted by antigen profiling analysis fitted boolean models.," Bioengineered, vol. 10, p. 190–196, 2019.
    [Bibtex]
    @Article{Cecil:19,
    author = {Cecil, Alexander and Gentschev, Ivaylo and Adelfinger, Marion and Dandekar, Thomas and Szalay, Aladar A.},
    journal = {Bioengineered},
    title = {Vaccinia virus injected human tumors: oncolytic virus efficiency predicted by antigen profiling analysis fitted boolean models.},
    year = {2019},
    pages = {190--196},
    volume = {10},
    abstract = {Virotherapy on the basis of oncolytic vaccinia virus (VACV) strains is a promising approach for cancer therapy. Recently, we showed that the oncolytic vaccinia virus GLV-1h68 has a therapeutic potential in treating human prostate and hepatocellular carcinomas in xenografted mice. In this study, we describe the use of dynamic boolean modeling for tumor growth prediction of vaccinia virus-injected human tumors. Antigen profiling data of vaccinia virus GLV-1h68-injected human xenografted mice were obtained, analyzed and used to calculate differences in the tumor growth signaling network by tumor type and gender. Our model combines networks for apoptosis, MAPK, p53, WNT, Hedgehog, the T-killer cell mediated cell death, Interferon and Interleukin signaling networks. The findings conform very well with findings of tumor growth. Similar to a previously published analysis of vaccinia virus-injected canine tumors, we were able to confirm the suitability of our boolean modeling for prediction of human tumor growth after virus infection in the current study as well. In summary, these findings indicate that our boolean models could be a useful tool for testing of the efficacy of VACV-mediated cancer therapy already before its use in human patients.},
    doi = {10.1080/21655979.2019.1622220},
    issue = {1},
    keywords = {Animals; Apoptosis, physiology; Cell Line, Tumor; Dogs; Humans; Male; Mice; Mitogen-Activated Protein Kinases, metabolism; Oncolytic Virotherapy, methods; Oncolytic Viruses, physiology; Vaccinia virus, physiology; Xenograft Model Antitumor Assays; Oncolytic virus; boolean modeling; cancer therapy; human xenografted mouse models},
    pmid = {31142183},
    pubstate = {ppublish},
    }
  • [DOI] M. Perotti and L. Perez, "Virus-like particles and nanoparticles for vaccine development against HCMV," Viruses, vol. 12, iss. 1, p. 35, 2019.
    [Bibtex]
    @Article{Perotti:19,
    author = {Michela Perotti and Laurent Perez},
    title = {Virus-Like Particles and Nanoparticles for Vaccine Development against {HCMV}},
    journal = {Viruses},
    year = {2019},
    volume = {12},
    number = {1},
    pages = {35},
    doi = {10.3390/v12010035},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] K. C. Wolthers, P. Susi, D. Jochmans, J. Koskinen, O. Landt, N. Sanchez, K. Palm, J. Neyts, and S. J. Butcher, "Progress in human picornavirus research: new findings from the AIROPico consortium," Antiviral Res, vol. 161, p. 100–107, 2019.
    [Bibtex]
    @Article{Wolthers:19,
    author = {Katja C. Wolthers and Petri Susi and Dirk Jochmans and Janne Koskinen and Olfert Landt and Neus Sanchez and Kaia Palm and Johan Neyts and Sarah J. Butcher},
    title = {Progress in human picornavirus research: New findings from the {AIROPico} consortium},
    journal = {{Antiviral Res}},
    year = {2019},
    volume = {161},
    pages = {100--107},
    doi = {10.1016/j.antiviral.2018.11.010},
    publisher = {Elsevier {BV}},
    }
  • [DOI] P. A. de Jonge, F. L. Nobrega, S. J. J. Brouns, and B. E. Dutilh, "Molecular and evolutionary determinants of bacteriophage host range," Trends Microbiol, vol. 27, iss. 1, p. 51–63, 2019.
    [Bibtex]
    @Article{Jonge:19,
    author = {Patrick A. de Jonge and Franklin L. Nobrega and Stan J.J. Brouns and Bas E. Dutilh},
    title = {Molecular and Evolutionary Determinants of Bacteriophage Host Range},
    journal = {{Trends Microbiol}},
    year = {2019},
    volume = {27},
    number = {1},
    pages = {51--63},
    doi = {10.1016/j.tim.2018.08.006},
    publisher = {Elsevier {BV}},
    }
  • D. Desirò, M. Hölzer, B. Ibrahim, and M. Marz, "SilentMutations (SIM): a tool for analyzing long-range RNA–RNA interactions in viral genomes and structured RNAs," Virus Res, vol. 260, p. 135–141, 2019.
    [Bibtex]
    @Article{Desiro:19,
    author = {Desir{\`{o}}, Daniel and H{\"o}lzer, Martin and Ibrahim, Bashar and Marz, Manja},
    title = {{S}ilent{M}utations ({SIM}): A tool for analyzing long-range {RNA}--{RNA} interactions in viral genomes and structured {RNA}s},
    journal = {{Virus Res}},
    year = {2019},
    volume = {260},
    pages = {135--141},
    publisher = {Elsevier},
    }
  • [DOI] J. D. Wuerth and F. Weber, "Ferreting out viral pathogenesis," Nat Microbiol, vol. 4, iss. 3, p. 384–385, 2019.
    [Bibtex]
    @Article{Wuerth:19,
    author = {Jennifer Deborah Wuerth and Friedemann Weber},
    title = {Ferreting out viral pathogenesis},
    journal = {{Nat Microbiol}},
    year = {2019},
    volume = {4},
    number = {3},
    pages = {384--385},
    doi = {10.1038/s41564-019-0390-0},
    publisher = {Springer Nature},
    }
  • [DOI] A. Sulovari and D. Li, "VIpower: simulation-based tool for estimating power of viral integration detection via high-throughput sequencing," Genomics, 2019.
    [Bibtex]
    @Article{Sulovari:19,
    author = {Arvis Sulovari and Dawei Li},
    title = {{VIpower}: Simulation-based tool for estimating power of viral integration detection via high-throughput sequencing},
    journal = {Genomics},
    year = {2019},
    doi = {10.1016/j.ygeno.2019.01.015},
    publisher = {Elsevier {BV}},
    }
  • [DOI] A. Fritz, P. Hofmann, S. Majda, E. Dahms, J. Dröge, J. Fiedler, T. R. Lesker, P. Belmann, M. Z. DeMaere, A. E. Darling, A. Sczyrba, A. Bremges, and A. C. McHardy, "CAMISIM: simulating metagenomes and microbial communities," Microbiome, vol. 7, iss. 1, 2019.
    [Bibtex]
    @Article{Fritz:19,
    author = {Adrian Fritz and Peter Hofmann and Stephan Majda and Eik Dahms and Johannes Dröge and Jessika Fiedler and Till R. Lesker and Peter Belmann and Matthew Z. DeMaere and Aaron E. Darling and Alexander Sczyrba and Andreas Bremges and Alice C. McHardy},
    title = {{CAMISIM}: simulating metagenomes and microbial communities},
    journal = {Microbiome},
    year = {2019},
    volume = {7},
    number = {1},
    doi = {10.1186/s40168-019-0633-6},
    publisher = {Springer Nature},
    }
  • [DOI] T. Kustin, G. Ling, S. Sharabi, D. Ram, N. Friedman, N. Zuckerman, E. D. Bucris, A. Glatman-Freedman, A. Stern, and M. Mandelboim, "A method to identify respiratory virus infections in clinical samples using next-generation sequencing," Sci Rep, vol. 9, iss. 1, 2019.
    [Bibtex]
    @Article{Kustin:19,
    author = {Talia Kustin and Guy Ling and Sivan Sharabi and Daniela Ram and Nehemya Friedman and Neta Zuckerman and Efrat Dahan Bucris and Aharona Glatman-Freedman and Adi Stern and Michal Mandelboim},
    title = {A method to identify respiratory virus infections in clinical samples using next-generation sequencing},
    journal = {{Sci Rep}},
    year = {2019},
    volume = {9},
    number = {1},
    doi = {10.1038/s41598-018-37483-w},
    publisher = {Springer Nature},
    }
  • [DOI] S. Kouchaki, A. Tapinos, and D. L. Robertson, "A signal processing method for alignment-free metagenomic binning: multi-resolution genomic binary patterns," Sci Rep, vol. 9, iss. 1, 2019.
    [Bibtex]
    @Article{Kouchaki:19,
    author = {Samaneh Kouchaki and Avraam Tapinos and David L. Robertson},
    title = {A signal processing method for alignment-free metagenomic binning: multi-resolution genomic binary patterns},
    journal = {{Sci Rep}},
    year = {2019},
    volume = {9},
    number = {1},
    doi = {10.1038/s41598-018-38197-9},
    publisher = {Springer Nature},
    }
  • [DOI] V. Ravindran, J. C. Nacher, T. Akutsu, M. Ishitsuka, A. Osadcenco, V. Sunitha, G. Bagler, J. Schwartz, and D. L. Robertson, "Network controllability analysis of intracellular signalling reveals viruses are actively controlling molecular systems," Sci Rep, vol. 9, iss. 1, 2019.
    [Bibtex]
    @Article{Ravindran:19,
    author = {Vandana Ravindran and Jose C. Nacher and Tatsuya Akutsu and Masayuki Ishitsuka and Adrian Osadcenco and V. Sunitha and Ganesh Bagler and Jean-Marc Schwartz and David L. Robertson},
    title = {Network controllability analysis of intracellular signalling reveals viruses are actively controlling molecular systems},
    journal = {{Sci Rep}},
    year = {2019},
    volume = {9},
    number = {1},
    doi = {10.1038/s41598-018-38224-9},
    publisher = {Springer Nature},
    }
  • [DOI] M. Ahmad, V. Helms, O. V. Kalinina, and T. Lengauer, "Relative principal components analysis: application to analyzing biomolecular conformational changes," J Chem Theory Comput, 2019.
    [Bibtex]
    @Article{Ahmad:19,
    author = {Mazen Ahmad and Volkhard Helms and Olga V. Kalinina and Thomas Lengauer},
    title = {Relative Principal Components Analysis: Application to Analyzing Biomolecular Conformational Changes},
    journal = {{J Chem Theory Comput}},
    year = {2019},
    doi = {10.1021/acs.jctc.8b01074},
    publisher = {American Chemical Society ({ACS})},
    }
  • [DOI] R. I. Amann, S. Baichoo, B. J. Blencowe, P. Bork, M. Borodovsky, C. Brooksbank, P. S. G. Chain, R. R. Colwell, D. G. Daffonchio, A. Danchin, V. de Lorenzo, P. C. Dorrestein, R. D. Finn, C. M. Fraser, J. A. Gilbert, S. J. Hallam, P. Hugenholtz, J. P. A. Ioannidis, J. K. Jansson, J. F. Kim, H. Klenk, M. G. Klotz, R. Knight, K. T. Konstantinidis, N. C. Kyrpides, C. E. Mason, A. C. McHardy, F. Meyer, C. A. Ouzounis, A. A. N. Patrinos, M. Podar, K. S. Pollard, J. Ravel, A. R. Muñoz, R. J. Roberts, R. Rosselló-Móra, S. Sansone, P. D. Schloss, L. M. Schriml, J. C. Setubal, R. Sorek, R. L. Stevens, J. M. Tiedje, A. Turjanski, G. W. Tyson, D. W. Ussery, G. M. Weinstock, O. White, W. B. Whitman, and I. Xenarios, "Toward unrestricted use of public genomic data," Science, vol. 363, iss. 6425, p. 350–352, 2019.
    [Bibtex]
    @Article{Amann:19,
    author = {Rudolf I. Amann and Shakuntala Baichoo and Benjamin J. Blencowe and Peer Bork and Mark Borodovsky and Cath Brooksbank and Patrick S. G. Chain and Rita R. Colwell and Daniele G. Daffonchio and Antoine Danchin and Victor de Lorenzo and Pieter C. Dorrestein and Robert D. Finn and Claire M. Fraser and Jack A. Gilbert and Steven J. Hallam and Philip Hugenholtz and John P. A. Ioannidis and Janet K. Jansson and Jihyun F. Kim and Hans-Peter Klenk and Martin G. Klotz and Rob Knight and Konstantinos T. Konstantinidis and Nikos C. Kyrpides and Christopher E. Mason and Alice C. McHardy and Folker Meyer and Christos A. Ouzounis and Aristides A. N. Patrinos and Mircea Podar and Katherine S. Pollard and Jacques Ravel and Alejandro Reyes Mu{\~{n}}oz and Richard J. Roberts and Ramon Rossell{\'{o}}-M{\'{o}}ra and Susanna-Assunta Sansone and Patrick D. Schloss and Lynn M. Schriml and Jo{\~{a}}o C. Setubal and Rotem Sorek and Rick L. Stevens and James M. Tiedje and Adrian Turjanski and Gene W. Tyson and David W. Ussery and George M. Weinstock and Owen White and William B. Whitman and Ioannis Xenarios},
    title = {Toward unrestricted use of public genomic data},
    journal = {Science},
    year = {2019},
    volume = {363},
    number = {6425},
    pages = {350--352},
    doi = {10.1126/science.aaw1280},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
  • [DOI] M. Golumbeanu, S. Desfarges, C. Hernandez, M. Quadroni, S. Rato, P. Mohammadi, A. Telenti, N. Beerenwinkel, and A. Ciuffi, "Proteo-transcriptomic dynamics of cellular response to HIV-1 infection," Sci Rep, vol. 9, iss. 1, 2019.
    [Bibtex]
    @Article{Golumbeanu:19,
    author = {Monica Golumbeanu and S{\'{e}}bastien Desfarges and C{\'{e}}line Hernandez and Manfredo Quadroni and Sylvie Rato and Pejman Mohammadi and Amalio Telenti and Niko Beerenwinkel and Angela Ciuffi},
    title = {Proteo-Transcriptomic Dynamics of Cellular Response to {HIV}-1 Infection},
    journal = {{Sci Rep}},
    year = {2019},
    volume = {9},
    number = {1},
    doi = {10.1038/s41598-018-36135-3},
    publisher = {Springer Nature},
    }
  • [DOI] C. M. Zmasek, D. M. Knipe, P. E. Pellett, and R. H. Scheuermann, "Classification of human Herpesviridae proteins using domain-architecture aware inference of orthologs (DAIO)," Virology, vol. 529, p. 29–42, 2019.
    [Bibtex]
    @Article{Zmasek:19,
    author = {Christian M. Zmasek and David M. Knipe and Philip E. Pellett and Richard H. Scheuermann},
    title = {Classification of human {H}erpesviridae proteins using Domain-architecture Aware Inference of Orthologs ({DAIO})},
    journal = {Virology},
    year = {2019},
    volume = {529},
    pages = {29--42},
    doi = {10.1016/j.virol.2019.01.005},
    publisher = {Elsevier {BV}},
    }
  • [DOI] S. F. Cotmore, M. Agbandje-McKenna, M. Canuti, J. A. Chiorini, A. Eis-Hubinger, J. Hughes, M. Mietzsch, S. Modha, M. Ogliastro, J. J. Pénzes, D. J. Pintel, J. Qiu, M. Soderlund-Venermo, P. Tattersall, and P. T. and, "ICTV virus taxonomy profile: Parvoviridae," J Gen Virol, vol. 100, iss. 3, p. 367–368, 2019.
    [Bibtex]
    @Article{Cotmore:19,
    author = {Susan F. Cotmore and Mavis Agbandje-McKenna and Marta Canuti and John A. Chiorini and Anna-Maria Eis-Hubinger and Joseph Hughes and Mario Mietzsch and Sejal Modha and Myl{\`{e}}ne Ogliastro and Judit J. P{\'{e}}nzes and David J. Pintel and Jianming Qiu and Maria Soderlund-Venermo and Peter Tattersall and Peter Tijssen and},
    title = {{ICTV} Virus Taxonomy Profile: {P}arvoviridae},
    journal = {{J Gen Virol}},
    year = {2019},
    volume = {100},
    number = {3},
    pages = {367--368},
    doi = {10.1099/jgv.0.001212},
    publisher = {Microbiology Society},
    }
  • [DOI] S. G. Siddell, P. J. Walker, E. J. Lefkowitz, A. R. Mushegian, M. J. Adams, B. E. Dutilh, A. E. Gorbalenya, B. Harrach, R. L. Harrison, S. Junglen, N. J. Knowles, A. M. Kropinski, M. Krupovic, J. H. Kuhn, M. Nibert, L. Rubino, S. Sabanadzovic, H. Sanfaçon, P. Simmonds, A. Varsani, F. M. Zerbini, and A. J. Davison, "Additional changes to taxonomy ratified in a special vote by the International Committee on Taxonomy of Viruses (October 2018)," Arch Virol, vol. 164, iss. 3, p. 943–946, 2019.
    [Bibtex]
    @Article{Siddell:19,
    author = {Stuart G. Siddell and Peter J. Walker and Elliot J. Lefkowitz and Arcady R. Mushegian and Michael J. Adams and Bas E. Dutilh and Alexander E. Gorbalenya and Bal{\'{a}}zs Harrach and Robert L. Harrison and Sandra Junglen and Nick J. Knowles and Andrew M. Kropinski and Mart Krupovic and Jens H. Kuhn and Max Nibert and Luisa Rubino and Sead Sabanadzovic and H{\'{e}}l{\`{e}}ne Sanfa{\c{c}}on and Peter Simmonds and Arvind Varsani and Francisco Murilo Zerbini and Andrew J. Davison},
    title = {Additional changes to taxonomy ratified in a special vote by the {International Committee on Taxonomy of Viruses} ({O}ctober 2018)},
    journal = {{Arch Virol}},
    year = {2019},
    volume = {164},
    number = {3},
    pages = {943--946},
    doi = {10.1007/s00705-018-04136-2},
    publisher = {Springer Nature},
    }
  • [DOI] U. Ashraf, C. Benoit-Pilven, V. Lacroix, V. Navratil, and N. Naffakh, "Advances in analyzing virus-induced alterations of host cell splicing," Trends Microbiol, vol. 27, iss. 3, p. 268–281, 2019.
    [Bibtex]
    @Article{Ashraf:19,
    author = {Usama Ashraf and Clara Benoit-Pilven and Vincent Lacroix and Vincent Navratil and Nadia Naffakh},
    title = {Advances in Analyzing Virus-Induced Alterations of Host Cell Splicing},
    journal = {{Trends Microbiol}},
    year = {2019},
    volume = {27},
    number = {3},
    pages = {268--281},
    doi = {10.1016/j.tim.2018.11.004},
    publisher = {Elsevier {BV}},
    }
  • [DOI] C. M. Kinsella, M. Deijs, and L. van der Hoek, "Enhanced bioinformatic profiling of VIDISCA libraries for virus detection and discovery," Virus Res, vol. 263, p. 21–26, 2019.
    [Bibtex]
    @Article{Kinsella:19,
    author = {Cormac M. Kinsella and Martin Deijs and Lia van der Hoek},
    title = {Enhanced bioinformatic profiling of {VIDISCA} libraries for virus detection and discovery},
    journal = {{Virus Res}},
    year = {2019},
    volume = {263},
    pages = {21--26},
    doi = {10.1016/j.virusres.2018.12.010},
    publisher = {Elsevier {BV}},
    }
  • [DOI] K. Wernike and M. Beer, "Misinterpretation of Schmallenberg virus sequence variations: the sample material makes the difference," Virus Genes, 2019.
    [Bibtex]
    @Article{Wernike:19,
    author = {Kerstin Wernike and Martin Beer},
    title = {Misinterpretation of {S}chmallenberg virus sequence variations: the sample material makes the difference},
    journal = {{Virus Genes}},
    year = {2019},
    doi = {10.1007/s11262-018-1628-2},
    publisher = {Springer Nature},
    }
  • [DOI] P. Hubel, C. Urban, V. Bergant, W. M. Schneider, B. Knauer, A. Stukalov, P. Scaturro, A. Mann, L. Brunotte, H. H. Hoffmann, J. W. Schoggins, M. Schwemmle, M. Mann, C. M. Rice, and A. Pichlmair, "A protein-interaction network of interferon-stimulated genes extends the innate immune system landscape," Nat Immunol, 2019.
    [Bibtex]
    @Article{Hubel:19,
    author = {Philipp Hubel and Christian Urban and Valter Bergant and William M. Schneider and Barbara Knauer and Alexey Stukalov and Pietro Scaturro and Angelika Mann and Linda Brunotte and Heinrich H. Hoffmann and John W. Schoggins and Martin Schwemmle and Matthias Mann and Charles M. Rice and Andreas Pichlmair},
    title = {A protein-interaction network of interferon-stimulated genes extends the innate immune system landscape},
    journal = {{Nat Immunol}},
    year = {2019},
    doi = {10.1038/s41590-019-0323-3},
    publisher = {Springer Nature},
    }
  • [DOI] K. Brown, I. Olendraite, S. M. Valles, A. E. Firth, Y. Chen, D. M. A. Guérin, Y. Hashimoto, S. Herrero, J. R. de Miranda, E. Ryabov, and ICTV Report Consortium, "ICTV virus taxonomy profile: Solinviviridae," J Gen Virol, 2019.
    [Bibtex]
    @Article{Brown:19,
    author = {Katherine Brown and Ingrida Olendraite and Steven M. Valles and Andrew E. Firth and Yanping Chen and Diego M. A. Gu{\'{e}}rin and Yoshifumi Hashimoto and Salvador Herrero and Joachim R. de Miranda and Eugene Ryabov and {ICTV Report Consortium}},
    title = {{ICTV} Virus Taxonomy Profile: {S}olinviviridae},
    journal = {{J Gen Virol}},
    year = {2019},
    doi = {10.1099/jgv.0.001242},
    publisher = {Microbiology Society},
    }
  • [DOI] I. Olendraite, K. Brown, S. M. Valles, A. E. Firth, Y. Chen, D. M. A. Guérin, Y. Hashimoto, S. Herrero, J. R. de Miranda, E. Ryabov, and ICTV Report Consortium, "ICTV virus taxonomy profile: Polycipiviridae," J Gen Virol, 2019.
    [Bibtex]
    @Article{Olendraite:19,
    author = {Ingrida Olendraite and Katherine Brown and Steven M. Valles and Andrew E. Firth and Yanping Chen and Diego M. A. Gu{\'{e}}rin and Yoshifumi Hashimoto and Salvador Herrero and Joachim R. de Miranda and Eugene Ryabov and {ICTV Report Consortium}},
    title = {{ICTV} Virus Taxonomy Profile: {P}olycipiviridae},
    journal = {{J Gen Virol}},
    year = {2019},
    doi = {10.1099/jgv.0.001241},
    publisher = {Microbiology Society},
    }
  • [DOI] S. Hansen, S. Hotop, O. Faye, O. Ndiaye, S. Böhlken-Fascher, R. Pessôa, F. Hufert, C. Stahl-Hennig, R. Frank, C. Czerny, J. Schmidt-Chanasit, S. S. Sanabani, A. A. Sall, M. Niedrig, M. Brönstrup, H. Fritz, and A. A. E. Wahed, "Diagnosing Zika virus infection against a background of other flaviviruses: studies in high resolution serological analysis," Sci Rep, vol. 9, iss. 1, 2019.
    [Bibtex]
    @Article{Hansen:19,
    author = {Sören Hansen and Sven-Kevin Hotop and Oumar Faye and Oumar Ndiaye and Susanne B\"{o}hlken-Fascher and Rodrigo Pess{\^{o}}a and Frank Hufert and Christiane Stahl-Hennig and Ronald Frank and Claus-Peter Czerny and Jonas Schmidt-Chanasit and Sabri S. Sanabani and Amadou A. Sall and Matthias Niedrig and Mark Br\"{o}nstrup and Hans-Joachim Fritz and Ahmed Abd El Wahed},
    title = {Diagnosing {Z}ika virus infection against a background of other flaviviruses: Studies in high resolution serological analysis},
    journal = {{Sci Rep}},
    year = {2019},
    volume = {9},
    number = {1},
    doi = {10.1038/s41598-019-40224-2},
    publisher = {Springer Nature},
    }
  • [DOI] M. Thijssen, P. Lemey, S. Amini-Bavil-Olyaee, S. Dellicour, S. M. Alavian, F. Tacke, C. Verslype, F. Nevens, and M. R. Pourkarim, "Mass migration to Europe: an opportunity for elimination of hepatitis B virus?," Lancet Gastroenterol Hepatol, vol. 4, p. 315–323, 2019.
    [Bibtex]
    @Article{Thijssen:19,
    author = {Thijssen, Marijn and Lemey, Philippe and Amini-Bavil-Olyaee, Samad and Dellicour, Simon and Alavian, Seyed Moayed and Tacke, Frank and Verslype, Chris and Nevens, Frederik and Pourkarim, Mahmoud Reza},
    title = {Mass migration to {E}urope: an opportunity for elimination of hepatitis {B} virus?},
    journal = {{Lancet Gastroenterol Hepatol}},
    year = {2019},
    volume = {4},
    pages = {315--323},
    abstract = {People from low-to-middle income countries have been migrating to western Europe on a large scale in recent years. Data indicate that the number of first-time asylum applications by non-EU members increased from 290 000 in 2011 to more than 1·3 million in 2015. During the peak period of migration, The Global Health Sector Strategy on Viral Hepatitis was adopted by WHO. Viral hepatitis, and particularly hepatitis B virus (HBV), is an important disease because of its high prevalence and associated mortality. In some cases, HBV can be carried by refugees arriving from regions of high and intermediate prevalence. Refugees with HBV might not show clinical symptoms and not be diagnosed in destination countries with a low prevalence, where screening is not regularly done. Although transmission to the host population is low, dedicated surveillance and tailored public health policies are required. It is important to note that some of the countries that receive many migrants do not have a universal HBV vaccination programme. In this Viewpoint, we argue that the current large-scale movement from regions with high or intermediate HBV prevalence should be taken as an opportunity to achieve viral hepatitis elimination targets, by establishing a well prepared infrastructure for HBV screening, vaccination, and treatment.},
    doi = {10.1016/S2468-1253(19)30014-7},
    issue = {4},
    pmid = {30860067},
    }
  • [DOI] A. Jariani, C. Warth, K. Deforche, P. Libin, A. J. Drummond, A. Rambaut, F. A. Matsen IV, and K. Theys, "SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination," Virus Evol, vol. 5, iss. 1, 2019.
    [Bibtex]
    @Article{Jariani:19,
    author = {Abbas Jariani and Christopher Warth and Koen Deforche and Pieter Libin and Alexei J Drummond and Andrew Rambaut and Frederick A {Matsen IV} and Kristof Theys},
    title = {{SANTA}-{SIM}: simulating viral sequence evolution dynamics under selection and recombination},
    journal = {{Virus Evol}},
    year = {2019},
    volume = {5},
    number = {1},
    doi = {10.1093/ve/vez003},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] X. Chen and D. Li, "ERVcaller: identifying polymorphic endogenous retrovirus and other transposable element insertions using whole-genome sequencing data," Bioinformatics, 2019.
    [Bibtex]
    @Article{Chen:19,
    author = {Xun Chen and Dawei Li},
    title = {{ERVcaller}: Identifying polymorphic endogenous retrovirus and other transposable element insertions using whole-genome sequencing data},
    journal = {Bioinformatics},
    year = {2019},
    doi = {10.1093/bioinformatics/btz205},
    editor = {Inanc Birol},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] N. Altan-Bonnet, C. Perales, and E. Domingo, "Extracellular vesicles: vehicles of en bloc viral transmission.," Virus Res, 2019.
    [Bibtex]
    @Article{Altan-Bonnet:19,
    author = {Altan-Bonnet, Nihal and Perales, Celia and Domingo, Esteban},
    title = {Extracellular vesicles: vehicles of en bloc viral transmission.},
    journal = {{Virus Res}},
    year = {2019},
    abstract = {En Bloc transmission of viruses allow multiple genomes to collectivelly penetrate and initiate infection in the same cell, often resulting in enhanced infectivity. Given the quasispecies (mutant cloud) nature of RNA viruses and many DNA viruses, the multiple genomes provide different starting points in sequence space to initiate adaptive walks. Moreover, en bloc transmission has implications for modulation of viral fitness and for the response of viral populations to lethal mutagenesis. Mechanisms that can enable multiple viral genomes to be transported en bloc among hosts has only recently been gaining attention. A growing body of research suggests that extracellular vesicles (EV) are highly prevalent and robust vehicles for en bloc delivery of viral particles and naked infectious genomes among organisms. Both RNA and DNA viruses exploit these vesicles to increase multiplicity of infection and enhance virulence.},
    doi = {10.1016/j.virusres.2019.03.023},
    pmid = {30928427},
    }
  • [DOI] O. Ratmann, K. M. and Grabowski, M. Hall, T. Golubchik, C. Wymant, L. Abeler-Dörner, D. Bonsall, A. Hoppe, A. L. Brown, T. de Oliveira, A. Gall, P. Kellam, D. Pillay, J. Kagaayi, G. Kigozi, T. C. Quinn, M. J. Wawer, O. Laeyendecker, D. Serwadda, R. H. Gray, and C. Fraser, "Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis," Nat Commun, vol. 10, iss. 1, 2019.
    [Bibtex]
    @Article{Ratmann:19,
    author = {Oliver Ratmann and and M. Kate Grabowski and Matthew Hall and Tanya Golubchik and Chris Wymant and Lucie Abeler-Dörner and David Bonsall and Anne Hoppe and Andrew Leigh Brown and Tulio de Oliveira and Astrid Gall and Paul Kellam and Deenan Pillay and Joseph Kagaayi and Godfrey Kigozi and Thomas C. Quinn and Maria J. Wawer and Oliver Laeyendecker and David Serwadda and Ronald H. Gray and Christophe Fraser},
    title = {Inferring {HIV}-1 transmission networks and sources of epidemic spread in {A}frica with deep-sequence phylogenetic analysis},
    journal = {{Nat Commun}},
    year = {2019},
    volume = {10},
    number = {1},
    doi = {10.1038/s41467-019-09139-4},
    publisher = {Springer Nature},
    }
  • [DOI] H. F. Löchel, D. Eger, T. Sperlea, and D. Heider, "Deep learning on chaos game representation for proteins," bioRxiv, p. 575324, 2019.
    [Bibtex]
    @Article{Löchel:19,
    author = {Hannah F. Löchel and Dominic Eger and Theodor Sperlea and Dominik Heider},
    title = {Deep Learning on Chaos Game Representation for Proteins},
    journal = {{bioRxiv}},
    year = {2019},
    pages = {575324},
    doi = {10.1101/575324},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] L. de Borba, S. M. Villordo, F. L. Marsico, J. M. Carballeda, C. V. Filomatori, L. G. Gebhard, H. M. Pallarés, S. Lequime, L. Lambrechts, I. S. Vargas, C. D. Blair, and A. V. Gamarnik, "RNA structure duplication in the dengue virus 3' UTR: redundancy or host specificity?," mBio, vol. 10, iss. 1, 2019.
    [Bibtex]
    @Article{Borba:19,
    author = {Luana de Borba and Sergio M. Villordo and Franco L. Marsico and Juan M. Carballeda and Claudia V. Filomatori and Leopoldo G. Gebhard and Horacio M. Pallar{\'{e}}s and Sebastian Lequime and Louis Lambrechts and Irma S{\'{a}}nchez Vargas and Carol D. Blair and Andrea V. Gamarnik},
    title = {{RNA} Structure Duplication in the Dengue Virus 3' {UTR}: Redundancy or Host Specificity?},
    journal = {{mBio}},
    year = {2019},
    volume = {10},
    number = {1},
    doi = {10.1128/mbio.02506-18},
    editor = {Carolyn B. Coyne},
    publisher = {American Society for Microbiology},
    }
  • [DOI] R. Bouckaert, T. G. Vaughan, J. Barido-Sottani, S. Duchêne, M. Fourment, A. Gavryushkina, J. Heled, G. Jones, D. Kühnert, N. D. Maio, M. Matschiner, F. K. Mendes, N. F. Müller, H. A. Ogilvie, L. du Plessis, A. Popinga, A. Rambaut, D. Rasmussen, I. Siveroni, M. A. Suchard, C. Wu, D. Xie, C. Zhang, T. Stadler, and A. J. Drummond, "BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis," PLOS Comput Biol, vol. 15, iss. 4, p. e1006650, 2019.
    [Bibtex]
    @Article{Bouckaert:19,
    author = {Remco Bouckaert and Timothy G. Vaughan and Joëlle Barido-Sottani and Sebasti{\'{a}}n Duch{\^{e}}ne and Mathieu Fourment and Alexandra Gavryushkina and Joseph Heled and Graham Jones and Denise Kühnert and Nicola De Maio and Michael Matschiner and F{\'{a}}bio K. Mendes and Nicola F. Müller and Huw A. Ogilvie and Louis du Plessis and Alex Popinga and Andrew Rambaut and David Rasmussen and Igor Siveroni and Marc A. Suchard and Chieh-Hsi Wu and Dong Xie and Chi Zhang and Tanja Stadler and Alexei J. Drummond},
    title = {{BEAST} 2.5: An advanced software platform for {B}ayesian evolutionary analysis},
    journal = {{PLOS Comput Biol}},
    year = {2019},
    volume = {15},
    number = {4},
    pages = {e1006650},
    doi = {10.1371/journal.pcbi.1006650},
    editor = {Mihaela Pertea},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] E. Domingo, A. I. de Ávila, I. Gallego, J. Sheldon, and C. Perales, "Viral fitness: history and relevance for viral pathogenesis and antiviral interventions," Pathog Dis, 2019.
    [Bibtex]
    @Article{Domingo:19,
    author = {Esteban Domingo and Ana I de {\'{A}}vila and Isabel Gallego and Julie Sheldon and Celia Perales},
    title = {Viral fitness: history and relevance for viral pathogenesis and antiviral interventions},
    journal = {{Pathog Dis}},
    year = {2019},
    doi = {10.1093/femspd/ftz021},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] J. V. Membrebe, M. A. Suchard, A. Rambaut, G. Baele, and P. Lemey, "Bayesian inference of evolutionary histories under time-dependent substitution rates," Mol Biol Evol, 2019.
    [Bibtex]
    @Article{Membrebe:19,
    author = {Jade Vincent Membrebe and Marc A Suchard and Andrew Rambaut and Guy Baele and Philippe Lemey},
    title = {Bayesian inference of evolutionary histories under time-dependent substitution rates},
    journal = {{Mol Biol Evol}},
    year = {2019},
    doi = {10.1093/molbev/msz094},
    editor = {Jeffrey Thorne},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] J. Singer, E. Thomson, J. Hughes, E. Aranday-Cortes, J. McLauchlan, A. S. da Filipe, L. Tong, C. Manso, R. J. Gifford, D. L. Robertson, E. Barnes, M. Ansari, J. Mbisa, D. Bibby, D. Bradshaw, and D. Smith, "Interpreting viral deep sequencing data with GLUE," Viruses, vol. 11, iss. 4, p. 323, 2019.
    [Bibtex]
    @Article{Singer:19,
    author = {Joshua Singer and Emma Thomson and Joseph Hughes and Elihu Aranday-Cortes and John McLauchlan and Ana da Silva Filipe and Lily Tong and Carmen Manso and Robert J. Gifford and David L. Robertson and Eleanor Barnes and M. Ansari and Jean Mbisa and David Bibby and Daniel Bradshaw and David Smith},
    title = {Interpreting Viral Deep Sequencing Data with {GLUE}},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {4},
    pages = {323},
    doi = {10.3390/v11040323},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] S. Nachtweide and M. Stanke, "Multi-genome annotation with AUGUSTUS," in Methods Mol Biol, Springer new york, 2019, p. 139–160.
    [Bibtex]
    @InCollection{Nachtweide:19,
    author = {Stefanie Nachtweide and Mario Stanke},
    title = {Multi-Genome Annotation with {AUGUSTUS}},
    booktitle = {{Methods Mol Biol}},
    publisher = {Springer New York},
    year = {2019},
    pages = {139--160},
    doi = {10.1007/978-1-4939-9173-0_8},
    }
  • [DOI] A. B. de Schneider and M. T. Wolfinger, "Musashi binding elements in Zika and related Flavivirus 3'UTRs: a comparative study in silico," Sci Rep, vol. 9, iss. 1, 2019.
    [Bibtex]
    @Article{BernardiSchneider:19,
    author = {Adriano de Bernardi Schneider and Michael T. Wolfinger},
    title = {Musashi binding elements in {Z}ika and related {F}lavivirus 3'{UTRs}: A comparative study in silico},
    journal = {{Sci Rep}},
    year = {2019},
    volume = {9},
    number = {1},
    doi = {10.1038/s41598-019-43390-5},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] F. Hufsky, B. Ibrahim, S. Modha, M. R. J. Clokie, S. Deinhardt-Emmer, B. E. Dutilh, S. Lycett, P. Simmonds, V. Thiel, A. Abroi, E. M. Adriaenssens, M. Escalera-Zamudio, J. N. Kelly, K. Lamkiewicz, L. Lu, J. Susat, T. Sicheritz, D. L. Robertson, and M. Marz, "The third annual meeting of the European Virus Bioinformatics Center," Viruses, vol. 11, iss. 5, p. 420, 2019.
    [Bibtex]
    @Article{Hufsky:19,
    author = {Franziska Hufsky and Bashar Ibrahim and Sejal Modha and Martha R. J. Clokie and Stefanie Deinhardt-Emmer and Bas E. Dutilh and Samantha Lycett and Peter Simmonds and Volker Thiel and Aare Abroi and Evelien M. Adriaenssens and Marina Escalera-Zamudio and Jenna Nicole Kelly and Kevin Lamkiewicz and Lu Lu and Julian Susat and Thomas Sicheritz and David L. Robertson and Manja Marz},
    title = {The Third Annual Meeting of the {E}uropean {V}irus {B}ioinformatics {C}enter},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {5},
    pages = {420},
    doi = {10.3390/v11050420},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] S. Peter, M. Hölzer, K. Lamkiewicz, P. S. di Fenizio, H. A. Hwaeer, M. Marz, S. Schuster, P. Dittrich, and B. Ibrahim, "Structure and hierarchy of influenza virus models revealed by reaction network analysis," Viruses, vol. 11, iss. 5, p. 449, 2019.
    [Bibtex]
    @Article{Peter:19,
    author = {Stephan Peter and Martin Hölzer and Kevin Lamkiewicz and Pietro Speroni di Fenizio and Hassan Al Hwaeer and Manja Marz and Stefan Schuster and Peter Dittrich and Bashar Ibrahim},
    title = {Structure and Hierarchy of Influenza Virus Models Revealed by Reaction Network Analysis},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {5},
    pages = {449},
    doi = {10.3390/v11050449},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] M. Kiening, R. Ochsenreiter, H. Hellinger, T. Rattei, I. L. Hofacker, and D. Frishman, "Conserved secondary structures in viral mRNAs," Viruses, vol. 11, iss. 5, p. 401, 2019.
    [Bibtex]
    @Article{Kiening:19,
    author = {Michael Kiening and Roman Ochsenreiter and Hans-Jörg Hellinger and Thomas Rattei and Ivo L. Hofacker and Dmitrij Frishman},
    title = {Conserved Secondary Structures in Viral {mRNAs}},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {5},
    pages = {401},
    doi = {10.3390/v11050401},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] A. C. Gregory, A. A. Zayed, N. Conceição-Neto, B. Temperton, B. Bolduc, A. Alberti, M. Ardyna, K. Arkhipova, M. Carmichael, C. Cruaud, C. Dimier, G. Domínguez-Huerta, J. Ferland, S. Kandels, Y. Liu, C. Marec, S. Pesant, M. Picheral, S. Pisarev, J. Poulain, J. Tremblay, D. Vik, M. Babin, C. Bowler, A. I. Culley, C. de Vargas, B. E. Dutilh, D. Iudicone, L. Karp-Boss, S. Roux, S. Sunagawa, P. Wincker, M. B. Sullivan, S. G. Acinas, M. Babin, P. Bork, E. Boss, C. Bowler, G. Cochrane, C. de Vargas, M. Follows, G. Gorsky, N. Grimsley, L. Guidi, P. Hingamp, D. Iudicone, O. Jaillon, S. Kandels-Lewis, L. Karp-Boss, E. Karsenti, F. Not, H. Ogata, S. Pesant, N. Poulton, J. Raes, C. Sardet, S. Speich, L. Stemmann, M. B. Sullivan, S. Sunagawa, and P. Wincker, "Marine DNA viral macro- and microdiversity from pole to pole," Cell, vol. 177, iss. 5, p. 1109–1123.e14, 2019.
    [Bibtex]
    @Article{Gregory:19,
    author = {Ann C. Gregory and Ahmed A. Zayed and N{\'{a}}dia Concei{\c{c}}{\~{a}}o-Neto and Ben Temperton and Ben Bolduc and Adriana Alberti and Mathieu Ardyna and Ksenia Arkhipova and Margaux Carmichael and Corinne Cruaud and C{\'{e}}line Dimier and Guillermo Dom{\'{\i}}nguez-Huerta and Joannie Ferland and Stefanie Kandels and Yunxiao Liu and Claudie Marec and St{\'{e}}phane Pesant and Marc Picheral and Sergey Pisarev and Julie Poulain and Jean-{\'{E}}ric Tremblay and Dean Vik and Marcel Babin and Chris Bowler and Alexander I. Culley and Colomban de Vargas and Bas E. Dutilh and Daniele Iudicone and Lee Karp-Boss and Simon Roux and Shinichi Sunagawa and Patrick Wincker and Matthew B. Sullivan and Silvia G. Acinas and Marcel Babin and Peer Bork and Emmanuel Boss and Chris Bowler and Guy Cochrane and Colomban de Vargas and Michael Follows and Gabriel Gorsky and Nigel Grimsley and Lionel Guidi and Pascal Hingamp and Daniele Iudicone and Olivier Jaillon and Stefanie Kandels-Lewis and Lee Karp-Boss and Eric Karsenti and Fabrice Not and Hiroyuki Ogata and St{\'{e}}phane Pesant and Nicole Poulton and Jeroen Raes and Christian Sardet and Sabrina Speich and Lars Stemmann and Matthew B. Sullivan and Shinichi Sunagawa and Patrick Wincker},
    title = {Marine {DNA} Viral Macro- and Microdiversity from Pole to Pole},
    journal = {Cell},
    year = {2019},
    volume = {177},
    number = {5},
    pages = {1109--1123.e14},
    doi = {10.1016/j.cell.2019.03.040},
    publisher = {Elsevier {BV}},
    }
  • [DOI] A. Tapinos, B. Constantinides, M. V. T. Phan, S. Kouchaki, M. Cotten, and D. L. Robertson, "The utility of data transformation for alignment, de novo assembly and classification of short read virus sequences," Viruses, vol. 11, iss. 5, p. 394, 2019.
    [Bibtex]
    @Article{Tapinos:19a,
    author = {Avraam Tapinos and Bede Constantinides and My V. T. Phan and Samaneh Kouchaki and Matthew Cotten and David L. Robertson},
    title = {The Utility of Data Transformation for Alignment, de novo Assembly and Classification of Short Read Virus Sequences},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {5},
    pages = {394},
    doi = {10.3390/v11050394},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] B. Zhao, C. Dewald, M. Hennig, J. Bossert, M. Bauer, M. W. Pletz, and K. D. Jandt, "Microorganisms at materials surfaces in aircraft: potential risks for public health? - A systematic review," Travel Med Infect Dis, vol. 28, p. 6–14, 2019.
    [Bibtex]
    @Article{Zhao:19,
    author = {Bin Zhao and Carolin Dewald and Max Hennig and Jörg Bossert and Michael Bauer and Mathias W. Pletz and Klaus D. Jandt},
    title = {Microorganisms at materials surfaces in aircraft: Potential risks for public health? - {A} systematic review},
    journal = {{Travel Med Infect Dis}},
    year = {2019},
    volume = {28},
    pages = {6--14},
    doi = {10.1016/j.tmaid.2018.07.011},
    publisher = {Elsevier {BV}},
    }
  • [DOI] V. Fonseca, P. J. K. Libin, K. Theys, N. R. Faria, M. R. T. Nunes, M. I. Restovic, M. Freire, M. Giovanetti, L. Cuypers, A. Nowé, A. B. Abecasis, K. Deforche, G. A. Santiago, I. C. de Siqueira, E. J. San, K. C. B. Machado, V. Azevedo, A. M. B. Filippis, R. V. da Cunha, O. G. Pybus, A. Vandamme, L. C. J. Alcantara, and T. de Oliveira, "A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes," PLoS Negl Trop Dis, vol. 13, iss. 5, p. e0007231, 2019.
    [Bibtex]
    @Article{Fonseca:19,
    author = {Vagner Fonseca and Pieter J. K. Libin and Kristof Theys and Nuno R. Faria and Marcio R. T. Nunes and Maria I. Restovic and Murilo Freire and Marta Giovanetti and Lize Cuypers and Ann Now{\'{e}} and Ana B. Abecasis and Koen Deforche and Gilberto A. Santiago and Isadora C. de Siqueira and Emmanuel J. San and Kaliane C. B. Machado and Vasco Azevedo and Ana Maria Bispo-de Filippis and Rivaldo Ven{\^{a}}ncio da Cunha and Oliver G. Pybus and Anne-Mieke Vandamme and Luiz C. J. Alcantara and Tulio de Oliveira},
    title = {A computational method for the identification of {D}engue, {Z}ika and {C}hikungunya virus species and genotypes},
    journal = {{PLoS Negl Trop Dis}},
    year = {2019},
    volume = {13},
    number = {5},
    pages = {e0007231},
    doi = {10.1371/journal.pntd.0007231},
    editor = {Isabel Rodriguez-Barraquer},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] M. Hölzer and M. Marz, "De novo transcriptome assembly: a comprehensive cross-species comparison of short-read RNA-seq assemblers," GigaScience, vol. 8, iss. 5, 2019.
    [Bibtex]
    @Article{Hölzer:19,
    author = {Martin Hölzer and Manja Marz},
    title = {{D}e novo transcriptome assembly: A comprehensive cross-species comparison of short-read {RNA}-Seq assemblers},
    journal = {{GigaScience}},
    year = {2019},
    volume = {8},
    number = {5},
    doi = {10.1093/gigascience/giz039},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] S. Schuster, P. Miesen, and R. P. van Rij, "Antiviral RNAi in insects and mammals: parallels and differences," Viruses, vol. 11, iss. 5, p. 448, 2019.
    [Bibtex]
    @Article{Schuster:19,
    author = {Susan Schuster and Pascal Miesen and Ronald P. van Rij},
    title = {Antiviral {RNAi} in Insects and Mammals: Parallels and Differences},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {5},
    pages = {448},
    doi = {10.3390/v11050448},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] F. Pfaff, S. Hägglund, M. Zoli, S. Blaise-Boisseau, E. Laloy, S. Koethe, D. Zühlke, K. Riedel, S. Zientara, L. Bakkali-Kassimi, J. Valarcher, D. Höper, M. Beer, and M. Eschbaumer, "Proteogenomics uncovers critical elements of host response in bovine soft palate epithelial cells following in vitro infection with foot-and-mouth disease virus," Viruses, vol. 11, iss. 1, p. 53, 2019.
    [Bibtex]
    @Article{Pfaff:19,
    author = {Florian Pfaff and Sara Hägglund and Martina Zoli and Sandra Blaise-Boisseau and Eve Laloy and Susanne Koethe and Daniela Zühlke and Katharina Riedel and Stephan Zientara and Labib Bakkali-Kassimi and Jean-Fran{\c{c}}ois Valarcher and Dirk Höper and Martin Beer and Michael Eschbaumer},
    title = {Proteogenomics Uncovers Critical Elements of Host Response in Bovine Soft Palate Epithelial Cells Following In Vitro Infection with Foot-And-Mouth Disease Virus},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {1},
    pages = {53},
    doi = {10.3390/v11010053},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] B. Röder, N. Kersten, M. Herr, N. K. Speicher, and N. Pfeifer, "Web-rMKL: a web server for dimensionality reduction and sample clustering of multi-view data based on unsupervised multiple kernel learning," Nucleic Acids Res, 2019.
    [Bibtex]
    @Article{Röder:19,
    author = {Benedict Röder and Nicolas Kersten and Marius Herr and Nora K Speicher and Nico Pfeifer},
    title = {web-{rMKL}: a web server for dimensionality reduction and sample clustering of multi-view data based on unsupervised multiple kernel learning},
    journal = {{Nucleic Acids Res}},
    year = {2019},
    doi = {10.1093/nar/gkz422},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] K. Theys, P. J. K. Libin, K. V. Laethem, and A. B. Abecasis, "An evolutionary-based approach to quantify the genetic barrier to drug resistance in fast-evolving viruses: an application to HIV-1 subtypes and integrase inhibitors.," Antimicrob Agents Chemother, 2019.
    [Bibtex]
    @Article{Theys:19,
    author = {Kristof Theys and Pieter J. K. Libin and Kristel Van Laethem and Ana B Abecasis},
    title = {An evolutionary-based approach to quantify the genetic barrier to drug resistance in fast-evolving viruses: an application to {HIV}-1 subtypes and integrase inhibitors.},
    journal = {{Antimicrob Agents Chemother}},
    year = {2019},
    doi = {10.1128/aac.00539-19},
    publisher = {American Society for Microbiology},
    }
  • [DOI] R. Kallies, M. Hölzer, R. Brizola Toscan, U. Nunes da Rocha, J. Anders, M. Marz, and A. Chatzinotas, "Evaluation of sequencing library preparation protocols for viral metagenomic analysis from pristine aquifer groundwaters.," Viruses, vol. 11, 2019.
    [Bibtex]
    @Article{Kallies:19,
    author = {Kallies, René and Hölzer, Martin and Brizola Toscan, Rodolfo and Nunes da Rocha, Ulisses and Anders, John and Marz, Manja and Chatzinotas, Antonis},
    title = {Evaluation of Sequencing Library Preparation Protocols for Viral Metagenomic Analysis from Pristine Aquifer Groundwaters.},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    abstract = {Viral ecology of terrestrial habitats is yet-to be extensively explored, in particular the terrestrial subsurface. One problem in obtaining viral sequences from groundwater aquifer samples is the relatively low amount of virus particles. As a result, the amount of extracted DNA may not be sufficient for direct sequencing of such samples. Here we compared three DNA amplification methods to enrich viral DNA from three pristine limestone aquifer assemblages of the Hainich Critical Zone Exploratory to evaluate potential bias created by the different amplification methods as determined by viral metagenomics. Linker amplification shotgun libraries resulted in lowest redundancy among the sequencing reads and showed the highest diversity, while multiple displacement amplification produced the highest number of contigs with the longest average contig size, suggesting a combination of these two methods is suitable for the successful enrichment of viral DNA from pristine groundwater samples. In total, we identified 27,173, 5,886 and 32,613 viral contigs from the three samples from which 11.92 to 18.65% could be assigned to taxonomy using blast. Among these, members of the order were the most abundant group (52.20 to 69.12%) dominated by and . Those, and the high number of unknown viral sequences, substantially expand the known virosphere.},
    doi = {10.3390/v11060484},
    issue = {6},
    keywords = {AquaDiva; aquifer; groundwater; sequencing library preparation; viral metagenome},
    pmid = {31141902},
    }
  • [DOI] A. Dukhovny, K. Lamkiewicz, Q. Chen, M. Fricke, N. Jabrane-Ferrat, M. Marz, J. U. Jung, and E. H. Sklan, "A CRISPR activation screen identifies genes protecting from Zika virus infection," J Virol, 2019.
    [Bibtex]
    @Article{Dukhovny:19,
    author = {Dukhovny, Anna and Lamkiewicz, Kevin and Chen, Qian and Fricke, Markus and Jabrane-Ferrat, Nabila and Marz, Manja and Jung, Jae U. and Sklan, Ella H.},
    title = {A {CRISPR} activation screen identifies genes protecting from {Z}ika virus infection},
    journal = {{J Virol}},
    year = {2019},
    abstract = {Zika virus (ZIKV) is an arthropod borne emerging pathogen causing febrile illness. ZIKV is associated Guillain-Barr{\'e} syndrome and other neurological complications. Infection during pregnancy is associated with pregnancy complications and developmental and neurological abnormalities collectively defined as congenital Zika syndrome. There is still no vaccine or specific treatment for ZIKV infection. To identify host factors that can rescue cells from ZIKV infection we used a genome scale CRISPR activation screen. Our highly ranking hits included a short list of interferon stimulated genes (ISGs) previously reported to have antiviral activity. Validation of the screen results highlighted IFNL2 and IFI6 as genes providing high levels of protection from ZIKV. Activation of these genes had an effect on an early stage in viral infection. In addition, infected cells expressing sgRNAs for both of these genes displayed lower levels of cell death compared to controls. Furthermore, the identified genes were significantly induced in ZIKV infected placenta explants. Thus, these results highlight a set of ISGs directly relevant for rescuing cells from ZIKV infection or its associated cell death and substantiates CRISPR activation screens as a tool to identify host factors impeding pathogen infection.IMPORTANCE Zika virus (ZIKV) is an emerging vector-borne pathogen causing a febrile disease. ZIKV infection might also trigger Guillain-Barr{\'e} syndrome, neuropathy and myelitis. Vertical transmission of ZIKV can cause fetus demise, still birth or severe congenital abnormalities and neurological complications. There is no vaccine or specific antiviral treatment against ZIKV. We used a genome wide CRISPR activation screen, where genes are activated from their native promoters to identify host cell factors that protect cells from ZIKV infection or associated cell death. The results provide better understanding of key host factors that protect cells from ZIKV infection and might assist in identifying novel antiviral targets.},
    doi = {10.1128/JVI.00211-19},
    elocation-id = {JVI.00211-19},
    eprint = {https://jvi.asm.org/content/early/2019/05/23/JVI.00211-19.full.pdf},
    publisher = {American Society for Microbiology Journals},
    url = {https://jvi.asm.org/content/early/2019/05/23/JVI.00211-19},
    }
  • [DOI] S. Jansen, A. Heitmann, R. Lühken, M. Leggewie, M. Helms, M. Badusche, G. Rossini, J. Schmidt-Chanasit, and E. Tannich, "Culex torrentium: a potent vector for the transmission of West Nile Virus in central europe," Viruses, vol. 11, iss. 6, p. 492, 2019.
    [Bibtex]
    @Article{Jansen:19,
    author = {Stephanie Jansen and Anna Heitmann and Renke Lühken and Mayke Leggewie and Michelle Helms and Marlis Badusche and Giada Rossini and Jonas Schmidt-Chanasit and Egbert Tannich},
    title = {{C}ulex torrentium: A Potent Vector for the Transmission of {W}est {N}ile {V}irus in Central Europe},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {6},
    pages = {492},
    doi = {10.3390/v11060492},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] L. A. Carlisle, T. Turk, K. Kusejko, K. J. Metzner, C. Leemann, C. Schenkel, N. Bachmann, S. Posada, N. Beerenwinkel, J. Böni, S. Yerly, T. Klimkait, M. Perreau, D. L. Braun, A. Rauch, A. Calmy, M. Cavassini, M. Battegay, P. Vernazza, E. Bernasconi, H. F. Günthard, R. D. Kouyos, and Swiss HIV Cohort Study, "Viral diversity from next-generation sequencing of HIV-1 samples provides precise estimates of infection recency and time since infection.," J Infect Dis, 2019.
    [Bibtex]
    @Article{Carlisle:19,
    author = {Carlisle, Louisa A and Turk, Teja and Kusejko, Katharina and Metzner, Karin J and Leemann, Christine and Schenkel, Corinne and Bachmann, Nadine and Posada, Susana and Beerenwinkel, Niko and Böni, Jürg and Yerly, Sabine and Klimkait, Thomas and Perreau, Matthieu and Braun, Dominique L and Rauch, Andri and Calmy, Alexandra and Cavassini, Matthias and Battegay, Manuel and Vernazza, Pietro and Bernasconi, Enos and Günthard, Huldrych F and Kouyos, Roger D and {Swiss HIV Cohort Study}},
    title = {Viral diversity from next-generation sequencing of {HIV}-1 samples provides precise estimates of infection recency and time since infection.},
    journal = {{J Infect Dis}},
    year = {2019},
    abstract = {HIV-1 genetic diversity increases over the course of infection, and can be used to infer time since infection (TSI) and consequently also infection recency, crucial quantities for HIV-1 surveillance and the understanding of viral pathogenesis. We considered 313 HIV-infected individuals for whom reliable estimates of infection dates and next-generation sequencing (NGS)-derived nucleotide frequency data were available. Fraction of ambiguous nucleotides (FAN) obtained by population sequencing were available for 207 samples. We assessed whether average pairwise diversity (APD) calculated using NGS sequences provided a more exact prediction of TSI and classification of infection recency (<1 year post-infection) compared to FAN. NGS-derived APD classifies an infection as recent with a sensitivity of 88% and specificity of 85%. When considering only the 207 samples for which FAN were available, NGS-derived APD exhibited a higher sensitivity (90% vs 78%) and specificity (95% vs 67%) than FAN. Additionally, APD can estimate TSI with a mean absolute error of 0.84 years, compared to 1.03 years for FAN.},
    doi = {10.1093/infdis/jiz094},
    keywords = {HIV-1; diversity; infection recency; next-generation sequencing; time since infection},
    pmid = {30835266},
    }
  • [DOI] V. Kinast, T. L. Burkard, D. Todt, and E. Steinmann, "Hepatitis E virus drug development.," Viruses, vol. 11, 2019.
    [Bibtex]
    @Article{Kinast:19,
    author = {Kinast, Volker and Burkard, Thomas L and Todt, Daniel and Steinmann, Eike},
    title = {Hepatitis {E} Virus Drug Development.},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    abstract = {Hepatitis E virus (HEV) is an underestimated disease, leading to estimated 20 million infections and up to 70,000 deaths annually. Infections are mostly asymptomatic but can reach mortality rates up to 25% in pregnant women or become chronic in immunocompromised patients. The current therapy options are limited to the unspecific antivirals Ribavirin (RBV) and pegylated Interferon-α (pegIFN-α). RBV leads to viral clearance in only 80% of patients treated, and is, similar to pegIFN-α, contraindicated in the major risk group of pregnant women, emphasizing the importance of new therapy options. In this review, we focus on the urgent need and current efforts in HEV drug development. We provide an overview of the current status of HEV antiviral research. Furthermore, we discuss strategies for drug development and the limitations of the approaches with respect to HEV.},
    doi = {10.3390/v11060485},
    issue = {6},
    keywords = {antivirals; drug development; hepatitis E virus; ribavirin; sofosbuvir; therapy; vaccine},
    pmid = {31141919},
    }
  • [DOI] A. Brinkmann, A. Andrusch, A. Belka, C. Wylezich, D. Höper, A. Pohlmann, T. N. Petersen, P. Lucas, Y. Blanchard, A. Papa, A. Melidou, B. B. Oude Munnink, J. Matthijnssens, W. Deboutte, R. J. Ellis, F. Hansmann, W. Baumgärtner, E. van der Vries, A. Osterhaus, C. Camma, I. Mangone, A. Lorusso, M. Maracci, A. Nunes, M. Pinto, V. Borges, A. Kroneman, D. Schmitz, V. M. Corman, C. Drosten, T. C. Jones, R. S. Hendriksen, F. M. Aarestrup, M. Koopmans, M. Beer, and A. Nitsche, "Proficiency testing of virus diagnostics based on bioinformatics analysis of simulated in silico high-throughput sequencing datasets.," J Clin Microbiol, 2019.
    [Bibtex]
    @Article{Brinkmann:19,
    author = {Brinkmann, Annika and Andrusch, Andreas and Belka, Ariane and Wylezich, Claudia and Höper, Dirk and Pohlmann, Anne and Petersen, Thomas Nordahl and Lucas, Pierrick and Blanchard, Yannick and Papa, Anna and Melidou, Angeliki and Oude Munnink, Bas B and Matthijnssens, Jelle and Deboutte, Ward and Ellis, Richard J and Hansmann, Florian and Baumgärtner, Wolfgang and van der Vries, Erhard and Osterhaus, Albert and Camma, Cesare and Mangone, Iolanda and Lorusso, Alessio and Maracci, Maurilia and Nunes, Alexandra and Pinto, Miguel and Borges, Vítor and Kroneman, Annelies and Schmitz, Dennis and Corman, Victor Max and Drosten, Christian and Jones, Terry C and Hendriksen, Rene S and Aarestrup, Frank M and Koopmans, Marion and Beer, Martin and Nitsche, Andreas},
    title = {Proficiency testing of virus diagnostics based on bioinformatics analysis of simulated in silico high-throughput sequencing datasets.},
    journal = {{J Clin Microbiol}},
    year = {2019},
    abstract = {Quality management and independent assessment of high-throughput sequencing-based virus diagnostics have not yet been established as a mandatory approach for ensuring comparable results. Sensitivity and specificity of viral high-throughput sequence data analysis are highly affected by bioinformatics processing, using publicly available and custom tools and databases, and differ widely between individuals and institutions.Here, we present the results of the COMPARE (COllaborative Management Platform for detection and Analyses of [Re-] emerging and foodborne outbreaks in Europe) virus proficiency test. An artificial, simulated dataset of Illumina HiSeq sequences was provided to 13 different European institutes for bioinformatics analysis towards the identification of viral pathogens in high-throughput sequence data. Comparison of the participants' analyses shows that the use of different tools, programs, and databases for bioinformatics analyses can impact the correct identification of viral sequences from a simple dataset. The identification of slightly mutated and highly divergent virus genomes has been identified as being most challenging: Furthermore, the interpretation of the results together with a fictitious case report by the participants showed that in addition to the bioinformatics analysis, the virological evaluation of the results can be important in clinical settings.External quality assessment and proficiency testing should become an important part of validating high-throughput sequencing-based virus diagnostics and could improve harmonization, comparability, and reproducibility of results. Similar to what is established for conventional laboratory tests like PCR, there is a need for the establishment of international proficiency testing for bioinformatics pipelines and interpretation of such results.},
    doi = {10.1128/JCM.00466-19},
    pmid = {31167846},
    }
  • [DOI] P. J. Walker, S. G. Siddell, E. J. Lefkowitz, A. R. Mushegian, D. M. Dempsey, B. E. Dutilh, B. Harrach, R. L. Harrison, C. R. Hendrickson, S. Junglen, N. J. Knowles, A. M. Kropinski, M. Krupovic, J. H. Kuhn, M. Nibert, L. Rubino, S. Sabanadzovic, P. Simmonds, A. Varsani, F. M. Zerbini, and A. J. Davison, "Changes to virus taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2019)," Arch Virol, 2019.
    [Bibtex]
    @Article{Walker:19,
    author = {Peter J. Walker and Stuart G. Siddell and Elliot J. Lefkowitz and Arcady R. Mushegian and Donald M. Dempsey and Bas E. Dutilh and Bal{\'{a}}zs Harrach and Robert L. Harrison and R. Curtis Hendrickson and Sandra Junglen and Nick J. Knowles and Andrew M. Kropinski and Mart Krupovic and Jens H. Kuhn and Max Nibert and Luisa Rubino and Sead Sabanadzovic and Peter Simmonds and Arvind Varsani and Francisco Murilo Zerbini and Andrew J. Davison},
    title = {Changes to virus taxonomy and the {I}nternational {C}ode of {V}irus {C}lassification and {N}omenclature ratified by the {I}nternational {C}ommittee on {T}axonomy of {V}iruses (2019)},
    journal = {{Arch Virol}},
    year = {2019},
    doi = {10.1007/s00705-019-04306-w},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] J. Lechner, F. Hartkopf, P. Hiort, A. Nitsche, M. Grossegesse, J. Doellinger, B. Y. Renard, and T. Muth, "Purple: a computational workflow for strategic selection of peptides for viral diagnostics using MS-based targeted proteomics.," Viruses, vol. 11, 2019.
    [Bibtex]
    @Article{Lechner:19,
    author = {Lechner, Johanna and Hartkopf, Felix and Hiort, Pauline and Nitsche, Andreas and Grossegesse, Marica and Doellinger, Joerg and Renard, Bernhard Y and Muth, Thilo},
    title = {Purple: A Computational Workflow for Strategic Selection of Peptides for Viral Diagnostics Using {MS}-Based Targeted Proteomics.},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    abstract = {Emerging virus diseases present a global threat to public health. To detect viral pathogens in time-critical scenarios, accurate and fast diagnostic assays are required. Such assays can now be established using mass spectrometry-based targeted proteomics, by which viral proteins can be rapidly detected from complex samples down to the strain-level with high sensitivity and reproducibility. Developing such targeted assays involves tedious steps of peptide candidate selection, peptide synthesis, and assay optimization. Peptide selection requires extensive preprocessing by comparing candidate peptides against a large search space of background proteins. Here we present Purple (Picking unique relevant peptides for viral experiments), a software tool for selecting target-specific peptide candidates directly from given proteome sequence data. It comes with an intuitive graphical user interface, various parameter options and a threshold-based filtering strategy for homologous sequences. Purple enables peptide candidate selection across various taxonomic levels and filtering against backgrounds of varying complexity. Its functionality is demonstrated using data from different virus species and strains. Our software enables to build taxon-specific targeted assays and paves the way to time-efficient and robust viral diagnostics using targeted proteomics.},
    doi = {10.3390/v11060536},
    issue = {6},
    keywords = {data analysis; mass spectrometry; parallel reaction monitoring; peptide selection; targeted proteomics; virus diagnostics; virus proteomics},
    pmid = {31181768},
    }
  • [DOI] E. Karatzas, G. Kolios, and G. M. Spyrou, "An application of computational drug repurposing based on transcriptomic signatures.," Methods Mol Biol, vol. 1903, p. 149–177, 2019.
    [Bibtex]
    @Article{Karatzas:19,
    author = {Karatzas, Evangelos and Kolios, George and Spyrou, George M},
    title = {An Application of Computational Drug Repurposing Based on Transcriptomic Signatures.},
    journal = {{Methods Mol Biol}},
    year = {2019},
    volume = {1903},
    pages = {149--177},
    abstract = {Drug repurposing is a methodology where already existing drugs are tested against diseases outside their initial usage, in order to reduce the high cost and long periods of new drug development. In silico drug repurposing further speeds up the process, by testing a large number of drugs against the biological signatures of known diseases. In this chapter, we present a step-by-step methodology of a transcriptomics-based computational drug repurposing pipeline providing a comprehensive guide to the whole procedure, from proper dataset selection to short list derivation of repurposed drugs which might act as inhibitors against the studied disease. The presented pipeline contains the selection and curation of proper transcriptomics datasets, statistical analysis of the datasets in order to extract the top over- and under-expressed gene identifiers, appropriate identifier conversion, drug repurposing analysis, repurposed drugs filtering, cross-tool screening, drug-list re-ranking, and results' validation.},
    doi = {10.1007/978-1-4939-8955-3_9},
    keywords = {Algorithms; Computational Biology, methods; Databases, Pharmaceutical; Drug Repositioning, methods; Gene Expression Profiling; Gene Expression Regulation, drug effects; Humans; Reproducibility of Results; Software; Transcriptome; User-Computer Interface; Web Browser; Workflow; Computational pipeline; Drug repositioning; Drug repurposing; Gene expression; Microarrays; RNA-Seq; Transcriptomics},
    pmid = {30547441},
    }
  • [DOI] L. Beller and J. Matthijnssens, "What is (not) known about the dynamics of the human gut virome in health and disease.," Curr Opin Virol, vol. 37, p. 52–57, 2019.
    [Bibtex]
    @Article{Beller:19,
    author = {Beller, Leen and Matthijnssens, Jelle},
    title = {What is (not) known about the dynamics of the human gut virome in health and disease.},
    journal = {{Curr Opin Virol}},
    year = {2019},
    volume = {37},
    pages = {52--57},
    abstract = {The human gut virome has an important role in human health but its dynamics remain poorly understood. Few longitudinal studies in healthy adults showed a stable temporal gut virome, with high inter-individual diversity. In contrast, the infant virome shows a high temporal intra-individual diversity. Unfortunately, these virome studies ignore an enormous amount of unknown 'dark matter' sequences, leading to incomplete analyses and possibly incorrect conclusions. Also, the interactions between prokaryotes and bacteriophages in the gut seem to be too complex for currently available models. Therefore, there is a huge need of larger longitudinal cohort studies focusing on both the bacterial and viral component of the microbiome to be able to describe and understand this complex ecosystem.},
    doi = {10.1016/j.coviro.2019.05.013},
    pmid = {31255903},
    }
  • [DOI] S. Tu and C. Upton, "Bioinformatics for analysis of poxvirus genomes.," Methods Mol Biol, vol. 2023, p. 29–62, 2019.
    [Bibtex]
    @Article{Tu:19,
    author = {Tu, Shin-Lin and Upton, Chris},
    title = {Bioinformatics for Analysis of Poxvirus Genomes.},
    journal = {{Methods Mol Biol}},
    year = {2019},
    volume = {2023},
    pages = {29--62},
    abstract = {In recent years, there have been numerous technological advances in the field of molecular biology; these include next- and third-generation sequencing of DNA genomes and mRNA transcripts and mass spectrometry of proteins. Perhaps, however, it is genome sequencing that impacts a virologist the most. In 2017, more than 480 complete genome sequences of poxviruses have been generated, and are constantly used in many different ways by almost all molecular virologists. Matching this growth in data acquisition is an explosion of the relatively new field of bioinformatics, providing databases to store and organize this valuable/expensive data and algorithms to analyze it. For the bench virologist, access to intuitive, easy-to-use, software is often critical for performing bioinformatics-based experiments. Three common hurdles for the researcher are (1) selection, retrieval, and reformatting genomics data from large databases; (2) use of tools to compare/analyze the genomics data; and (3) display and interpretation of complex sets of results. This chapter is directed at the bench virologist and describes the software that helps overcome these obstacles, with a focus on the comparison and analysis of poxvirus genomes. Although poxvirus genomes are stored in public databases such as GenBank, this resource can be cumbersome and tedious to use if large amounts of data must to be collected. Therefore, we also highlight our Viral Orthologous Clusters database system and integrated tools that we developed specifically for the management and analysis of complete viral genomes.},
    doi = {10.1007/978-1-4939-9593-6_2},
    keywords = {BBB; BLAST; Bioinformatics; Dotplot; Genomics; JDotter; MSA; Multiple sequence alignment; Poxvirus; Smallpox; VGO; VOCs; Vaccinia virus},
    pmid = {31240669},
    }
  • [DOI] A. Ariza-Mateos, C. Briones, C. Perales, E. Domingo, and J. Gómez, "The archaeology of coding RNA.," Ann NY Acad Sci, 2019.
    [Bibtex]
    @Article{Ariza-Mateos:19,
    author = {Ariza-Mateos, Ascensión and Briones, Carlos and Perales, Celia and Domingo, Esteban and Gómez, Jordi},
    title = {The archaeology of coding {RNA}.},
    journal = {{Ann NY Acad Sci}},
    year = {2019},
    abstract = {Different theories concerning the origin of RNA (and, in particular, mRNA) point to the concatenation and expansion of proto-tRNA-like structures. Different biochemical and biophysical tools have been used to search for ancient-like RNA elements with a specific structure in genomic viral RNAs, including that of the hepatitis C virus, as well as in cellular mRNA populations, in particular those of human hepatocytes. We define this method as "archaeological," and it has been designed to discover evolutionary patterns through a nonphylogenetic and nonrepresentational strategy. tRNA-like elements were found in structurally or functionally relevant positions both in viral RNA and in one of the liver mRNAs examined, the antagonist interferon-alpha subtype 5 (IFNA5) mRNA. Additionally, tRNA-like elements are highly represented within the hepatic mRNA population, which suggests that they could have participated in the formation of coding RNAs in the distant past. Expanding on this finding, we have observed a recurring dsRNA-like motif next to the tRNA-like elements in both viral RNAs and IFNA5 mRNA. This suggested that the concatenation of these RNA motifs was an activity present in the RNA pools that might have been relevant in the RNA world. The extensive alteration of sequences that likely triggered the transition from the predecessors of coding RNAs to the first fully functional mRNAs (which was not the case in the stepwise construction of noncoding rRNAs) hinders the phylogeny-based identification of RNA elements (both sequences and structures) that might have been active before the advent of protein synthesis. Therefore, our RNA archaeological method is presented as a way to better understand the structural/functional versatility of a variety of RNA elements, which might represent "the losers" in the process of RNA evolution as they had to adapt to the selective pressures favoring the coding capacity of the progressively longer mRNAs.},
    doi = {10.1111/nyas.14173},
    keywords = {RNA world; RNase III; RNase P; biocommunication; biosemiotics; quasispecies},
    pmid = {31237363},
    }
  • [DOI] R. A. Edwards, A. A. Vega, H. M. Norman, M. Ohaeri, K. Levi, E. A. Dinsdale, O. Cinek, R. K. Aziz, K. McNair, J. J. Barr, K. Bibby, S. J. J. Brouns, A. Cazares, P. A. de Jonge, C. Desnues, S. D. L. Muñoz, P. C. Fineran, A. Kurilshikov, R. Lavigne, K. Mazankova, D. T. McCarthy, F. L. Nobrega, A. R. Muñoz, G. Tapia, N. Trefault, A. V. Tyakht, P. Vinuesa, J. Wagemans, A. Zhernakova, F. M. Aarestrup, G. Ahmadov, A. Alassaf, J. Anton, A. Asangba, E. K. Billings, V. A. Cantu, J. M. Carlton, D. Cazares, G. Cho, T. Condeff, P. Cortés, M. Cranfield, D. A. Cuevas, R. D. la Iglesia, P. Decewicz, M. P. Doane, N. J. Dominy, L. Dziewit, B. M. Elwasila, M. A. Eren, C. Franz, J. Fu, C. Garcia-Aljaro, E. Ghedin, K. M. Gulino, J. M. Haggerty, S. R. Head, R. S. Hendriksen, C. Hill, H. Hyöty, E. N. Ilina, M. T. Irwin, T. C. Jeffries, J. Jofre, R. E. Junge, S. T. Kelley, M. K. Mirzaei, M. Kowalewski, D. Kumaresan, S. R. Leigh, D. Lipson, E. S. Lisitsyna, M. Llagostera, J. M. Maritz, L. C. Marr, A. McCann, S. Molshanski-Mor, S. Monteiro, B. Moreira-Grez, M. Morris, L. Mugisha, M. Muniesa, H. Neve, N. Nguyen, O. D. Nigro, A. S. Nilsson, T. O'Connell, R. Odeh, A. Oliver, M. Piuri, A. P. J. II, U. Qimron, Z. Quan, P. Rainetova, A. Ramírez-Rojas, R. Raya, K. Reasor, G. A. O. Rice, A. Rossi, R. Santos, J. Shimashita, E. N. Stachler, L. C. Stene, R. Strain, R. Stumpf, P. J. Torres, A. Twaddle, M. U. Ibekwe, N. Villagra, S. Wandro, B. White, A. Whiteley, K. L. Whiteson, C. Wijmenga, M. M. Zambrano, H. Zschach, and B. E. Dutilh, "Global phylogeography and ancient evolution of the widespread human gut virus crAssphage," Nat Microbiol, 2019.
    [Bibtex]
    @Article{Edwards:19,
    author = {Robert A. Edwards and Alejandro A. Vega and Holly M. Norman and Maria Ohaeri and Kyle Levi and Elizabeth A. Dinsdale and Ondrej Cinek and Ramy K. Aziz and Katelyn McNair and Jeremy J. Barr and Kyle Bibby and Stan J. J. Brouns and Adrian Cazares and Patrick A. de Jonge and Christelle Desnues and Samuel L. D{\'{\i}}az Mu{\~{n}}oz and Peter C. Fineran and Alexander Kurilshikov and Rob Lavigne and Karla Mazankova and David T. McCarthy and Franklin L. Nobrega and Alejandro Reyes Mu{\~{n}}oz and German Tapia and Nicole Trefault and Alexander V. Tyakht and Pablo Vinuesa and Jeroen Wagemans and Alexandra Zhernakova and Frank M. Aarestrup and Gunduz Ahmadov and Abeer Alassaf and Josefa Anton and Abigail Asangba and Emma K. Billings and Vito Adrian Cantu and Jane M. Carlton and Daniel Cazares and Gyu-Sung Cho and Tess Condeff and Pilar Cort{\'{e}}s and Mike Cranfield and Daniel A. Cuevas and Rodrigo De la Iglesia and Przemyslaw Decewicz and Michael P. Doane and Nathaniel J. Dominy and Lukasz Dziewit and Bashir Mukhtar Elwasila and A. Murat Eren and Charles Franz and Jingyuan Fu and Cristina Garcia-Aljaro and Elodie Ghedin and Kristen M. Gulino and John M. Haggerty and Steven R. Head and Rene S. Hendriksen and Colin Hill and Heikki Hyöty and Elena N. Ilina and Mitchell T. Irwin and Thomas C. Jeffries and Juan Jofre and Randall E. Junge and Scott T. Kelley and Mohammadali Khan Mirzaei and Martin Kowalewski and Deepak Kumaresan and Steven R. Leigh and David Lipson and Eugenia S. Lisitsyna and Montserrat Llagostera and Julia M. Maritz and Linsey C. Marr and Angela McCann and Shahar Molshanski-Mor and Silvia Monteiro and Benjamin Moreira-Grez and Megan Morris and Lawrence Mugisha and Maite Muniesa and Horst Neve and Nam-phuong Nguyen and Olivia D. Nigro and Anders S. Nilsson and Taylor O'Connell and Rasha Odeh and Andrew Oliver and Mariana Piuri and Aaron J. Prussin II and Udi Qimron and Zhe-Xue Quan and Petra Rainetova and Ad{\'{a}}n Ram{\'{\i}}rez-Rojas and Raul Raya and Kim Reasor and Gillian A. O. Rice and Alessandro Rossi and Ricardo Santos and John Shimashita and Elyse N. Stachler and Lars C. Stene and Ronan Strain and Rebecca Stumpf and Pedro J. Torres and Alan Twaddle and MaryAnn Ugochi Ibekwe and Nicol{\'{a}}s Villagra and Stephen Wandro and Bryan White and Andy Whiteley and Katrine L. Whiteson and Cisca Wijmenga and Maria M. Zambrano and Henrike Zschach and Bas E. Dutilh},
    title = {Global phylogeography and ancient evolution of the widespread human gut virus {crAssphage}},
    journal = {{Nat Microbiol}},
    year = {2019},
    doi = {10.1038/s41564-019-0494-6},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] H. B. Jang, B. Bolduc, O. D. Zablocki, J. H. Kuhn, S. Roux, E. M. Adriaenssens, R. J. Brister, A. M. Kropinski, M. Krupovic, R. Lavigne, D. Turner, and M. B. Sullivan, "Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks," Nat Biotechnol, vol. 37, iss. 6, p. 632–639, 2019.
    [Bibtex]
    @Article{Jang:19,
    author = {Ho Bin Jang and Benjamin Bolduc and Olivier D. Zablocki and Jens H. Kuhn and Simon Roux and Evelien M. Adriaenssens and J. Rodney Brister and Andrew M Kropinski and Mart Krupovic and Rob Lavigne and Dann Turner and Matthew B. Sullivan},
    title = {Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks},
    journal = {{Nat Biotechnol}},
    year = {2019},
    volume = {37},
    number = {6},
    pages = {632--639},
    doi = {10.1038/s41587-019-0100-8},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] F. Erhard, M. A. P. Baptista, T. Krammer, T. Hennig, M. Lange, P. Arampatzi, C. S. Jürges, F. J. Theis, A. Saliba, and L. Dölken, "scSLAM-seq reveals core features of transcription dynamics in single cells.," Nature, 2019.
    [Bibtex]
    @Article{Erhard:19,
    author = {Erhard, Florian and Baptista, Marisa A P and Krammer, Tobias and Hennig, Thomas and Lange, Marius and Arampatzi, Panagiota and Jürges, Christopher S and Theis, Fabian J and Saliba, Antoine-Emmanuel and Dölken, Lars},
    title = {{scSLAM-seq} reveals core features of transcription dynamics in single cells.},
    journal = {Nature},
    year = {2019},
    abstract = {Single-cell RNA sequencing (scRNA-seq) has highlighted the important role of intercellular heterogeneity in phenotype variability in both health and disease . However, current scRNA-seq approaches provide only a snapshot of gene expression and convey little information on the true temporal dynamics and stochastic nature of transcription. A further key limitation of scRNA-seq analysis is that the RNA profile of each individual cell can be analysed only once. Here we introduce single-cell, thiol-(SH)-linked alkylation of RNA for metabolic labelling sequencing (scSLAM-seq), which integrates metabolic RNA labelling , biochemical nucleoside conversion and scRNA-seq to record transcriptional activity directly by differentiating between new and old RNA for thousands of genes per single cell. We use scSLAM-seq to study the onset of infection with lytic cytomegalovirus in single mouse fibroblasts. The cell-cycle state and dose of infection deduced from old RNA enable dose-response analysis based on new RNA. scSLAM-seq thereby both visualizes and explains differences in transcriptional activity at the single-cell level. Furthermore, it depicts 'on-off' switches and transcriptional burst kinetics in host gene expression with extensive gene-specific differences that correlate with promoter-intrinsic features (TBP-TATA-box interactions and DNA methylation). Thus, gene-specific, and not cell-specific, features explain the heterogeneity in transcriptomes between individual cells and the transcriptional response to perturbations.},
    doi = {10.1038/s41586-019-1369-y},
    pmid = {31292545},
    }
  • [DOI] C. N. Agoti, M. V. T. Phan, P. K. Munywoki, G. Githinji, G. F. Medley, P. A. Cane, P. Kellam, M. Cotten, and J. D. Nokes, "Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant.," Sci Rep, vol. 9, p. 10076, 2019.
    [Bibtex]
    @Article{Agoti:19,
    author = {Agoti, Charles N and Phan, My V T and Munywoki, Patrick K and Githinji, George and Medley, Graham F and Cane, Patricia A and Kellam, Paul and Cotten, Matthew and Nokes, D James},
    title = {Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant.},
    journal = {{Sci Rep}},
    year = {2019},
    volume = {9},
    pages = {10076},
    abstract = {Infants (under 1-year-old) are at most risk of life threatening respiratory syncytial virus (RSV) disease. RSV epidemiological data alone has been insufficient in defining who acquires infection from whom (WAIFW) within households. We investigated RSV genomic variation within and between infected individuals and assessed its potential utility in tracking transmission in households. Over an entire single RSV season in coastal Kenya, nasal swabs were collected from members of 20 households every 3-4 days regardless of symptom status and screened for RSV nucleic acid. Next generation sequencing was used to generate >90% RSV full-length genomes for 51.1% of positive samples (191/374). Single nucleotide polymorphisms (SNPs) observed during household infection outbreaks ranged from 0-21 (median: 3) while SNPs observed during single-host infection episodes ranged from 0-17 (median: 1). Using the viral genomic data alone there was insufficient resolution to fully reconstruct within-household transmission chains. For households with clear index cases, the most likely source of infant infection was via a toddler (aged 1 to <3 years-old) or school-aged (aged 6 to <12 years-old) co-occupant. However, for best resolution of WAIFW within households, we suggest an integrated analysis of RSV genomic and epidemiological data.},
    doi = {10.1038/s41598-019-46509-w},
    issue = {1},
    pmid = {31296922},
    }
  • [DOI] J. M. Bartoszewicz, A. Seidel, R. Rentzsch, and B. Y. Renard, "DeePaC: predicting pathogenic potential of novel dna with reverse-complement neural networks.," Bioinformatics, 2019.
    [Bibtex]
    @Article{Bartoszewicz:19,
    author = {Bartoszewicz, Jakub M and Seidel, Anja and Rentzsch, Robert and Renard, Bernhard Y},
    title = {{DeePaC}: Predicting pathogenic potential of novel DNA with reverse-complement neural networks.},
    journal = {Bioinformatics},
    year = {2019},
    abstract = {We expect novel pathogens to arise due to their fast-paced evolution, and new species to be discovered thanks to advances in DNA sequencing and metagenomics. Moreover, recent developments in synthetic biology raise concerns that some strains of bacteria could be modified for malicious purposes. Traditional approaches to open-view pathogen detection depend on databases of known organisms, which limits their performance on unknown, unrecognized, and unmapped sequences. In contrast, machine learning methods can infer pathogenic phenotypes from single NGS reads, even though the biological context is unavailable. We present DeePaC, a Deep Learning Approach to Pathogenicity Classification. It includes a flexible framework allowing easy evaluation of neural architectures with reverse-complement parameter sharing. We show that convolutional neural networks and LSTMs outperform the state-of-the-art based on both sequence homology and machine learning. Combining a deep learning approach with integrating the predictions for both mates in a read pair results in cutting the error rate almost in half in comparison to the previous state-of-the-art. The code and the models are available at: https://gitlab.com/rki_bioinformatics/DeePaC. Supplementary data are available at Bioinformatics online.},
    doi = {10.1093/bioinformatics/btz541},
    pmid = {31298694},
    }
  • [DOI] N. Bachmann, C. von Siebenthal, V. Vongrad, T. Turk, K. Neumann, N. Beerenwinkel, J. Bogojeska, J. Fellay, V. Roth, Y. L. Kok, C. W. Thorball, A. Borghesi, S. Parbhoo, M. Wieser, J. Böni, M. Perreau, T. Klimkait, S. Yerly, M. Battegay, A. Rauch, M. Hoffmann, E. Bernasconi, M. Cavassini, R. D. Kouyos, H. F. Günthard, K. J. Metzner, and S. H. C. Study, "Determinants of HIV-1 reservoir size and long-term dynamics during suppressive ART.," Nat Commun, vol. 10, p. 3193, 2019.
    [Bibtex]
    @Article{Bachmann:19,
    author = {Bachmann, Nadine and von Siebenthal, Chantal and Vongrad, Valentina and Turk, Teja and Neumann, Kathrin and Beerenwinkel, Niko and Bogojeska, Jasmina and Fellay, Jaques and Roth, Volker and Kok, Yik Lim and Thorball, Christian W and Borghesi, Alessandro and Parbhoo, Sonali and Wieser, Mario and Böni, Jürg and Perreau, Matthieu and Klimkait, Thomas and Yerly, Sabine and Battegay, Manuel and Rauch, Andri and Hoffmann, Matthias and Bernasconi, Enos and Cavassini, Matthias and Kouyos, Roger D and Günthard, Huldrych F and Metzner, Karin J and Swiss HIV Cohort Study},
    title = {Determinants of {HIV}-1 reservoir size and long-term dynamics during suppressive {ART}.},
    journal = {{Nat Commun}},
    year = {2019},
    volume = {10},
    pages = {3193},
    abstract = {The HIV-1 reservoir is the major hurdle to a cure. We here evaluate viral and host characteristics associated with reservoir size and long-term dynamics in 1,057 individuals on suppressive antiretroviral therapy for a median of 5.4 years. At the population level, the reservoir decreases with diminishing differences over time, but increases in 26.6% of individuals. Viral blips and low-level viremia are significantly associated with slower reservoir decay. Initiation of ART within the first year of infection, pretreatment viral load, and ethnicity affect reservoir size, but less so long-term dynamics. Viral blips and low-level viremia are thus relevant for reservoir and cure studies.},
    doi = {10.1038/s41467-019-10884-9},
    investigator = {Anagnostopoulos, Alexia and Battegay, Manuel and Bernasconi, Enos and Böni, Jürg and Braun, Dominique L and Bucher, Heiner C and Calmy, Alexandra and Cavassini, Matthias and Ciuffi, Angela and Dollenmaier, Günter and Egger, Matthias and Elzi, Luigia and Fehr, Jan and Fellay, Jacques and Furrer, Hansjakob and Fux, Christoph A and Günthard, Huldrych F and Haerry, David and Hasse, Barbara and Hirsch, Hans H and Hoffmann, Matthias and Hösli, Irene and Huber, Michael and Kahlert, Christian and Kaiser, Laurent and Keiser, Olivia and Klimkait, Thomas and Kouyos, Roger D and Kovari, Helen and Ledergerber, Bruno and Martinetti, Gladys and Tejada, Begona Martinez de and Marzolini, Catia and Metzner, Karin J and Müller, Nicolas and Nicca, Dunja and Paioni, Paolo and Pantaleo, Guiseppe and Perreau, Matthieu and Rauch, Andri and Rudin, Christoph and Scherrer, Alexandra U and Schmid, Patrick and Speck, Roberto and Stöckle, Marcel and Tarr, Philip and Trkola, Alexandra and Vernazza, Pietro and Wandeler, Gilles and Weber, Rainer and Yerly, Sabine},
    issue = {1},
    pmid = {31324762},
    }
  • [DOI] A. Michelitsch, K. Wernike, C. Klaus, G. Dobler, and M. Beer, "Exploring the reservoir hosts of tick-borne encephalitis virus," Viruses, vol. 11, iss. 7, p. 669, 2019.
    [Bibtex]
    @Article{Michelitsch:19,
    author = {Anna Michelitsch and Kerstin Wernike and Christine Klaus and Gerhard Dobler and Martin Beer},
    title = {Exploring the Reservoir Hosts of Tick-Borne Encephalitis Virus},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    number = {7},
    pages = {669},
    doi = {10.3390/v11070669},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] M. Döring, C. Kreer, N. Lehnen, F. Klein, and N. Pfeifer, "Modeling the amplification of immunoglobulins through machine learning on sequence-specific features," Sci Rep, vol. 9, iss. 1, 2019.
    [Bibtex]
    @Article{Döring:19,
    author = {Matthias Döring and Christoph Kreer and Nathalie Lehnen and Florian Klein and Nico Pfeifer},
    title = {Modeling the Amplification of Immunoglobulins through Machine Learning on Sequence-Specific Features},
    journal = {{Sci Rep}},
    year = {2019},
    volume = {9},
    number = {1},
    doi = {10.1038/s41598-019-47173-w},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] C. Wylezich, A. Belka, D. Hanke, M. Beer, S. Blome, and D. Höper, "Metagenomics for broad and improved parasite detection: a proof-of-concept study using swine faecal samples.," Int J Parasitol, 2019.
    [Bibtex]
    @Article{Wylezich:19,
    author = {Wylezich, Claudia and Belka, Ariane and Hanke, Dennis and Beer, Martin and Blome, Sandra and Höper, Dirk},
    title = {Metagenomics for broad and improved parasite detection: a proof-of-concept study using swine faecal samples.},
    journal = {{Int J Parasitol}},
    year = {2019},
    abstract = {Efficient and reliable identification of emerging pathogens is crucial for the design and implementation of timely and proportionate control strategies. This is difficult if the pathogen is so far unknown or only distantly related with known pathogens. Diagnostic metagenomics - an undirected, broad and sensitive method for the efficient identification of pathogens - was frequently used for virus and bacteria detection, but seldom applied to parasite identification. Here, metagenomics datasets prepared from swine faeces using an unbiased sample processing approach with RNA serving as starting material were re-analysed with respect to parasite detection. The taxonomic identification tool RIEMS, used for initial detection, provided basic hints on potential pathogens contained in the datasets. The suspected parasites/intestinal protists (Blastocystis, Entamoeba, Iodamoeba, Neobalantidium, Tetratrichomonas) were verified using subsequently applied reference mapping analyses on the base of rRNA sequences. Nearly full-length gene sequences could be extracted from the RNA-derived datasets. In the case of Blastocystis, subtyping was possible with subtype (ST)15 discovered for the first known time in swine faeces. Using RIEMS, some of the suspected candidates turned out to be false-positives caused by the poor status of sequences in publicly available databases. Altogether, 11 different species/STs of parasites/intestinal protists were detected in 34 out of 41 datasets extracted from metagenomics data. The approach operates without any primer bias that typically hampers the analysis of amplicon-based approaches, and allows the detection and taxonomic classification including subtyping of protist and metazoan endobionts (parasites, commensals or mutualists) based on an abundant biomarker, the 18S rRNA. The generic nature of the approach also allows evaluation of interdependencies that induce mutualistic or pathogenic effects that are often not clear for many intestinal protists and perhaps other parasites. Thus, metagenomics has the potential for generic pathogen identification beyond the characterization of viruses and bacteria when starting from RNA instead of DNA.},
    doi = {10.1016/j.ijpara.2019.04.007},
    keywords = {False-positives; Intestinal protists; Parasite detection; Pig faeces; RIEMS; Shotgun metagenomics; Subtyping; Taxonomic assignment},
    pmid = {31361998},
    }
  • [DOI] I. H. E. Korf, J. P. Meier-Kolthoff, E. M. Adriaenssens, A. M. Kropinski, M. Nimtz, M. Rohde, M. J. van Raaij, and J. Wittmann, "Still something to discover: novel insights into Escherichia coli phage diversity and taxonomy.," Viruses, vol. 11, 2019.
    [Bibtex]
    @Article{Korf:19,
    author = {Korf, Imke H E and Meier-Kolthoff, Jan P and Adriaenssens, Evelien M and Kropinski, Andrew M and Nimtz, Manfred and Rohde, Manfred and van Raaij, Mark J and Wittmann, Johannes},
    title = {Still Something to Discover: Novel Insights into {Escherichia coli} Phage Diversity and Taxonomy.},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    abstract = {The aim of this study was to gain further insight into the diversity of Escherichia coli phagesfollowed by enhanced work on taxonomic issues in that field. Therefore, we present the genomiccharacterization and taxonomic classification of 50 bacteriophages against isolated fromvarious sources, such as manure or sewage. All phages were examined for their host range on a setof different strains, originating, e.g., from human diagnostic laboratories or poultry farms.Transmission electron microscopy revealed a diversity of morphotypes (70% Myo-, 22% Sipho-, and8% Podoviruses), and genome sequencing resulted in genomes sizes from ~44 to ~370 kb.Annotation and comparison with databases showed similarities in particular to T4- and T5-likephages, but also to less-known groups. Though various phages against are already describedin literature and databases, we still isolated phages that showed no or only few similarities to otherphages, namely phages Goslar, PTXU04, and KWBSE43-6. Genome-based phylogeny andclassification of the newly isolated phages using VICTOR resulted in the proposal of new generaand led to an enhanced taxonomic classification of phages.},
    doi = {10.3390/v11050454},
    issue = {5},
    keywords = {Escherichia coli; bacteriophage; diversity; genomics; taxonomy},
    pmid = {31109012},
    }
  • [DOI] M. Džunková, S. J. Low, J. N. Daly, L. Deng, C. Rinke, and P. Hugenholtz, "Defining the human gut host-phage network through single-cell viral tagging.," Nat Microbiol, 2019.
    [Bibtex]
    @Article{Dzunkova:19,
    author = {Džunková, Mária and Low, Soo Jen and Daly, Joshua N and Deng, Li and Rinke, Christian and Hugenholtz, Philip},
    title = {Defining the human gut host-phage network through single-cell viral tagging.},
    journal = {{Nat Microbiol}},
    year = {2019},
    abstract = {Viral discovery is accelerating at an unprecedented rate due to continuing advances in culture-independent sequence-based analyses. One important facet of this discovery is identification of the hosts of these recently characterized uncultured viruses. To this end, we have adapted the viral tagging approach, which bypasses the need for culture-based methods to identify host-phage pairings. Fluorescently labelled anonymous virions adsorb to unlabelled anonymous bacterial host cells, which are then individually sorted as host-phage pairs, followed by genome amplification and high-throughput sequencing to establish the identities of both the host and the attached virus(es). We demonstrate single-cell viral tagging using the faecal microbiome, including cross-tagging of viruses and bacteria between human subjects. A total of 363 unique host-phage pairings were predicted, most of which were subject-specific and involved previously uncharacterized viruses despite the majority of their bacterial hosts having known taxonomy. One-fifth of these pairs were confirmed by multiple individual tagged cells. Viruses targeting more than one bacterial species were conspicuously absent in the host-phage network, suggesting that phages are not major vectors of inter-species horizontal gene transfer in the human gut. A high level of cross-reactivity between phages and bacteria from different subjects was noted despite subject-specific viral profiles, which has implications for faecal microbiota transplant therapy.},
    doi = {10.1038/s41564-019-0526-2},
    pmid = {31384000},
    }
  • [DOI] M. Hölzer, A. Schoen, J. Wulle, M. A. Müller, C. Drosten, M. Marz, and F. Weber, "Virus- and interferon alpha-induced transcriptomes of cells from the microbat Myotis daubentonii," iScience, 2019.
    [Bibtex]
    @Article{Hölzer:19a,
    author = {Martin Hölzer and Andreas Schoen and Julia Wulle and Marcel A. Müller and Christian Drosten and Manja Marz and Friedemann Weber},
    title = {Virus- and interferon alpha-induced transcriptomes of cells from the microbat {Myotis daubentonii}},
    journal = {{iScience}},
    year = {2019},
    doi = {10.1016/j.isci.2019.08.016},
    publisher = {Elsevier {BV}},
    }
  • [DOI] N. C. Bilz, E. Willscher, H. Binder, J. Böhnke, M. L. Stanifer, D. Hübner, S. Boulant, U. G. Liebert, and C. Claus, "Teratogenic rubella virus alters the endodermal differentiation capacity of human induced pluripotent stem cells.," Cells, vol. 8, 2019.
    [Bibtex]
    @Article{Bilz:19,
    author = {Bilz, Nicole C and Willscher, Edith and Binder, Hans and Böhnke, Janik and Stanifer, Megan L and Hübner, Denise and Boulant, Steeve and Liebert, Uwe G and Claus, Claudia},
    title = {Teratogenic Rubella Virus Alters the Endodermal Differentiation Capacity of Human Induced Pluripotent Stem Cells.},
    journal = {Cells},
    year = {2019},
    volume = {8},
    abstract = {The study of congenital virus infections in humans requires suitable ex vivo platforms for the species-specific events during embryonal development. A prominent example for these infections is rubella virus (RV) which most commonly leads to defects in ear, heart, and eye development. We applied teratogenic RV to human induced pluripotent stem cells (iPSCs) followed by differentiation into cells of the three embryonic lineages (ecto-, meso-, and endoderm) as a cell culture model for blastocyst- and gastrulation-like stages. In the presence of RV, lineage-specific differentiation markers were expressed, indicating that lineage identity was maintained. However, portrait analysis of the transcriptomic expression signatures of all samples revealed that mock- and RV-infected endodermal cells were less related to each other than their ecto- and mesodermal counterparts. Markers for definitive endoderm were increased during RV infection. Profound alterations of the epigenetic landscape including the expression level of components of the chromatin remodeling complexes and an induction of type III interferons were found, especially after endodermal differentiation of RV-infected iPSCs. Moreover, the eye field transcription factors RAX and SIX3 and components of the gene set vasculogenesis were identified as dysregulated transcripts. Although iPSC morphology was maintained, the formation of embryoid bodies as three-dimensional cell aggregates and as such cellular adhesion capacity was impaired during RV infection. The correlation of the molecular alterations induced by RV during differentiation of iPSCs with the clinical signs of congenital rubella syndrome suggests mechanisms of viral impairment of human development.},
    doi = {10.3390/cells8080870},
    issue = {8},
    keywords = {TGF-β and Wnt/β-catenin pathway; ectoderm; embryogenesis; embryoid body; epigenetic signature; human development; interferon response; interferon-induced genes; mesoderm; self-organizing map (SOM) data portrayal},
    pmid = {31405163},
    }
  • [DOI] H. R. Jonsdottir, S. Marti, D. Geerts, R. Rodriguez, V. Thiel, and R. Dijkman, "Establishment of primary transgenic human airway epithelial cell cultures to study respiratory virus-host interactions.," Viruses, vol. 11, 2019.
    [Bibtex]
    @Article{Jonsdottir:19,
    author = {Jonsdottir, Hulda R and Marti, Sabrina and Geerts, Dirk and Rodriguez, Regulo and Thiel, Volker and Dijkman, Ronald},
    title = {Establishment of Primary Transgenic Human Airway Epithelial Cell Cultures to Study Respiratory Virus-Host Interactions.},
    journal = {Viruses},
    year = {2019},
    volume = {11},
    abstract = {Primary human airway epithelial cell (hAEC) cultures represent a universal platform to propagate respiratory viruses and characterize their host interactions in authentic target cells. To further elucidate specific interactions between human respiratory viruses and important host factors in the airway epithelium, it is important to make hAEC cultures amenable to genetic modification. However, the short and finite lifespan of primary cells in cell culture creates a bottleneck for the genetic modification of these cultures. In the current study, we show that the incorporation of the Rho-associated protein kinase (ROCK) inhibitor (Y-27632) during cell propagation extends the life span of primary human cells in vitro and thereby facilitates the incorporation of lentivirus-based expression systems. Using fluorescent reporters for fluorescence-activated cell sorting (FACS)-based sorting, we generated homogenously fluorescent hAEC cultures that differentiate normally after lentiviral transduction. As a proof-of-principle, we demonstrate that host gene expression can be modulated post-differentiation via inducible short hairpin (sh)RNA-mediated knockdown. Importantly, functional characterization of these transgenic hAEC cultures with exogenous poly (I:C), as a proxy for virus infection, demonstrates that such modifications do not influence the host innate immune response. Moreover, the propagation kinetics of both human coronavirus 229E (HCoV-229E) and human respiratory syncytial virus (hRSV) were not affected. Combined, these results validate our newly established protocol for the genetic modification of hAEC cultures, thereby unlocking a unique potential for detailed molecular characterization of virus-host interactions in human respiratory epithelium.},
    doi = {10.3390/v11080747},
    issue = {8},
    keywords = {human airway epithelial cell cultures; respiratory viruses; virus-host interactions},
    pmid = {31412613},
    }
  • [DOI] A. Viehweger, S. Krautwurst, K. Lamkiewicz, R. Madhugiri, J. Ziebuhr, M. Hölzer, and M. Marz, "Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis.," Genome Res, 2019.
    [Bibtex]
    @Article{Viehweger:19,
    author = {Viehweger, Adrian and Krautwurst, Sebastian and Lamkiewicz, Kevin and Madhugiri, Ramakanth and Ziebuhr, John and Hölzer, Martin and Marz, Manja},
    title = {Direct {RNA} nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis.},
    journal = {{Genome Res}},
    year = {2019},
    abstract = {Sequence analyses of RNA virus genomes remain challenging owing to the exceptional genetic plasticity of these viruses. Because of high mutation and recombination rates, genome replication by viral RNA-dependent RNA polymerases leads to populations of closely related viruses, so-called "quasispecies." Standard (short-read) sequencing technologies are ill-suited to reconstruct large numbers of full-length haplotypes of (1) RNA virus genomes and (2) subgenome-length (sg) RNAs composed of noncontiguous genome regions. Here, we used a full-length, direct RNA sequencing (DRS) approach based on nanopores to characterize viral RNAs produced in cells infected with a human coronavirus. By using DRS, we were able to map the longest (∼26-kb) contiguous read to the viral reference genome. By combining Illumina and Oxford Nanopore sequencing, we reconstructed a highly accurate consensus sequence of the human coronavirus (HCoV)-229E genome (27.3 kb). Furthermore, by using long reads that did not require an assembly step, we were able to identify, in infected cells, diverse and novel HCoV-229E sg RNAs that remain to be characterized. Also, the DRS approach, which circumvents reverse transcription and amplification of RNA, allowed us to detect methylation sites in viral RNAs. Our work paves the way for haplotype-based analyses of viral quasispecies by showing the feasibility of intra-sample haplotype separation. Even though several technical challenges remain to be addressed to exploit the potential of the nanopore technology fully, our work illustrates that DRS may significantly advance genomic studies of complex virus populations, including predictions on long-range interactions in individual full-length viral RNA haplotypes.},
    doi = {10.1101/gr.247064.118},
    pmid = {31439691},
    }
  • [DOI] S. Gago-Zachert, J. Schuck, C. Weinholdt, M. Knoblich, V. Pantaleo, I. Grosse, T. Gursinsky, and S. Behrens, "Highly efficacious antiviral protection of plants by small interfering RNAs identified in vitro.," Nucleic Acids Res, 2019.
    [Bibtex]
    @Article{Gago-Zachert:19,
    author = {Gago-Zachert, Selma and Schuck, Jana and Weinholdt, Claus and Knoblich, Marie and Pantaleo, Vitantonio and Grosse, Ivo and Gursinsky, Torsten and Behrens, Sven-Erik},
    title = {Highly efficacious antiviral protection of plants by small interfering {RNAs} identified in vitro.},
    journal = {{Nucleic Acids Res}},
    year = {2019},
    abstract = {In response to a viral infection, the plant's RNA silencing machinery processes viral RNAs into a huge number of small interfering RNAs (siRNAs). However, a very few of these siRNAs actually interfere with viral replication. A reliable approach to identify these immunologically effective siRNAs (esiRNAs) and to define the characteristics underlying their activity has not been available so far. Here, we develop a novel screening approach that enables a rapid functional identification of antiviral esiRNAs. Tests on the efficacy of such identified esiRNAs of a model virus achieved a virtual full protection of plants against a massive subsequent infection in transient applications. We find that the functionality of esiRNAs depends crucially on two properties: the binding affinity to Argonaute proteins and the ability to access the target RNA. The ability to rapidly identify functional esiRNAs could be of great benefit for all RNA silencing-based plant protection measures against viruses and other pathogens.},
    doi = {10.1093/nar/gkz678},
    pmid = {31433052},
    }
  • [DOI] K. Theys, P. Lemey, A. Vandamme, and G. Baele, "Advances in visualization tools for phylogenomic and phylodynamic studies of viral diseases.," Front Public Health, vol. 7, p. 208, 2019.
    [Bibtex]
    @Article{Theys:19a,
    author = {Theys, Kristof and Lemey, Philippe and Vandamme, Anne-Mieke and Baele, Guy},
    title = {Advances in Visualization Tools for Phylogenomic and Phylodynamic Studies of Viral Diseases.},
    journal = {{Front Public Health}},
    year = {2019},
    volume = {7},
    pages = {208},
    abstract = {Genomic and epidemiological monitoring have become an integral part of our response to emerging and ongoing epidemics of viral infectious diseases. Advances in high-throughput sequencing, including portable genomic sequencing at reduced costs and turnaround time, are paralleled by continuing developments in methodology to infer evolutionary histories (dynamics/patterns) and to identify factors driving viral spread in space and time. The traditionally static nature of visualizing phylogenetic trees that represent these evolutionary relationships/processes has also evolved, albeit perhaps at a slower rate. Advanced visualization tools with increased resolution assist in drawing conclusions from phylogenetic estimates and may even have potential to better inform public health and treatment decisions, but the design (and choice of what analyses are shown) is hindered by the complexity of information embedded within current phylogenetic models and the integration of available meta-data. In this review, we discuss visualization challenges for the interpretation and exploration of reconstructed histories of viral epidemics that arose from increasing volumes of sequence data and the wealth of additional data layers that can be integrated. We focus on solutions that address joint temporal and spatial visualization but also consider what the future may bring in terms of visualization and how this may become of value for the coming era of real-time digital pathogen surveillance, where actionable results and adequate intervention strategies need to be obtained within days.},
    doi = {10.3389/fpubh.2019.00208},
    keywords = {epidemiology; evolution; infectious disease; phylodynamics; phylogenetics; phylogenomics; visualization},
    pmid = {31428595},
    }
  • [DOI] C. Shi, L. Beller, W. Deboutte, K. C. Yinda, L. Delang, A. Vega-Rúa, A. Failloux, and J. Matthijnssens, "Stable distinct core eukaryotic viromes in different mosquito species from Guadeloupe, using single mosquito viral metagenomics.," Microbiome, vol. 7, p. 121, 2019.
    [Bibtex]
    @Article{Shi:19,
    author = {Shi, Chenyan and Beller, Leen and Deboutte, Ward and Yinda, Kwe Claude and Delang, Leen and Vega-Rúa, Anubis and Failloux, Anna-Bella and Matthijnssens, Jelle},
    title = {Stable distinct core eukaryotic viromes in different mosquito species from {G}uadeloupe, using single mosquito viral metagenomics.},
    journal = {Microbiome},
    year = {2019},
    volume = {7},
    pages = {121},
    abstract = {Mosquitoes are the most important invertebrate viral vectors in humans and harbor a high diversity of understudied viruses, which has been shown in many mosquito virome studies in recent years. These studies generally performed metagenomics sequencing on pools of mosquitoes, without assessment of the viral diversity in individual mosquitoes. To address this issue, we applied our optimized viral met