Authors: Type:

2021

  • [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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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. 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. 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. 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] 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] 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. 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] 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. 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] 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] 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] 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] 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] 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] 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})},
    }
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    @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},
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    publisher = {American Physiological Society},
    }
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    @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},
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    title = {Analytical methodologies for the detection of {SARS}-{CoV}-2 in wastewater: Protocols and future perspectives},
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    @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},
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    @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. 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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] 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] 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] 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},
    }
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    [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},
    }
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    [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] 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})},
    }
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    [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}},
    }
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    [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})},
    }
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    [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},
    }
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    [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}},
    }
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    [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] 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})},
    }
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    [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] 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})},
    }
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    [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})},
    }
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    [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},
    }
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    [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},
    }
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    [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},
    }
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    [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},
    }
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    [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},
    }
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    [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},
    }
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    [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}},
    }
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    [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})},
    }
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    [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},
    }
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    [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},
    }
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    @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}},
    }
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    [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}},
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    [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},
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    [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},
    }
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    [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},
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    }
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    [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}},
    }
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    @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}},
    }
  • 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},
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    publisher = {Nature Publishing Group},
    }
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    @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},
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    @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}},
    }
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    @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}},
    }
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    @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}},
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    doi = {10.1002/cmdc.202000548},
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    @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}},
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    @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}},
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    @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},
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    publisher = {Springer Science and Business Media {LLC}},
    }
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    [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},
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    publisher = {Cold Spring Harbor Laboratory},
    }
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    [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},
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    publisher = {Research Square},
    }
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    [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},
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    publisher = {Cold Spring Harbor Laboratory},
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    [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}},
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    [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}},
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    }
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    [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}},
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    [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},
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    publisher = {Cold Spring Harbor Laboratory},
    }
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    [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}},
    }
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    [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})},
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    @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}},
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    [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}},
    }
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    [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}},
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    @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},
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    [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}},
    }
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    [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}},
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    [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},
    }
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    [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] 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] 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] 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] 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] 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}},
    }
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    [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}},
    }
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    @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}},
    }
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    @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},
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    }
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    @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},
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    @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}},
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    @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})},
    }
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    @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},
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    publisher = {Springer Science and Business Media {LLC}},
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    @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},
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    doi = {10.2807/1560-7917.es.2020.25.24.2001057},
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    @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},
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    @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}},
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    [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},
    }
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    @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},
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    @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},
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    publisher = {Elsevier {BV}},
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    @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},
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    @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}},
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    @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},
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    publisher = {Cold Spring Harbor Laboratory},
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    @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},
    }
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    @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},
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    pages = {571},
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    publisher = {{BMJ}},
    }
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    @Article{Vandamme:20,
    author = {Anne-Mieke Vandamme and ToTran Nguyen},
    title = {{B}elgium -- concerns about coronavirus contact-tracing apps},
    journal = {Nature},
    year = {2020},
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    pages = {384},
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    publisher = {Springer Science and Business Media {LLC}},
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    @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},
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    doi = {10.3201/eid2608.201525},
    publisher = {Centers for Disease Control and Prevention ({CDC})},
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    @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}},
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    publisher = {Elsevier {BV}},
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    @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},
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    publisher = {Cold Spring Harbor Laboratory},
    }
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    [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},
    }
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    @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},
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    publisher = {Cold Spring Harbor Laboratory},
    }
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    @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},
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    title = {The emergence of {SARS}-{CoV}-2 in {Europe} and the {US}},
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    author = {Oscar A. MacLean and Spyros Lytras and Joshua B. Singer and Steven Weaver and Sergei L. Kosakovsky Pond and David L. Robertson},
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    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},
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    @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},
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    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},
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    pages = {561--565},
    doi = {10.1038/s41586-020-2294-9},
    publisher = {Springer Science and Business Media {LLC}},
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    @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}},
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    @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},
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    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},
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    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}},
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    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},
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    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}},
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    @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}},
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    @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},
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    @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}},
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    @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}},
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    publisher = {Cold Spring Harbor Laboratory},
    }
  • [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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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},
    }

2019

  • [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},
    }

2018

  • [DOI] J. Cui, F. Li, and Z. Shi, “Origin and evolution of pathogenic coronaviruses,” Nat Rev Microbiol, vol. 17, iss. 3, p. 181–192, 2018.
    [Bibtex]
    @Article{Cui:18,
    author = {Jie Cui and Fang Li and Zheng-Li Shi},
    title = {Origin and evolution of pathogenic coronaviruses},
    journal = {{Nat Rev Microbiol}},
    year = {2018},
    volume = {17},
    number = {3},
    pages = {181--192},
    doi = {10.1038/s41579-018-0118-9},
    publisher = {Springer Nature},
    }
  • [DOI] A. Viehweger, S. Krautwurst, K. Lamkiewicz, R. Madhugiri, J. Ziebuhr, M. Hölzer, and M. Marz, “Nanopore direct RNA sequencing reveals modification in full-length coronavirus genomes,” bioRxiv, 2018.
    [Bibtex]
    @Article{Viehweger:18,
    author = {Adrian Viehweger and Sebastian Krautwurst and Kevin Lamkiewicz and Ramakanth Madhugiri and John Ziebuhr and Martin Hölzer and Manja Marz},
    title = {Nanopore direct {RNA} sequencing reveals modification in full-length coronavirus genomes},
    journal = {{bioRxiv}},
    year = {2018},
    doi = {10.1101/483693},
    publisher = {Cold Spring Harbor Laboratory},
    }