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

Authors: Type:

2021

  • [DOI] C. Bäuerl, W. Randazzo, G. Sánchez, M. Selma-Royo, E. Garcia-Verdevio, L. Martínez, A. Parra-Llorca, C. Lerin, V. Fumadó, F. Crovetto, F. Crispi, F. J. Pérez-Cano, G. Rodríguez, G. Ruiz-Redondo, C. Campoy, C. Martínez-Costa, and M. C. Collado, “SARS-CoV-2 RNA and antibody detection in breast milk from a prospective multicentre study in Spain,” Arch Dis Child Fetal Neonatal Ed, p. fetalneonatal–2021–322463, 2021.
    [Bibtex]
    @Article{Baeuerl:21,
    author = {Christine Bäuerl and Walter Randazzo and Gloria S{\'{a}}nchez and Marta Selma-Royo and Elia Garcia-Verdevio and Laura Mart{\'{\i}}nez and Anna Parra-Llorca and Carles Lerin and Victoria Fumad{\'{o}} and Francesca Crovetto and Fatima Crispi and Francisco J P{\'{e}}rez-Cano and Gerardo Rodr{\'{\i}}guez and Gemma Ruiz-Redondo and Cristina Campoy and Cecilia Mart{\'{\i}}nez-Costa and Maria Carmen Collado},
    journal = {{Arch Dis Child Fetal Neonatal Ed}},
    title = {{SARS}-{CoV}-2 {RNA} and antibody detection in breast milk from a prospective multicentre study in {S}pain},
    year = {2021},
    pages = {fetalneonatal--2021--322463},
    doi = {10.1136/archdischild-2021-322463},
    publisher = {{BMJ}},
    }
  • [DOI] Y. Chen, L. Graf, T. Chen, Q. Liao, T. Bai, P. P. Petric, W. Zhu, L. Yang, J. Dong, J. Lu, Y. Chen, J. Shen, O. Haller, P. Staeheli, G. Kochs, D. Wang, M. Schwemmle, and Y. Shu, “Rare variant MX1 alleles increase human susceptibility to zoonotic H7N9 influenza virus,” Science, vol. 373, iss. 6557, p. 918–922, 2021.
    [Bibtex]
    @Article{Chen:21b,
    author = {Yongkun Chen and Laura Graf and Tao Chen and Qijun Liao and Tian Bai and Philipp P. Petric and Wenfei Zhu and Lei Yang and Jie Dong and Jian Lu and Ying Chen and Juan Shen and Otto Haller and Peter Staeheli and Georg Kochs and Dayan Wang and Martin Schwemmle and Yuelong Shu},
    journal = {Science},
    title = {Rare variant {MX}1 alleles increase human susceptibility to zoonotic {H7N9} influenza virus},
    year = {2021},
    number = {6557},
    pages = {918--922},
    volume = {373},
    doi = {10.1126/science.abg5953},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
  • [DOI] M. Krupovic, D. Turner, V. Morozova, M. Dyall-Smith, H. M. Oksanen, R. Edwards, B. E. Dutilh, S. M. Lehman, A. Reyes, D. P. Baquero, M. B. Sullivan, J. Uchiyama, J. Nakavuma, J. Barylski, M. J. Young, S. Du, P. Alfenas-Zerbini, A. Kushkina, A. M. Kropinski, I. Kurtböke, R. J. Brister, C. Lood, B. L. Sarkar, T. Yigang, Y. Liu, L. Huang, J. Wittmann, N. Chanishvili, L. J. van Zyl, J. Rumnieks, T. Mochizuki, M. Jalasvuori, R. K. Aziz, M. L, K. M. Stedman, A. N. Shkoporov, A. Gillis, X. Peng, F. Enault, P. Knezevic, R. Lavigne, S. Rhee, V. Cvirkaite-Krupovic, C. Moraru, A. M. I. Switt, M. M. Poranen, A. Millard, D. Prangishvili, and E. M. Adriaenssens, “Bacterial viruses subcommittee and archaeal viruses subcommittee of the ICTV: update of taxonomy changes in 2021,” Arch Virol, 2021.
    [Bibtex]
    @Article{Krupovic:21,
    author = {Mart Krupovic and Dann Turner and Vera Morozova and Mike Dyall-Smith and Hanna M. Oksanen and Rob Edwards and Bas E. Dutilh and Susan M. Lehman and Alejandro Reyes and Diana P. Baquero and Matthew B. Sullivan and Jumpei Uchiyama and Jesca Nakavuma and Jakub Barylski and Mark J. Young and Shishen Du and Poliane Alfenas-Zerbini and Alla Kushkina and Andrew M. Kropinski and Ipek Kurtböke and J. Rodney Brister and C{\'{e}}dric Lood and B. L. Sarkar and Tong Yigang and Ying Liu and Li Huang and Johannes Wittmann and Nina Chanishvili and Leonardo J. van Zyl and Janis Rumnieks and Tomohiro Mochizuki and Matti Jalasvuori and Ramy K. Aziz and Ma{\l}gorzata {\L}obocka and Kenneth M. Stedman and Andrey N. Shkoporov and Annika Gillis and Xu Peng and Fran{\c{c}}ois Enault and Petar Knezevic and Rob Lavigne and Sung-Keun Rhee and Virginija Cvirkaite-Krupovic and Cristina Moraru and Andrea I. Moreno Switt and Minna M. Poranen and Andrew Millard and David Prangishvili and Evelien M. Adriaenssens},
    journal = {{Arch Virol}},
    title = {Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the {ICTV}: update of taxonomy changes in 2021},
    year = {2021},
    doi = {10.1007/s00705-021-05205-9},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] S. Lytras, W. Xia, J. Hughes, X. Jiang, and D. L. Robertson, “The animal origin of SARS-CoV-2,” Science, vol. 373, iss. 6558, p. 968–970, 2021.
    [Bibtex]
    @Article{Lytras:21b,
    author = {Spyros Lytras and Wei Xia and Joseph Hughes and Xiaowei Jiang and David L. Robertson},
    journal = {Science},
    title = {The animal origin of {SARS}-{CoV}-2},
    year = {2021},
    number = {6558},
    pages = {968--970},
    volume = {373},
    doi = {10.1126/science.abh0117},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
  • [DOI] E. M. Adriaenssens, “Phage diversity in the human gut microbiome: a taxonomist’s perspective,” mSystems, vol. 6, iss. 4, 2021.
    [Bibtex]
    @Article{Adriaenssens:21,
    author = {Evelien M. Adriaenssens},
    journal = {{mSystems}},
    title = {Phage Diversity in the Human Gut Microbiome: a Taxonomist's Perspective},
    year = {2021},
    number = {4},
    volume = {6},
    doi = {10.1128/msystems.00799-21},
    publisher = {American Society for Microbiology},
    }
  • [DOI] J. Zahradník, S. Marciano, M. Shemesh, E. Zoler, D. Harari, J. Chiaravalli, B. Meyer, Y. Rudich, C. Li, I. Marton, O. Dym, N. Elad, M. G. Lewis, H. Andersen, M. Gagne, R. A. Seder, D. C. Douek, and G. Schreiber, “SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution,” Nat Microbiol, vol. 6, iss. 9, p. 1188–1198, 2021.
    [Bibtex]
    @Article{Zahradnik:21,
    author = {Ji{\v{r}}{\'{\i}} Zahradn{\'{\i}}k and Shir Marciano and Maya Shemesh and Eyal Zoler and Daniel Harari and Jeanne Chiaravalli and Björn Meyer and Yinon Rudich and Chunlin Li and Ira Marton and Orly Dym and Nadav Elad and Mark G. Lewis and Hanne Andersen and Matthew Gagne and Robert A. Seder and Daniel C. Douek and Gideon Schreiber},
    journal = {{Nat Microbiol}},
    title = {{SARS}-{CoV}-2 variant prediction and antiviral drug design are enabled by {RBD} in vitro evolution},
    year = {2021},
    number = {9},
    pages = {1188--1198},
    volume = {6},
    doi = {10.1038/s41564-021-00954-4},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] C. Brandt, S. Krautwurst, R. Spott, M. Lohde, M. Jundzill, M. Marquet, and M. Hölzer, “poreCov-an easy to use, fast, and robust workflow for SARS-CoV-2 genome reconstruction via nanopore sequencing,” Front Genet, vol. 12, 2021.
    [Bibtex]
    @Article{Brandt:21a,
    author = {Christian Brandt and Sebastian Krautwurst and Riccardo Spott and Mara Lohde and Mateusz Jundzill and Mike Marquet and Martin Hölzer},
    journal = {{Front Genet}},
    title = {{poreCov}-An Easy to Use, Fast, and Robust Workflow for {SARS}-{CoV}-2 Genome Reconstruction via Nanopore Sequencing},
    year = {2021},
    volume = {12},
    doi = {10.3389/fgene.2021.711437},
    publisher = {Frontiers Media {SA}},
    }
  • [DOI] D. Hillus, T. Schwarz, P. Tober-Lau, K. Vanshylla, H. Hastor, C. Thibeault, S. Jentzsch, E. T. Helbig, L. J. Lippert, P. Tscheak, M. L. Schmidt, J. Riege, A. Solarek, C. von Kalle, C. Dang-Heine, H. Gruell, P. Kopankiewicz, N. Suttorp, C. Drosten, H. Bias, J. Seybold, F. Klein, F. Kurth, V. M. Corman, L. E. Sander, B. Al-Rim, L. Bardtke, J. I. Beheim-Schwarzbach, K. Behn, L. Bergfeld, N. Bethke, T. Bleicker, D. Briesemeister, S. Brumhard, C. Conrad, S. Dieckmann, D. Frey, J. Gabelich, P. Georg, U. Gläser, L. Hasler, A. Hetey, A. L. Hiller, A. Horn, C. Hülso, L. Kegel, W. Koch, A. Krannich, P. Kroneberg, M. Lisy, P. Mackeldanz, B. Maeß, F. Münn, N. Olk, C. Peiser, K. Pohl, A. Hermel, M. Rönnefarth, C. Rubisch, A. S. Rezza, I. Schellenberger, V. Schenkel, J. Schlesinger, S. Schmidt, G. Schwanitz, A. Sinnigen, P. Stubbemann, J. Tesch, D. Treue, D. Wendisch, and S. Zvorc, “Safety, reactogenicity, and immunogenicity of homologous and heterologous prime-boost immunisation with ChAdOx1 nCoV-19 and BNT162b2: a prospective cohort study,” Lancet Respir Med, 2021.
    [Bibtex]
    @Article{Hillus:21,
    author = {David Hillus and Tatjana Schwarz and Pinkus Tober-Lau and Kanika Vanshylla and Hana Hastor and Charlotte Thibeault and Stefanie Jentzsch and Elisa T Helbig and Lena J Lippert and Patricia Tscheak and Marie Luisa Schmidt and Johanna Riege and Andr{\'{e}} Solarek and Christof von Kalle and Chantip Dang-Heine and Henning Gruell and Piotr Kopankiewicz and Norbert Suttorp and Christian Drosten and Harald Bias and Joachim Seybold and Florian Klein and Florian Kurth and Victor Max Corman and Leif Erik Sander and Ben Al-Rim and Lara Bardtke and Jörn Ilmo Beheim-Schwarzbach and Kerstin Behn and Leon Bergfeld and Norma Bethke and Tobias Bleicker and Dana Briesemeister and Sophia Brumhard and Claudia Conrad and Sebastian Dieckmann and Doris Frey and Julie-Anne Gabelich and Philipp Georg and Ute Gläser and Lisbeth Hasler and Andreas Hetey and Anna Luisa Hiller and Alexandra Horn and Claudia Hülso and Luisa Kegel and Willi Koch and Alexander Krannich and Paolo Kroneberg and Michelle Lisy and Petra Mackeldanz and Birgit Mae{\ss} and Friederike Münn and Nadine Olk and Christian Peiser and Kai Pohl and Annelie Hermel and Maria Rönnefarth and Carolin Rubisch and Angela Sanchez Rezza and Isabelle Schellenberger and Viktoria Schenkel and Jenny Schlesinger and Sein Schmidt and Georg Schwanitz and Anne-Sophie Sinnigen and Paula Stubbemann and Julia Tesch and Denise Treue and Daniel Wendisch and Saskia Zvorc},
    journal = {{Lancet Respir Med}},
    title = {Safety, reactogenicity, and immunogenicity of homologous and heterologous prime-boost immunisation with {ChAdOx}1 {nCoV}-19 and {BNT}162b2: a prospective cohort study},
    year = {2021},
    doi = {10.1016/s2213-2600(21)00357-x},
    publisher = {Elsevier {BV}},
    }
  • [DOI] K. D. Nahata, N. Bollen, M. S. Gill, M. Layan, H. Bourhy, S. Dellicour, and G. Baele, “On the use of phylogeographic inference to infer the dispersal history of rabies virus: a review study,” Viruses, vol. 13, iss. 8, p. 1628, 2021.
    [Bibtex]
    @Article{Nahata:21,
    author = {Kanika D. Nahata and Nena Bollen and Mandev S. Gill and Maylis Layan and Herv{\'{e}} Bourhy and Simon Dellicour and Guy Baele},
    journal = {Viruses},
    title = {On the Use of Phylogeographic Inference to Infer the Dispersal History of Rabies Virus: A Review Study},
    year = {2021},
    number = {8},
    pages = {1628},
    volume = {13},
    doi = {10.3390/v13081628},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] C. M. Donato and J. E. Bines, “Rotaviruses and rotavirus vaccines,” Pathogens, vol. 10, iss. 8, p. 959, 2021.
    [Bibtex]
    @Article{Donato:21,
    author = {Celeste M. Donato and Julie E. Bines},
    journal = {Pathogens},
    title = {Rotaviruses and Rotavirus Vaccines},
    year = {2021},
    number = {8},
    pages = {959},
    volume = {10},
    doi = {10.3390/pathogens10080959},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] E. M. Adriaenssens, K. Farkas, J. E. McDonald, D. L. Jones, H. E. Allison, and A. J. McCarthy, “Tracing the fate of wastewater viruses reveals catchment-scale virome diversity and connectivity,” Water research, vol. 203, p. 117568, 2021.
    [Bibtex]
    @Article{Adriaenssens:21a,
    author = {Evelien M. Adriaenssens and Kata Farkas and James E. McDonald and David L. Jones and Heather E. Allison and Alan J. McCarthy},
    journal = {Water Research},
    title = {Tracing the fate of wastewater viruses reveals catchment-scale virome diversity and connectivity},
    year = {2021},
    pages = {117568},
    volume = {203},
    doi = {10.1016/j.watres.2021.117568},
    publisher = {Elsevier {BV}},
    }
  • [DOI] M. Bousali, G. Papatheodoridis, D. Paraskevis, and T. Karamitros, “Hepatitis B virus DNA integration, chronic infections and hepatocellular carcinoma,” Microorganisms, vol. 9, iss. 8, p. 1787, 2021.
    [Bibtex]
    @Article{Bousali:21a,
    author = {Maria Bousali and George Papatheodoridis and Dimitrios Paraskevis and Timokratis Karamitros},
    journal = {Microorganisms},
    title = {Hepatitis {B} Virus {DNA} Integration, Chronic Infections and Hepatocellular Carcinoma},
    year = {2021},
    number = {8},
    pages = {1787},
    volume = {9},
    doi = {10.3390/microorganisms9081787},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] T. Ma, J. Ru, J. Xue, S. Schulz, M. K. Mirzaei, K. Janssen, M. Quante, and L. Deng, “Differences in gut virome related to barrett esophagus and esophageal adenocarcinoma,” Microorganisms, vol. 9, iss. 8, p. 1701, 2021.
    [Bibtex]
    @Article{Ma:21,
    author = {Tianli Ma and Jinlong Ru and Jinling Xue and Sarah Schulz and Mohammadali Khan Mirzaei and Klaus-Peter Janssen and Michael Quante and Li Deng},
    journal = {Microorganisms},
    title = {Differences in Gut Virome Related to Barrett Esophagus and Esophageal Adenocarcinoma},
    year = {2021},
    number = {8},
    pages = {1701},
    volume = {9},
    doi = {10.3390/microorganisms9081701},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] I. Guerrero-Arguero, C. M. Tellez-Freitas, S. K. Weber, B. K. Berges, R. A. Robison, and B. E. Pickett, “Alphaviruses: host pathogenesis, immune response, and vaccine & treatment updates,” J Gen Virol, vol. 102, iss. 8, 2021.
    [Bibtex]
    @Article{GuerreroArguero:21,
    author = {Israel Guerrero-Arguero and Claudia M. Tellez-Freitas and K. Scott Weber and Bradford K. Berges and Richard A. Robison and Brett E. Pickett},
    journal = {{J Gen Virol}},
    title = {Alphaviruses: Host pathogenesis, immune response, and vaccine {\&} treatment updates},
    year = {2021},
    number = {8},
    volume = {102},
    doi = {10.1099/jgv.0.001644},
    publisher = {Microbiology Society},
    }
  • [DOI] J. Matschinske, N. Alcaraz, A. Benis, M. Golebiewski, D. G. Grimm, L. Heumos, T. Kacprowski, O. Lazareva, M. List, Z. Louadi, J. K. Pauling, N. Pfeifer, R. Röttger, V. Schwämmle, G. Sturm, A. Traverso, K. V. Steen, M. V. de Freitas, G. C. V. Silva, L. Wee, N. K. Wenke, M. Zanin, O. Zolotareva, J. Baumbach, and D. B. Blumenthal, “The AIMe registry for artificial intelligence in biomedical research,” Nat Methods, 2021.
    [Bibtex]
    @Article{Matschinske:21,
    author = {Julian Matschinske and Nicolas Alcaraz and Arriel Benis and Martin Golebiewski and Dominik G. Grimm and Lukas Heumos and Tim Kacprowski and Olga Lazareva and Markus List and Zakaria Louadi and Josch K. Pauling and Nico Pfeifer and Richard Röttger and Veit Schwämmle and Gregor Sturm and Alberto Traverso and Kristel Van Steen and Martiela Vaz de Freitas and Gerda Cristal Villalba Silva and Leonard Wee and Nina K. Wenke and Massimiliano Zanin and Olga Zolotareva and Jan Baumbach and David B. Blumenthal},
    journal = {{Nat Methods}},
    title = {The {AIMe} registry for artificial intelligence in biomedical research},
    year = {2021},
    doi = {10.1038/s41592-021-01241-0},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] S. C. Bera, M. Seifert, R. N. Kirchdoerfer, P. van Nies, Y. Wubulikasimu, S. Quack, F. S. Papini, J. J. Arnold, B. Canard, C. E. Cameron, M. Depken, and D. Dulin, “The nucleotide addition cycle of the SARS-CoV-2 polymerase,” Cell Rep, vol. 36, iss. 9, p. 109650, 2021.
    [Bibtex]
    @Article{Bera:21,
    author = {Subhas Chandra Bera and Mona Seifert and Robert N. Kirchdoerfer and Pauline van Nies and Yibulayin Wubulikasimu and Salina Quack and Fl{\'{a}}via S. Papini and Jamie J. Arnold and Bruno Canard and Craig E. Cameron and Martin Depken and David Dulin},
    journal = {{Cell Rep}},
    title = {The nucleotide addition cycle of the {SARS}-{CoV}-2 polymerase},
    year = {2021},
    number = {9},
    pages = {109650},
    volume = {36},
    doi = {10.1016/j.celrep.2021.109650},
    publisher = {Elsevier {BV}},
    }
  • [DOI] M. Grossegesse, P. Leupold, J. Doellinger, L. Schaade, and A. Nitsche, “Inactivation of coronaviruses during sample preparation for proteomics experiments,” J Proteome Res, vol. 20, iss. 9, p. 4598–4602, 2021.
    [Bibtex]
    @Article{Grossegesse:21a,
    author = {Marica Grossegesse and Paula Leupold and Joerg Doellinger and Lars Schaade and Andreas Nitsche},
    journal = {{J Proteome Res}},
    title = {Inactivation of Coronaviruses during Sample Preparation for Proteomics Experiments},
    year = {2021},
    number = {9},
    pages = {4598--4602},
    volume = {20},
    doi = {10.1021/acs.jproteome.1c00320},
    publisher = {American Chemical Society ({ACS})},
    }
  • [DOI] P. Tober-Lau, T. Schwarz, K. Vanshylla, D. Hillus, H. Gruell, N. Suttorp, I. Landgraf, K. Kappert, J. Seybold, C. Drosten, F. Klein, F. Kurth, V. M. Corman, and L. E. S. and, “Long-term immunogenicity of BNT162b2 vaccination in the elderly and in younger health care workers,” medRxiv, 2021.
    [Bibtex]
    @Article{ToberLau:21,
    author = {Pinkus Tober-Lau and Tatjana Schwarz and Kanika Vanshylla and David Hillus and Henning Gruell and Norbert Suttorp and Irmgard Landgraf and Kai Kappert and Joachim Seybold and Christian Drosten and Florian Klein and Florian Kurth and Victor Max Corman and Leif Erik Sander and},
    journal = {{medRxiv}},
    title = {Long-term immunogenicity of {BNT}162b2 vaccination in the elderly and in younger health care workers},
    year = {2021},
    doi = {10.1101/2021.08.26.21262468},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] J. Zhou, T. P. Peacock, J. C. Brown, D. H. Goldhill, A. M. E. Elrefaey, R. Penrice-Randal, V. M. Cowton, G. D. Lorenzo, W. Furnon, W. T. Harvey, R. Kugathasan, R. Frise, L. Baillon, R. Lassaunière, N. Thakur, G. Gallo, H. Goldswain, I. Donovan-Banfield, X. Dong, N. P. Randle, F. Sweeney, M. C. Glynn, J. L. Quantrill, P. F. McKay, A. H. Patel, M. Palmarini, J. A. Hiscox, D. Bailey, and W. S. Barclay, “Mutations that adapt SARS-CoV-2 to mustelid hosts do not increase fitness in the human airway,” bioRxiv, 2021.
    [Bibtex]
    @Article{Zhou:21a,
    author = {Jie Zhou and Thomas P. Peacock and Jonathan C. Brown and Daniel H. Goldhill and Ahmed M.E. Elrefaey and Rebekah Penrice-Randal and Vanessa M. Cowton and Giuditta De Lorenzo and Wilhelm Furnon and William T. Harvey and Ruthiran Kugathasan and Rebecca Frise and Laury Baillon and Ria Lassauni{\`{e}}re and Nazia Thakur and Giulia Gallo and Hannah Goldswain and I'ah Donovan-Banfield and Xiaofeng Dong and Nadine P. Randle and Fiachra Sweeney and Martha C. Glynn and Jessica L. Quantrill and Paul F. McKay and Arvind H. Patel and Massimo Palmarini and Julian A. Hiscox and Dalan Bailey and Wendy S. Barclay},
    journal = {{bioRxiv}},
    title = {Mutations that adapt {SARS}-{CoV}-2 to mustelid hosts do not increase fitness in the human airway},
    year = {2021},
    doi = {10.1101/2021.08.20.456972},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] T. M. Scott, S. Jensen, and B. E. Pickett, “A signaling pathway-driven bioinformatics pipeline for predicting therapeutics against emerging infectious diseases,” F1000Research, vol. 10, p. 330, 2021.
    [Bibtex]
    @Article{Scott:21,
    author = {Tiana M. Scott and Sam Jensen and Brett E. Pickett},
    journal = {{F1000Research}},
    title = {A signaling pathway-driven bioinformatics pipeline for predicting therapeutics against emerging infectious diseases},
    year = {2021},
    pages = {330},
    volume = {10},
    doi = {10.12688/f1000research.52412.2},
    publisher = {F1000 Research Ltd},
    }
  • [DOI] M. J. Roach, K. McNair, S. K. Giles, L. K. Inglis, E. Pargin, S. Roux, P. l, and R. A. Edwards, “Philympics 2021: prophage predictions perplex programs,” F1000research, vol. 10, p. 758, 2021.
    [Bibtex]
    @Article{Roach:21,
    author = {Michael J. Roach and Katelyn McNair and Sarah K Giles and Laura K Inglis and Evan Pargin and Simon Roux and Przemys{\l}aw Decewicz and Robert A. Edwards},
    journal = {F1000Research},
    title = {Philympics 2021: Prophage Predictions Perplex Programs},
    year = {2021},
    pages = {758},
    volume = {10},
    doi = {10.12688/f1000research.54449.1},
    publisher = {F1000 Research Ltd},
    }
  • [DOI] S. Iannuzzi and M. von Kleist, “Mathematical modelling of the molecular mechanisms of interaction of tenofovir with emtricitabine against HIV,” Viruses, vol. 13, iss. 7, p. 1354, 2021.
    [Bibtex]
    @Article{Iannuzzi:21,
    author = {Sara Iannuzzi and Max von Kleist},
    journal = {Viruses},
    title = {Mathematical Modelling of the Molecular Mechanisms of Interaction of Tenofovir with Emtricitabine against {HIV}},
    year = {2021},
    number = {7},
    pages = {1354},
    volume = {13},
    doi = {10.3390/v13071354},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] F. Amaro, L. Zé-Zé, J. Lourenço, M. Giovanetti, S. C. Becker, and M. J. Alves, “Phylogenetic analysis of massilia phlebovirus in portugal,” Viruses, vol. 13, iss. 7, p. 1412, 2021.
    [Bibtex]
    @Article{Amaro:21,
    author = {F{\'{a}}tima Amaro and L{\'{\i}}bia Z{\'{e}}-Z{\'{e}} and Jos{\'{e}} Louren{\c{c}}o and Marta Giovanetti and Stefanie Christine Becker and Maria Jo{\~{a}}o Alves},
    journal = {Viruses},
    title = {Phylogenetic Analysis of Massilia phlebovirus in Portugal},
    year = {2021},
    number = {7},
    pages = {1412},
    volume = {13},
    doi = {10.3390/v13071412},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] D. P. Depledge and J. Breuer, “Varicella-zoster virus – genetics, molecular evolution and recombination.,” Curr Top Microbiol Immunol, 2021.
    [Bibtex]
    @Article{Depledge:21,
    author = {Depledge, Daniel P. and Breuer, Judith},
    journal = {{Curr Top Microbiol Immunol}},
    title = {Varicella-Zoster Virus -- Genetics, Molecular Evolution and Recombination.},
    year = {2021},
    abstract = {This chapter first details the structure, organization and coding content of the VZV genome to provide a foundation on which the molecular evolution of the virus can be projected. We subsequently describe the evolution of molecular profiling approaches from restriction fragment length polymorphisms to single nucleotide polymorphism profiling to modern day high-throughput sequencing approaches. We describe how the application of these methodologies led to our current model of VZV phylogeograpy including the number and structure of geographic clades and the role of recombination in reshaping these.},
    doi = {10.1007/82_2021_238},
    keywords = {Expression kinetics; Genome; Molecular evolution; Phylogeny; Recombination; Transcriptome; Varicella-Zoster virus},
    pmid = {34374828},
    pubstate = {aheadofprint},
    }
  • [DOI] P. Terzian, E. Olo~Ndela, C. Galiez, J. Lossouarn, R. Pérez~Bucio, R. Mom, A. Toussaint, M. Petit, and F. Enault, “PHROG: families of prokaryotic virus proteins clustered using remote homology,” NAR Genom Bioinform, vol. 3, iss. 3, 2021.
    [Bibtex]
    @Article{Terzian:21,
    author = {Paul Terzian and Eric Olo~Ndela and Clovis Galiez and Julien Lossouarn and Rub{\'{e}}n~Enrique P{\'{e}}rez~Bucio and Robin Mom and Ariane Toussaint and Marie-Agn{\`{e}}s Petit and Fran{\c{c}}ois Enault},
    journal = {{NAR Genom Bioinform}},
    title = {{PHROG}: families of prokaryotic virus proteins clustered using remote homology},
    year = {2021},
    number = {3},
    volume = {3},
    doi = {10.1093/nargab/lqab067},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] S. Pach, T. N. Nguyen, J. Trimpert, D. Kunec, N. Osterrieder, and G. Wolber, “ACE2-variants indicate potential SARS-CoV-2-susceptibility in animals: a molecular dynamics study,” Mol Inform, 2021.
    [Bibtex]
    @Article{Pach:21,
    author = {Szymon Pach and Trung Ngoc Nguyen and Jakob Trimpert and Dusan Kunec and Nikolaus Osterrieder and Gerhard Wolber},
    journal = {{Mol Inform}},
    title = {{ACE}2-Variants Indicate Potential {SARS}-{CoV}-2-Susceptibility in Animals: A Molecular Dynamics Study},
    year = {2021},
    doi = {10.1002/minf.202100031},
    publisher = {Wiley},
    }
  • [DOI] G. Nouailles, E. Wyler, P. Pennitz, D. Postmus, D. Vladimirova, J. Kazmierski, F. Pott, K. Dietert, M. Muelleder, V. Farztdinov, B. Obermayer, S. Wienhold, S. Andreotti, T. Hoefler, 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, “Temporal omics analysis in syrian hamsters unravel cellular effector responses to moderate COVID-19,” Nat Commun, vol. 12, iss. 1, 2021.
    [Bibtex]
    @Article{Nouailles:21a,
    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 Muelleder and Vadim Farztdinov and Benedikt Obermayer and Sandra-Maria Wienhold and Sandro Andreotti and Thomas Hoefler and Birgit Sawitzki and Christian Drosten and Leif E. Sander and Norbert Suttorp and Markus Ralser and Dieter Beule and Achim D. Gruber and Christine Goffinet and Markus Landthaler and Jakob Trimpert and Martin Witzenrath},
    journal = {{Nat Commun}},
    title = {Temporal omics analysis in Syrian hamsters unravel cellular effector responses to moderate {COVID}-19},
    year = {2021},
    number = {1},
    volume = {12},
    doi = {10.1038/s41467-021-25030-7},
    publisher = {Springer Science and Business Media {LLC}},
    }
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    [Bibtex]
    @Article{Scholz:21,
    author = {Juliane Scholz and Wibke Wetzker and Annika Licht and Rainer Heintzmann and Andr{\'{e}} Scherag and Sebastian Weis and Mathias Pletz and Cornelia Betsch and Michael Bauer and Petra Dickmann and},
    journal = {{PLoS One}},
    title = {The role of risk communication in public health interventions. An analysis of risk communication for a community quarantine in Germany to curb the {SARS}-{CoV}-2 pandemic},
    year = {2021},
    number = {8},
    pages = {e0256113},
    volume = {16},
    doi = {10.1371/journal.pone.0256113},
    editor = {Rosemary Frey},
    publisher = {Public Library of Science ({PLoS})},
    }
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    [Bibtex]
    @Article{Bergwerk:21,
    author = {Moriah Bergwerk and Tal Gonen and Yaniv Lustig and Sharon Amit and Marc Lipsitch and Carmit Cohen and Michal Mandelboim and Einav Gal Levin and Carmit Rubin and Victoria Indenbaum and Ilana Tal and Malka Zavitan and Neta Zuckerman and Adina Bar-Chaim and Yitshak Kreiss and Gili Regev-Yochay},
    journal = {{N Engl J Med}},
    title = {Covid-19 Breakthrough Infections in Vaccinated Health Care Workers},
    year = {2021},
    doi = {10.1056/nejmoa2109072},
    publisher = {Massachusetts Medical Society},
    }
  • [DOI] J. Trimpert, K. Dietert, T. C. Firsching, N. Ebert, T. T. N. Thao, D. Vladimirova, S. Kaufer, F. Labroussaa, A. Abdelgawad, A. Conradie, T. Höfler, J. M. Adler, L. D. Bertzbach, J. Jores, A. D. Gruber, V. Thiel, N. Osterrieder, and D. Kunec, “Development of safe and highly protective live-attenuated SARS-CoV-2 vaccine candidates by genome recoding,” Cell Rep, vol. 36, iss. 5, p. 109493, 2021.
    [Bibtex]
    @Article{Trimpert:21,
    author = {Jakob Trimpert and Kristina Dietert and Theresa C. Firsching and Nadine Ebert and Tran Thi Nhu Thao and Daria Vladimirova and Susanne Kaufer and Fabien Labroussaa and Azza Abdelgawad and Andel{\'{e}} Conradie and Thomas Höfler and Julia M. Adler and Luca D. Bertzbach and Joerg Jores and Achim D. Gruber and Volker Thiel and Nikolaus Osterrieder and Dusan Kunec},
    journal = {{Cell Rep}},
    title = {Development of safe and highly protective live-attenuated {SARS}-{CoV}-2 vaccine candidates by genome recoding},
    year = {2021},
    number = {5},
    pages = {109493},
    volume = {36},
    doi = {10.1016/j.celrep.2021.109493},
    publisher = {Elsevier {BV}},
    }
  • [DOI] V. Oberhardt, H. Luxenburger, J. Kemming, I. Schulien, K. Ciminski, S. Giese, B. Csernalabics, J. Lang-Meli, I. Janowska, J. Staniek, K. Wild, K. Basho, M. S. Marinescu, J. Fuchs, F. Topfstedt, A. Janda, O. Sogukpinar, H. Hilger, K. Stete, F. Emmerich, B. Bengsch, C. F. Waller, S. Rieg, Sagar, T. Boettler, K. Zoldan, G. Kochs, M. Schwemmle, M. Rizzi, R. Thimme, C. Neumann-Haefelin, and M. Hofmann, “Rapid and stable mobilization of CD8+ t cells by SARS-CoV-2 mRNA vaccine,” Nature, 2021.
    [Bibtex]
    @Article{Oberhardt:21,
    author = {Valerie Oberhardt and Hendrik Luxenburger and Janine Kemming and Isabel Schulien and Kevin Ciminski and Sebastian Giese and Benedikt Csernalabics and Julia Lang-Meli and Iga Janowska and Julian Staniek and Katharina Wild and Kristi Basho and Mircea Stefan Marinescu and Jonas Fuchs and Fernando Topfstedt and Ales Janda and Oezlem Sogukpinar and Hanna Hilger and Katarina Stete and Florian Emmerich and Bertram Bengsch and Cornelius F. Waller and Siegbert Rieg and Sagar and Tobias Boettler and Katharina Zoldan and Georg Kochs and Martin Schwemmle and Marta Rizzi and Robert Thimme and Christoph Neumann-Haefelin and Maike Hofmann},
    journal = {Nature},
    title = {Rapid and stable mobilization of {CD}8+ T cells by {SARS}-{CoV}-2 {mRNA} vaccine},
    year = {2021},
    doi = {10.1038/s41586-021-03841-4},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] R. Parry, R. J. Gifford, S. Lytras, S. C. Ray, and L. J. M. Coin, “No evidence of SARS-CoV-2 reverse transcription and integration as the origin of chimeric transcripts in patient tissues,” Proc Natl Acad Sci, vol. 118, iss. 33, p. e2109066118, 2021.
    [Bibtex]
    @Article{Parry:21,
    author = {Rhys Parry and Robert J. Gifford and Spyros Lytras and Stuart C. Ray and Lachlan J. M. Coin},
    journal = {{Proc Natl Acad Sci}},
    title = {No evidence of {SARS}-{CoV}-2 reverse transcription and integration as the origin of chimeric transcripts in patient tissues},
    year = {2021},
    number = {33},
    pages = {e2109066118},
    volume = {118},
    doi = {10.1073/pnas.2109066118},
    publisher = {Proceedings of the National Academy of Sciences},
    }
  • [DOI] K. Kieft, A. M. Breister, P. Huss, A. M. Linz, E. Zanetakos, Z. Zhou, J. Rahlff, S. P. Esser, A. J. Probst, S. Raman, S. Roux, and K. Anantharaman, “Virus-associated organosulfur metabolism in human and environmental systems,” Cell Rep, vol. 36, iss. 5, p. 109471, 2021.
    [Bibtex]
    @Article{Kieft:21,
    author = {Kristopher Kieft and Adam M. Breister and Phil Huss and Alexandra M. Linz and Elizabeth Zanetakos and Zhichao Zhou and Janina Rahlff and Sarah P. Esser and Alexander J. Probst and Srivatsan Raman and Simon Roux and Karthik Anantharaman},
    journal = {{Cell Rep}},
    title = {Virus-associated organosulfur metabolism in human and environmental systems},
    year = {2021},
    number = {5},
    pages = {109471},
    volume = {36},
    doi = {10.1016/j.celrep.2021.109471},
    publisher = {Elsevier {BV}},
    }
  • [DOI] R. Zell, N. J. Knowles, and P. Simmonds, “A proposed division of the family Picornaviridae into subfamilies based on phylogenetic relationships and functional genomic organization,” Arch Virol, 2021.
    [Bibtex]
    @Article{Zell:21,
    author = {Roland Zell and Nick J. Knowles and Peter Simmonds},
    journal = {{Arch Virol}},
    title = {A proposed division of the family {P}icornaviridae into subfamilies based on phylogenetic relationships and functional genomic organization},
    year = {2021},
    doi = {10.1007/s00705-021-05178-9},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] A. A. Guzmán-Solís, V. Villa-Islas, M. J. Bravo-López, M. Sandoval-Velasco, J. K. Wesp, J. A. Gómez-Valdés, M. L. de la Moreno-Cabrera, A. Meraz, G. Solís-Pichardo, P. Schaaf, B. R. tenOever, D. Blanco-Melo, and M. Á. C. Arcos, “Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade,” eLife, vol. 10, 2021.
    [Bibtex]
    @Article{GuzmanSolis:21,
    author = {Axel A Guzm{\'{a}}n-Sol{\'{\i}}s and Viridiana Villa-Islas and Miriam J Bravo-L{\'{o}}pez and Marcela Sandoval-Velasco and Julie K Wesp and Jorge A G{\'{o}}mez-Vald{\'{e}}s and Mar{\'{\i}}a de la Luz Moreno-Cabrera and Alejandro Meraz and Gabriela Sol{\'{\i}}s-Pichardo and Peter Schaaf and Benjamin R tenOever and Daniel Blanco-Melo and Mar{\'{\i}}a C {\'{A}}vila Arcos},
    journal = {{eLife}},
    title = {Ancient viral genomes reveal introduction of human pathogenic viruses into {M}exico during the transatlantic slave trade},
    year = {2021},
    volume = {10},
    doi = {10.7554/elife.68612},
    publisher = {{eLife} Sciences Publications, Ltd},
    }
  • [DOI] S. Calvignac-Spencer, A. Düx, J. F. Gogarten, F. H. Leendertz, and L. V. Patrono, “A great ape perspective on the origins and evolution of human viruses,” in Adv Virus Res, Elsevier, 2021, p. 1–26.
    [Bibtex]
    @InCollection{CalvignacSpencer:21,
    author = {S{\'{e}}bastien Calvignac-Spencer and Ariane Düx and Jan F. Gogarten and Fabian H. Leendertz and Livia V. Patrono},
    booktitle = {{Adv Virus Res}},
    publisher = {Elsevier},
    title = {A great ape perspective on the origins and evolution of human viruses},
    year = {2021},
    pages = {1--26},
    doi = {10.1016/bs.aivir.2021.06.001},
    }
  • [DOI] A. Michelitsch, K. Wernike, L. Ulrich, T. C. Mettenleiter, and M. Beer, “SARS-CoV-2 in animals: from potential hosts to animal models,” in Adv Virus Res, Elsevier, 2021, p. 59–102.
    [Bibtex]
    @InCollection{Michelitsch:21a,
    author = {Anna Michelitsch and Kerstin Wernike and Lorenz Ulrich and Thomas C. Mettenleiter and Martin Beer},
    booktitle = {{Adv Virus Res}},
    publisher = {Elsevier},
    title = {{SARS}-{CoV}-2 in animals: From potential hosts to animal models},
    year = {2021},
    pages = {59--102},
    doi = {10.1016/bs.aivir.2021.03.004},
    }
  • [DOI] M. A. Brinton, A. A. Gulyaeva, U. B. R. Balasuriya, M. Dunowska, K. S. Faaberg, T. Goldberg, F. C. C. Leung, H. J. Nauwynck, E. J. Snijder, T. Stadejek, and A. E. Gorbalenya, “ICTV virus taxonomy profile: arteriviridae 2021,” Journal of general virology, vol. 102, iss. 8, 2021.
    [Bibtex]
    @Article{Brinton:21,
    author = {Margo A. Brinton and Anastasia A. Gulyaeva and Udeni B. R. Balasuriya and Magda Dunowska and Kay S. Faaberg and Tony Goldberg and Frederick C. C. Leung and Hans J. Nauwynck and Eric J. Snijder and Tomasz Stadejek and Alexander E. Gorbalenya},
    journal = {Journal of General Virology},
    title = {{ICTV} Virus Taxonomy Profile: Arteriviridae 2021},
    year = {2021},
    number = {8},
    volume = {102},
    doi = {10.1099/jgv.0.001632},
    publisher = {Microbiology Society},
    }
  • [DOI] M. Kohls, B. Saremi, I. Muchsin, N. Fischer, P. Becher, and K. Jung, “A resampling strategy for studying robustness in virus detection pipelines,” Comput Biol Chem, vol. 94, p. 107555, 2021.
    [Bibtex]
    @Article{Kohls:21,
    author = {Moritz Kohls and Babak Saremi and Ihsan Muchsin and Nicole Fischer and Paul Becher and Klaus Jung},
    journal = {{Comput Biol Chem}},
    title = {A resampling strategy for studying robustness in virus detection pipelines},
    year = {2021},
    pages = {107555},
    volume = {94},
    doi = {10.1016/j.compbiolchem.2021.107555},
    publisher = {Elsevier {BV}},
    }
  • [DOI] M. U. G. Kraemer, V. Hill, C. Ruis, S. Dellicour, S. Bajaj, J. T. McCrone, G. Baele, K. V. Parag, A. L. Battle, B. Gutierrez, B. Jackson, R. Colquhoun, Á. O’Toole, B. Klein, A. Vespignani, E. Volz, N. R. Faria, D. Aanensen, N. J. Loman, L. du Plessis, S. Cauchemez, A. Rambaut, S. V. Scarpino, and O. P. G. and, “Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence,” Science, p. eabj0113, 2021.
    [Bibtex]
    @Article{Kraemer:21,
    author = {Moritz U.G. Kraemer and Verity Hill and Christopher Ruis and Simon Dellicour and Sumali Bajaj and John T. McCrone and Guy Baele and Kris V. Parag and Anya Lindström Battle and Bernardo Gutierrez and Ben Jackson and Rachel Colquhoun and {\'{A}}ine O'Toole and Brennan Klein and Alessandro Vespignani and Erik Volz and Nuno R. Faria and David Aanensen and Nicholas J. Loman and Louis du Plessis and Simon Cauchemez and Andrew Rambaut and Samuel V. Scarpino and Oliver G. Pybus and},
    journal = {Science},
    title = {Spatiotemporal invasion dynamics of {SARS}-{CoV}-2 lineage {B}.1.1.7 emergence},
    year = {2021},
    pages = {eabj0113},
    doi = {10.1126/science.abj0113},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
  • [DOI] J. M. Bartoszewicz, U. Genske, and B. Y. Renard, “Deep learning-based real-time detection of novel pathogens during sequencing,” Brief Bioinform, 2021.
    [Bibtex]
    @Article{Bartoszewicz:21,
    author = {Jakub M Bartoszewicz and Ulrich Genske and Bernhard Y Renard},
    journal = {{Brief Bioinform}},
    title = {Deep learning-based real-time detection of novel pathogens during sequencing},
    year = {2021},
    doi = {10.1093/bib/bbab269},
    publisher = {Oxford University Press ({OUP})},
    }
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    [Bibtex]
    @Article{Hauschild:21,
    author = {Anne-Christin Hauschild and Lisa Eick and Joachim Wienbeck and Dominik Heider},
    journal = {{iScience}},
    title = {Fostering reproducibility, reusability, and technology transfer in health informatics},
    year = {2021},
    number = {7},
    pages = {102803},
    volume = {24},
    doi = {10.1016/j.isci.2021.102803},
    publisher = {Elsevier {BV}},
    }
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    [Bibtex]
    @Article{Coutinho:21,
    author = {Felipe Hernandes Coutinho and Asier Zaragoza-Solas and Mario L{\'{o}}pez-P{\'{e}}rez and Jakub Barylski and Andrzej Zielezinski and Bas E. Dutilh and Robert Edwards and Francisco Rodriguez-Valera},
    journal = {Patterns},
    title = {{RaFAH}: Host prediction for viruses of Bacteria and Archaea based on protein content},
    year = {2021},
    number = {7},
    pages = {100274},
    volume = {2},
    doi = {10.1016/j.patter.2021.100274},
    publisher = {Elsevier {BV}},
    }
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    [Bibtex]
    @Article{Zhong:21,
    author = {Zhi-Ping Zhong and Funing Tian and Simon Roux and M. Consuelo Gazit{\'{u}}a and Natalie E. Solonenko and Yueh-Fen Li and Mary E. Davis and James L. Van Etten and Ellen Mosley-Thompson and Virginia I. Rich and Matthew B. Sullivan and Lonnie G. Thompson},
    journal = {Microbiome},
    title = {Glacier ice archives nearly 15,000-year-old microbes and phages},
    year = {2021},
    number = {1},
    volume = {9},
    doi = {10.1186/s40168-021-01106-w},
    publisher = {Springer Science and Business Media {LLC}},
    }
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    [Bibtex]
    @Article{Fritz:21,
    author = {Adrian Fritz and Andreas Bremges and Zhi-Luo Deng and Till Robin Lesker and Jasper Götting and Tina Ganzenmueller and Alexander Sczyrba and Alexander Dilthey and Frank Klawonn and Alice Carolyn McHardy},
    journal = {{Genome Biol}},
    title = {Haploflow: strain-resolved de novo assembly of viral genomes},
    year = {2021},
    number = {1},
    volume = {22},
    doi = {10.1186/s13059-021-02426-8},
    publisher = {Springer Science and Business Media {LLC}},
    }
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    [Bibtex]
    @Article{Brinkmann:21,
    author = {Annika Brinkmann and Sophie-Luisa Ulm and Steven Uddin and Sophie Förster and Dominique Seifert and Rainer Oehme and Merle Corty and Lars Schaade and Janine Michel and Andreas Nitsche},
    journal = {{Front Microbiol}},
    title = {{AmpliCoV}: Rapid Whole-Genome Sequencing Using Multiplex {PCR} Amplification and Real-Time Oxford Nanopore {MinION} Sequencing Enables Rapid Variant Identification of {SARS}-{CoV}-2},
    year = {2021},
    volume = {12},
    doi = {10.3389/fmicb.2021.651151},
    publisher = {Frontiers Media {SA}},
    }
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    [Bibtex]
    @Article{Mock:21,
    author = {Florian Mock and Fleming Kretschmer and Anton Kriese and Sebastian Böcker and Manja Marz},
    journal = {{bioRxiv}},
    title = {{BERTax}: taxonomic classification of {DNA} sequences with {D}eep {N}eural {N}etworks},
    year = {2021},
    doi = {10.1101/2021.07.09.451778},
    publisher = {Cold Spring Harbor Laboratory},
    }
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    [Bibtex]
    @Article{Michalik:21,
    author = {Stephan Michalik and Florian Siegerist and Raghavendra Palankar and Kati Franzke and Maximilian Schindler and Alexander Reder and Ulrike Seifert and Clemens Cammann and Jan Wesche and Leif Steil and Christian Hentschker and Manuela Gesell-Salazar and Emil Reisinger and Martin Beer and Nicole Endlich and Andreas Greinacher and Uwe Völker},
    journal = {{Research Square}},
    title = {Comparative analysis of {ChAdOx}1 {nCoV}-19 and Ad26.{COV}2.S {SARS}-{CoV}-2 vector vaccines},
    year = {2021},
    doi = {10.21203/rs.3.rs-736157/v1},
    publisher = {Research Square Platform {LLC}},
    }
  • [DOI] N. Yin, S. Dellicour, V. Daubie, N. Franco, M. Wautier, C. Faes, D. V. Cauteren, L. Nymark, N. Hens, M. Gilbert, M. Hallin, and O. Vandenberg, “Leveraging of SARS-CoV-2 PCR cycle thresholds values (ct) to forecast COVID-19 trends,” medRxiv, 2021.
    [Bibtex]
    @Article{Yin:21,
    author = {Nicolas Yin and Simon Dellicour and Valery Daubie and Nicolas Franco and Magali Wautier and Christel Faes and Dieter Van Cauteren and Liv Nymark and Niel Hens and Marius Gilbert and Marie Hallin and Olivier Vandenberg},
    journal = {{medRxiv}},
    title = {Leveraging of {SARS}-{CoV}-2 {PCR} cycle thresholds values (Ct) to forecast {COVID}-19 trends},
    year = {2021},
    doi = {10.1101/2021.07.17.21260679},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] R. Rose, F. Neumann, O. Grobe, T. Lorentz, H. Fickenscher, and A. Krumbholz, “Heterologous immunisation with vector vaccine as prime followed by mRNA vaccine as boost leads to humoral immune response against SARS-CoV-2, which is comparable to that according to a homologous mRNA vaccination scheme,” medRxiv, 2021.
    [Bibtex]
    @Article{Rose:21,
    author = {Ruben Rose and Franziska Neumann and Olaf Grobe and Thomas Lorentz and Helmut Fickenscher and Andi Krumbholz},
    journal = {{medRxiv}},
    title = {Heterologous immunisation with vector vaccine as prime followed by {mRNA} vaccine as boost leads to humoral immune response against {SARS}-{CoV}-2, which is comparable to that according to a homologous {mRNA} vaccination scheme},
    year = {2021},
    doi = {10.1101/2021.07.09.21260251},
    publisher = {Cold Spring Harbor Laboratory},
    }
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    @Article{Davis:21,
    author = {Chris Davis and Nicola Logan and Grace Tyson and Richard Orton and William Harvey and John Haughney and Jon Perkins and Thomas P. Peacock and Wendy S. Barclay and Peter Cherepanov and Massimo Palmarini and Pablo R. Murcia and Arvind H. Patel and David L. Robertson and Emma C. Thomson and Brian J. Willett and},
    journal = {{medRxiv}},
    title = {Reduced neutralisation of the {D}elta ({B}.1.617.2) {SARS}-{CoV}-2 variant of concern following vaccination},
    year = {2021},
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    @Article{Shah:21,
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    title = {Hundreds of viral families in the healthy infant gut},
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    @Article{Pratama:21,
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    journal = {{PeerJ}},
    title = {Expanding standards in viromics: in silico evaluation of {dsDNA} viral genome identification, classification, and auxiliary metabolic gene curation},
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    @Article{Bahai:21,
    author = {Akash Bahai and Ehsaneddin Asgari and Mohammad R K Mofrad and Andreas Kloetgen and Alice C McHardy},
    journal = {Bioinformatics},
    title = {{EpitopeVec}: Linear Epitope Prediction Using Deep Protein Sequence Embeddings},
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    @Article{Huddleston:21,
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    journal = {{J Open Source Softw}},
    title = {Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens},
    year = {2021},
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    title = {Untangling introductions and persistence in {COVID}-19 resurgence in {E}urope},
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    @Article{Hoffmann:21a,
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    year = {2021},
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    author = {Claudia Kohl and Andreas Nitsche and Andreas Kurth},
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    title = {Update on Potentially Zoonotic Viruses of European Bats},
    year = {2021},
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    journal = {Viruses},
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    year = {2021},
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    @Article{Muzeniek:21,
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    journal = {Vaccines},
    title = {Detection of Alpha- and Betacoronaviruses in {M}iniopterus fuliginosus and {R}ousettus leschenaultii, two species of {S}ri {L}ankan Bats},
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    @Article{Mavian:21,
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    journal = {Viruses},
    title = {Comparative Pathogenesis, Genomics and Phylogeography of Mousepox},
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    @Article{Vakulenko:21,
    author = {Yulia Vakulenko and Andrei Deviatkin and Jan Felix Drexler and Alexander Lukashev},
    journal = {Viruses},
    title = {Modular Evolution of Coronavirus Genomes},
    year = {2021},
    number = {7},
    pages = {1270},
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    journal = {{Virus Evol}},
    title = {Molecular detection and genomic characterization of diverse hepaciviruses in {A}frican rodents},
    year = {2021},
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    @Article{Bekliz:21,
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    journal = {{Lancet Microbe}},
    title = {{SARS}-{CoV}-2 rapid diagnostic tests for emerging variants},
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    author = {Petar Knezevic and Evelien M. Adriaenssens and {ICTV Report Consortium}},
    journal = {{J Gen Virol}},
    title = {{ICTV} Virus Taxonomy Profile: Inoviridae},
    year = {2021},
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    @Article{Walker:21,
    author = {Peter J. Walker and Stuart G. Siddell and Elliot J. Lefkowitz and Arcady R. Mushegian and Evelien M. Adriaenssens and Poliane Alfenas-Zerbini and Andrew J. Davison and Donald M. Dempsey and Bas E. Dutilh and Mar{\'{\i}}a Laura Garc{\'{\i}}a and Bal{\'{a}}zs Harrach and Robert L. Harrison and R. Curtis Hendrickson and Sandra Junglen and Nick J. Knowles and Mart Krupovic and Jens H. Kuhn and Amy J. Lambert and Ma{\l}gorzata {\L}obocka and Max L. Nibert and Hanna M. Oksanen and Richard J. Orton and David L. Robertson and Luisa Rubino and Sead Sabanadzovic and Peter Simmonds and Donald B. Smith and Nobuhiro Suzuki and Koenraad Van Dooerslaer and Anne-Mieke Vandamme and Arvind Varsani and Francisco Murilo Zerbini},
    journal = {{Arch Virol}},
    title = {Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021)},
    year = {2021},
    doi = {10.1007/s00705-021-05156-1},
    publisher = {Springer Science and Business Media {LLC}},
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    @Article{Calisher:21,
    author = {Charles H Calisher and Dennis Carroll and Rita Colwell and Ronald B Corley and Peter Daszak and Christian Drosten and Luis Enjuanes and Jeremy Farrar and Hume Field and Josie Golding and Alexander E Gorbalenya and Bart Haagmans and James M Hughes and Gerald T Keusch and Sai Kit Lam and Juan Lubroth and John S Mackenzie and Larry Madoff and Jonna Keener Mazet and Stanley M Perlman and Leo Poon and Linda Saif and Kanta Subbarao and Michael Turner},
    journal = {{Lancet}},
    title = {Science, not speculation, is essential to determine how {SARS}-{CoV}-2 reached humans},
    year = {2021},
    number = {10296},
    pages = {209--211},
    volume = {398},
    doi = {10.1016/s0140-6736(21)01419-7},
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    author = {Marcos C. Vieira and Celeste M. Donato and Philip Arevalo and Guus F. Rimmelzwaan and Timothy Wood and Liza Lopez and Q. Sue Huang and Vijaykrishna Dhanasekaran and Katia Koelle and Sarah Cobey},
    journal = {{Nat Commun}},
    title = {Lineage-specific protection and immune imprinting shape the age distributions of influenza {B} cases},
    year = {2021},
    number = {1},
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    @Article{Fischer:21,
    author = {Thea K Fischer and Peter Simmonds and Heli Harvala},
    journal = {{Lancet Infect Dis}},
    title = {The importance of enterovirus surveillance in a post-polio world},
    year = {2021},
    doi = {10.1016/s1473-3099(20)30852-5},
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    @Article{Morais:21,
    author = {Paulo Morais and N{\'{\i}}dia S. Trov{\~{a}}o and Ana B. Abecasis and Ricardo Parreira},
    journal = {{Virus Res}},
    title = {Genetic lineage characterization and spatiotemporal dynamics of classical insect-specific flaviviruses: outcomes and limitations},
    year = {2021},
    pages = {198507},
    volume = {303},
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    @Article{Vries:21b,
    author = {Jutte J.C. de Vries and Julianne R. Brown and Nicole Fischer and Igor A. Sidorov and Sofia Morfopoulou and Jiabin Huang and Bas B. Oude Munnink and Arzu Sayiner and Alihan Bulgurcu and Christophe Rodriguez and Guillaume Gricourt and Els Keyaerts and Leen Beller and Claudia Bachofen and Jakub Kubacki and Cordey Samuel and Laubscher Florian and Schmitz Dennis and Martin Beer and Dirk Hoeper and Michael Huber and Verena Kufner and Maryam Zaheri and Aitana Lebrand and Anna Papa and Sander van Boheemen and Aloys C.M. Kroes and Judith Breuer and F. Xavier Lopez-Labrador and Eric C.J. Claas},
    journal = {{J Clin Virol}},
    title = {Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples},
    year = {2021},
    pages = {104908},
    volume = {141},
    doi = {10.1016/j.jcv.2021.104908},
    publisher = {Elsevier {BV}},
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    [Bibtex]
    @Article{Conforti:21,
    author = {Antonella Conforti and Emanuele Marra and Fabio Palombo and Giuseppe Roscilli and Micol Rav{\`{a}} and Valeria Fumagalli and Alessia Muzi and Mariano Maffei and Laura Luberto and Lucia Lione and Erika Salvatori and Mirco Compagnone and Eleonora Pinto and Emiliano Pavoni and Federica Bucci and Grazia Vitagliano and Daniela Stoppoloni and Maria Lucrezia Pacello and Manuela Cappelletti and Fabiana Fosca Ferrara and Emanuela D'Acunto and Valerio Chiarini and Roberto Arriga and Abraham Nyska and Pietro Di Lucia and Davide Marotta and Elisa Bono and Leonardo Giustini and Eleonora Sala and Chiara Perucchini and Jemma Paterson and Kathryn Ann Ryan and Amy-Rose Challis and Giulia Matusali and Francesca Colavita and Gianfranco Caselli and Elena Criscuolo and Nicola Clementi and Nicasio Mancini and Rüdiger Gro{\ss} and Alina Seidel and Lukas Wettstein and Jan Münch and Lorena Donnici and Matteo Conti and Raffaele De Francesco and Mirela Kuka and Gennaro Ciliberto and Concetta Castilletti and Maria Rosaria Capobianchi and Giuseppe Ippolito and Luca G. Guidotti and Lucio Rovati and Matteo Iannacone and Luigi Aurisicchio},
    journal = {{bioRxiv}},
    title = {{COVID}-{eVax}, an electroporated plasmid {DNA} vaccine candidate encoding the {SARS}-{CoV}-2 Receptor Binding Domain, elicits protective immune responses in animal models of {COVID}-19},
    year = {2021},
    doi = {10.1101/2021.06.14.448343},
    publisher = {Cold Spring Harbor Laboratory},
    }
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    [Bibtex]
    @Article{Althaus:21,
    author = {Christian L. Althaus and Stephanie Baggio and Martina L. Reichmuth and Emma B. Hodcroft and Julien Riou and Richard A. Neher and Fr{\'{e}}d{\'{e}}rique Jacquerioz and Herv{\'{e}} Spechbach and Julien Salamun and Pauline Vetter and Carolyn Williamson and Nei-yuan Hsiao and Wolfgang Preiser and Mary-Ann Davies and Richard J. Lessells and Tulio de Olivera and Laurent Kaiser and Isabella Eckerle},
    journal = {{medRxiv}},
    title = {A tale of two variants: Spread of {SARS}-{CoV}-2 variants {A}lpha in {G}eneva, {S}witzerland, and {B}eta in {S}outh {A}frica},
    year = {2021},
    doi = {10.1101/2021.06.10.21258468},
    publisher = {Cold Spring Harbor Laboratory},
    }
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    [Bibtex]
    @Article{Demina:21,
    author = {Tatiana A. Demina and Anne-Mari Luhtanen and Simon Roux and Hanna M. Oksanen},
    journal = {{bioRxiv}},
    title = {Characteristics of genetically diverse {A}ntarctic sea ice bacteriophages allow adaptation to changing environmental conditions},
    year = {2021},
    doi = {10.1101/2021.05.28.446129},
    publisher = {Cold Spring Harbor Laboratory},
    }
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    @Article{Gulyaeva:21,
    author = {Anastasia Gulyaeva and Sanzhima Garmaeva and Renate A.A.A. Ruigrok and Daoming Wang and Niels P. Riksen and Mihai G. Netea and Cisca Wijmenga and Rinse K. Weersma and Jingyuan Fu and Arnau Vich Vila and Alexander Kurilshikov and Alexandra Zhernakova},
    journal = {{bioRxiv}},
    title = {Discovery, diversity and functional associations of {crAss}-like phages in human gut metagenomes from four {D}utch cohorts},
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    [Bibtex]
    @Article{McNaughton:21a,
    author = {Anna L. McNaughton and Robert S. Paton and Matthew Edmans and Jonathan Youngs and Judith Wellens and Prabhjeet Phalora and Alex Fyfe and Sandra Belij-rammerstorfer and Jai S. Bolton and Jonathan Ball and George Carnell and Wanwisa Dejnirattisai and Christina Dold and David W. Eyre and Philip Hopkins and Alison Howarth and Kreepa Kooblall and Hannah Klim and Susannah Leaver and Lian Lee and Cesar Lopez-Camacho and Sheila Lumley and Derek Macallan and Alexander J. Mentzer and Nicholas Provine and Jeremy Ratcliff and Jose Slon-Campos and Donal Skelly and Lucas Stolle and Piyada Supasa and Nigel Temperton and Chris Walker and Beibei Wang and Duncan Wyncoll and OPTIC consortium and SNBTS consortium and Peter Simmonds and Teresa Lambe and J. Kenneth Baillie and Malcolm Semple and Peter Openshaw and Uri Obolski and Marc Turner and Miles W. Carroll and Juthathip Mongkolspaya and Gavin R. Screaton and Stephen H. Kennedy and Lisa Jarvis and Eleanor Barnes and Susanna Dunachie and Jos{\'{e}} Louren{\c{c}}o and Philippa Matthews and Tihana Bicanic and Paul Klenerman and Sunetra Gupta and Craig P. Thompson},
    journal = {{SSRN}},
    title = {Fatal {COVID}-19 Outcomes are Associated with an Antibody Response Targeting Epitopes Shared with Endemic Coronaviruses},
    year = {2021},
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    publisher = {Elsevier {BV}},
    }
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    [Bibtex]
    @Article{Jackson:21,
    author = {Ben Jackson and Maciej F Boni and Matthew J Bull and Amy Colleran and Rachel M Colquhoun and Alistair Darby and Sam Haldenby and Verity Hill and Anita Lucaci and John T McCrone and Samuel Nicholls and {\'{A}}ine O'Toole and Nicole Pacchiarini and Radoslaw Poplawski and Emily Scher and Flora Todd and Hermione Webster and Mark Whitehead and Claudia Wierzbicki and Nicholas J Loman and Thomas R Connor and David L Robertson and Oliver G Pybus and Andrew Rambaut and},
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    title = {Generation and transmission of inter-lineage recombinants in the {SARS}-{CoV}-2 pandemic},
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    [Bibtex]
    @Article{Maher:21,
    author = {M. Cyrus Maher and Istvan Bartha and Steven Weaver and Julia di Iulio and Elena Ferri and Leah Soriaga and Florian A. Lempp and Brian L. Hie and Bryan Bryson and Bonnie Berger and David L. Robertson and Gyorgy Snell and Davide Corti and Herbert W. Virgin and Sergei L. Kosakovsky Pond and Amalio Telenti},
    journal = {{medRxiv}},
    title = {Predicting the mutational drivers of future {SARS}-{CoV}-2 variants of concern},
    year = {2021},
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    @Article{Ankerhold:21,
    author = {Jakob Ankerhold and Sebastian Giese and Philipp Kolb and Andrea Maul-Pavicic and Nathalie Goeppert and Kevin Ciminski and Clemens Kreutz and Achim Lother and Ulrich Salzer and Wolfgang Bildl and Tim Welsink and Nils Morgenthaler and Andrea Busse Grawitz and Daniela Huzly and Martin Schwemmle and Hartmut Hengel and Valeria Falcone},
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    year = {2021},
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    [Bibtex]
    @Article{Ferron:21,
    author = {Fran{\c{c}}ois Ferron and Bhawna Sama and Etienne Decroly and Bruno Canard},
    journal = {{Trends Biochem Sci}},
    title = {The enzymes for genome size increase and maintenance of large (+){RNA} viruses},
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    @Article{Burgess:21,
    author = {Hannah M. Burgess and Daniel P. Depledge and Letitia Thompson and Kalanghad Puthankalam Srinivas and Rebecca C. Grande and Elizabeth I. Vink and Jonathan S. Abebe and Wesley P. Blackaby and Alan Hendrick and Mark R. Albertella and Tony Kouzarides and Kenneth A. Stapleford and Angus C. Wilson and Ian Mohr},
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    @Article{Meng:21,
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Fairley and Matthew W. Loose and Joanne Watkins and Rich Livett and Samuel Moses and Roberto Amato and Sam Nicholls and Matthew Bull and Darren L. Smith and Jeff Barrett and David M. Aanensen and Martin D. Curran and Surendra Parmar and Dinesh Aggarwal and James G. Shepherd and Matthew D. Parker and Sharon Glaysher and Matthew Bashton and Anthony P. Underwood and Nicole Pacchiarini and Katie F. Loveson and Kate E. Templeton and Cordelia F. Langford and John Sillitoe and Thushan I. de Silva and Dennis Wang and Dominic Kwiatkowski and Andrew Rambaut and Justin O'Grady and Simon Cottrell and Matthew T.G. Holden and Emma C. Thomson and Husam Osman and Monique Andersson and Anoop J. Chauhan and Mohammed O. Hassan-Ibrahim and Mara Lawniczak and Alex Alderton and Meera Chand and Chrystala Constantinidou and Meera Unnikrishnan and Alistair C. Darby and Julian A. Hiscox and Steve Paterson and Inigo Martincorena and Erik M. Volz and Andrew J. Page and Oliver G. Pybus and Andrew R. Bassett and Cristina V. Ariani and Michael H. Spencer Chapman and Kathy K. Li and Rajiv N. Shah and Natasha G. Jesudason and Yusri Taha and Martin P. McHugh and Rebecca Dewar and Aminu S. Jahun and Claire McMurray and Sarojini Pandey and James P. McKenna and Andrew Nelson and Gregory R. Young and Clare M. McCann and Scott Elliott and Hannah Lowe and Ben Temperton and Sunando Roy and Anna Price and Sara Rey and Matthew Wyles and Stefan Rooke and Sharif Shaaban and Mariateresa de Cesare and Laura Letchford and Siona Silveira and Emanuela Pelosi and Eleri Wilson-Davies and Myra Hosmillo and {\'{A}}ine O'Toole and Andrew R. Hesketh and Richard Stark and Louis du Plessis and Chris Ruis and Helen Adams and Yann Bourgeois and Stephen L. Michell and Dimitris Gramatopoulos and Jonathan Edgeworth and Judith Breuer and John A. Todd and Christophe Fraser and David Buck and Michaela John and Gemma L. Kay and Steve Palmer and Sharon J. Peacock and David Heyburn and Danni Weldon and Esther Robinson and Alan McNally and Peter Muir and Ian B. Vipond and John Boyes and Venkat Sivaprakasam and Tranprit Salluja and Samir Dervisevic and Emma J. Meader and Naomi R. Park and Karen Oliver and Aaron R. Jeffries and Sascha Ott and Ana da Silva Filipe and David A. Simpson and Chris Williams and Jane A.H. Masoli and Bridget A. Knight and Christopher R. Jones and Cherian Koshy and Amy Ash and Anna Casey and Andrew Bosworth and Liz Ratcliffe and Li Xu-McCrae and Hannah M. Pymont and Stephanie Hutchings and Lisa Berry and Katie Jones and Fenella Halstead and Thomas Davis and Christopher Holmes and Miren Iturriza-Gomara and Anita O. Lucaci and Paul Anthony Randell and Alison Cox and Pinglawathee Madona and Kathryn Ann Harris and Julianne Rose Brown and Tabitha W. Mahungu and Dianne Irish-Tavares and Tanzina Haque and Jennifer Hart and Eric Witele and Melisa Louise Fenton and Steven Liggett and Clive Graham and Emma Swindells and Jennifer Collins and Gary Eltringham and Sharon Campbell and Patrick C. McClure and Gemma Clark and Tim J. Sloan and Carl Jones and Jessica Lynch and Ben Warne and Steven Leonard and Jillian Durham and Thomas Williams and Sam T. Haldenby and Nathaniel Storey and Nabil-Fareed Alikhan and Nadine Holmes and Christopher Moore and Matthew Carlile and Malorie Perry and Noel Craine and Ronan A. Lyons and Angela H. Beckett and Salman Goudarzi and Christopher Fearn and Kate Cook and Hannah Dent and Hannah Paul and Robert Davies and Beth Blane and Sophia T. Girgis and Mathew A. Beale and Katherine L. Bellis and Matthew J. Dorman and Eleanor Drury and Leanne Kane and Sally Kay and Samantha McGuigan and Rachel Nelson and Liam Prestwood and Shavanthi Rajatileka and Rahul Batra and Rachel J. Williams and Mark Kristiansen and Angie Green and Anita Justice and Adhyana I.K. Mahanama and Buddhini Samaraweera and Nazreen F. Hadjirin and Joshua Quick and Radoslaw Poplawski and Leanne M. Kermack and Nicola Reynolds and Grant Hall and Yasmin Chaudhry and Malte L. Pinckert and Iliana Georgana and Robin J. Moll and Alicia Thornton and Richard Myers and Joanne Stockton and Charlotte A. Williams and Wen C. Yew and Alexander J. Trotter and Amy Trebes and George MacIntyre-Cockett and Alec Birchley and Alexander Adams and Amy Plimmer and Bree Gatica-Wilcox and Caoimhe McKerr and Ember Hilvers and Hannah Jones and Hibo Asad and Jason Coombes and Johnathan M. Evans and Laia Fina and Lauren Gilbert and Lee Graham and Michelle Cronin and Sara Kumziene-Summerhayes and Sarah Taylor and Sophie Jones and Danielle C. Groves and Peijun Zhang and Marta Gallis and Stavroula F. Louka and Igor Starinskij and Chris Jackson and Marina Gourtovaia and Gerry Tonkin-Hill and Kevin Lewis and Jaime M. Tovar-Corona and Keith James and Laura Baxter and Mohammad T. Alam and Richard J. Orton and Joseph Hughes and Sreenu Vattipally and Manon Ragonnet-Cronin and Fabricia F. Nascimento and David Jorgensen and Olivia Boyd and Lily Geidelberg and Alex E. Zarebski and Jayna Raghwani and Moritz U.G. Kraemer and Joel Southgate and Benjamin B. Lindsey and Timothy M. Freeman and Jon-Paul Keatley and Joshua B. Singer and Leonardo de Oliveira Martins and Corin A. Yeats and Khalil Abudahab and Ben E.W. Taylor and Mirko Menegazzo and John Danesh and Wendy Hogsden and Sahar Eldirdiri and Anita Kenyon and Jenifer Mason and Trevor I. Robinson and Alison Holmes and James Price and John A. Hartley and Tanya Curran and Alison E. Mather and Giri Shankar and Rachel Jones and Robin Howe and Sian Morgan and Elizabeth Wastenge and Michael R. Chapman and Siddharth Mookerjee and Rachael Stanley and Wendy Smith and Timothy Peto and David Eyre and Derrick Crook and Gabrielle Vernet and Christine Kitchen and Huw Gulliver and Ian Merrick and Martyn Guest and Robert Munn and Declan T. Bradley and Tim Wyatt and Charlotte Beaver and Luke Foulser and Sophie Palmer and Carol M. Churcher and Ellena Brooks and Kim S. Smith and Katerina Galai and Georgina M. McManus and Frances Bolt and Francesc Coll and Lizzie Meadows and Stephen W. Attwood and Alisha Davies and Elen De Lacy and Fatima Downing and Sue Edwards and Garry P. Scarlett and Sarah Jeremiah and Nikki Smith and Danielle Leek and Sushmita Sridhar and Sally Forrest and Claire Cormie and Harmeet K. Gill and Joana Dias and Ellen E. Higginson and Mailis Maes and Jamie Young and Michelle Wantoch and Dorota Jamrozy and Stephanie Lo and Minal Patel and Verity Hill and Claire M. Bewshea and Sian Ellard and Cressida Auckland and Ian Harrison and Chloe Bishop and Vicki Chalker and Alex Richter and Andrew Beggs and Angus Best and Benita Percival and Jeremy Mirza and Oliver Megram and Megan Mayhew and Liam Crawford and Fiona Ashcroft and Emma Moles-Garcia and Nicola Cumley and Richard Hopes and Patawee Asamaphan and Marc O. Niebel and Rory N. Gunson and Amanda Bradley and Alasdair Maclean and Guy Mollett and Rachel Blacow and Paul Bird and Thomas Helmer and Karlie Fallon and Julian Tang and Antony D. Hale and Louissa R. Macfarlane-Smith and Katherine L. Harper and Holli Carden and Nicholas W. Machin and Kathryn A. Jackson and Shazaad S.Y. Ahmad and Ryan P. George and Lance Turtle and Elaine O'Toole and Joanne Watts and Cassie Breen and Angela Cowell and Adela Alcolea-Medina and Themoula Charalampous and Amita Patel and Lisa J. Levett and Judith Heaney and Aileen Rowan and Graham P. Taylor and Divya Shah and Laura Atkinson and Jack C.D. Lee and Adam P. Westhorpe and Riaz Jannoo and Helen L. Lowe and Angeliki Karamani and Leah Ensell and Wendy Chatterton and Monika Pusok and Ashok Dadrah and Amanda Symmonds and Graciela Sluga and Zoltan Molnar and Paul Baker and Stephen Bonner and Sarah Essex and Edward Barton and Debra Padgett and Garren Scott and Jane Greenaway and Brendan A.I. Payne and Shirelle Burton-Fanning and Sheila Waugh and Veena Raviprakash and Nicola Sheriff and Victoria Blakey and Lesley-Anne Williams and Jonathan Moore and Susanne Stonehouse and Louise Smith and Rose K. Davidson and Luke Bedford and Lindsay Coupland and Victoria Wright and Joseph G. Chappell and Theocharis Tsoleridis and Jonathan Ball 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 Nichola Duckworth and Sarah Walsh and Emma Wise and Nathan Moore and Matilde Mori and Nick Cortes and Stephen Kidd and Rebecca Williams and Laura Gifford and Kelly Bicknell and Sarah Wyllie and Allyson Lloyd and Robert Impey and Cassandra S. Malone and Benjamin J. Cogger and Nick Levene and Lynn Monaghan and Alexander J. Keeley and David G. Partridge and Mohammad Raza and Cariad Evans and Kate Johnson and Emma Betteridge and Ben W. Farr and Scott Goodwin and Michael A. Quail and Carol Scott and Lesley Shirley and Scott A.J. Thurston and Diana Rajan and Iraad F. Bronner and Louise Aigrain and Nicholas M. Redshaw and Stefanie V. Lensing and Shane McCarthy and Alex Makunin and Carlos E. Balcazar and Michael D. Gallagher and Kathleen A. Williamson and Thomas D. Stanton 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 Angie Lackenby and Tamyo Mbisa and Steven Platt and Shahjahan Miah and David Bibby and Carmen Manso and Jonathan Hubb and Gavin Dabrera and Mary Ramsay and Daniel Bradshaw and Ulf Schaefer and Natalie Groves and Eileen Gallagher and David Lee and David Williams and Nicholas Ellaby and Hassan Hartman and Nikos Manesis and Vineet Patel and Juan Ledesma and Katherine A. Twohig and Elias Allara and Clare Pearson and Jeffrey K.J. Cheng and Hannah E. Bridgewater and Lucy R. Frost and Grace Taylor-Joyce and Paul E. Brown and Lily Tong and Alice Broos and Daniel Mair and Jenna Nichols and Stephen N. Carmichael and Katherine L. Smollett and Kyriaki Nomikou and Elihu Aranday-Cortes and Natasha Johnson and Seema Nickbakhsh and Edith E. Vamos and Margaret Hughes and Lucille Rainbow and Richard Eccles and Charlotte Nelson and Mark Whitehead and Richard Gregory and Matthew Gemmell and Claudia Wierzbicki and Hermione J. Webster and Chloe L. Fisher and Adrian W. Signell and Gilberto Betancor and Harry D. Wilson and Gaia Nebbia and Flavia Flaviani and Alberto C. Cerda and Tammy V. Merrill and Rebekah E. Wilson and Marius Cotic and Nadua Bayzid and Thomas Thompson and Erwan Acheson and Steven Rushton and Sarah O'Brien and David J. Baker and Steven Rudder and Alp Aydin and Fei Sang and Johnny Debebe and Sarah Francois and Tetyana I. Vasylyeva and Marina Escalera Zamudio and Bernardo Gutierrez and Angela Marchbank and Joshua Maksimovic and Karla Spellman and Kathryn McCluggage and Mari Morgan and Robert Beer and Safiah Afifi and Trudy Workman and William Fuller and Catherine Bresner and Adrienn Angyal and Luke R. Green and Paul J. Parsons and Rachel M. Tucker and Rebecca Brown and Max Whiteley and James Bonfield and Christoph Puethe and Andrew Whitwham and Jennifier Liddle and Will Rowe and Igor Siveroni and Thanh Le-Viet and Amy Gaskin and Rob Johnson and Irina Abnizova and Mozam Ali and Laura Allen and Ralph Anderson and Cristina Ariani and Siobhan Austin-Guest and Sendu Bala and Jeffrey Barrett and Andrew Bassett and Kristina Battleday and James Beal and Mathew Beale and Sam Bellany and Tristram Bellerby and Katie Bellis and Duncan Berger and Matt Berriman and Paul Bevan and Simon Binley and Jason Bishop and Kirsty Blackburn and Nick Boughton and Sam Bowker and Timothy Brendler-Spaeth and Iraad Bronner and Tanya Brooklyn and Sarah Kay Buddenborg and Robert Bush and Catarina Caetano and Alex Cagan and Nicola Carter and Joanna Cartwright and Tiago Carvalho Monteiro and Liz Chapman and Tracey-Jane Chillingworth and Peter Clapham and Richard Clark and Adrian Clarke and Catriona Clarke and Daryl Cole and Elizabeth Cook and Maria Coppola and Linda Cornell and Clare Cornwell and Craig Corton and Abby Crackett and Alison Cranage and Harriet Craven and Sarah Craw and Mark Crawford and Tim Cutts and Monika Dabrowska and Matt Davies and Joseph Dawson and Callum Day and Aiden Densem and Thomas Dibling and Cat Dockree and David Dodd and Sunil Dogga and Matthew Dorman and Gordon Dougan and Martin Dougherty and Alexander Dove and Lucy Drummond and Monika Dudek and Laura Durrant and Elizabeth Easthope and Sabine Eckert and Pete Ellis and Ben Farr and Michael Fenton and Marcella Ferrero and Neil Flack and Howerd Fordham and Grace Forsythe and Matt Francis and Audrey Fraser and Adam Freeman and Anastasia Galvin and Maria Garcia-Casado and Alex Gedny and Sophia Girgis and James Glover and Oliver Gould and Andy Gray and Emma Gray and Coline Griffiths and Yong Gu and Florence Guerin and Will Hamilton and Hannah Hanks and Ewan Harrison and Alexandria Harrott and Edward Harry and Julia Harvison and Paul Heath and Anastasia Hernandez-Koutoucheva and Rhiannon Hobbs and Dave Holland and Sarah Holmes and Gary Hornett and Nicholas Hough and Liz Huckle and Lena Hughes-Hallet and Adam Hunter and Stephen Inglis and Sameena Iqbal and Adam Jackson and David Jackson and Carlos Jimenez Verdejo and Matthew Jones and Kalyan Kallepally and Keely Kay and Jon Keatley and Alan Keith and Alison King and Lucy Kitchin and Matt Kleanthous and Martina Klimekova and Petra Korlevic and Ksenia Krasheninnkova and Greg Lane and Cordelia Langford and Adam Laverack and Katharine Law and Stefanie Lensing and Amanah Lewis-Wade and Jennifer Liddle and Quan Lin and Sarah Lindsay and Sally Linsdell and Rhona Long and Jamie Lovell and Jon Lovell and James Mack and Mark Maddison and Aleksei Makunin and Irfan Mamun and Jenny Mansfield and Neil Marriott and Matt Martin and Matthew Mayho and Jo McClintock and Sandra McHugh and Liz MapcMinn and Carl Meadows and Emily Mobley and Robin Moll and Maria Morra and Leanne Morrow and Kathryn Murie and Sian Nash and Claire Nathwani and Plamena Naydenova and Alexandra Neaverson and Ed Nerou and Jon Nicholson and Tabea Nimz and Guillaume G. Noell and Sarah O'Meara and Valeriu Ohan and Charles Olney and Doug Ormond and Agnes Oszlanczi and Yoke Fei Pang and Barbora Pardubska and Naomi Park and Aaron Parmar and Gaurang Patel and Maggie Payne and Sharon Peacock and Arabella Petersen and Deborah Plowman and Tom Preston and Michael Quail and Richard Rance and Suzannah Rawlings and Nicholas Redshaw and Joe Reynolds and Mark Reynolds and Simon Rice and Matt Richardson and Connor Roberts and Katrina Robinson and Melanie Robinson and David Robinson and Hazel Rogers and Eduardo Martin Rojo and Daljit Roopra and Mark Rose and Luke Rudd and Ramin Sadri and Nicholas Salmon and David Saul and Frank Schwach and Phil Seekings and Alison Simms and Matt Sinnott and Shanthi Sivadasan and Bart Siwek and Dale Sizer and Kenneth Skeldon and Jason Skelton and Joanna Slater-Tunstill and Lisa Sloper and Nathalie Smerdon and Chris Smith and Christen Smith and James Smith and Katie Smith and Michelle Smith and Sean Smith and Tina Smith and Leighton Sneade and Carmen Diaz Soria and Catarina Sousa and Emily Souster and Andrew Sparkes and Michael Spencer-Chapman and Janet Squares and Robert Stanley and Claire Steed and Tim Stickland and Ian Still and Mike Stratton and Michelle Strickland and Allen Swann and Agnieszka Swiatkowska and Neil Sycamore and Emma Swift and Edward Symons and Suzanne Szluha and Emma Taluy and Nunu Tao and Katy Taylor and Sam Taylor and Stacey Thompson and Mark Thompson and Mark Thomson and Nicholas Thomson and Scott Thurston and Dee Toombs and Benjamin Topping and Jaime Tovar-Corona and Daniel Ungureanu and James Uphill and Jana Urbanova and Philip Jansen Van and Valerie Vancollie and Paul Voak and Danielle Walker and Matthew Walker and Matt Waller and Gary Ward and Charlie Weatherhogg and Niki Webb and Alan Wells and Eloise Wells and Luke Westwood and Theo Whipp and Thomas Whiteley and Georgia Whitton and Sara Widaa and Mia Williams and Mark Wilson and Sean Wright},
    journal = {{Cell Rep}},
    title = {Recurrent emergence of {SARS}-{CoV}-2 spike deletion {H69/V70} and its role in the {A}lpha variant {B.1.1.7}},
    year = {2021},
    pages = {109292},
    doi = {10.1016/j.celrep.2021.109292},
    publisher = {Elsevier {BV}},
    }
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    [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 = {{NatMicrobiol}},
    title = {Emergence and spread of a {SARS}-{CoV}-2 lineage {A} variant ({A}.23.1) with altered spike protein in {U}ganda},
    year = {2021},
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    publisher = {Springer Science and Business Media {LLC}},
    }
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    [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 Ivan Odak 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 Serra 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 = {{Proc Natl Acad.Sci}},
    title = {Immunogenicity and efficacy of the {COVID}-19 candidate vector vaccine {MVA}-{SARS}-2-S in preclinical vaccination},
    year = {2021},
    number = {28},
    pages = {e2026207118},
    volume = {118},
    doi = {10.1073/pnas.2026207118},
    publisher = {Proceedings of the National Academy of Sciences},
    }
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    [Bibtex]
    @Article{Gassen:21,
    author = {Nils C. Gassen and Jan Papies and Thomas Bajaj and Jackson Emanuel and Frederik Dethloff and Robert Lorenz Chua and Jakob Trimpert and Nicolas Heinemann and Christine Niemeyer and Friderike Weege and Katja Hönzke and Tom Aschman and Daniel E. Heinz and Katja Weckmann and Tim Ebert and Andreas Zellner and Martina Lennarz and Emanuel Wyler and Simon Schroeder and Anja Richter and Daniela Niemeyer and Karen Hoffmann and Thomas F. Meyer and Frank L. Heppner and Victor M. Corman and Markus Landthaler and Andreas C. Hocke and Markus Morkel and Nikolaus Osterrieder and Christian Conrad and Roland Eils and Helena Radbruch and Patrick Giavalisco and Christian Drosten and Marcel A. Müller},
    journal = {{Nat Commun}},
    title = {{SARS}-{CoV}-2-mediated dysregulation of metabolism and autophagy uncovers host-targeting antivirals},
    year = {2021},
    number = {1},
    volume = {12},
    doi = {10.1038/s41467-021-24007-w},
    publisher = {Springer Science and Business Media {LLC}},
    }
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    [Bibtex]
    @Article{Fuhrmann:21,
    author = {Lara Fuhrmann and Kim Philipp Jablonski and Niko Beerenwinkel},
    journal = {{Curr Opin Virol}},
    title = {Quantitative measures of within-host viral genetic diversity},
    year = {2021},
    pages = {157--163},
    volume = {49},
    doi = {10.1016/j.coviro.2021.06.002},
    publisher = {Elsevier {BV}},
    }
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    [Bibtex]
    @Article{Lindner:21,
    author = {Andreas K. Lindner and Olga Nikolai and Chiara Rohardt and Franka Kausch and Mia Wintel and Maximilian Gertler and Susen Burock and Merle Hörig and Julian Bernhard and Frank Tobian and Mary Gaeddert and Federica Lainati and Victor M. Corman and Terry C. Jones and Jilian A. Sacks and Joachim Seybold and Claudia M. Denkinger and Frank P. Mockenhaupt},
    journal = {{J Clin Virol}},
    title = {Diagnostic accuracy and feasibility of patient self-testing with a {SARS}-{CoV}-2 antigen-detecting rapid test},
    year = {2021},
    pages = {104874},
    volume = {141},
    doi = {10.1016/j.jcv.2021.104874},
    publisher = {Elsevier {BV}},
    }
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    [Bibtex]
    @Article{EchavarriaConsuegra:21,
    author = {Liliana Echavarr{\'{\i}}a-Consuegra and Georgia M. Cook and Idoia Busnadiego and Charlotte Lef{\`{e}}vre and Sarah Keep and Katherine Brown and Nicole Doyle and Giulia Dowgier and Krzysztof Franaszek and Nathan A. Moore and Stuart G. Siddell and Erica Bickerton and Benjamin G. Hale and Andrew E. Firth and Ian Brierley and Nerea Irigoyen},
    journal = {{PLoS Pathog}},
    title = {Manipulation of the unfolded protein response: A pharmacological strategy against coronavirus infection},
    year = {2021},
    number = {6},
    pages = {e1009644},
    volume = {17},
    doi = {10.1371/journal.ppat.1009644},
    editor = {Benhur Lee},
    publisher = {Public Library of Science ({PLoS})},
    }
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    @Article{Pantazis:21,
    author = {Nikos Pantazis and Magdalena Rosinska and Ard VAN Sighem and Chantal Quinten and Teymur Noori and Fiona Burns and Helena Cortes Martins and Peter D Kirwan and Kate O'donnell and Dimitrios Paraskevis and C{\'{e}}cile Sommen and Dominik Zenner and Anastasia Pharris},
    journal = {{J Acquir Immune Defic Syndr}},
    title = {Discriminating between pre-migration and post-migration {HIV} acquisition using surveillance data},
    year = {2021},
    volume = {Publish Ahead of Print},
    doi = {10.1097/qai.0000000000002745},
    publisher = {Ovid Technologies (Wolters Kluwer Health)},
    }
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    [Bibtex]
    @Article{Zayed:21,
    author = {Ahmed A Zayed and Dominik Lücking and Mohamed Mohssen and Dylan Cronin and Ben Bolduc and Ann C Gregory and Katherine R Hargreaves and Paul D Piehowski and Richard A White and Eric L Huang and Joshua N Adkins and Simon Roux and Cristina Moraru and Matthew B Sullivan},
    journal = {Bioinformatics},
    title = {{efam}: an expanded, metaproteome-supported {HMM} profile database of viral protein families},
    year = {2021},
    doi = {10.1093/bioinformatics/btab451},
    editor = {Peter Robinson},
    publisher = {Oxford University Press ({OUP})},
    }
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    [Bibtex]
    @Article{Bi:21,
    author = {Qifang Bi and Justin Lessler and Isabella Eckerle and Stephen A. Lauer and Laurent Kaiser and Nicolas Vuilleumier and Derek A. T. Cummings and Antoine Flahault and Dusan Petrovic and Idris Guessous and Silvia Stringhini and Andrew S. Azman and Silvia Stringhini and Idris Guessous and H{\'{e}}l{\`{e}}ne Baysson and Prune Collombet and David De Ridder and Paola d'Ippolito and Matilde D'asaro-Aglieri Rinella and Yaron Dibner and Nacira El Merjani and Natalie Francioli and Marion Frangville and Kailing Marcus and Chantal Martinez and Natacha Noel and Francesco Pennacchio and Javier Perez-Saez and Dusan Petrovic and Attilio Picazio and Alborz Pishkenari and Giovanni Piumatti and Jane Portier and Caroline Pugin and Barinjaka Rakotomiaramanana and Aude Richard and Lilas Salzmann-Bellard and Stephanie Schrempft and Maria-Eugenia Zaballa and Zo{\'{e}} Waldmann and Ania Wisniak and Alioucha Davidovic and Jos{\'{e}}phine Duc and Julie Gu{\'{e}}rin and Fanny Lombard and Manon Will and Antoine Flahault and Isabelle Arm Vernez and Olivia Keiser and Loan Mattera and Magdalena Schellongova and Laurent Kaiser and Isabella Eckerle and Pierre Lescuyer and Benjamin Meyer and G{\'{e}}raldine Poulain and Nicolas Vuilleumier and Sabine Yerly and Fran{\c{c}}ois Chappuis and Sylvie Welker and Delphine Courvoisier and Laurent G{\'{e}}taz and Mayssam Nehme and Febronio Pardo and Guillemette Violot and Samia Hurst and Philippe Matute and Jean-Michel Maugey and Didier Pittet and Arnaud G. L'Huillier and Klara M. Posfay-Barbe and Jean-Fran{\c{c}}ois Pradeau and Michel Tacchino and Didier Trono and},
    journal = {{Nat Commun}},
    title = {Insights into household transmission of {SARS}-{CoV}-2 from a population-based serological survey},
    year = {2021},
    number = {1},
    volume = {12},
    doi = {10.1038/s41467-021-23733-5},
    publisher = {Springer Science and Business Media {LLC}},
    }
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    [Bibtex]
    @Article{Coclet:21,
    author = {Cl{\'{e}}ment Coclet and Simon Roux},
    journal = {{Curr Opin Virol}},
    title = {Global overview and major challenges of host prediction methods for uncultivated phages},
    year = {2021},
    pages = {117--126},
    volume = {49},
    doi = {10.1016/j.coviro.2021.05.003},
    publisher = {Elsevier {BV}},
    }
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    [Bibtex]
    @Article{Onisiforou:21,
    author = {Anna Onisiforou and George M Spyrou},
    journal = {{Brief Bioinform}},
    title = {Identification of viral-mediated pathogenic mechanisms in neurodegenerative diseases using network-based approaches},
    year = {2021},
    doi = {10.1093/bib/bbab141},
    publisher = {Oxford University Press ({OUP})},
    }
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    @Article{Tomazou:21,
    author = {Marios Tomazou and Marilena M Bourdakou and George Minadakis and Margarita Zachariou and Anastasis Oulas and Evangelos Karatzas and Eleni M Loizidou and Andrea C Kakouri and Christiana C Christodoulou and Kyriaki Savva and Maria Zanti and Anna Onisiforou and Sotiroula Afxenti and Jan Richter and Christina G Christodoulou and Theodoros Kyprianou and George Kolios and Nikolas Dietis and George M Spyrou},
    journal = {{Brief Bioinform}},
    title = {Multi-omics data integration and network-based analysis drives a multiplex drug repurposing approach to a shortlist of candidate drugs against {COVID}-19},
    year = {2021},
    doi = {10.1093/bib/bbab114},
    publisher = {Oxford University Press ({OUP})},
    }
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    [Bibtex]
    @Article{Ratcliff:21a,
    author = {Jeremy Ratcliff and Dung Nguyen and Matthew Fish and Jennifer Rynne 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 A Ciccone and Ullrich Leuscher and Wendy Slack and Emma Laing and Paul R Mouncey and Sheba Ziyenge and Marta Oliveira 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 = {{J Infect Dis}},
    title = {Virological and serological characterization of critically ill patients with {COVID}-19 in the {UK}: Interactions of viral load, antibody status and {B.1.1.7} variant infection},
    year = {2021},
    doi = {10.1093/infdis/jiab283},
    publisher = {Oxford University Press ({OUP})},
    }
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    [Bibtex]
    @Article{Gifford:21,
    author = {Robert J. Gifford},
    journal = {{Proc Natl Acad Sci}},
    title = {Mapping the evolution of bornaviruses across geological timescales},
    year = {2021},
    number = {26},
    pages = {e2108123118},
    volume = {118},
    doi = {10.1073/pnas.2108123118},
    publisher = {Proceedings of the National Academy of Sciences},
    }
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    [Bibtex]
    @Article{SternGinossar:21,
    author = {Noam Stern-Ginossar and Thirumala-Devi Kanneganti and Craig E. Cameron and Zhiyong Lou and Sara Cherry and Jonathan Abraham and Laura Martin-Sancho},
    journal = {{Mol Cell}},
    title = {Rising to the challenge of {COVID}-19: Working on {SARS}-{CoV}-2 during the pandemic},
    year = {2021},
    number = {11},
    pages = {2261--2265},
    volume = {81},
    doi = {10.1016/j.molcel.2021.05.021},
    publisher = {Elsevier {BV}},
    }
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    @Article{Lo:21,
    author = {Ho Sing Lo and Kenrie Pui Yan Hui and Hei-Ming Lai and Xu He and Khadija Shahed Khan and Simranjeet Kaur and Junzhe Huang and Zhongqi Li and Anthony K. N. Chan and Hayley Hei-Yin Cheung and Ka-Chun Ng and John Chi Wang Ho and Yu Wai Chen and Bowen Ma and Peter Man-Hin Cheung and Donghyuk Shin and Kaidao Wang and Meng-Hsuan Lee and Barbara Selisko and Cecilia Eydoux and Jean-Claude Guillemot and Bruno Canard and Kuen-Phon Wu and Po-Huang Liang and Ivan Dikic and Zhong Zuo and Francis K. L. Chan and David S. C. Hui and Vincent C. T. Mok and Kam-Bo Wong and Chris Ka Pun Mok and Ho Ko and Wei Shen Aik and Michael Chi Wai Chan and Wai-Lung Ng},
    journal = {{ACS Cent Sci}},
    title = {{S}imeprevir Potently Suppresses {SARS}-{CoV}-2 Replication and Synergizes with {R}emdesivir},
    year = {2021},
    number = {5},
    pages = {792--802},
    volume = {7},
    doi = {10.1021/acscentsci.0c01186},
    publisher = {American Chemical Society ({ACS})},
    }
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    [Bibtex]
    @Article{Harvey:21,
    author = {William T. Harvey and and Alessandro M. Carabelli and Ben Jackson and Ravindra K. Gupta and Emma C. Thomson and Ewan M. Harrison and Catherine Ludden and Richard Reeve and Andrew Rambaut and Sharon J. Peacock and David L. Robertson},
    journal = {{Nat Rev Microbiol}},
    title = {{SARS}-{CoV}-2 variants, spike mutations and immune escape},
    year = {2021},
    doi = {10.1038/s41579-021-00573-0},
    publisher = {Springer Science and Business Media {LLC}},
    }
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    [Bibtex]
    @Article{Michelitsch:21,
    author = {Anna Michelitsch and Jacob Schön and Donata Hoffmann and Martin Beer and Kerstin Wernike},
    journal = {Viruses},
    title = {The Second Wave of {SARS}-{CoV}-2 Circulation{\textemdash}Antibody Detection in the Domestic Cat Population in {G}ermany},
    year = {2021},
    number = {6},
    pages = {1009},
    volume = {13},
    doi = {10.3390/v13061009},
    publisher = {{MDPI} {AG}},
    }
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    [Bibtex]
    @Article{Cadar:21,
    author = {D{\'{a}}niel Cadar and Jonas Schmidt-Chanasit and Dennis Tappe},
    journal = {Microorganisms},
    title = {Genomic and Micro-Evolutionary Features of Mammalian 2 orthobornavirus (Variegated Squirrel Bornavirus 1, {VSBV}-1)},
    year = {2021},
    number = {6},
    pages = {1141},
    volume = {9},
    doi = {10.3390/microorganisms9061141},
    publisher = {{MDPI} {AG}},
    }
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    [Bibtex]
    @Article{Doelken:21,
    author = {Lars Dölken and August Stich and Christoph D. Spinner},
    journal = {Viruses},
    title = {Remdesivir for Early {COVID}-19 Treatment of High-Risk Individuals Prior to or at Early Disease Onset{\textemdash}Lessons Learned},
    year = {2021},
    number = {6},
    pages = {963},
    volume = {13},
    doi = {10.3390/v13060963},
    publisher = {{MDPI} {AG}},
    }
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    [Bibtex]
    @Article{Simmonds:21,
    author = {Peter Simmonds and M. Azim Ansari},
    journal = {{PLoS Pathog}},
    title = {Extensive {C}->{U} transition biases in the genomes of a wide range of mammalian {RNA} viruses; potential associations with transcriptional mutations, damage- or host-mediated editing of viral {RNA}},
    year = {2021},
    number = {6},
    pages = {e1009596},
    volume = {17},
    doi = {10.1371/journal.ppat.1009596},
    editor = {Andreas Pichlmair},
    publisher = {Public Library of Science ({PLoS})},
    }
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    [Bibtex]
    @Article{Meisel:21,
    author = {Christian Meisel and Bengisu Akbil and Tim Meyer and Erwin Lankes and Victor M. Corman and Olga Staudacher and Nadine Unterwalder and Uwe Kölsch and Christian Drosten and Marcus A. Mall and Tilmann Kallinich and Dirk Schnabel and Christine Goffinet and Horst von Bernuth},
    journal = {Journal of Clinical Investigation},
    title = {Mild {COVID}-19 despite autoantibodies to type {I} {IFNs} in {Autoimmune-Polyendocrine-Syndrome} {T}ype 1 ({APS}-1)},
    year = {2021},
    doi = {10.1172/jci150867},
    publisher = {American Society for Clinical Investigation},
    }
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    @Article{Aschman:21,
    author = {Tom Aschman and Julia Schneider and Selina Greuel and Jenny Meinhardt and Simon Streit and Hans-Hilmar Goebel and Ivana Büttnerova and Sefer Elezkurtaj and Franziska Scheibe and Josefine Radke and Christian Meisel and Christian Drosten and Helena Radbruch and Frank L. Heppner and Victor Max Corman and Werner Stenzel},
    journal = {{JAMA Neurol}},
    title = {Association Between {SARS}-{CoV}-2 Infection and Immune-Mediated Myopathy in Patients Who Have Died},
    year = {2021},
    doi = {10.1001/jamaneurol.2021.2004},
    publisher = {American Medical Association ({AMA})},
    }
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    [Bibtex]
    @Article{Decroly:21,
    author = {Decroly, Etienne and Claverie, Jean-Michel and Canard, Bruno},
    journal = {{Virologie (Montrouge)}},
    title = {The {WHO} mission report struggles to trace the origins of the {SARS-CoV}-2 epidemic.},
    year = {2021},
    doi = {10.1684/vir.2021.0902},
    pmid = {34112630},
    pubstate = {aheadofprint},
    }
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    [Bibtex]
    @Article{Konings:21,
    author = {Frank Konings and Mark D. Perkins and Jens H. Kuhn and Mark J. Pallen and Erik J. Alm and Brett N. Archer and Amal Barakat and Trevor Bedford and Jinal N. Bhiman and Leon Caly and Lisa L. Carter and Anne Cullinane and Tulio de Oliveira and Julian Druce and Ihab El Masry and Roger Evans and George F. Gao and Alexander E. Gorbalenya and Esther Hamblion and Belinda L. Herring and Emma Hodcroft and Edward C. Holmes and Manish Kakkar and Shagun Khare and Marion P. G. Koopmans and Bette Korber and Juliana Leite and Duncan MacCannell and Marco Marklewitz and Sebastian Maurer-Stroh and Jairo Andres Mendez Rico and Vincent J. Munster and Richard A. Neher and Bas B. {Oude Munnink} and Boris I. Pavlin and Malik Peiris and Leo Poon and Oliver Pybus and Andrew Rambaut and Paola Resende and Lorenzo Subissi and Volker Thiel and Suxiang Tong and Sylvie van der Werf and Anne von Gottberg and John Ziebuhr and Maria D. Van Kerkhove},
    journal = {{Nat Microbiol}},
    title = {{SARS}-{CoV}-2 Variants of Interest and Concern naming scheme conducive for global discourse},
    year = {2021},
    doi = {10.1038/s41564-021-00932-w},
    publisher = {Springer Science and Business Media {LLC}},
    }
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    [Bibtex]
    @Article{Rafiee:21,
    author = {Mohammad Rafiee and Siavash Isazadeh and Anoushiravan Mohseni-Bandpei and Seyed Reza Mohebbi and Mahsa Jahangiri-rad and Akbar Eslami and Hossein Dabiri and Kasra Roostaei and Mohammad Tanhaei and Fatemeh Amereh},
    journal = {{Sci Total Environ}},
    title = {Moore swab performs equal to composite and outperforms grab sampling for {SARS}-{CoV}-2 monitoring in wastewater},
    year = {2021},
    pages = {148205},
    volume = {790},
    doi = {10.1016/j.scitotenv.2021.148205},
    publisher = {Elsevier {BV}},
    }
  • [DOI] T. Schwarz, P. Tober-Lau, D. Hillus, E. T. Helbig, L. J. Lippert, C. Thibeault, W. Koch, I. Landgraf, J. Michel, L. Bergfeld, D. Niemeyer, B. Mühlemann, C. Conrad, C. Dang-Heine, S. Kasper, F. Münn, K. Kappert, A. Nitsche, R. Tauber, S. Schmidt, P. Kopankiewicz, H. Bias, J. Seybold, C. von Kalle, T. C. Jones, N. Suttorp, C. Drosten, L. E. Sander, V. M. Corman, and F. Kurth, “Delayed antibody and T-cell response to BNT162b2 vaccination in the Elderly, Germany.,” Emerging infectious diseases, vol. 27, 2021.
    [Bibtex]
    @Article{Schwarz:21a,
    author = {Schwarz, Tatjana and Tober-Lau, Pinkus and Hillus, David and Helbig, Elisa T. and Lippert, Lena J. and Thibeault, Charlotte and Koch, Willi and Landgraf, Irmgard and Michel, Janine and Bergfeld, Leon and Niemeyer, Daniela and Mühlemann, Barbara and Conrad, Claudia and Dang-Heine, Chantip and Kasper, Stefanie and Münn, Friederike and Kappert, Kai and Nitsche, Andreas and Tauber, Rudolf and Schmidt, Sein and Kopankiewicz, Piotr and Bias, Harald and Seybold, Joachim and von Kalle, Christof and Jones, Terry C. and Suttorp, Norbert and Drosten, Christian and Sander, Leif Erik and Corman, Victor M. and Kurth, Florian},
    journal = {Emerging infectious diseases},
    title = {Delayed Antibody and {T}-Cell Response to {BNT162b2} Vaccination in the {E}lderly, {G}ermany.},
    year = {2021},
    volume = {27},
    abstract = {We detected delayed and reduced antibody and T-cell responses after BNT162b2 vaccination in 71 elderly persons (median age 81 years) compared with 123 healthcare workers (median age 34 years) in Germany. These data emphasize that nonpharmaceutical interventions for coronavirus disease remain crucial and that additional immunizations for the elderly might become necessary.},
    doi = {10.3201/eid2708.211145},
    issue = {8},
    keywords = {B cell; Berlin; COVID-19; Germany; SARS-CoV-2; T cell; antibody; coronavirus disease; immunity; mRNA; respiratory infections; severe acute respiratory syndrome coronavirus 2; vaccine; viruses; zoonoses},
    pmid = {34102097},
    pubstate = {aheadofprint},
    }
  • [DOI] E. B. Hodcroft, M. Zuber, S. Nadeau, T. G. Vaughan, K. H. D. Crawford, C. L. Althaus, M. L. Reichmuth, J. E. Bowen, A. C. Walls, D. Corti, J. D. Bloom, D. Veesler, D. Mateo, A. Hernando, I. Comas, F. G. Candelas, S. V. I. D. -S. P. A. I. N. consortium, T. Stadler, and R. A. Neher, “Spread of a SARS-CoV-2 variant through Europe in the summer of 2020.,” Nature, 2021.
    [Bibtex]
    @Article{Hodcroft:21a,
    author = {Hodcroft, Emma B. and Zuber, Moira and Nadeau, Sarah and Vaughan, Timothy G. and Crawford, Katharine H. D. and Althaus, Christian L. and Reichmuth, Martina L. and Bowen, John E. and Walls, Alexandra C. and Corti, Davide and Bloom, Jesse D. and Veesler, David and Mateo, David and Hernando, Alberto and Comas, Iñaki and Candelas, Fernando González and consortium, SeqCO. V. I. D.-S. P. A. I. N. and Stadler, Tanja and Neher, Richard A.},
    journal = {Nature},
    title = {Spread of a {SARS-CoV}-2 variant through {E}urope in the summer of 2020.},
    year = {2021},
    abstract = {Following its emergence in late 2019, the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been tracked via phylogenetic analysis of viral genome sequences in unprecedented detail . While the virus spread globally in early 2020 before borders closed, intercontinental travel has since been greatly reduced. However, within Europe travel resumed in the summer of 2020. Here we report on a novel SARS-CoV-2 variant, 20E (EU1), that emerged in Spain in early summer, and subsequently spread across Europe. We find no evidence of increased transmissibility, but instead demonstrate how rising incidence in Spain, resumption of travel, and lack of effective screening and containment may explain the variant's success. Despite travel restrictions, we estimate 20E (EU1) was introduced hundreds of times to European countries by summertime travelers, likely undermining local efforts to keep SARS-CoV-2 cases low. Our results demonstrate how a variant can rapidly become dominant even in absence of a substantial transmission advantage in favorable epidemiological settings. Genomic surveillance is critical to understanding how travel can impact SARS-CoV-2 transmission, and thus for informing future containment strategies as travel resumes.},
    doi = {10.1038/s41586-021-03677-y},
    investigator = {Comas, Iñaki and González-Candelas, Fernando and Goig, Galo Adrian and Chiner-Oms, Álvaro and Cancino-Muñoz, Irving and López, Mariana Gabriela and Torres-Puente, Manuela and Gomez-Navarro, Inmaculada and Jiménez-Serrano, Santiago and Ruiz-Roldán, Lidia and Bracho, María Alma and García-González, Neris and Martínez-Priego, Llúcia and Galán-Vendrell, Inmaculada and Ruiz-Hueso, Paula and Marco, Griselda De and Ferrús, Maria Loreto and Carbó-Ramírez, Sandra and D'Auria, Giuseppe and Coscollá, Mireia and Ruiz-Rodríguez, Paula and Roig-Sena, Francisco Javier and Sanmartín, Isabel and Garcia-Souto, Daniel and Pequeno-Valtierra, Ana and Tubio, Jose M C and Rodríguez-Castro, Jorge and Rabella, Nuria and Navarro, Ferrán and Miró, Elisenda and Rodríguez-Iglesias, Manuel and Galán-Sanchez, Fátima and Rodriguez-Pallares, Salud and de Toro, María and Escudero, María Bea and Azcona-Gutiérrez, José Manuel and Alberdi, Miriam Blasco and Mayor, Alfredo and García-Basteiro, Alberto L and Moncunill, Gemma and Dobaño, Carlota and Cisteró, Pau and García-de-Viedma, Darío and Pérez-Lago, Laura and Herranz, Marta and Sicilia, Jon and Catalán-Alonso, Pilar and Muñoz, Patricia and Muñoz-Cuevas, Cristina and Rodríguez-Rodríguez, Guadalupe and Alberola-Enguidanos, Juan and Nogueira, Jose Miguel and Camarena, Juan José and Rezusta, Antonio and Tristancho-Baró, Alexander and Milagro, Ana and Martínez-Cameo, Nieves Felisa and Gracia-Grataloup, Yolanda and Martró, Elisa and Bordoy, Antoni E and Not, Anna and Antuori-Torres, Adrián and Benito, Rafael and Algarate, Sonia and Bueno, Jessica and Del Pozo, Jose Luis and Boga, Jose Antonio and Castelló-Abietar, Cristián and Rojo-Alba, Susana and Alvarez-Argüelles, Marta Elena and Melon, Santiago and Aranzamendi-Zaldumbide, Maitane and Vergara-Gómez, Andrea and Fernández-Pinero, Jovita and Martínez, Miguel J and Vila, Jordi and Rubio, Elisa and Peiró-Mestres, Aida and Navero-Castillejos, Jessica and Posada, David and Valverde, Diana and Estévez-Gómez, Nuria and Fernandez-Silva, Iria and de Chiara, Loretta and Gallego-García, Pilar and Varela, Nair and Moreno, Rosario and Tirado, Maria Dolores and Gomez-Pinedo, Ulises and Gozalo-Margüello, Mónica and Eliecer-Cano, Maria and Méndez-Legaza, José Manuel and Rodríguez-Lozano, Jesus and Siller, María and Pablo-Marcos, Daniel and Oliver, Antonio and Reina, Jordi and López-Causapé, Carla and Canut-Blasco, Andrés and Hernáez-Crespo, Silvia and Cordón, Maria Luz A and Lecároz-Agara, María-Concepción and Gómez-González, Carmen and Aguirre-Quiñonero, Amaia and López-Mirones, José Israel and Fernández-Torres, Marina and Almela-Ferrer, Maria Rosario and Gonzalo-Jiménez, Nieves and Ruiz-García, Maria Montserrat and Galiana, Antonio and Sanchez-Almendro, Judith and Cilla, Gustavo and Montes, Milagrosa and Piñeiro, Luis and Sorarrain, Ane and Marimón, José María and Gomez-Ruiz, Maria Dolores and López-Hontangas, José Luis and González Barberá, Eva M and Navarro-Marí, José María and Pedrosa-Corral, Irene and Sanbonmatsu-Gámez, Sara and Pérez-González, Carmen and Chamizo-López, Francisco and Bordes-Benítez, Ana and Navarro, David and Albert, Eliseo and Torres, Ignacio and Gascón, Isabel and Torregrosa-Hetland, Cristina Juana and Pastor-Boix, Eva and Cascales-Ramos, Paloma and Fuster-Escrivá, Begoña and Gimeno-Cardona, Concepción and Ocete, María Dolores and Medina-Gonzalez, Rafael and González-Cantó, Julia and Martínez-Macias, Olalla and Palop-Borrás, Begoña and de Toro, Inmaculada and Mediavilla-Gradolph, Maria Concepción and Pérez-Ruiz, Mercedes and González-Recio, Óscar and Gutiérrez-Rivas, Mónica and Simarro-Córdoba, Encarnación and Lozano-Serra, Julia and Robles-Fonseca, Lorena and de Salazar, Adolfo and Viñuela-González, Laura and Chueca, Natalia and García, Federico and Gómez-Camarasa, Cristina and Carvajal, Ana and de la Puente, Raul and Martín-Sánchez, Vicente and Fregeneda-Grandes, Juan-Miguel and Molina, Antonio José and Argüello, Héctor and Fernández-Villa, Tania and Farga-Martí, Maria Amparo and Domínguez-Márquez, Victoria and Costa-Alcalde, José Javier and Trastoy, Rocío and Barbeito-Castiñeiras, Gema and Coira, Amparo and Pérez-Del-Molino, María Luisa and Aguilera, Antonio and Planas, Anna M and Soriano, Alex and Fernandez-Cádenas, Israel and Pérez-Tur, Jordi and Marcos, Maria Ángeles and Moreno-Docón, Antonio and Viedma, Esther and Mingorance, Jesús and Galán-Montemayor, Juan Carlos and Parra-Grande, Mónica},
    pmid = {34098568},
    pubstate = {aheadofprint},
    }
  • [DOI] M. Roncoroni, B. Droesbeke, I. Eguinoa, K. D. Ruyck, F. D’Anna, D. Yusuf, B. Grüning, R. Backofen, and F. Coppens, “A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive,” Bioinformatics, 2021.
    [Bibtex]
    @Article{Roncoroni:21,
    author = {Miguel Roncoroni and Bert Droesbeke and Ignacio Eguinoa and Kim De Ruyck and Flora D'Anna and Dilmurat Yusuf and Björn Grüning and Rolf Backofen and Frederik Coppens},
    journal = {Bioinformatics},
    title = {A {SARS}-{CoV}-2 sequence submission tool for the {E}uropean {N}ucleotide {A}rchive},
    year = {2021},
    doi = {10.1093/bioinformatics/btab421},
    editor = {Zhiyong Lu},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] Á. O’Toole, V. Hill, O. G. Pybus, A. Watts, I. I. Bogoch, K. Khan, J. P. Messina, H. Tegally, R. R. Lessells, J. Giandhari, S. Pillay, K. A. Tumedi, G. Nyepetsi, M. Kebabonye, M. Matsheka, M. Mine, S. Tokajian, H. Hassan, T. Salloum, G. Merhi, J. Koweyes, J. L. Geoghegan, J. de Ligt, X. Ren, M. Storey, N. E. Freed, C. Pattabiraman, P. Prasad, A. S. Desai, R. Vasanthapuram, T. F. Schulz, L. Steinbrück, T. Stadler, A. Parisi, A. Bianco, D. G. de Viedma, S. Buenestado-Serrano, V. Borges, J. Isidro, S. Duarte, J. P. Gomes, N. Zuckerman, M. Mandelboim, O. Mor, T. Seemann, A. Arnott, J. Draper, M. Gall, W. Rawlinson, I. Deveson, S. Schlebusch, J. McMahon, L. Leong, C. K. Lim, M. Chironna, D. Loconsole, A. Bal, L. Josset, E. Holmes, K. S. George, E. Lasek-Nesselquist, R. S. Sikkema, B. B. Oude Munnink, M. Koopmans, M. Brytting, S. V. rani, S. Pavani, T. Smura, A. Heim, S. Kurkela, M. Umair, M. Salman, B. Bartolini, M. Rueca, C. Drosten, T. Wolff, O. Silander, D. Eggink, C. Reusken, H. Vennema, A. Park, C. Carrington, N. Sahadeo, M. Carr, G. Gonzalez, T. de Oliveira, N. Faria, A. Rambaut, M. U. G. Kraemer, and, and, and, and, and and and, “Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2,” Wellcome Open Res, vol. 6, p. 121, 2021.
    [Bibtex]
    @Article{OToole:21,
    author = {{\'{A}}ine O'Toole and Verity Hill and Oliver G. Pybus and Alexander Watts and Issac I. Bogoch and Kamran Khan and Jane P. Messina and Houriiyah Tegally and Richard R. Lessells and Jennifer Giandhari and Sureshnee Pillay and Kefentse Arnold Tumedi and Gape Nyepetsi and Malebogo Kebabonye and Maitshwarelo Matsheka and Madisa Mine and Sima Tokajian and Hamad Hassan and Tamara Salloum and Georgi Merhi and Jad Koweyes and Jemma L. Geoghegan and Joep de Ligt and Xiaoyun Ren and Matthew Storey and Nikki E. Freed and Chitra Pattabiraman and Pramada Prasad and Anita S. Desai and Ravi Vasanthapuram and Thomas F. Schulz and Lars Steinbrück and Tanja Stadler and Antonio Parisi and Angelica Bianco and Dar{\'{\i}}o Garc{\'{\i}}a de Viedma and Sergio Buenestado-Serrano and V{\'{\i}}tor Borges and Joana Isidro and S{\'{\i}}lvia Duarte and Jo{\~{a}}o Paulo Gomes and Neta Zuckerman and Michal Mandelboim and Orna Mor and Torsten Seemann and Alicia Arnott and Jenny Draper and Mailie Gall and William Rawlinson and Ira Deveson and Sanmari{\'{e}} Schlebusch and Jamie McMahon and Lex Leong and Chuan Kok Lim and Maria Chironna and Daniela Loconsole and Antonin Bal and Laurence Josset and Edward Holmes and Kirsten St. George and Erica Lasek-Nesselquist and Reina S. Sikkema and Bas B. {Oude Munnink} and Marion Koopmans and Mia Brytting and V. Sudha rani and S. Pavani and Teemu Smura and Albert Heim and Satu Kurkela and Massab Umair and Muhammad Salman and Barbara Bartolini and Martina Rueca and Christian Drosten and Thorsten Wolff and Olin Silander and Dirk Eggink and Chantal Reusken and Harry Vennema and Aekyung Park and Christine Carrington and Nikita Sahadeo and Michael Carr and Gabo Gonzalez and Tulio de Oliveira and Nuno Faria and Andrew Rambaut and Moritz U. G. Kraemer and and and and and and and and and and and},
    journal = {{Wellcome Open Res}},
    title = {Tracking the international spread of {SARS}-{CoV}-2 lineages {B}.1.1.7 and {B}.1.351/501{Y}-{V2}},
    year = {2021},
    pages = {121},
    volume = {6},
    doi = {10.12688/wellcomeopenres.16661.1},
    publisher = {F1000 Research Ltd},
    }
  • [DOI] T. C. Jones, G. Biele, B. Mühlemann, T. Veith, J. Schneider, J. Beheim-Schwarzbach, T. Bleicker, J. Tesch, M. L. Schmidt, L. E. Sander, F. Kurth, P. Menzel, R. Schwarzer, M. Zuchowski, J. Hofmann, A. Krumbholz, A. Stein, A. Edelmann, V. M. Corman, and C. Drosten, “Estimating infectiousness throughout SARS-CoV-2 infection course,” Science, p. eabi5273, 2021.
    [Bibtex]
    @Article{Jones:21,
    author = {Terry C. Jones and Guido Biele and Barbara Mühlemann and Talitha Veith and Julia Schneider and Jörn Beheim-Schwarzbach and Tobias Bleicker and Julia Tesch and Marie Luisa Schmidt and Leif Erik Sander and Florian Kurth and Peter Menzel and Rolf Schwarzer and Marta Zuchowski and Jörg Hofmann and Andi Krumbholz and Angela Stein and Anke Edelmann and Victor Max Corman and Christian Drosten},
    journal = {Science},
    title = {Estimating infectiousness throughout {SARS}-{CoV}-2 infection course},
    year = {2021},
    pages = {eabi5273},
    doi = {10.1126/science.abi5273},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
  • [DOI] S. Roux, B. G. Paul, S. C. Bagby, S. Nayfach, M. A. Allen, G. Attwood, R. Cavicchioli, L. Chistoserdova, R. J. Gruninger, S. J. Hallam, M. E. Hernandez, M. Hess, W. Liu, T. A. McAllister, M. A. O’Malley, X. Peng, V. I. Rich, S. R. Saleska, and E. A. Eloe-Fadrosh, “Ecology and molecular targets of hypermutation in the global microbiome,” Nat Commun, vol. 12, iss. 1, 2021.
    [Bibtex]
    @Article{Roux:21,
    author = {Simon Roux and Blair G. Paul and Sarah C. Bagby and Stephen Nayfach and Michelle A. Allen and Graeme Attwood and Ricardo Cavicchioli and Ludmila Chistoserdova and Robert J. Gruninger and Steven J. Hallam and Maria E. Hernandez and Matthias Hess and Wen-Tso Liu and Tim A. McAllister and Michelle A. O'Malley and Xuefeng Peng and Virginia I. Rich and Scott R. Saleska and Emiley A. Eloe-Fadrosh},
    journal = {{Nat Commun}},
    title = {Ecology and molecular targets of hypermutation in the global microbiome},
    year = {2021},
    number = {1},
    volume = {12},
    doi = {10.1038/s41467-021-23402-7},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] P. R. Bhatt, A. Scaiola, G. Loughran, M. Leibundgut, A. Kratzel, R. Meurs, R. Dreos, K. M. O’Connor, A. McMillan, J. W. Bode, V. Thiel, D. Gatfield, J. F. Atkins, and N. Ban, “Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome,” Science, p. eabf3546, 2021.
    [Bibtex]
    @Article{Bhatt:21,
    author = {Pramod R. Bhatt and Alain Scaiola and Gary Loughran and Marc Leibundgut and Annika Kratzel and Romane Meurs and Ren{\'{e}} Dreos and Kate M. O'Connor and Angus McMillan and Jeffrey W. Bode and Volker Thiel and David Gatfield and John F. Atkins and Nenad Ban},
    journal = {Science},
    title = {Structural basis of ribosomal frameshifting during translation of the {SARS}-{CoV}-2 {RNA} genome},
    year = {2021},
    pages = {eabf3546},
    doi = {10.1126/science.abf3546},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
  • [DOI] S. Paraskevopoulou, S. Käfer, F. Zirkel, A. Donath, M. Petersen, S. Liu, X. Zhou, C. Drosten, B. Misof, and S. Junglen, “Viromics of extant insect orders unveil the evolution of the flavi-like superfamily,” Virus Evol, vol. 7, iss. 1, 2021.
    [Bibtex]
    @Article{Paraskevopoulou:21,
    author = {Sofia Paraskevopoulou and Simon Käfer and Florian Zirkel and Alexander Donath and Malte Petersen and Shanlin Liu and Xin Zhou and Christian Drosten and Bernhard Misof and Sandra Junglen},
    journal = {{Virus Evol}},
    title = {Viromics of extant insect orders unveil the evolution of the flavi-like superfamily},
    year = {2021},
    number = {1},
    volume = {7},
    doi = {10.1093/ve/veab030},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] M. Barlev-Gross, S. Weiss, N. Paran, Y. Yahalom-Ronen, O. Israeli, I. Nemet, L. Kliker, N. Zuckerman, I. Glinert, T. Noy-Porat, R. Alcalay, R. Rosenfeld, H. Levy, O. Mazor, M. Mandelboim, E. Mendelson, A. Beth-Din, T. Israely, and A. Mechaly, “Sensitive immunodetection of SARS-CoV-2 variants-of-concern 501Y.V2 and 501Y.V1,” J Infect Dis, 2021.
    [Bibtex]
    @Article{BarlevGross:21,
    author = {Moria Barlev-Gross and Shay Weiss and Nir Paran and Yfat Yahalom-Ronen and Ofir Israeli and Ital Nemet and Limor Kliker and Neta Zuckerman and Itai Glinert and Tal Noy-Porat and Ron Alcalay and Ronit Rosenfeld and Haim Levy and Ohad Mazor and Michal Mandelboim and Ella Mendelson and Adi Beth-Din and Tomer Israely and Adva Mechaly},
    journal = {{J Infect Dis}},
    title = {Sensitive immunodetection of {SARS}-{CoV}-2 variants-of-concern {501Y.V2} and {501Y.V1}},
    year = {2021},
    doi = {10.1093/infdis/jiab278},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] S. G. Acinas, P. Sánchez, G. Salazar, F. M. Cornejo-Castillo, M. Sebastián, R. Logares, M. Royo-Llonch, L. Paoli, S. Sunagawa, P. Hingamp, H. Ogata, G. Lima-Mendez, S. Roux, J. M. González, J. M. Arrieta, I. S. Alam, A. Kamau, C. Bowler, J. Raes, S. Pesant, P. Bork, S. Agustí, T. Gojobori, D. Vaqué, M. B. Sullivan, C. Pedrós-Alió, R. Massana, C. M. Duarte, and J. M. Gasol, “Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities,” Commun Biol, vol. 4, iss. 1, 2021.
    [Bibtex]
    @Article{Acinas:21,
    author = {Silvia G. Acinas and Pablo S{\'{a}}nchez and Guillem Salazar and Francisco M. Cornejo-Castillo and Marta Sebasti{\'{a}}n and Ramiro Logares and Marta Royo-Llonch and Lucas Paoli and Shinichi Sunagawa and Pascal Hingamp and Hiroyuki Ogata and Gipsi Lima-Mendez and Simon Roux and Jos{\'{e}} M. Gonz{\'{a}}lez and Jes{\'{u}}s M. Arrieta and Intikhab S. Alam and Allan Kamau and Chris Bowler and Jeroen Raes and St{\'{e}}phane Pesant and Peer Bork and Susana Agust{\'{\i}} and Takashi Gojobori and Dolors Vaqu{\'{e}} and Matthew B. Sullivan and Carlos Pedr{\'{o}}s-Ali{\'{o}} and Ramon Massana and Carlos M. Duarte and Josep M. Gasol},
    journal = {{Commun Biol}},
    title = {Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities},
    year = {2021},
    number = {1},
    volume = {4},
    doi = {10.1038/s42003-021-02112-2},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] M. K. Mirzaei and L. Deng, “New technologies for developing phage-based tools to manipulate the human microbiome,” Trends Microbiol, 2021.
    [Bibtex]
    @Article{Mirzaei:21,
    author = {Mohammadali Khan Mirzaei and Li Deng},
    journal = {{Trends Microbiol}},
    title = {New technologies for developing phage-based tools to manipulate the human microbiome},
    year = {2021},
    doi = {10.1016/j.tim.2021.04.007},
    publisher = {Elsevier {BV}},
    }
  • [DOI] E. Boehm, I. Kronig, R. A. Neher, I. Eckerle, P. Vetter, and L. Kaiser, “Novel SARS-CoV-2 variants: the pandemics within the pandemic,” Clin Microbiol Infec, 2021.
    [Bibtex]
    @Article{Boehm:21,
    author = {Erik Boehm and Ilona Kronig and Richard A. Neher and Isabella Eckerle and Pauline Vetter and Laurent Kaiser},
    journal = {{Clin Microbiol Infec}},
    title = {Novel {SARS}-{CoV}-2 variants: the pandemics within the pandemic},
    year = {2021},
    doi = {10.1016/j.cmi.2021.05.022},
    publisher = {Elsevier {BV}},
    }
  • [DOI] S. Dellicour, S. L. Hong, B. Vrancken, A. Chaillon, M. S. Gill, M. T. Maurano, S. Ramaswami, P. Zappile, C. Marier, G. W. Harkins, G. Baele, R. Duerr, and A. Heguy, “Dispersal dynamics of SARS-CoV-2 lineages during the first epidemic wave in New York City,” PLoS Pathog, vol. 17, iss. 5, p. e1009571, 2021.
    [Bibtex]
    @Article{Dellicour:21a,
    author = {Simon Dellicour and Samuel L. Hong and Bram Vrancken and Antoine Chaillon and Mandev S. Gill and Matthew T. Maurano and Sitharam Ramaswami and Paul Zappile and Christian Marier and Gordon W. Harkins and Guy Baele and Ralf Duerr and Adriana Heguy},
    journal = {{PLoS Pathog}},
    title = {Dispersal dynamics of {SARS}-{CoV}-2 lineages during the first epidemic wave in {N}ew {Y}ork {C}ity},
    year = {2021},
    number = {5},
    pages = {e1009571},
    volume = {17},
    doi = {10.1371/journal.ppat.1009571},
    editor = {Adam S. Lauring},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] S. Garmaeva, A. Gulyaeva, T. Sinha, A. N. Shkoporov, A. G. Clooney, S. R. Stockdale, J. E. Spreckels, T. D. S. Sutton, L. A. Draper, B. E. Dutilh, C. Wijmenga, A. Kurilshikov, J. Fu, C. Hill, and A. Zhernakova, “Stability of the human gut virome and effect of gluten-free diet,” Cell Rep, vol. 35, iss. 7, p. 109132, 2021.
    [Bibtex]
    @Article{Garmaeva:21,
    author = {Sanzhima Garmaeva and Anastasia Gulyaeva and Trishla Sinha and Andrey N. Shkoporov and Adam G. Clooney and Stephen R. Stockdale and Johanne E. Spreckels and Thomas D.S. Sutton and Lorraine A. Draper and Bas E. Dutilh and Cisca Wijmenga and Alexander Kurilshikov and Jingyuan Fu and Colin Hill and Alexandra Zhernakova},
    journal = {{Cell Rep}},
    title = {Stability of the human gut virome and effect of gluten-free diet},
    year = {2021},
    number = {7},
    pages = {109132},
    volume = {35},
    doi = {10.1016/j.celrep.2021.109132},
    publisher = {Elsevier {BV}},
    }
  • [DOI] A. Munsey, F. N. Mwiine, S. Ochwo, L. Velazquez-Salinas, Z. Ahmed, F. Maree, L. L. Rodriguez, E. Rieder, A. Perez, S. Dellicour, and K. VanderWaal, “Phylogeographic analysis of foot-and-mouth disease virus serotype O dispersal and associated drivers in East Africa,” Mol Ecol, 2021.
    [Bibtex]
    @Article{Munsey:21,
    author = {Anna Munsey and Frank Norbert Mwiine and Sylvester Ochwo and Lauro Velazquez-Salinas and Zaheer Ahmed and Francois Maree and Luis L. Rodriguez and Elizabeth Rieder and Andres Perez and Simon Dellicour and Kimberly VanderWaal},
    journal = {{Mol Ecol}},
    title = {Phylogeographic analysis of foot-and-mouth disease virus serotype {O} dispersal and associated drivers in {E}ast {A}frica},
    year = {2021},
    doi = {10.1111/mec.15991},
    publisher = {Wiley},
    }
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    [Bibtex]
    @Article{Clum:21,
    author = {Alicia Clum and Marcel Huntemann and Brian Bushnell and Brian Foster and Bryce Foster and Simon Roux and Patrick P. Hajek and Neha Varghese and Supratim Mukherjee and T. B. K. Reddy and Chris Daum and Yuko Yoshinaga and Ronan O'Malley and Rekha Seshadri and Nikos C. Kyrpides and Emiley A. Eloe-Fadrosh and I-Min A. Chen and Alex Copeland and Natalia N. Ivanova},
    journal = {{mSystems}},
    title = {{DOE} {JGI} Metagenome Workflow},
    year = {2021},
    number = {3},
    volume = {6},
    doi = {10.1128/msystems.00804-20},
    editor = {Nicola Segata},
    publisher = {American Society for Microbiology},
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    [Bibtex]
    @Article{Low:21,
    author = {Jun Siong Low and Daniela Vaqueirinho and Federico Mele and Mathilde Foglierini and Josipa Jerak and Michela Perotti and David Jarrossay and Sandra Jovic and Laurent Perez and Rosalia Cacciatore and Tatiana Terrot and Alessandra Franzetti Pellanda and Maira Biggiogero and Christian Garzoni and Paolo Ferrari and Alessandro Ceschi and Antonio Lanzavecchia and Federica Sallusto and Antonino Cassotta},
    journal = {Science},
    title = {Clonal analysis of immunodominance and cross-reactivity of the {CD}4 {T} cell response to {SARS}-{CoV}-2},
    year = {2021},
    pages = {eabg8985},
    doi = {10.1126/science.abg8985},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
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    [Bibtex]
    @Article{Ferrarini:21,
    author = {Mariana G. Ferrarini and Avantika Lal and Rita Rebollo and Andreas J. 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},
    journal = {{Commun Biol}},
    title = {Genome-wide bioinformatic analyses predict key host and viral factors in {SARS}-{CoV}-2 pathogenesis},
    year = {2021},
    number = {1},
    volume = {4},
    doi = {10.1038/s42003-021-02095-0},
    publisher = {Springer Science and Business Media {LLC}},
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    [Bibtex]
    @Article{Unterer:21,
    author = {Magdalena Unterer and Mohammadali Khan Mirzaei and Li Deng},
    journal = {{Signal Transduct Target Ther}},
    title = {{G}ut {P}hage {D}atabase: phage mining in the cave of wonders},
    year = {2021},
    number = {1},
    volume = {6},
    doi = {10.1038/s41392-021-00615-2},
    publisher = {Springer Science and Business Media {LLC}},
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    [Bibtex]
    @Article{Liu:21,
    author = {Ying Liu and Tatiana A. Demina and Simon Roux and Pakorn Aiewsakun and Darius Kazlauskas and Peter Simmonds and David Prangishvili and Hanna M. Oksanen and Mart Krupovic},
    journal = {{bioRxiv}},
    title = {Diversity, taxonomy and evolution of archaeal viruses of the class {C}audoviricetes},
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    publisher = {Cold Spring Harbor Laboratory},
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    @Article{Billaud:21,
    author = {Maud Billaud and Quentin Lamy-Besnier and Julien Lossouarn and Elisabeth Moncaut and Moira B. Dion and Sylvain Moineau and Fatoumata Traor{\'{e}} and Emmanuelle Le Chatelier and Catherine Denis and Jordi Estelle and Caroline Achard and Olivier Zemb and Marie Agnès Petit},
    journal = {{bioRxiv}},
    title = {Analysis of viromes and microbiomes from pig fecal samples reveals that phages and prophages are not vectors of antibiotic resistance genes},
    year = {2021},
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    [Bibtex]
    @Article{Smith:21,
    author = {Maureen Rebecca Smith and Maria Trofimova and Ariane Weber and Yannick Duport and Denise Kühnert and Max von Kleist},
    journal = {{medRxiv}},
    title = {Rapid incidence estimation from {SARS}-{CoV}-2 genomes reveals decreased case detection in {E}urope during summer 2020},
    year = {2021},
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    publisher = {Cold Spring Harbor Laboratory},
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    [Bibtex]
    @Article{Baltoumas:21,
    author = {Fotis A. Baltoumas and Sofia Zafeiropoulou and Evangelos Karatzas and Savvas Paragkamian and Foteini Thanati and Ioannis Iliopoulos and Aristides G. Eliopoulos and Reinhard Schneider and Lars Juhl Jensen and Evangelos Pafilis and Georgios A. Pavlopoulos},
    journal = {{bioRxiv}},
    title = {{OnTheFly}2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis},
    year = {2021},
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    [Bibtex]
    @Article{VanHelden:21,
    author = {Van Helden, Jacques and Butler, Colin D and Canard, Bruno and Achaz, Guillaume and Graner, François and Segreto, Rossana and Deigin, Yuri and Colombo, Fabien and Morand, Serge and Sirotkin, Dan and Sirotkin, Karl and Decroly, Etienne and Halloy, José},
    journal = {{arXiv}},
    title = {An appeal for an open scientific debate about the proximal origin of {SARS-CoV-2}},
    year = {2021},
    doi = {10.13140/RG.2.2.15356.46727},
    publisher = {Unpublished},
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    [Bibtex]
    @InCollection{Oliveira:21,
    author = {Liliane Santana Oliveira and Arthur Gruber},
    booktitle = {Bioinformatics},
    publisher = {Exon Publications},
    title = {Rational Design of Profile Hidden Markov Models for Viral Classification and Discovery},
    year = {2021},
    pages = {151--170},
    doi = {10.36255/exonpublications.bioinformatics.2021.ch9},
    }
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    [Bibtex]
    @Article{Chepkwony:21,
    author = {Sharon Chepkwony and Anna Parys and Elien Vandoorn and Wojciech Stadejek and Jiexiong Xie and Jacqueline King and Annika Graaf and Anne Pohlmann and Martin Beer and Timm Harder and Kristien Van Reeth},
    journal = {{Sci Rep}},
    title = {Genetic and antigenic evolution of {H1} swine influenza {A} viruses isolated in {B}elgium and the {N}etherlands from 2014 through 2019},
    year = {2021},
    number = {1},
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    [Bibtex]
    @Article{Harrison:21,
    author = {Peter W Harrison and Rodrigo Lopez and Nadim Rahman and Stefan Gutnick Allen and Raheela Aslam and Nicola Buso and Carla Cummins and Yasmin Fathy and Eloy Felix and Mihai Glont and Suran Jayathilaka and Sandeep Kadam and Manish Kumar and Katharina~B Lauer and Geetika Malhotra and Abayomi Mosaku and Ossama Edbali and Young Mi Park and Andrew Parton and Matt Pearce and Jose Francisco Estrada~Pena and Joseph Rossetto and Craig Russell and Sandeep Selvakumar and X{\`{e}}nia P{\'{e}}rez Sitj{\`{a}} and Alexey Sokolov and Ross Thorne and Marianna Ventouratou and Peter Walter and Galabina Yordanova and Amonida Zadissa and Guy Cochrane and Niklas Blomberg and Rolf Apweiler},
    journal = {{Nucleic Acids Res}},
    title = {The {COVID}-19 Data Portal: accelerating {SARS}-{CoV}-2 and {COVID}-19 research through rapid open access data sharing},
    year = {2021},
    doi = {10.1093/nar/gkab417},
    publisher = {Oxford University Press ({OUP})},
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    @Article{Spaenig:21,
    author = {Sebastian Spänig and Siba Mohsen and Georges Hattab and Anne-Christin Hauschild and Dominik Heider},
    journal = {{NAR} Genomics and Bioinformatics},
    title = {A large-scale comparative study on peptide encodings for biomedical classification},
    year = {2021},
    number = {2},
    volume = {3},
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    publisher = {Oxford University Press ({OUP})},
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    [Bibtex]
    @Article{Layan:21,
    author = {Maylis Layan and Simon Dellicour and Guy Baele and Simon Cauchemez and Herv{\'{e}} Bourhy},
    journal = {{PLoS Negl Trop Dis}},
    title = {Mathematical modelling and phylodynamics for the study of dog rabies dynamics and control: A scoping review},
    year = {2021},
    number = {5},
    pages = {e0009449},
    volume = {15},
    doi = {10.1371/journal.pntd.0009449},
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    [Bibtex]
    @Article{Shoraka:21,
    author = {Shahrzad Shoraka and Maria Lucia Brito Ferreira and Seyed Reza Mohebbi and Amir Ghaemi},
    journal = {{Front Immunol}},
    title = {{SARS}-{CoV}-2 Infection and Guillain-Barr{\'{e}} Syndrome: A Review on Potential Pathogenic Mechanisms},
    year = {2021},
    volume = {12},
    doi = {10.3389/fimmu.2021.674922},
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    [Bibtex]
    @Article{Cordey:21,
    author = {Samuel Cordey and Florian Laubscher and Mary-Anne Hartley and Thomas Junier and Kristina Keitel and Myl{\`{e}}ne Docquier and Nicolas Guex and Christian Iseli and Gael Vieille and Philippe {Le Mercier} and Anne Gleizes and Josephine Samaka and Tarsis Mlaganile and Frank Kagoro and John Masimba and Zamzam Said and Hosiana Temba and Gasser H. Elbanna and Caroline Tapparel and Marie-Celine Zanella and Ioannis Xenarios and Jacques Fellay and Val{\'{e}}rie D'Acremont and Laurent Kaiser},
    journal = {{Emerg Microbes Infect}},
    title = {Blood Virosphere in Febrile {T}anzanian Children},
    year = {2021},
    pages = {1--237},
    doi = {10.1080/22221751.2021.1925161},
    publisher = {Informa {UK} Limited},
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    [Bibtex]
    @Article{FolgueirasGonzalez:21,
    author = {Alba Folgueiras-Gonz{\'{a}}lez and Robin van den Braak and Martin Deijs and Lia van der Hoek and Ad de Groof},
    journal = {Diagnostics},
    title = {A Versatile Processing Workflow to Enable Pathogen Detection in Clinical Samples from Organs Using {VIDISCA}},
    year = {2021},
    number = {5},
    pages = {791},
    volume = {11},
    doi = {10.3390/diagnostics11050791},
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    }
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    [Bibtex]
    @Article{Kudryavtsev:21,
    author = {Igor Kudryavtsev and Olga V. Kalinina and Vadim Bezrukikh and Olesya Melnik and Alexey Golovkin},
    journal = {Viruses},
    title = {The Significance of Phenotyping and Quantification of Plasma Extracellular Vesicles Levels Using High-Sensitivity Flow Cytometry during {COVID}-19 Treatment},
    year = {2021},
    number = {5},
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    publisher = {{MDPI} {AG}},
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    [Bibtex]
    @Article{Goettsch:21,
    author = {Winfried Goettsch and Niko Beerenwinkel and Li Deng and Lars Dölken and Bas E. Dutilh and Florian Erhard and Lars Kaderali and Max von Kleist and Roland Marquet and Jelle Matthijnssens and Shawna McCallin and Dino P. McMahon and Thomas Rattei and Ronald P. van Rij and David L. Robertson and Martin Schwemmle and Noam Stern-Ginossar and Manja Marz},
    journal = {Viruses},
    title = {{ITN}{\textemdash}{VIROINF}: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics},
    year = {2021},
    number = {5},
    pages = {766},
    volume = {13},
    doi = {10.3390/v13050766},
    publisher = {{MDPI} {AG}},
    }
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    [Bibtex]
    @Article{Kostaki:21a,
    author = {Evangelia-Georgia Kostaki and Ioulia Tseti and Sotirios Tsiodras and George N. Pavlakis and Petros P. Sfikakis and Dimitrios Paraskevis},
    journal = {Life},
    title = {Temporal Dominance of {B.1.1.7} over {B.1.354} {SARS}-{CoV}-2 Variant: A Hypothesis Based on Areas of Variant Co-Circulation},
    year = {2021},
    number = {5},
    pages = {375},
    volume = {11},
    doi = {10.3390/life11050375},
    publisher = {{MDPI} {AG}},
    }
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    [Bibtex]
    @Article{Kutnjak:21,
    author = {Denis Kutnjak and Lucie Tamisier and Ian Adams and Neil Boonham and Thierry Candresse and Michela Chiumenti and Kris De Jonghe and Jan F. Kreuze and Marie Lefebvre and Gon{\c{c}}alo Silva and Martha Malapi-Wight and Paolo Margaria and Irena Mavri{\v{c}} Ple{\v{s}}ko and Sam McGreig and Laura Miozzi and Benoit Remenant and Jean-Sebastien Reynard and Johan Rollin and Mike Rott and Olivier Schumpp and S{\'{e}}bastien Massart and Annelies Haegeman},
    journal = {Microorganisms},
    title = {A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses},
    year = {2021},
    number = {4},
    pages = {841},
    volume = {9},
    doi = {10.3390/microorganisms9040841},
    publisher = {{MDPI} {AG}},
    }
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    [Bibtex]
    @Article{Widera:21a,
    author = {Marek Widera and Barbara Mühlemann and Victor M. Corman and Tuna Toptan and Jörn Beheim-Schwarzbach and Niko Kohmer and Julia Schneider and Annemarie Berger and Talitha Veith and Christiane Pallas and Tobias Bleicker and Udo Goetsch and Julia Tesch and Rene Gottschalk and Terry C. Jones and Sandra Ciesek and Christian Drosten},
    journal = {Microorganisms},
    title = {Surveillance of {SARS}-{CoV}-2 in {F}rankfurt am {M}ain from {O}ctober to {D}ecember 2020 Reveals High Viral Diversity Including Spike Mutation {N501Y} in {B}.1.1.70 and {B}.1.1.7},
    year = {2021},
    number = {4},
    pages = {748},
    volume = {9},
    doi = {10.3390/microorganisms9040748},
    publisher = {{MDPI} {AG}},
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    [Bibtex]
    @Article{Kitazawa:21,
    author = {Koji Kitazawa and Stefanie Deinhardt-Emmer and Takenori Inomata and Sharvari Deshpande and Chie Sotozono},
    journal = {Cells},
    title = {The Transmission of {SARS}-{CoV}-2 Infection on the Ocular Surface and Prevention Strategies},
    year = {2021},
    number = {4},
    pages = {796},
    volume = {10},
    doi = {10.3390/cells10040796},
    publisher = {{MDPI} {AG}},
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    @Article{Sand:21,
    author = {Lukas van de Sand and Maren Bormann and Mira Alt and Leonie Schipper and Christiane Silke Heilingloh and Eike Steinmann and Daniel Todt and Ulf Dittmer and Carina Elsner and Oliver Witzke and Adalbert Krawczyk},
    journal = {Viruses},
    title = {Glycyrrhizin Effectively Inhibits {SARS}-{CoV}-2 Replication by Inhibiting the Viral Main Protease},
    year = {2021},
    number = {4},
    pages = {609},
    volume = {13},
    doi = {10.3390/v13040609},
    publisher = {{MDPI} {AG}},
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    @Article{GonzalezCandelas:21,
    author = {Fernando Gonz{\'{a}}lez-Candelas and Marie-Anne Shaw and Tung Phan and Urmila Kulkarni-Kale and Dimitrios Paraskevis and Fabio Luciani and Hirokazu Kimura and Manuela Sironi},
    journal = {Infection, Genetics and Evolution},
    title = {One year into the pandemic: Short-term evolution of {SARS}-{CoV}-2 and emergence of new lineages},
    year = {2021},
    pages = {104869},
    volume = {92},
    doi = {10.1016/j.meegid.2021.104869},
    publisher = {Elsevier {BV}},
    }
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    [Bibtex]
    @Article{GarciaNicolas:21,
    author = {Obdulio Garc{\'{\i}}a-Nicol{\'{a}}s and Philip V'kovski and Ferdinand Zettl and Gert Zimmer and Volker Thiel and Artur Summerfield},
    journal = {{Front Cell Infect Microbiol}},
    title = {No Evidence for Human Monocyte-Derived Macrophage Infection and Antibody-Mediated Enhancement of {SARS}-{CoV}-2 Infection},
    year = {2021},
    volume = {11},
    doi = {10.3389/fcimb.2021.644574},
    publisher = {Frontiers Media {SA}},
    }
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    [Bibtex]
    @Article{Gestuveo:21,
    author = {Rommel J. Gestuveo and Jamie Royle and Claire L. Donald and Douglas J. Lamont and Edward C. Hutchinson and Andres Merits and Alain Kohl and Margus Varjak},
    journal = {{Nat Commun}},
    title = {Analysis of {Z}ika virus capsid-{A}edes aegypti mosquito interactome reveals pro-viral host factors critical for establishing infection},
    year = {2021},
    number = {1},
    volume = {12},
    doi = {10.1038/s41467-021-22966-8},
    publisher = {Springer Science and Business Media {LLC}},
    }
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    [Bibtex]
    @Article{Bloom:21,
    author = {Jesse D. Bloom and Yujia Alina Chan and Ralph S. Baric and Pamela J. Bjorkman and Sarah Cobey and Benjamin E. Deverman and David N. Fisman and Ravindra Gupta and Akiko Iwasaki and Marc Lipsitch and Ruslan Medzhitov and Richard A. Neher and Rasmus Nielsen and Nick Patterson and Tim Stearns and Erik van Nimwegen and Michael Worobey and David A. Relman},
    journal = {Science},
    title = {Investigate the origins of {COVID}-19},
    year = {2021},
    number = {6543},
    pages = {6941--694},
    volume = {372},
    doi = {10.1126/science.abj0016},
    editor = {Jennifer Sills},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
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    [Bibtex]
    @Article{Polo:21,
    author = {David Polo and Marta Lois and Mar{\'{\i}}a Teresa Fern{\'{a}}ndez-N{\'{u}}{\~{n}}ez and Jes{\'{u}}s L. Romalde},
    journal = {{Sci Total Environ}},
    title = {Detection of {SARS}-{CoV}-2 {RNA} in bivalve mollusks and marine sediments},
    year = {2021},
    pages = {147534},
    volume = {786},
    doi = {10.1016/j.scitotenv.2021.147534},
    publisher = {Elsevier {BV}},
    }
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    [Bibtex]
    @Article{Vanshylla:21a,
    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 Matthias Zehner 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 Birgit Gathof and Gerd Fätkenheuer and Nico Pfeifer and Ralf Eggeling and Max Augustin and Clara Lehmann and Florian Klein},
    journal = {{Cell Host Microbe}},
    title = {Kinetics and correlates of the neutralizing antibody response to {SARS}-{CoV}-2 infection in humans},
    year = {2021},
    doi = {10.1016/j.chom.2021.04.015},
    publisher = {Elsevier {BV}},
    }
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    [Bibtex]
    @Article{Berg:21,
    author = {Maureen Berg and Simon Roux},
    journal = {{Nat Rev Microbiol}},
    title = {Extreme dimensions {\textemdash} how big (or small) can tailed phages be?},
    year = {2021},
    doi = {10.1038/s41579-021-00574-z},
    publisher = {Springer Science and Business Media {LLC}},
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    [Bibtex]
    @Article{Jahrsdoerfer:21,
    author = {Bernd Jahrsdörfer and Rüdiger Gro{\ss} and Alina Seidel and Lukas Wettstein and Carolin Ludwig and Tatjana Schwarz and Sixten Körper and Markus Rojewski and Ramin Lotfi and Christoph Weinstock and Erhard Seifried and Victor Max Corman and Christian Drosten and Jan Münch and Hubert Schrezenmeier},
    journal = {{J Immunol}},
    title = {Characterization of the {SARS}-{CoV}-2 Neutralization Potential of {COVID}-19{\textendash}Convalescent Donors},
    year = {2021},
    pages = {ji2100036},
    doi = {10.4049/jimmunol.2100036},
    publisher = {The American Association of Immunologists},
    }
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    [Bibtex]
    @Article{Finkel:21,
    author = {Yaara Finkel and Avi Gluck and Aharon Nachshon and Roni Winkler and Tal Fisher and Batsheva Rozman and Orel Mizrahi and Yoav Lubelsky and Binyamin Zuckerman and Boris Slobodin and Yfat Yahalom-Ronen and Hadas Tamir and Igor Ulitsky and Tomer Israely and Nir Paran and Michal Schwartz and Noam Stern-Ginossar},
    journal = {Nature},
    title = {{SARS}-{CoV}-2 uses a multipronged strategy to impede host protein synthesis},
    year = {2021},
    doi = {10.1038/s41586-021-03610-3},
    publisher = {Springer Science and Business Media {LLC}},
    }
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    [Bibtex]
    @Article{Dudas:21,
    author = {Gytis Dudas and Samuel L. Hong and Barney Potter and S{\'{e}}bastien Calvignac-Spencer and Fr{\'{e}}d{\'{e}}ric S. Niatou-Singa and Thais B. Tombolomako and Terence Fuh-Neba and Ulrich Vickos and Markus Ulrich and Fabian H. Leendertz and Kamran Khan and Alexander Watts and Ingrida Olendrait{\.{e}} and Joost Snijder and Kim N. Wijnant and Alexandre M.J.J. Bonvin and Pascale Martres and Sylvie Behillil and Ahidjo Ayouba and Martin Foudi Maidadi and Dowbiss Meta Djomsi and Celestin Godwe and Christelle Butel and Aistis {\v{S}}imaitis and Migl{\.{e}} Gabrielait{\.{e}} and Monika Kat{\.{e}}nait{\.{e}} and Rimvydas Norvilas and Ligita Raugait{\.{e}} and Rimvydas Jonikas and Inga Nasvytien{\.{e}} and {\v{Z}}ivil{\.{e}} {\v{Z}}emeckien{\.{e}} and Dovydas Ge{\v{c}}ys and Kamil{\.{e}} Tamu{\v{s}}auskait{\.{e}} and Milda Norkien{\.{e}} and Emilija Vasili{\={u}}nait{\.{e}} and Danguol{\.{e}} {\v{Z}}iogien{\.{e}} and Albertas Timinskas and Marius {\v{S}}ukys and Mantas {\v{S}}arauskas and Gediminas Alzbutas and Dovil{\.{e}} Juozapait{\.{e}} and Daniel Naumovas and Arnoldas Pautienius and Astra Vitkauskien{\.{e}} and Rasa Ugenskien{\.{e}} and Alma Gedvilait{\.{e}} and Darius {\v{C}}ere{\v{s}}kevi{\v{c}}ius and Vaiva Lesauskait{\.{e}} and Lukas {\v{Z}}emaitis and Laimonas Gri{\v{s}}kevi{\v{c}}ius and Guy Baele},
    journal = {{medRxiv}},
    title = {Travel-driven emergence and spread of {SARS}-{CoV}-2 lineage {B.1.620} with multiple {VOC}-like mutations and deletions in {E}urope},
    year = {2021},
    doi = {10.1101/2021.05.04.21256637},
    publisher = {Cold Spring Harbor Laboratory},
    }
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    [Bibtex]
    @Article{Wilkinson:21,
    author = {Eduan Wilkinson and Marta Giovanetti and Houriiyah Tegally and James E. San and Richard Lessels and Diego Cuadros and Darren P. Martin and Abdel-Rahman N. Zekri and Abdoul K. Sangare and Abdoul-Salam Ouedraogo and Abdul K. Sesay and Adn{\`{e}}ne Hammami and Adrienne A. Amuri and Ahmad Sayed and Ahmed Rebai and Aida Elargoubi and Alexander J. Trotter and Alpha K. Keita and Amadou A. Sall and Amadou Kone and Amal Souissi and Ana V. Gutierrez and Andrew J. Page and Arash Iranzadeh and Arnold Lambisia and Augustina Sylverken and Azeddine Ibrahimi and Beatrice Dhaala and Bourema Kouriba and Bronwyn Kleinhans and Cara Brook and Carolyn Williamson and Catherine B. Pratt and Chantal G. Akoua-Koffi and Charles N. Agoti and Collins M. Morang'a and D. James Nokes and Daniel J. Bridges and Daniel L. Bugembe and David Baker and Deelan Doolabh and Deogratius Ssemwanga and Derek Tshabuila and Diarra Bassirou and Dominic S.Y. Amuzu and Dominique Goedhals and Dorcas Maruapula and Ebenezer Foster-Nyarko and Eddy K. Lusamaki and Edgar Simulundu and Edidah Moraa and Edith N. Ngabana and Elmostafa El Fahime and Emerald Jacob and Emmanuel Lokilo and Enatha Mukantwari and Essia Belarbi and Etienne Simon-Loriere and Etil{\'{e}} A. Anoh and Fabian Leendertz and Faida Ajili and Fares Wasfi and Faustinos T. Takawira and Fawzi Derrar and Feriel Bouzid and Francisca M. Muyembe and Frank Tanser and Gabriel K. Mbunsu and Gaetan Thilliez and Gemma Kay and George Githinji and Gert van Zyl and Gordon A. Awandare and Grit Schubert and Gugu P. Maphalala and Hafaliana C. Ranaivoson and Hajar Lemriss and Haruka Abe and Hela H. Karray and Hellen Nansumba and Hesham A. Elgahzaly and Hlanai Gumbo and Ibtihel Smeti and Ikhlas B. Ayed and Ilhem Boutiba-Ben Boubaker and Imed Gaaloul and Inbal Gazy and Isaac Ssewanyana and Jean B. Lekana-Douk and Jean-Claude C. Makangara and Jean-Jacques M. Tamfum and Jean-Michel Heraud and Jeffrey G. Shaffer and Jennifer Giandhari and Jingjing Li and Jiro Yasuda and Joana Q. Mends and Jocelyn Kiconco and John Morobe and John N. Nkengasong and John O. Gyapong and John T. Kayiwa and Johnathan A. Edwards and Jones Gyamfi and Jouali Farah and Joyce M. Ngoi and Joyce Namulondo and Julia C. Andeko and Julius J. Lutwama and Justin O'Grady and Kefentse A. Tumedi and Khadija M. Said and Kim Hae-Young and Kwabena O. Duedu and Lahcen Belyamani and Lavanya Singh and Leonardo de O. Martins and Madisa Mine and Magalutcheemee Ramuth and Maha Mastouri and Mahjoub Aouni and Mahmoud el Hefnawi and Maitshwarelo I. Matsheka and Malebogo Kebabonye and Manel Turki and Martin M. Nyaga and Mathabo Mareka and Matoke Damaris and Matthew Cotten and Maureen W. Mburu and Maximillian Mpina and Michael Owusu and Michael R. Wiley and Mohamed A. Ali and Mohamed Abouelhoda and Mohamed G. Seadawy and Mohamed K. Khalifa and Mooko Sekhele and Mouna Ouadghiri and Mulenga Mwenda and Mushal Allam and My V.T. Phan and Nabil Abid and Nadia Touil and Najla Kharrat and Nalia Ismael and Nedio Mabunda and Nei-yuan Hsiao and Nelson B. Silochi and Ngonda Saasa and Nicola Mulder and Patrice Combe and Patrick Semanda and Paul E. Oluniyi and Paulo Arnaldo and Peter K. Quashie and Philip A. Bester and Philippe Dussart and Placide K. Mbala and Pontiano Kaleebu and Reuben Ayivor-Djanie and Richard Njouom and Richard O. Phillips and Richmond Gorman and Robert A. Kingsley and Rosina A.A. Carr and Sa{\^{a}}d El Kabbaj and Saba Gargouri and Saber Masmoudi and Samar Kassim and Sameh Trabelsi and Sami Kammoun and Sana{\^{a}} Lemriss and Sara H. Agwa and S{\'{e}}bastien Calvignac-Spencer and Seydou Doumbia and Sheila M. Mandanda and Sherihane Aryeetey and Shymaa S. Ahmed and Sikhulile Moyo and Simani Gaseitsiwe and Sonia Lekana-Douki and Sophie Prosolek and Soumeya Ouangraoua and Steve A. Mundeke and Steven Rudder and Sumir Panji and Sureshnee Pillay and Susan Engelbrecht and Susan Nabadda and Sylvie Behillil and Sylvie L. Budiaki and Sylvie van der Werf and Tapfumanei Mashe and Tarik Aanniz and Thabo Mohale and Thanh Le-Viet and Tobias Schindler and Ugochukwu J. Anyaneji and Upasana Ramphal and Vagner Fonseca and Vincent Enouf and Vivianne Gorova and Wael H. Roshdy and William K. Ampofo and Wolfgang Preiser and Wonderful T. Choga and Yaw Bediako and Yenew K Tebeje and Yeshnee Naidoo and Zaydah R. de Laurent and Sofonias K. Tessema and Tulio de Oliveira},
    journal = {{medRxiv}},
    title = {A year of genomic surveillance reveals how the {SARS}-{CoV}-2 pandemic unfolded in {A}frica},
    year = {2021},
    doi = {10.1101/2021.05.12.21257080},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] L. V. Patrono, B. Vrancken, M. Budt, A. Duex, S. Lequime, S. Boral, T. M. P. Gilbert, J. F. Gogarten, L. Hoffmann, D. Horst, K. Merkel, D. Morens, B. Prepoint, J. Schlotterbeck, V. Schuenemann, M. A. Suchard, J. K. Taubenberger, L. Tenkhoff, C. Urban, N. Widulin, E. Winter, M. Worobey, F. H. Leendertz, T. Schnalke, T. Wolff, P. Lemey, and S. Calvignac-Spencer, “Archival influenza virus genomes from Europe reveal genomic and phenotypic variability during the 1918 pandemic,” bioRxiv, 2021.
    [Bibtex]
    @Article{Patrono:21,
    author = {Livia V Patrono and Bram Vrancken and Matthias Budt and Ariane Duex and Sebastian Lequime and Senguel Boral and M Thomas P Gilbert and Jan F Gogarten and Luisa Hoffmann and David Horst and Kevin Merkel and David Morens and Baptiste Prepoint and Jasmin Schlotterbeck and Verena Schuenemann and Marc A Suchard and Jeffery K Taubenberger and Luisa Tenkhoff and Christian Urban and Navena Widulin and Eduard Winter and Michael Worobey and Fabian H Leendertz and Thomas Schnalke and Thorsten Wolff and Philippe Lemey and Sebastien Calvignac-Spencer},
    journal = {{bioRxiv}},
    title = {Archival influenza virus genomes from {E}urope reveal genomic and phenotypic variability during the 1918 pandemic},
    year = {2021},
    doi = {10.1101/2021.05.14.444134},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] A. Wickenhagen, E. Sugrue, S. Lytras, S. Kuchi, M. L. Turnbull, C. Loney, V. Herder, J. Allan, I. Jarmson, N. Cameron-Ruiz, M. Varjak, R. M. Pinto, D. G. Stewart, S. Swingler, M. Noerenberg, E. J. D. Greenwood, T. W. M. Crozier, Q. Gu, S. Clohisey, B. Wang, F. T. M. Costa, M. F. Santana, L. C. L. de Ferreira, J. L. D. S. Filho, M. Marti, R. J. Stanton, E. C. Y. Wang, A. Castello-Palomares, A. Ho, K. Baillie, R. F. Jarrett, D. L. Robertson, M. Palmarini, P. J. Lehner, S. J. Rihn, and S. W. J. and, “A prenylated dsRNA sensor protects against severe COVID-19 and is absent in horseshoe bats,” medRxiv, 2021.
    [Bibtex]
    @Article{Wickenhagen:21,
    author = {Arthur Wickenhagen and Elena Sugrue and Spyros Lytras and Srikeerthana Kuchi and Matthew L Turnbull and Colin Loney and Vanessa Herder and Jay Allan and Innes Jarmson and Natalia Cameron-Ruiz and Margus Varjak and Rute M Pinto and Douglas G Stewart and Simon Swingler and Marko Noerenberg and Edward J D Greenwood and Thomas W M Crozier and Quan Gu and Sara Clohisey and Bo Wang and Fabio Trindade Maranh{\~{a}}o Costa and Monique Freire Santana and Luiz Carlos de Lima Ferreira and Joao Luiz Da Silva Filho and Matthias Marti and Richard J Stanton and Eddie C Y Wang and Alfredo Castello-Palomares and Antonia Ho and Kenneth Baillie and Ruth F Jarrett and David L Robertson and Massimo Palmarini and Paul J Lehner and Suzannah J Rihn and Sam J Wilson and},
    journal = {{medRxiv}},
    title = {A Prenylated {dsRNA} Sensor Protects Against Severe {COVID}-19 and is Absent in Horseshoe Bats},
    year = {2021},
    doi = {10.1101/2021.05.05.21256681},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] K. F. Föhse, B. Geckin, G. J. Overheul, J. van de Maat, G. Kilic, O. Bulut, H. Dijkstra, H. Lemmers, A. S. Sarlea, M. Reijnders, J. Hoogerwerf, J. ten Oever, E. Simonetti, F. L. van de Veerdonk, L. A. B. Joosten, B. L. Haagmans, R. van Crevel, Y. Li, R. P. van Rij, C. GeurtsvanKessel, M. I. de Jonge, J. Domínguez-Andrés, and M. G. Netea, “The BNT162b2 mRNA vaccine against SARS-CoV-2 reprograms both adaptive and innate immune responses,” medRxiv, 2021.
    [Bibtex]
    @Article{Foehse:21,
    author = {F. Konstantin Föhse and Büsranur Geckin and Gijs J. Overheul and Josephine van de Maat and Gizem Kilic and Ozlem Bulut and Helga Dijkstra and Heidi Lemmers and S. Andrei Sarlea and Maartje Reijnders and Jacobien Hoogerwerf and Jaap ten Oever and Elles Simonetti and Frank L. van de Veerdonk and Leo A.B. Joosten and Bart L. Haagmans and Reinout van Crevel and Yang Li and Ronald P. van Rij and Corine GeurtsvanKessel and Marien I. de Jonge and Jorge Dom{\'{\i}}nguez-Andr{\'{e}}s and Mihai G. Netea},
    journal = {{medRxiv}},
    title = {The {BNT}162b2 {mRNA} vaccine against {SARS}-{CoV}-2 reprograms both adaptive and innate immune responses},
    year = {2021},
    doi = {10.1101/2021.05.03.21256520},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] A. L. McNaughton, R. S. Paton, M. Edmans, J. Youngs, J. Wellens, P. Phalora, A. Fyfe, S. Belij-Rammerstorfer, J. S. Bolton, J. Ball, G. Carnell, W. Dejnirattisai, C. Dold, D. W. Eyre, P. Hopkins, A. Howarth, K. Kooblall, H. Klim, S. Leaver, L. Lee, C. López-Camacho, S. F. Lumley, D. Macallan, A. J. Mentzer, N. Provine, J. Ratcliff, J. Slon-Compos, D. Skelly, L. Stolle, P. Supasa, N. Temperton, C. Walker, B. Wang, D. Wyncoll, P. Simmonds, T. Lambe, K. Baillie, M. G. Semple, P. I. Openshaw, U. Obolski, M. Turner, M. Carroll, J. Mongkolsapaya, G. Screaton, S. H. Kennedy, L. Jarvis, E. Barnes, S. Dunachie, J. Lourenço, P. C. Matthews, T. Bicanic, P. Klenerman, S. Gupta, C. P. Thompson, and and and, “Fatal COVID-19 outcomes are associated with an antibody response targeting epitopes shared with endemic coronaviruses,” medRxiv, 2021.
    [Bibtex]
    @Article{McNaughton:21,
    author = {Anna L McNaughton and Robert S Paton and Matthew Edmans and Jonathan Youngs and Judith Wellens and Prabhjeet Phalora and Alex Fyfe and Sandra Belij-Rammerstorfer and Jai S Bolton and Jonathan Ball and George Carnell and Wanwisa Dejnirattisai and Christina Dold and David W Eyre and Philip Hopkins and Alison Howarth and Kreepa Kooblall and Hannah Klim and Susannah Leaver and Lian Lee and C{\'{e}}sar L{\'{o}}pez-Camacho and Sheila F Lumley and Derek Macallan and Alexander J Mentzer and Nicholas Provine and Jeremy Ratcliff and Jose Slon-Compos and Donal Skelly and Lucas Stolle and Piyada Supasa and Nigel Temperton and Chris Walker and Beibei Wang and Duncan Wyncoll and Peter Simmonds and Teresa Lambe and Kenneth Baillie and Malcolm G Semple and Peter IM Openshaw and Uri Obolski and Marc Turner and Miles Carroll and Juthathip Mongkolsapaya and Gavin Screaton and Stephen H Kennedy and Lisa Jarvis and Eleanor Barnes and Susanna Dunachie and Jos{\'{e}} Louren{\c{c}}o and Philippa C Matthews and Tihana Bicanic and Paul Klenerman and Sunetra Gupta and Craig P Thompson and and and},
    journal = {{medRxiv}},
    title = {Fatal {COVID}-19 outcomes are associated with an antibody response targeting epitopes shared with endemic coronaviruses},
    year = {2021},
    doi = {10.1101/2021.05.04.21256571},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] W. Proesmans, M. Albrecht, A. Gajda, P. Neumann, R. J. Paxton, M. Pioz, C. Polzin, O. Schweiger, J. Settele, H. Szentgyörgyi, H. Thulke, and A. J. Vanbergen, “Pathways for novel epidemiology: plan-pollinator-pathogen networks and global change,” Trends Ecol Evol, 2021.
    [Bibtex]
    @Article{Proesmans:21,
    author = {Willem Proesmans and Matthias Albrecht and Anna Gajda and Peter Neumann and Robert J. Paxton and Maryline Pioz and Christine Polzin and Oliver Schweiger and Josef Settele and Hajnalka Szentgyörgyi and Hans-Hermann Thulke and Adam J. Vanbergen},
    journal = {{Trends Ecol Evol}},
    title = {Pathways for Novel Epidemiology: Plan-Pollinator-Pathogen Networks and Global Change},
    year = {2021},
    doi = {10.1016/j.tree.2021.03.006},
    publisher = {Elsevier {BV}},
    }
  • [DOI] A. E. Gorbalenya and C. Lauber, “Phylogeny of viruses,” in Encyclopedia of virology, Elsevier, 2021, p. 116–123.
    [Bibtex]
    @InCollection{Gorbalenya:21a,
    author = {Alexander E. Gorbalenya and Chris Lauber},
    booktitle = {Encyclopedia of Virology},
    publisher = {Elsevier},
    title = {Phylogeny of Viruses},
    year = {2021},
    pages = {116--123},
    doi = {10.1016/b978-0-12-814515-9.00118-1},
    }
  • [DOI] K. K. Li, M. Y. Woo, O. Stirrup, J. Hughes, A. Ho, A. D. S. Filipe, N. Johnson, K. Smollett, D. Mair, S. Carmichael, L. Tong, J. Nichols, E. Aranday-Cortes, K. Brunker, Y. A. Parr, K. Nomikou, S. E. McDonald, M. Niebel, P. Asamaphan, V. B. Sreenu, D. L. Robertson, A. Taggart, N. Jesudason, R. Shah, J. Shepherd, J. Singer, A. H. M. Taylor, Z. Cousland, J. Price, J. S. Lees, T. P. W. Jones, C. V. Lopez, A. MacLean, I. Starinskij, R. Gunson, S. T. W. Morris, P. C. Thomson, C. C. Geddes, J. P. Traynor, J. Breuer, E. C. Thomson, and P. B. Mark, “Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units – a high risk community-hospital interface,” J Infect, 2021.
    [Bibtex]
    @Article{Li:21,
    author = {Kathy K. Li and Y. Mun Woo and Oliver Stirrup and Joseph Hughes and Antonia Ho and Ana Da Silva Filipe and Natasha Johnson and Katherine Smollett and Daniel Mair and Stephen Carmichael and Lily Tong and Jenna Nichols and Elihu Aranday-Cortes and Kirstyn Brunker and Yasmin A. Parr and Kyriaki Nomikou and Sarah E. McDonald and Marc Niebel and Patawee Asamaphan and Vattipally B Sreenu and David L. Robertson and Aislynn Taggart and Natasha Jesudason and Rajiv Shah and James Shepherd and Josh Singer and Alison H.M. Taylor and Zoe Cousland and Jonathan Price and Jennifer S. Lees and Timothy P.W. Jones and Carlos Varon Lopez and Alasdair MacLean and Igor Starinskij and Rory Gunson and Scott T.W. Morris and Peter C. Thomson and Colin C. Geddes and Jamie P. Traynor and Judith Breuer and Emma C. Thomson and Patrick B. Mark},
    journal = {{J Infect}},
    title = {Genetic epidemiology of {SARS}-{CoV}-2 transmission in renal dialysis units - a high risk community-hospital interface},
    year = {2021},
    doi = {10.1016/j.jinf.2021.04.020},
    publisher = {Elsevier {BV}},
    }
  • [DOI] S. Dallari, T. Heaney, A. Rosas-Villegas, J. A. Neil, S. Wong, J. J. Brown, K. Urbanek, C. Herrmann, D. P. Depledge, T. S. Dermody, and K. Cadwell, “Enteric viruses evoke broad host immune responses resembling those elicited by the bacterial microbiome.,” Cell Host Microbe, 2021.
    [Bibtex]
    @Article{Dallari:21,
    author = {Dallari, Simone and Heaney, Thomas and Rosas-Villegas, Adriana and Neil, Jessica A. and Wong, Serre-Yu and Brown, Judy J. and Urbanek, Kelly and Herrmann, Christin and Depledge, Daniel P. and Dermody, Terence S. and Cadwell, Ken},
    journal = {{Cell Host Microbe}},
    title = {Enteric viruses evoke broad host immune responses resembling those elicited by the bacterial microbiome.},
    year = {2021},
    abstract = {The contributions of the viral component of the microbiome-the virome-to the development of innate and adaptive immunity are largely unknown. Here, we systematically defined the host response in mice to a panel of eukaryotic enteric viruses representing six different families. Infections with most of these viruses were asymptomatic in the mice, the magnitude and duration of which was dependent on the microbiota. Flow cytometric and transcriptional profiling of mice mono-associated with these viruses unveiled general adaptations by the host, such as lymphocyte differentiation and IL-22 signatures in the intestine, as well as numerous viral-strain-specific responses that persisted. Comparison with a dataset derived from analogous bacterial mono-association in mice identified bacterial species that evoke an immune response comparable with the viruses we examined. These results expand an understanding of the immune space occupied by the enteric virome and underscore the importance of viral exposure events.},
    doi = {10.1016/j.chom.2021.03.015},
    keywords = {enteric virome; host-virome relationship; regulation of the enteric immune system; virome; virus},
    pmid = {33894129},
    pubstate = {aheadofprint},
    }
  • [DOI] L. Wang, A. L. Rosales Rosas, L. De Coninck, C. Shi, J. Bouckaert, J. Matthijnssens, and L. Delang, “Establishment of Culex modestus in belgium and a glance into the virome of Belgian mosquito species.,” Msphere, vol. 6, 2021.
    [Bibtex]
    @Article{Wang:21,
    author = {Wang, Lanjiao and Rosales Rosas, Ana Lucia and De Coninck, Lander and Shi, Chenyan and Bouckaert, Johanna and Matthijnssens, Jelle and Delang, Leen},
    journal = {mSphere},
    title = {Establishment of {C}ulex modestus in Belgium and a Glance into the Virome of {B}elgian Mosquito Species.},
    year = {2021},
    volume = {6},
    abstract = {mosquitoes are considered potential transmission vectors of West Nile virus and Usutu virus. Their presence has been reported across several European countries, including one larva detected in Belgium in 2018. In this study, mosquitoes were collected in the city of Leuven and surrounding areas in the summers of 2019 and 2020. Species identification was performed based on morphological features and partial sequences of the mitochondrial cytochrome oxidase subunit I (COI) gene. The 107 mosquitoes collected in 2019 belonged to eight mosquito species, (24.3%), (48.6%), (0.9%), (0.9%), (0.9%), (14.0%), (9.3%), and (0.9%), suggesting the presence of an established population in Belgium. The collection of mosquitoes at the same locations in 2020 confirmed their establishment in the region. Haplotype network analysis of the COI sequences for showed that the Belgian population is rather diverse, suggesting that it may have been established in Belgium for some time. The Belgian population was most closely related to populations from the United Kingdom and Germany. Characterization of the virome of the collected mosquitoes resulted in the identification of at least 33 eukaryotic viral species. Nine (nearly) complete genomes belonging to 6 viral species were identified, all of which were closely related to known viruses. In conclusion, here, we report the presence of in the surrounding areas of Leuven, Belgium. As this species is considered to be a vector of several arboviruses, the implementation of vector surveillance programs to monitor this species is recommended. mosquitoes are considered to be a potential "bridge" vector, being able to transmit pathogens between birds as well as from birds to mammals, including humans. In Belgium, this mosquito species was considered absent until the finding of one larva in 2018 and subsequent evidence of a large population in 2019 to 2020 described here. We collected mosquitoes in the summers of 2019 and 2020 in the city of Leuven and surrounding areas. The mosquito species was identified by morphological and molecular methods, demonstrating the presence of in this region. The ability of mosquitoes to transmit pathogens can depend on several factors, one of them being their natural virus composition. Therefore, we identified the mosquito-specific viruses harbored by Belgian mosquitoes. As is able to transmit viruses such as West Nile virus and Usutu virus, the establishment of this mosquito species may increase the risk of virus transmission in the region. It is thus advisable to implement mosquito surveillance programs to monitor this species.},
    doi = {10.1128/mSphere.01229-20},
    issue = {2},
    keywords = {Belgium; Culex modestus; haplotype; mosquito; virome},
    pmid = {33883261},
    pubstate = {epublish},
    }
  • [DOI] J. Lei, Y. Ma-Lauer, Y. Han, M. Thoms, R. Buschauer, J. Jores, V. Thiel, R. Beckmann, W. Deng, H. Leonhardt, R. Hilgenfeld, and A. von Brunn, “The SARS-unique domain (SUD) of SARS-CoV and SARS-CoV-2 interacts with human paip1 to enhance viral RNA translation,” EMBO J, 2021.
    [Bibtex]
    @Article{Lei:21,
    author = {Jian Lei and Yue Ma-Lauer and Yinze Han and Matthias Thoms and Robert Buschauer and Joerg Jores and Volker Thiel and Roland Beckmann and Wen Deng and Heinrich Leonhardt and Rolf Hilgenfeld and Albrecht von Brunn},
    journal = {{EMBO J}},
    title = {The {SARS}-unique domain ({SUD}) of {SARS}-{CoV} and {SARS}-{CoV}-2 interacts with human Paip1 to enhance viral {RNA} translation},
    year = {2021},
    doi = {10.15252/embj.2019102277},
    publisher = {{EMBO}},
    }
  • [DOI] J. F. Gogarten, M. Rühlemann, E. Archie, J. Tung, C. Akoua-Koffi, C. Bang, T. Deschner, J. Muyembe-Tamfun, M. M. Robbins, G. Schubert, M. Surbeck, R. M. Wittig, K. Zuberbühler, J. F. Baines, A. Franke, F. H. Leendertz, and S. Calvignac-Spencer, “Primate phageomes are structured by superhost phylogeny and environment,” Proc Natl Acad Sci, vol. 118, iss. 15, p. e2013535118, 2021.
    [Bibtex]
    @Article{Gogarten:21,
    author = {Jan F. Gogarten and Malte Rühlemann and Elizabeth Archie and Jenny Tung and Chantal Akoua-Koffi and Corinna Bang and Tobias Deschner and Jean-Jacques Muyembe-Tamfun and Martha M. Robbins and Grit Schubert and Martin Surbeck and Roman M. Wittig and Klaus Zuberbühler and John F. Baines and Andre Franke and Fabian H. Leendertz and S{\'{e}}bastien Calvignac-Spencer},
    journal = {{Proc Natl Acad Sci}},
    title = {Primate phageomes are structured by superhost phylogeny and environment},
    year = {2021},
    number = {15},
    pages = {e2013535118},
    volume = {118},
    doi = {10.1073/pnas.2013535118},
    publisher = {Proceedings of the National Academy of Sciences},
    }
  • [DOI] J. J. Fros, I. Visser, B. Tang, K. Yan, E. Nakayama, T. M. Visser, C. J. M. Koenraadt, M. M. van Oers, G. P. Pijlman, A. Suhrbier, and P. Simmonds, “The dinucleotide composition of the Zika virus genome is shaped by conflicting evolutionary pressures in mammalian hosts and mosquito vectors,” PLoS Biol, vol. 19, iss. 4, p. e3001201, 2021.
    [Bibtex]
    @Article{Fros:21,
    author = {Jelke J. Fros and Imke Visser and Bing Tang and Kexin Yan and Eri Nakayama and Tessa M. Visser and Constantianus J. M. Koenraadt and Monique M. van Oers and Gorben P. Pijlman and Andreas Suhrbier and Peter Simmonds},
    journal = {{PLoS Biol}},
    title = {The dinucleotide composition of the {Zika} virus genome is shaped by conflicting evolutionary pressures in mammalian hosts and mosquito vectors},
    year = {2021},
    number = {4},
    pages = {e3001201},
    volume = {19},
    doi = {10.1371/journal.pbio.3001201},
    editor = {Claudia Bank},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] R. Gilroy, A. Ravi, M. Getino, I. Pursley, D. L. Horton, N. Alikhan, D. Baker, K. Gharbi, N. Hall, M. Watson, E. M. Adriaenssens, E. Foster-Nyarko, S. Jarju, A. Secka, M. Antonio, A. Oren, R. R. Chaudhuri, R. L. Ragione, F. Hildebrand, and M. J. Pallen, “Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture,” PeerJ, vol. 9, p. e10941, 2021.
    [Bibtex]
    @Article{Gilroy:21,
    author = {Rachel Gilroy and Anuradha Ravi and Maria Getino and Isabella Pursley and Daniel L. Horton and Nabil-Fareed Alikhan and Dave Baker and Karim Gharbi and Neil Hall and Mick Watson and Evelien M. Adriaenssens and Ebenezer Foster-Nyarko and Sheikh Jarju and Arss Secka and Martin Antonio and Aharon Oren and Roy R. Chaudhuri and Roberto La Ragione and Falk Hildebrand and Mark J. Pallen},
    journal = {{PeerJ}},
    title = {Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture},
    year = {2021},
    pages = {e10941},
    volume = {9},
    doi = {10.7717/peerj.10941},
    publisher = {{PeerJ}},
    }
  • [DOI] A. Greinacher, K. Selleng, J. Wesche, S. Handtke, R. Palankar, K. Aurich, M. Lalk, K. Methling, U. Völker, C. Hentschker, S. Michalik, L. Steil, L. Schönborn, M. Beer, K. Franzke, C. Rangaswamy, R. K. Mailer, T. Thiele, S. Kochanek, L. Krutzke, F. Siegerist, N. Endlich, T. E. Warkentin, and T. Renné, “Towards understanding ChAdOx1 nCov-19 vaccine-induced immune thrombotic thrombocytopenia (VITT),” Research Square, 2021.
    [Bibtex]
    @Article{Greinacher:21,
    author = {Andreas Greinacher and Kathleen Selleng and Jan Wesche and Stefan Handtke and Raghavendra Palankar and Konstanze Aurich and Michael Lalk and Karen Methling and Uwe Völker and Christian Hentschker and Stephan Michalik and Leif Steil and Linda Schönborn and Martin Beer and Kati Franzke and Chandini Rangaswamy and Reiner K. Mailer and Thomas Thiele and Stefan Kochanek and Lea Krutzke and Florian Siegerist and Nicole Endlich and Theodore E. Warkentin and Thomas Renn{\'{e}}},
    journal = {{Research Square}},
    title = {Towards Understanding {ChAdOx}1 {nCov}-19 Vaccine-induced Immune Thrombotic Thrombocytopenia ({VITT})},
    year = {2021},
    doi = {10.21203/rs.3.rs-440461/v1},
    publisher = {Research Square Platform {LLC}},
    }
  • [DOI] L. Chen, D. Wang, S. Garmaeva, A. Kurilshikov, A. V. Vila, R. Gacesa, T. Sinha, E. Segal, R. K. Weersma, C. Wijmenga, A. Zhernakova, and J. Fu, “The long-term genetic stability and individual specificity of the human gut microbiome,” Cell, 2021.
    [Bibtex]
    @Article{Chen:21a,
    author = {Lianmin Chen and Daoming Wang and Sanzhima Garmaeva and Alexander Kurilshikov and Arnau Vich Vila and Ranko Gacesa and Trishla Sinha and Eran Segal and Rinse K. Weersma and Cisca Wijmenga and Alexandra Zhernakova and Jingyuan Fu},
    journal = {Cell},
    title = {The long-term genetic stability and individual specificity of the human gut microbiome},
    year = {2021},
    doi = {10.1016/j.cell.2021.03.024},
    publisher = {Elsevier {BV}},
    }
  • [DOI] A. N. Aziz, V. M. Corman, A. K. C. Echterhoff, M. A. Müller, A. Richter, A. Schmandke, M. L. Schmidt, T. H. Schmidt, F. M. de Vries, C. Drosten, and M. M. B. Breteler, “Seroprevalence and correlates of SARS-CoV-2 neutralizing antibodies from a population-based study in Bonn, Germany,” Nat Commun, vol. 12, iss. 1, 2021.
    [Bibtex]
    @Article{Aziz:21,
    author = {N. Ahmad Aziz and Victor M. Corman and Antje K. C. Echterhoff and Marcel A. Müller and Anja Richter and Antonio Schmandke and Marie Luisa Schmidt and Thomas H. Schmidt and Folgerdiena M. de Vries and Christian Drosten and Monique M. B. Breteler},
    journal = {{Nat Commun}},
    title = {Seroprevalence and correlates of {SARS}-{CoV}-2 neutralizing antibodies from a population-based study in {B}onn, {G}ermany},
    year = {2021},
    number = {1},
    volume = {12},
    doi = {10.1038/s41467-021-22351-5},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] S. L. Hong, P. Lemey, M. A. Suchard, and G. Baele, “Bayesian phylogeographic analysis incorporating predictors and individual travel histories in BEAST,” Current protocols, vol. 1, iss. 4, 2021.
    [Bibtex]
    @Article{Hong:21,
    author = {Samuel L. Hong and Philippe Lemey and Marc A. Suchard and Guy Baele},
    journal = {Current Protocols},
    title = {Bayesian Phylogeographic Analysis Incorporating Predictors and Individual Travel Histories in {BEAST}},
    year = {2021},
    number = {4},
    volume = {1},
    doi = {10.1002/cpz1.98},
    publisher = {Wiley},
    }
  • [DOI] T. Schwarz, K. Heiss, Y. Mahendran, F. Casilag, F. Kurth, L. E. Sander, C. Wendtner, M. A. Hoechstetter, M. A. Müller, R. Sekul, C. Drosten, V. Stadler, and V. M. Corman, “SARS-CoV-2 proteome-wide analysis revealed significant epitope signatures in COVID-19 patients,” Front Immunol, vol. 12, 2021.
    [Bibtex]
    @Article{Schwarz:21,
    author = {Tatjana Schwarz and Kirsten Heiss and Yuvaraj Mahendran and Fiordiligie Casilag and Florian Kurth and Leif E. Sander and Clemens-Martin Wendtner and Manuela A. Hoechstetter and Marcel A. Müller and Renate Sekul and Christian Drosten and Volker Stadler and Victor M. Corman},
    journal = {{Front Immunol}},
    title = {{SARS}-{CoV}-2 Proteome-Wide Analysis Revealed Significant Epitope Signatures in {COVID}-19 Patients},
    year = {2021},
    volume = {12},
    doi = {10.3389/fimmu.2021.629185},
    publisher = {Frontiers Media {SA}},
    }
  • [DOI] J. J. C. de Vries, J. R. Brown, N. Couto, M. Beer, P. Le Mercier, I. Sidorov, A. Papa, N. Fischer, B. B. Oude Munnink, C. Rodriquez, M. Zaheri, A. Sayiner, M. Hönemann, A. Pérez-Cataluña, E. C. Carbo, C. Bachofen, J. Kubacki, D. Schmitz, K. Tsioka, S. Matamoros, D. Höper, M. Hernandez, E. Puchhammer-Stöckl, A. Lebrand, M. Huber, P. Simmonds, E. C. J. Claas, and X. F. López-Labrador, “Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting,” J Clin Virol, vol. 138, p. 104812, 2021.
    [Bibtex]
    @Article{Vries:21,
    author = {Jutte J.C. de Vries and Julianne R. Brown and Natacha Couto and Martin Beer and Philippe {Le Mercier} and Igor Sidorov and Anna Papa and Nicole Fischer and Bas B. {Oude Munnink} and Christophe Rodriquez and Maryam Zaheri and Arzu Sayiner and Mario Hönemann and Alba Pérez-Cataluña and Ellen C. Carbo and Claudia Bachofen and Jakub Kubacki and Dennis Schmitz and Katerina Tsioka and S{\'{e}}bastien Matamoros and Dirk Höper and Marta Hernandez and Elisabeth Puchhammer-Stöckl and Aitana Lebrand and Michael Huber and Peter Simmonds and Eric C.J. Claas and F. Xavier L{\'{o}}pez-Labrador},
    journal = {{J Clin Virol}},
    title = {Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part {II}: bioinformatic analysis and reporting},
    year = {2021},
    pages = {104812},
    volume = {138},
    doi = {10.1016/j.jcv.2021.104812},
    publisher = {Elsevier {BV}},
    }
  • [DOI] N. R. Faria, T. A. Mellan, C. Whittaker, I. M. Claro, D. S. da Candido, S. Mishra, M. A. E. Crispim, F. C. S. Sales, I. Hawryluk, J. T. McCrone, R. J. G. Hulswit, L. A. M. Franco, M. S. Ramundo, J. G. de Jesus, P. S. Andrade, T. M. Coletti, G. M. Ferreira, C. A. M. Silva, E. R. Manuli, R. H. M. Pereira, P. S. Peixoto, M. U. G. Kraemer, N. Gaburo, C. C. da Camilo, H. Hoeltgebaum, W. M. Souza, E. C. Rocha, L. M. de Souza, M. C. de Pinho, L. J. T. Araujo, F. S. V. Malta, A. B. de Lima, J. P. do Silva, D. A. G. Zauli, A. C. S. de Ferreira, R. P. Schnekenberg, D. J. Laydon, P. G. T. Walker, H. M. Schlüter, A. L. P. dos Santos, M. S. Vidal, V. D. S. Caro, R. M. F. Filho, H. M. dos Santos, R. S. Aguiar, J. L. Proença-Modena, B. Nelson, J. A. Hay, M. Monod, X. Miscouridou, H. Coupland, R. Sonabend, M. Vollmer, A. Gandy, C. A. Prete, V. H. Nascimento, M. A. Suchard, T. A. Bowden, S. L. K. Pond, C. Wu, O. Ratmann, N. M. Ferguson, C. Dye, N. J. Loman, P. Lemey, A. Rambaut, N. A. Fraiji, M. P. S. S. do Carvalho, O. G. Pybus, S. Flaxman, S. Bhatt, and E. C. Sabino, “Genomics and epidemiology of the p.1 SARS-CoV-2 lineage in Manaus, Brazil,” Science, p. eabh2644, 2021.
    [Bibtex]
    @Article{Faria:21,
    author = {Nuno R. Faria and Thomas A. Mellan and Charles Whittaker and Ingra M. Claro and Darlan da S. Candido and Swapnil Mishra and Myuki A. E. Crispim and Flavia C. S. Sales and Iwona Hawryluk and John T. McCrone and Ruben J. G. Hulswit and Lucas A. M. Franco and Mariana S. Ramundo and Jaqueline G. de Jesus and Pamela S. Andrade and Thais M. Coletti and Giulia M. Ferreira and Camila A. M. Silva and Erika R. Manuli and Rafael H. M. Pereira and Pedro S. Peixoto and Moritz U. G. Kraemer and Nelson Gaburo and Cecilia da C. Camilo and Henrique Hoeltgebaum and William M. Souza and Esmenia C. Rocha and Leandro M. de Souza and Mariana C. de Pinho and Leonardo J. T Araujo and Frederico S. V. Malta and Aline B. de Lima and Joice do P. Silva and Danielle A. G. Zauli and Alessandro C. de S. Ferreira and Ricardo P Schnekenberg and Daniel J. Laydon and Patrick G. T. Walker and Hannah M. Schlüter and Ana L. P. dos Santos and Maria S. Vidal and Valentina S. Del Caro and Rosinaldo M. F. Filho and Helem M. dos Santos and Renato S. Aguiar and Jos{\'{e}} L. Proen{\c{c}}a-Modena and Bruce Nelson and James A. Hay and M{\'{e}}lodie Monod and Xenia Miscouridou and Helen Coupland and Raphael Sonabend and Michaela Vollmer and Axel Gandy and Carlos A. Prete and Vitor H. Nascimento and Marc A. Suchard and Thomas A. Bowden and Sergei L. K. Pond and Chieh-Hsi Wu and Oliver Ratmann and Neil M. Ferguson and Christopher Dye and Nick J. Loman and Philippe Lemey and Andrew Rambaut and Nelson A. Fraiji and Maria do P. S. S. Carvalho and Oliver G. Pybus and Seth Flaxman and Samir Bhatt and Ester C. Sabino},
    journal = {Science},
    title = {Genomics and epidemiology of the P.1 {SARS}-{CoV}-2 lineage in {M}anaus, {B}razil},
    year = {2021},
    pages = {eabh2644},
    doi = {10.1126/science.abh2644},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
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    [Bibtex]
    @Article{Zablocki:21,
    author = {Olivier D. Zablocki and Michelle Michelsen and Marie Burris and Natalie Solonenko and Joanna Warwick-Dugdale and Romik Ghosh and Jennifer Pett-Ridge and Matthew B. Sullivan and Ben Temperton},
    journal = {{PeerJ}},
    title = {{VirION}2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature},
    year = {2021},
    pages = {e11088},
    volume = {9},
    doi = {10.7717/peerj.11088},
    publisher = {{PeerJ}},
    }
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    [Bibtex]
    @Article{Steiner:21,
    author = {Andrea Steiner and Mathias W. 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}},
    }
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    [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}},
    }
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    [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}},
    }
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    [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},
    }
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    [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},
    }
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    [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},
    }
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    [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},
    }
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    [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},
    }
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    [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},
    }
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    [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},
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    publisher = {Cold Spring Harbor Laboratory},
    }
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    [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}},
    }
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    [Bibtex]
    @Article{TaroncherOldenburg:21,
    author = {Gaspar Taroncher-Oldenburg and Christin Müller and Wiebke Obermann and John Ziebuhr and Roland K. Hartmann and Arnold Grünweller},
    journal = {Microorganisms},
    title = {Targeting the {DEAD}-Box {RNA} Helicase {eIF}4A with Rocaglates{\textemdash}A Pan-Antiviral Strategy for Minimizing the Impact of Future {RNA} Virus Pandemics},
    year = {2021},
    number = {3},
    pages = {540},
    volume = {9},
    doi = {10.3390/microorganisms9030540},
    publisher = {{MDPI} {AG}},
    }
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    [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}},
    }
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    [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}},
    }
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    [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} {I}mplementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing},
    year = {2021},
    number = {4},
    pages = {677},
    volume = {9},
    doi = {10.3390/microorganisms9040677},
    publisher = {{MDPI} {AG}},
    }
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    [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}},
    }
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    [Bibtex]
    @Article{VelazquezMoctezuma:21,
    author = {Rodrigo Vel{\'{a}}zquez-Moctezuma and Elias H. Augestad and Matteo Castelli and Christina Holmboe Olesen and Nicola Clementi and Massimo Clementi and Nicasio Mancini and Jannick Prentoe},
    journal = {Vaccines},
    title = {Mechanisms of Hepatitis {C} Virus Escape from Vaccine-Relevant Neutralizing Antibodies},
    year = {2021},
    number = {3},
    pages = {291},
    volume = {9},
    doi = {10.3390/vaccines9030291},
    publisher = {{MDPI} {AG}},
    }
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    [Bibtex]
    @Article{Lorenzo:21,
    author = {Roberto J. Hermida Lorenzo and D{\'{a}}niel Cadar and Fara Raymond Koundouno and Javier Juste and Alexandra Bialonski and Heike Baum and Juan Luis Garc{\'{\i}}a-Mudarra and Henry Hakamaki and Andr{\'{a}}s Bencsik and Emily V. Nelson and Miles W. Carroll and N'Faly Magassouba and Stephan Günther and Jonas Schmidt-Chanasit and C{\'{e}}sar Mu{\~{n}}oz Fontela and Beatriz Escudero-P{\'{e}}rez},
    journal = {Microorganisms},
    title = {Metagenomic Snapshots of Viral Components in Guinean Bats},
    year = {2021},
    number = {3},
    pages = {599},
    volume = {9},
    doi = {10.3390/microorganisms9030599},
    publisher = {{MDPI} {AG}},
    }
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    [Bibtex]
    @Article{Turner:21,
    author = {Dann Turner and Andrew M. Kropinski and Evelien M. Adriaenssens},
    journal = {Viruses},
    title = {A Roadmap for Genome-Based Phage Taxonomy},
    year = {2021},
    number = {3},
    pages = {506},
    volume = {13},
    doi = {10.3390/v13030506},
    publisher = {{MDPI} {AG}},
    }
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    [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}},
    }
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    [Bibtex]
    @Article{Tsitsilonis:21,
    author = {Ourania E. Tsitsilonis and Dimitrios Paraskevis and Evi Lianidou and Evangelos Terpos and Athanasios Akalestos and Vassilios Pierros and Evangelia-Georgia Kostaki and Efstathios Kastritis and Paraskevi Moutsatsou and Marianna Politou and Andreas Scorilas and Thomas Sphicopoulos and Nikolaos Thomaidis and Ioannis P. Trougakos and Athanassios Tsakris and Nikolaos Voulgaris and Christina C. Daskalaki and Zoi Evangelakou and Christina Fouki and Despoina D. Gianniou and Sentiljana Gumeni and Ioannis V. Kostopoulos and Maria S. Manola and Nikolaos Orologas-Stavrou and Chrysanthi Panteli and Eleni-Dimitra Papanagnou and Pantelis Rousakis and Aimilia D. Sklirou and Stavroula Smilkou and Dimitra Stergiopoulou and Sotirios Tsiodras and Meletios-Athanasios Dimopoulos and Petros P. Sfikakis},
    journal = {Vaccines},
    title = {{SARS}-{CoV}-2 Infection Is Asymptomatic in Nearly Half of Adults with Robust Anti-Spike Protein Receptor-Binding Domain Antibody Response},
    year = {2021},
    number = {3},
    pages = {207},
    volume = {9},
    doi = {10.3390/vaccines9030207},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] C. Kohl, A. Brinkmann, A. Radonić, P. W. Dabrowski, K. Mühldorfer, A. Nitsche, G. Wibbelt, and A. Kurth, “The virome of German bats: comparing virus discovery approaches,” Sci Rep, vol. 11, iss. 1, 2021.
    [Bibtex]
    @Article{Kohl:21,
    author = {Claudia Kohl and Annika Brinkmann and Aleksandar Radoni{\'{c}} and Piotr Wojtek Dabrowski and Kristin Mühldorfer and Andreas Nitsche and Gudrun Wibbelt and Andreas Kurth},
    journal = {{Sci Rep}},
    title = {The virome of {G}erman bats: comparing virus discovery approaches},
    year = {2021},
    number = {1},
    volume = {11},
    doi = {10.1038/s41598-021-86435-4},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] A. Berger, M. T. N. Nsoga, F. J. Perez-Rodriguez, Y. A. Aad, P. Sattonnet-Roche, A. Gayet-Ageron, C. Jaksic, G. Torriani, E. Boehm, I. Kronig, J. A. Sacks, M. de Vos, F. J. Bausch, F. Chappuis, A. Renzoni, L. Kaiser, M. Schibler, and I. Eckerle, “Diagnostic accuracy of two commercial SARS-CoV-2 antigen-detecting rapid tests at the point of care in community-based testing centers,” PLoS One, vol. 16, iss. 3, p. e0248921, 2021.
    [Bibtex]
    @Article{Berger:21,
    author = {Alice Berger and Marie Therese Ngo Nsoga and Francisco Javier Perez-Rodriguez and Yasmine Abi Aad and Pascale Sattonnet-Roche and Ang{\`{e}}le Gayet-Ageron and Cyril Jaksic and Giulia Torriani and Erik Boehm and Ilona Kronig and Jilian A. Sacks and Margaretha de Vos and Fr{\'{e}}d{\'{e}}rique Jacquerioz Bausch and Fran{\c{c}}ois Chappuis and Adriana Renzoni and Laurent Kaiser and Manuel Schibler and Isabella Eckerle},
    journal = {{PLoS One}},
    title = {Diagnostic accuracy of two commercial {SARS}-{CoV}-2 antigen-detecting rapid tests at the point of care in community-based testing centers},
    year = {2021},
    number = {3},
    pages = {e0248921},
    volume = {16},
    doi = {10.1371/journal.pone.0248921},
    editor = {Nei-yuan Hsiao},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] S. Deinhardt-Emmer, D. Wittschieber, J. Sanft, S. Kleemann, S. Elschner, K. F. Haupt, V. Vau, C. Häring, J. Rödel, A. Henke, C. Ehrhardt, M. Bauer, M. Philipp, N. Gaßler, S. Nietzsche, B. Löffler, and G. Mall, “Early postmortem mapping of SARS-CoV-2 RNA in patients with COVID-19 and the correlation with tissue damage,” eLife, vol. 10, 2021.
    [Bibtex]
    @Article{DeinhardtEmmer:21a,
    author = {Stefanie Deinhardt-Emmer and Daniel Wittschieber and Juliane Sanft and Sandra Kleemann and Stefan Elschner and Karoline Frieda Haupt and Vanessa Vau and Clio Häring and Jürgen Rödel and Andreas Henke and Christina Ehrhardt and Michael Bauer and Mike Philipp and Nikolaus Ga{\ss}ler and Sandor Nietzsche and Bettina Löffler and Gita Mall},
    journal = {{eLife}},
    title = {Early postmortem mapping of {SARS}-{CoV}-2 {RNA} in patients with {COVID}-19 and the correlation with tissue damage},
    year = {2021},
    volume = {10},
    doi = {10.7554/elife.60361},
    publisher = {{eLife} Sciences Publications, Ltd},
    }
  • [DOI] P. V’kovski, M. Gultom, J. N. Kelly, S. Steiner, J. Russeil, B. Mangeat, E. Cora, J. Pezoldt, M. Holwerda, A. Kratzel, L. Laloli, M. Wider, J. Portmann, T. Tran, N. Ebert, H. Stalder, R. Hartmann, V. Gardeux, D. Alpern, B. Deplancke, V. Thiel, and R. Dijkman, “Disparate temperature-dependent virus-host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epithelium.,” PLoS Biol, vol. 19, p. e3001158, 2021.
    [Bibtex]
    @Article{Vkovski:21,
    author = {V'kovski, Philip and Gultom, Mitra and Kelly, Jenna N. and Steiner, Silvio and Russeil, Julie and Mangeat, Bastien and Cora, Elisa and Pezoldt, Joern and Holwerda, Melle and Kratzel, Annika and Laloli, Laura and Wider, Manon and Portmann, Jasmine and Tran, Thao and Ebert, Nadine and Stalder, Hanspeter and Hartmann, Rune and Gardeux, Vincent and Alpern, Daniel and Deplancke, Bart and Thiel, Volker and Dijkman, Ronald},
    journal = {{PLoS Biol}},
    title = {Disparate temperature-dependent virus-host dynamics for {SARS-CoV-2} and {SARS-CoV} in the human respiratory epithelium.},
    year = {2021},
    pages = {e3001158},
    volume = {19},
    abstract = {Since its emergence in December 2019, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread globally and become a major public health burden. Despite its close phylogenetic relationship to SARS-CoV, SARS-CoV-2 exhibits increased human-to-human transmission dynamics, likely due to efficient early replication in the upper respiratory epithelium of infected individuals. Since different temperatures encountered in the human upper and lower respiratory tract (33°C and 37°C, respectively) have been shown to affect the replication kinetics of several respiratory viruses, as well as host innate immune response dynamics, we investigated the impact of temperature on SARS-CoV-2 and SARS-CoV infection using the primary human airway epithelial cell culture model. SARS-CoV-2, in contrast to SARS-CoV, replicated to higher titers when infections were performed at 33°C rather than 37°C. Although both viruses were highly sensitive to type I and type III interferon pretreatment, a detailed time-resolved transcriptome analysis revealed temperature-dependent interferon and pro-inflammatory responses induced by SARS-CoV-2 that were inversely proportional to its replication efficiency at 33°C or 37°C. These data provide crucial insight on pivotal virus-host interaction dynamics and are in line with characteristic clinical features of SARS-CoV-2 and SARS-CoV, as well as their respective transmission efficiencies.},
    doi = {10.1371/journal.pbio.3001158},
    issue = {3},
    pmid = {33780434},
    pubstate = {epublish},
    }
  • [DOI] C. Chen, S. Nadeau, I. Topolsky, M. Manceau, J. S. Huisman, K. P. Jablonski, L. Fuhrmann, D. Dreifuss, K. Jahn, C. Beckmann, M. Redondo, O. Kobel, C. Noppen, L. Risch, M. Risch, N. Wohlwend, S. Kas, T. Bodmer, T. Roloff, M. Stange, A. Egli, I. Eckerle, R. Denes, M. Feldkamp, I. Nissen, N. Santacroce, E. Burcklen, C. Aquino, A. C. de Gouvea, M. D. Moccia, S. Grüter, T. Sykes, L. Opitz, G. White, L. Neff, D. Popovic, A. Patrignani, J. Tracy, R. Schlapbach, E. T. Dermitzakis, K. Harshman, I. Xenarios, H. Pegeot, L. Cerutti, D. Penet, A. Blin, M. Elies, C. Althaus, C. Beisel, N. Beerenwinkel, M. Ackermann, and T. Stadler, “Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland,” medRxiv, 2021.
    [Bibtex]
    @Article{Chen:21,
    author = {Chaoran Chen and Sarah Nadeau and Ivan Topolsky and Marc Manceau and Jana S. Huisman and Kim Philipp Jablonski and Lara Fuhrmann and David Dreifuss and Katharina Jahn and Christiane Beckmann and Maurice Redondo and Olivier Kobel and Christoph Noppen and Lorenz Risch and Martin Risch and Nadia Wohlwend and Sinem Kas and Thomas Bodmer and Tim Roloff and Madlen Stange and Adrian Egli and Isabella Eckerle and Rebecca Denes and Mirjam Feldkamp and Ina Nissen and Natascha Santacroce and Elodie Burcklen and Catharine Aquino and Andreia Cabral de Gouvea and Maria Domenica Moccia and Simon Grüter and Timothy Sykes and Lennart Opitz and Griffin White and Laura Neff and Doris Popovic and Andrea Patrignani and Jay Tracy and Ralph Schlapbach and Emmanouil T. Dermitzakis and Keith Harshman and Ioannis Xenarios and Henri Pegeot and Lorenzo Cerutti and Deborah Penet and Anthony Blin and Melyssa Elies and Christian Althaus and Christian Beisel and Niko Beerenwinkel and Martin Ackermann and Tanja Stadler},
    journal = {{medRxiv}},
    title = {Quantification of the spread of {SARS}-{CoV}-2 variant {B}.1.1.7 in {S}witzerland},
    year = {2021},
    doi = {10.1101/2021.03.05.21252520},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] K. T. T. Kwok, M. M. T. de Rooij, A. B. Messink, I. M. Wouters, L. A. M. Smit, D. J. J. Heederik, M. P. G. Koopmans, and M. V. T. Phan, “Comparative viral metagenomics from chicken feces and farm dust in the Netherlands,” bioRxiv, 2021.
    [Bibtex]
    @Article{Kwok:21,
    author = {Kirsty T. T. Kwok and Myrna M. T. de Rooij and Aniek B. Messink and Inge M. Wouters and Lidwien A. M. Smit and Dick J.J. Heederik and Marion P. G. Koopmans and My V. T. Phan},
    journal = {{bioRxiv}},
    title = {Comparative viral metagenomics from chicken feces and farm dust in the {N}etherlands},
    year = {2021},
    doi = {10.1101/2021.03.09.434704},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] L. Van Espen, E. G. Bak, L. Beller, L. Close, W. Deboutte, H. Bæk. Juel, T. Nielsen, D. Sinar, L. D. Coninck, C. F. o, C. E. Fonvig, S. Jacobsen, M. Kjærgaard, M. Thiele, A. Fullam, M. Kuhn, J. Holm, P. Bork, A. Krag, T. Hansen, M. Arumugam, and J. Matthijnssens, “A previously undescribed highly prevalent phage identified in a Danish enteric virome catalogue,” Research Square, 2021.
    [Bibtex]
    @Article{Espen:21,
    author = {Lore {Van Espen} and Emilie Glad Bak and Leen Beller and Lila Close and Ward Deboutte and Helene B{\ae}k Juel and Trine Nielsen and Deniz Sinar and Lander De Coninck and Christine Frithioff-B{\o}js{\o}e and Cilius Esmann Fonvig and Suganya Jacobsen and Maria Kj{\ae}rgaard and Maja Thiele and Anthony Fullam and Michael Kuhn and Jens-Christian Holm and Peer Bork and Aleksander Krag and Torben Hansen and Manimozhiyan Arumugam and Jelle Matthijnssens},
    journal = {{Research Square}},
    title = {A previously undescribed highly prevalent phage identified in a {D}anish enteric virome catalogue},
    year = {2021},
    doi = {10.21203/rs.3.rs-273865/v1},
    publisher = {Research Square},
    }
  • [DOI] B. Schepens, L. van Schie, W. Nerinckx, K. Roose, W. V. Breedam, D. Fijalkowska, S. Devos, W. Weyts, S. D. Cae, S. Vanmarcke, C. Lonigro, H. Eeckhaut, D. V. Herpe, J. Borloo, A. F. Oliveira, J. P. Catani, S. Creytens, D. D. Vlieger, G. Michielsen, J. C. Z. Marchan, G. D. Moschonas, I. Rossey, K. Sedeyn, A. V. Hecke, X. Zhang, L. Langendries, S. Jacobs, S. ter Horst, L. Seldeslachts, L. Liesenborghs, R. Boudewijns, H. J. Thibaut, K. Dallmeier, G. V. Velde, B. Weynand, J. Beer, D. Schnepf, A. Ohnemus, I. Remory, C. S. Foo, R. Abdelnabi, P. Maes, S. J. F. Kaptein, J. Rocha-Pereira, D. Jochmans, L. Delang, F. Peelman, P. Staeheli, M. Schwemmle, N. Devoogdt, D. Tersago, M. Germani, J. Heads, A. Henry, A. Popplewell, M. Ellis, K. Brady, A. Turner, B. Dombrecht, C. Stortelers, J. Neyts, N. Callewaert, and X. Saelens, “Drug development of an affinity enhanced, broadly neutralizing heavy chain-only antibody that restricts SARS-CoV-2 in rodents,” bioRxiv, 2021.
    [Bibtex]
    @Article{Schepens:21,
    author = {Bert Schepens and Loes van Schie and Wim Nerinckx and Kenny Roose and Wander Van Breedam and Daria Fijalkowska and Simon Devos and Wannes Weyts and Sieglinde De Cae and Sandrine Vanmarcke and Chiara Lonigro and Hannah Eeckhaut and Dries Van Herpe and Jimmy Borloo and Ana Filipa Oliveira and Joao Paulo Catani and Sarah Creytens and Dorien De Vlieger and Gitte Michielsen and Jackeline Cecilia Zavala Marchan and George D. Moschonas and Iebe Rossey and Koen Sedeyn and Annelies Van Hecke and Xin Zhang and Lana Langendries and Sofie Jacobs and Sebastiaan ter Horst and Laura Seldeslachts and Laurens Liesenborghs and Robbert Boudewijns and Hendrik Jan Thibaut and Kai Dallmeier and Greetje Vande Velde and Birgit Weynand and Julius Beer and Daniel Schnepf and Annette Ohnemus and Isabel Remory and Caroline S. Foo and Rana Abdelnabi and Piet Maes and Suzanne J. F. Kaptein and Joana Rocha-Pereira and Dirk Jochmans and Leen Delang and Frank Peelman and Peter Staeheli and Martin Schwemmle and Nick Devoogdt and Dominique Tersago and Massimiliano Germani and James Heads and Alistair Henry and Andrew Popplewell and Mark Ellis and Kevin Brady and Alison Turner and Bruno Dombrecht and Catelijne Stortelers and Johan Neyts and Nico Callewaert and Xavier Saelens},
    journal = {{bioRxiv}},
    title = {Drug development of an affinity enhanced, broadly neutralizing heavy chain-only antibody that restricts {SARS}-{CoV}-2 in rodents},
    year = {2021},
    doi = {10.1101/2021.03.08.433449},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] I. Jungreis, C. W. Nelson, Z. Ardern, Y. Finkel, N. J. Krogan, K. Sato, J. Ziebuhr, N. Stern-Ginossar, A. Pavesi, A. E. Firth, A. E. Gorbalenya, and M. Kellis, “Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: a homology-based resolution,” Virology, vol. 558, p. 145–151, 2021.
    [Bibtex]
    @Article{Jungreis:21,
    author = {Irwin Jungreis and Chase W. Nelson and Zachary Ardern and Yaara Finkel and Nevan J. Krogan and Kei Sato and John Ziebuhr and Noam Stern-Ginossar and Angelo Pavesi and Andrew E. Firth and Alexander E. Gorbalenya and Manolis Kellis},
    journal = {Virology},
    title = {Conflicting and ambiguous names of overlapping {ORFs} in the {SARS}-{CoV}-2 genome: A homology-based resolution},
    year = {2021},
    pages = {145--151},
    volume = {558},
    doi = {10.1016/j.virol.2021.02.013},
    publisher = {Elsevier {BV}},
    }
  • [DOI] W. K. Jo, C. Drosten, and J. F. Drexler, “The evolutionary dynamics of endemic human coronaviruses,” Virus Evol, vol. 7, iss. 1, 2021.
    [Bibtex]
    @Article{Jo:21,
    author = {Wendy K Jo and Christian Drosten and Jan Felix Drexler},
    journal = {{Virus Evol}},
    title = {The evolutionary dynamics of endemic human coronaviruses},
    year = {2021},
    number = {1},
    volume = {7},
    doi = {10.1093/ve/veab020},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] N. Huang, P. and Pérez, T. Kato, Y. Mikami, K. Okuda, R. C. Gilmore, C. D. Conde, B. Gasmi, S. Stein, M. Beach, E. Pelayo, J. O. Maldonado, B. A. Lafont, S. Jang, N. Nasir, R. J. Padilla, V. A. Murrah, R. Maile, W. Lovell, S. M. Wallet, N. M. Bowman, S. L. Meinig, M. C. Wolfgang, S. N. Choudhury, M. Novotny, B. D. Aevermann, R. H. Scheuermann, G. Cannon, C. W. Anderson, R. E. Lee, J. T. Marchesan, M. Bush, M. Freire, A. J. Kimple, D. L. Herr, J. Rabin, A. Grazioli, S. Das, B. N. French, T. Pranzatelli, J. A. Chiorini, D. E. Kleiner, S. Pittaluga, S. M. Hewitt, P. D. Burbelo, D. Chertow, K. Frank, J. Lee, R. C. Boucher, S. A. Teichmann, B. M. Warner, and K. B. M. and, “SARS-CoV-2 infection of the oral cavity and saliva,” Nat Med, 2021.
    [Bibtex]
    @Article{Huang:21,
    author = {Ni Huang and and Paola P{\'{e}}rez and Takafumi Kato and Yu Mikami and Kenichi Okuda and Rodney C. Gilmore and Cecilia Dom{\'{\i}}nguez Conde and Billel Gasmi and Sydney Stein and Margaret Beach and Eileen Pelayo and Jose O. Maldonado and Bernard A. Lafont and Shyh-Ing Jang and Nadia Nasir and Ricardo J. Padilla and Valerie A. Murrah and Robert Maile and William Lovell and Shannon M. Wallet and Natalie M. Bowman and Suzanne L. Meinig and Matthew C. Wolfgang and Saibyasachi N. Choudhury and Mark Novotny and Brian D. Aevermann and Richard H. Scheuermann and Gabrielle Cannon and Carlton W. Anderson and Rhianna E. Lee and Julie T. Marchesan and Mandy Bush and Marcelo Freire and Adam J. Kimple and Daniel L. Herr and Joseph Rabin and Alison Grazioli and Sanchita Das and Benjamin N. French and Thomas Pranzatelli and John A. Chiorini and David E. Kleiner and Stefania Pittaluga and Stephen M. Hewitt and Peter D. Burbelo and Daniel Chertow and Karen Frank and Janice Lee and Richard C. Boucher and Sarah A. Teichmann and Blake M. Warner and Kevin M. Byrd and},
    journal = {{Nat Med}},
    title = {{SARS}-{CoV}-2 infection of the oral cavity and saliva},
    year = {2021},
    doi = {10.1038/s41591-021-01296-8},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] M. O. Pohl, I. Busnadiego, V. Kufner, I. Glas, U. Karakus, S. Schmutz, M. Zaheri, I. Abela, A. Trkola, M. Huber, S. Stertz, and B. G. Hale, “SARS-CoV-2 variants reveal features critical for replication in primary human cells,” PLoS Biol, vol. 19, iss. 3, p. e3001006, 2021.
    [Bibtex]
    @Article{Pohl:21,
    author = {Marie O. Pohl and Idoia Busnadiego and Verena Kufner and Irina Glas and Umut Karakus and Stefan Schmutz and Maryam Zaheri and Irene Abela and Alexandra Trkola and Michael Huber and Silke Stertz and Benjamin G. Hale},
    journal = {{PLoS Biol}},
    title = {{SARS}-{CoV}-2 variants reveal features critical for replication in primary human cells},
    year = {2021},
    number = {3},
    pages = {e3001006},
    volume = {19},
    doi = {10.1371/journal.pbio.3001006},
    editor = {Stacey Schultz-Cherry},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] L. Ulrich, A. Michelitsch, N. Halwe, K. Wernike, D. Hoffmann, and M. Beer, “Experimental SARS-CoV-2 infection of bank voles,” Emerg Infect Dis., vol. 27, iss. 4, p. 1193–1195, 2021.
    [Bibtex]
    @Article{Ulrich:21,
    author = {Lorenz Ulrich and Anna Michelitsch and Nico Halwe and Kerstin Wernike and Donata Hoffmann and Martin Beer},
    journal = {{Emerg Infect Dis.}},
    title = {Experimental {SARS}-{CoV}-2 Infection of Bank Voles},
    year = {2021},
    number = {4},
    pages = {1193--1195},
    volume = {27},
    doi = {10.3201/eid2704.204945},
    publisher = {Centers for Disease Control and Prevention ({CDC})},
    }
  • [DOI] J. Beck, S. Seitz, C. Lauber, and M. Nassal, “Conservation of the HBV RNA element epsilon in nackednaviruses reveals ancient origin of protein-primed reverse transcription,” Proc Natl Acad Sci USA, vol. 118, iss. 13, p. e2022373118, 2021.
    [Bibtex]
    @Article{Beck:21,
    author = {Jürgen Beck and Stefan Seitz and Chris Lauber and Michael Nassal},
    journal = {{Proc Natl Acad Sci USA}},
    title = {Conservation of the {HBV} {RNA} element epsilon in nackednaviruses reveals ancient origin of protein-primed reverse transcription},
    year = {2021},
    number = {13},
    pages = {e2022373118},
    volume = {118},
    doi = {10.1073/pnas.2022373118},
    publisher = {Proceedings of the National Academy of Sciences},
    }
  • [DOI] P. Barrat-Charlaix, J. Huddleston, T. Bedford, and R. A. Neher, “Limited predictability of amino acid substitutions in seasonal influenza viruses,” Mol Biol Evol, 2021.
    [Bibtex]
    @Article{BarratCharlaix:21,
    author = {Pierre Barrat-Charlaix and John Huddleston and Trevor Bedford and Richard A Neher},
    journal = {{Mol Biol Evol}},
    title = {Limited Predictability of Amino Acid Substitutions in Seasonal Influenza Viruses},
    year = {2021},
    doi = {10.1093/molbev/msab065},
    editor = {Thomas Leitner},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] S. Lytras, G. Arriagada, and R. J. Gifford, “Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes,” Virus Evol, vol. 7, iss. 1, 2021.
    [Bibtex]
    @Article{Lytras:21a,
    author = {Spyros Lytras and Gloria Arriagada and Robert J Gifford},
    journal = {{Virus Evol}},
    title = {Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes},
    year = {2021},
    number = {1},
    volume = {7},
    doi = {10.1093/ve/veab012},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] A. Bataille, H. Salami, I. Seck, M. M. Lo, A. Ba, M. Diop, B. Sall, C. Faye, M. Lo, L. Kaba, Y. Sidime, M. Keyra, A. O. S. Diallo, M. Niang, C. A. K. Sidibe, A. Sery, M. Dakouo, A. B. E. Mamy, A. S. E. Arbi, Y. Barry, E. Isselmou, H. Habiboullah, A. S. Lella, B. Doumbia, M. B. Gueya, C. Coste, C. S. Diaw, O. Kwiatek, G. Libeau, and A. Apolloni, “Combining viral genetic and animal mobility network data to unravel peste des petits ruminants transmission dynamics in West Africa,” PLoS Pathog, vol. 17, iss. 3, p. e1009397, 2021.
    [Bibtex]
    @Article{Bataille:21,
    author = {Arnaud Bataille and Habib Salami and Ismaila Seck and Modou Moustapha Lo and Aminata Ba and Mariame Diop and Baba Sall and Coumba Faye and Mbargou Lo and Lanceï Kaba and Youssouf Sidime and Mohamed Keyra and Alpha Oumar Sily Diallo and Mamadou Niang and Cheick Abou Kounta Sidibe and Amadou Sery and Martin Dakouo and Ahmed Bezeid El Mamy and Ahmed Salem El Arbi and Yahya Barry and Ekaterina Isselmou and Habiboullah Habiboullah and Abdellahi Salem Lella and Baba Doumbia and Mohamed Baba Gueya and Caroline Coste and C{\'{e}}cile Squarzoni Diaw and Olivier Kwiatek and Genevi{\`{e}}ve Libeau and Andrea Apolloni},
    journal = {{PLoS Pathog}},
    title = {Combining viral genetic and animal mobility network data to unravel peste des petits ruminants transmission dynamics in {W}est {A}frica},
    year = {2021},
    number = {3},
    pages = {e1009397},
    volume = {17},
    doi = {10.1371/journal.ppat.1009397},
    editor = {Guillaume Fourni{\'{e}}},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] S. Mantip, A. Sigismeau, D. Shamaki, T. Y. Woma, O. Kwiatek, G. Libeau, S. Farougou, and A. Bataille, “Molecular epidemiology of peste des petits ruminants virus in Nigeria: an update,” Transbound Emerg Dis, 2021.
    [Bibtex]
    @Article{Mantip:21,
    author = {Samuel Mantip and Anthony Sigismeau and David Shamaki and Timothy Yusuf Woma and Olivier Kwiatek and Genevieve Libeau and Souabou Farougou and Arnaud Bataille},
    journal = {{Transbound Emerg Dis}},
    title = {Molecular epidemiology of peste des petits ruminants virus in {N}igeria: an update},
    year = {2021},
    doi = {10.1111/tbed.14073},
    publisher = {Wiley},
    }
  • [DOI] B. W. Haak, R. Argelaguet, C. M. Kinsella, R. F. J. Kullberg, J. M. Lankelma, M. Deijs, M. Klein, M. F. Jebbink, F. Hugenholtz, S. Kostidis, M. Giera, T. B. M. Hakvoort, W. J. de Jonge, M. J. Schultz, T. van Gool, T. van der Poll, W. M. de Vos, L. M. van der Hoek, and J. W. Wiersinga, “Integrative transkingdom analysis of the gut microbiome in antibiotic perturbation and critical illness,” mSystems, vol. 6, iss. 2, 2021.
    [Bibtex]
    @Article{Haak:21,
    author = {Bastiaan W. Haak and Ricard Argelaguet and Cormac M. Kinsella and Robert F. J. Kullberg and Jacqueline M. Lankelma and Martin Deijs and Michelle Klein and Maarten F. Jebbink and Floor Hugenholtz and Sarantos Kostidis and Martin Giera and Theodorus B. M. Hakvoort and Wouter J. de Jonge and Marcus J. Schultz and Tom van Gool and Tom van der Poll and Willem M. de Vos and Lia M. van der Hoek and W. Joost Wiersinga},
    journal = {{mSystems}},
    title = {Integrative Transkingdom Analysis of the Gut Microbiome in Antibiotic Perturbation and Critical Illness},
    year = {2021},
    number = {2},
    volume = {6},
    doi = {10.1128/msystems.01148-20},
    editor = {Nicholas Chia},
    publisher = {American Society for Microbiology},
    }
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    @Article{Wertheim:21,
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    @Article{Juerges:21,
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    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] E. C. Thomson, L. E. Rosen, J. G. Shepherd, R. Spreafico, A. da Silva Filipe, J. A. Wojcechowskyj, C. Davis, L. Piccoli, D. J. Pascall, J. Dillen, S. Lytras, N. Czudnochowski, R. Shah, M. Meury, N. Jesudason, A. De Marco, K. Li, J. Bassi, A. O’Toole, D. Pinto, R. M. Colquhoun, K. Culap, B. Jackson, F. Zatta, A. Rambaut, S. Jaconi, V. B. Sreenu, J. Nix, I. Zhang, R. F. Jarrett, W. G. Glass, M. Beltramello, K. Nomikou, M. Pizzuto, L. Tong, E. Cameroni, T. I. Croll, N. Johnson, J. Di Iulio, A. Wickenhagen, A. Ceschi, A. M. Harbison, D. Mair, P. Ferrari, K. Smollett, F. Sallusto, S. Carmichael, C. Garzoni, J. Nichols, M. Galli, J. Hughes, A. Riva, A. Ho, M. Schiuma, M. G. Semple, P. J. M. Openshaw, E. Fadda, K. J. Baillie, J. D. Chodera, The ISARIC4C Investigators, COVID-19 Genomics UK (COG-UK) consortium, S. J. Rihn, S. J. Lycett, H. W. Virgin, A. Telenti, D. Corti, D. L. Robertson, and G. Snell, “Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity.,” Cell, 2021.
    [Bibtex]
    @Article{Thomson:21,
    author = {Thomson, Emma C. and Rosen, Laura E. and Shepherd, James G. and Spreafico, Roberto and da Silva Filipe, Ana and Wojcechowskyj, Jason A. and Davis, Chris and Piccoli, Luca and Pascall, David J. and Dillen, Josh and Lytras, Spyros and Czudnochowski, Nadine and Shah, Rajiv and Meury, Marcel and Jesudason, Natasha and De Marco, Anna and Li, Kathy and Bassi, Jessica and O'Toole, Aine and Pinto, Dora and Colquhoun, Rachel M. and Culap, Katja and Jackson, Ben and Zatta, Fabrizia and Rambaut, Andrew and Jaconi, Stefano and Sreenu, Vattipally B. and Nix, Jay and Zhang, Ivy and Jarrett, Ruth F. and Glass, William G. and Beltramello, Martina and Nomikou, Kyriaki and Pizzuto, Matteo and Tong, Lily and Cameroni, Elisabetta and Croll, Tristan I. and Johnson, Natasha and Di Iulio, Julia and Wickenhagen, Arthur and Ceschi, Alessandro and Harbison, Aoife M. and Mair, Daniel and Ferrari, Paolo and Smollett, Katherine and Sallusto, Federica and Carmichael, Stephen and Garzoni, Christian and Nichols, Jenna and Galli, Massimo and Hughes, Joseph and Riva, Agostino and Ho, Antonia and Schiuma, Marco and Semple, Malcolm G. and Openshaw, Peter J. M. and Fadda, Elisa and Baillie, J. Kenneth and Chodera, John D. and {The ISARIC4C Investigators} and {COVID-19 Genomics UK (COG-UK) consortium} and Rihn, Suzannah J. and Lycett, Samantha J. and Virgin, Herbert W. and Telenti, Amalio and Corti, Davide and Robertson, David L. and Snell, Gyorgy},
    journal = {Cell},
    title = {Circulating {SARS-CoV-2} spike {N439K} variants maintain fitness while evading antibody-mediated immunity.},
    year = {2021},
    abstract = {SARS-CoV-2 can mutate and evade immunity, with consequences for efficacy of emerging vaccines and antibody therapeutics. Here, we demonstrate that the immunodominant SARS-CoV-2 spike (S) receptor binding motif (RBM) is a highly variable region of S and provide epidemiological, clinical, and molecular characterization of a prevalent, sentinel RBM mutation, N439K. We demonstrate N439K S protein has enhanced binding affinity to the hACE2 receptor, and N439K viruses have similar in vitro replication fitness and cause infections with similar clinical outcomes as compared to wild type. We show the N439K mutation confers resistance against several neutralizing monoclonal antibodies, including one authorized for emergency use by the US Food and Drug Administration (FDA), and reduces the activity of some polyclonal sera from persons recovered from infection. Immune evasion mutations that maintain virulence and fitness such as N439K can emerge within SARS-CoV-2 S, highlighting the need for ongoing molecular surveillance to guide development and usage of vaccines and therapeutics.},
    doi = {10.1016/j.cell.2021.01.037},
    keywords = {COVID-19; N439K; SARS-CoV-2; Spike; monoclonal antibody escape; mutation; protein structure; receptor binding motif; variant},
    pmid = {33621484},
    pubstate = {aheadofprint},
    }
  • [DOI] S. J. Rihn, A. Merits, S. Bakshi, M. L. Turnbull, A. Wickenhagen, A. J. T. Alexander, C. Baillie, B. Brennan, F. Brown, K. Brunker, S. R. Bryden, K. A. Burness, S. Carmichael, S. J. Cole, V. M. Cowton, P. Davies, C. Davis, G. De Lorenzo, C. L. Donald, M. Dorward, J. I. Dunlop, M. Elliott, M. Fares, A. da Silva Filipe, J. R. Freitas, W. Furnon, R. J. Gestuveo, A. Geyer, D. Giesel, D. M. Goldfarb, N. Goodman, R. Gunson, J. C. Hastie, V. Herder, J. Hughes, C. Johnson, N. Johnson, A. Kohl, K. Kerr, H. Leech, L. S. Lello, K. Li, G. Lieber, X. Liu, R. Lingala, C. Loney, D. Mair, M. J. McElwee, S. McFarlane, J. Nichols, K. Nomikou, A. Orr, R. J. Orton, M. Palmarini, Y. A. Parr, R. M. Pinto, S. Raggett, E. Reid, D. L. Robertson, J. Royle, N. Cameron-Ruiz, J. G. Shepherd, K. Smollett, D. G. Stewart, M. Stewart, E. Sugrue, A. M. Szemiel, A. Taggart, E. C. Thomson, L. Tong, L. S. Torrie, R. Toth, M. Varjak, S. Wang, S. G. Wilkinson, P. G. Wyatt, E. Zusinaite, D. R. Alessi, A. H. Patel, A. Zaid, S. J. Wilson, and S. Mahalingam, “A plasmid DNA-launched SARS-CoV-2 reverse genetics system and coronavirus toolkit for COVID-19 research.,” PLoS Biol, vol. 19, p. e3001091, 2021.
    [Bibtex]
    @Article{Rihn:21,
    author = {Rihn, Suzannah J. and Merits, Andres and Bakshi, Siddharth and Turnbull, Matthew L. and Wickenhagen, Arthur and Alexander, Akira J. T. and Baillie, Carla and Brennan, Benjamin and Brown, Fiona and Brunker, Kirstyn and Bryden, Steven R. and Burness, Kerry A. and Carmichael, Stephen and Cole, Sarah J. and Cowton, Vanessa M. and Davies, Paul and Davis, Chris and De Lorenzo, Giuditta and Donald, Claire L. and Dorward, Mark and Dunlop, James I. and Elliott, Matthew and Fares, Mazigh and da Silva Filipe, Ana and Freitas, Joseph R. and Furnon, Wilhelm and Gestuveo, Rommel J. and Geyer, Anna and Giesel, Daniel and Goldfarb, Daniel M. and Goodman, Nicola and Gunson, Rory and Hastie, C. James and Herder, Vanessa and Hughes, Joseph and Johnson, Clare and Johnson, Natasha and Kohl, Alain and Kerr, Karen and Leech, Hannah and Lello, Laura Sandra and Li, Kathy and Lieber, Gauthier and Liu, Xiang and Lingala, Rajendra and Loney, Colin and Mair, Daniel and McElwee, Marion J. and McFarlane, Steven and Nichols, Jenna and Nomikou, Kyriaki and Orr, Anne and Orton, Richard J. and Palmarini, Massimo and Parr, Yasmin A. and Pinto, Rute Maria and Raggett, Samantha and Reid, Elaine and Robertson, David L. and Royle, Jamie and Cameron-Ruiz, Natalia and Shepherd, James G. and Smollett, Katherine and Stewart, Douglas G. and Stewart, Meredith and Sugrue, Elena and Szemiel, Agnieszka M. and Taggart, Aislynn and Thomson, Emma C. and Tong, Lily and Torrie, Leah S. and Toth, Rachel and Varjak, Margus and Wang, Sainan and Wilkinson, Stuart G. and Wyatt, Paul G. and Zusinaite, Eva and Alessi, Dario R. and Patel, Arvind H. and Zaid, Ali and Wilson, Sam J. and Mahalingam, Suresh},
    journal = {{PLoS Biol}},
    title = {A plasmid {DNA}-launched {SARS-CoV-2} reverse genetics system and coronavirus toolkit for {COVID-19} research.},
    year = {2021},
    pages = {e3001091},
    volume = {19},
    abstract = {The recent emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the underlying cause of Coronavirus Disease 2019 (COVID-19), has led to a worldwide pandemic causing substantial morbidity, mortality, and economic devastation. In response, many laboratories have redirected attention to SARS-CoV-2, meaning there is an urgent need for tools that can be used in laboratories unaccustomed to working with coronaviruses. Here we report a range of tools for SARS-CoV-2 research. First, we describe a facile single plasmid SARS-CoV-2 reverse genetics system that is simple to genetically manipulate and can be used to rescue infectious virus through transient transfection (without in vitro transcription or additional expression plasmids). The rescue system is accompanied by our panel of SARS-CoV-2 antibodies (against nearly every viral protein), SARS-CoV-2 clinical isolates, and SARS-CoV-2 permissive cell lines, which are all openly available to the scientific community. Using these tools, we demonstrate here that the controversial ORF10 protein is expressed in infected cells. Furthermore, we show that the promising repurposed antiviral activity of apilimod is dependent on TMPRSS2 expression. Altogether, our SARS-CoV-2 toolkit, which can be directly accessed via our website at https://mrcppu-covid.bio/, constitutes a resource with considerable potential to advance COVID-19 vaccine design, drug testing, and discovery science.},
    doi = {10.1371/journal.pbio.3001091},
    issue = {2},
    pmid = {33630831},
    pubstate = {epublish},
    }
  • [DOI] S. Rüeger, C. Hammer, A. Loetscher, P. J. McLaren, D. Lawless, O. Naret, D. P. Depledge, S. Morfopoulou, J. Breuer, E. Zdobnov, J. Fellay, and S. C. H. I. V. Study, “The influence of human genetic variation on Epstein-barr virus sequence diversity.,” Sci Rep, vol. 11, p. 4586, 2021.
    [Bibtex]
    @Article{Rueeger:21,
    author = {Rüeger, Sina and Hammer, Christian and Loetscher, Alexis and McLaren, Paul J. and Lawless, Dylan and Naret, Olivier and Depledge, Daniel P. and Morfopoulou, Sofia and Breuer, Judith and Zdobnov, Evgeny and Fellay, Jacques and Study, Swiss H.I.V. Cohort},
    journal = {{Sci Rep}},
    title = {The influence of human genetic variation on {E}pstein-Barr virus sequence diversity.},
    year = {2021},
    pages = {4586},
    volume = {11},
    abstract = {Epstein-Barr virus (EBV) is one of the most common viruses latently infecting humans. Little is known about the impact of human genetic variation on the large inter-individual differences observed in response to EBV infection. To search for a potential imprint of host genomic variation on the EBV sequence, we jointly analyzed paired viral and human genomic data from 268 HIV-coinfected individuals with CD4 + T cell count < 200/mm and elevated EBV viremia. We hypothesized that the reactivated virus circulating in these patients could carry sequence variants acquired during primary EBV infection, thereby providing a snapshot of early adaptation to the pressure exerted on EBV by the individual immune response. We searched for associations between host and pathogen genetic variants, taking into account human and EBV population structure. Our analyses revealed significant associations between human and EBV sequence variation. Three polymorphic regions in the human genome were found to be associated with EBV variation: one at the amino acid level (BRLF1:p.Lys316Glu); and two at the gene level (burden testing of rare variants in BALF5 and BBRF1). Our findings confirm that jointly analyzing host and pathogen genomes can identify sites of genomic interactions, which could help dissect pathogenic mechanisms and suggest new therapeutic avenues.},
    doi = {10.1038/s41598-021-84070-7},
    investigator = {Aebi-Popp, Karoline and Anagnostopoulos, Alexia and Battegay, Manuel and Bernasconi, Enos and Böni, Jürg and Braun, Dominique and Bucher, Heiner and Calmy, Alexandra and Cavassini, Matthias and Ciuffi, Angela and Dollenmaier, Guenter and Egger, Matthias and Elzi, Luigia and Fehr, Jan and Fellay, Jacques and Furrer, Hansjakob and Fux, Christoph and Günthard, Huldrych and Haerry, David and Hasse, Barbara and Hirsch, Hans and Hoffmann, Matthias and Hösli, Irene and Huber, Michael and Kahlert, Christian and Kaiser, Laurent and Keiser, Olivia and Klimkait, Thomas and Kottanattu, Lisa and Kouyos, Roger and Kovari, Helen and Ledergerber, Bruno and Martinetti, Gladys and de Tejada, Begoña Martinez and Marzolini, Catia and Metzner, Karin and Müller, Nicolas and Nicca, Dunja and Paioni, Paolo and Pantaleo, Giuseppe and Perreau, Matthieu and Rauch, Andri and Rudin, Christoph and Scherrer, Alexandra and Schmid, Patrick and Speck, Roberto and Stöckle, Marcel and Tarr, Philip and Trkola, Alexandra and Vernazza, Pietro and Wagner, Noémie and Wandeler, Gilles and Weber, Rainer and Yerly, Sabine},
    issue = {1},
    pmid = {33633271},
    pubstate = {epublish},
    }
  • [DOI] B. Zhou, T. Thi Nhu Thao, D. Hoffmann, A. Taddeo, N. Ebert, F. Labroussaa, A. Pohlmann, J. King, S. Steiner, J. N. Kelly, J. Portmann, N. J. Halwe, L. Ulrich, B. S. Trüeb, X. Fan, B. Hoffmann, L. Wang, L. Thomann, X. Lin, H. Stalder, B. Pozzi, S. de Brot, N. Jiang, D. Cui, J. Hossain, M. Wilson, M. Keller, T. J. Stark, J. R. Barnes, R. Dijkman, J. Jores, C. Benarafa, D. E. Wentworth, V. Thiel, and M. Beer, "SARS-CoV-2 spike D614G change enhances replication and transmission.," Nature, 2021.
    [Bibtex]
    @Article{Zhou:21,
    author = {Zhou, Bin and Thi Nhu Thao, Tran and Hoffmann, Donata and Taddeo, Adriano and Ebert, Nadine and Labroussaa, Fabien and Pohlmann, Anne and King, Jacqueline and Steiner, Silvio and Kelly, Jenna N. and Portmann, Jasmine and Halwe, Nico Joel and Ulrich, Lorenz and Trüeb, Bettina Salome and Fan, Xiaoyu and Hoffmann, Bernd and Wang, Li and Thomann, Lisa and Lin, Xudong and Stalder, Hanspeter and Pozzi, Berta and de Brot, Simone and Jiang, Nannan and Cui, Dan and Hossain, Jaber and Wilson, Malania and Keller, Matthew and Stark, Thomas J. and Barnes, John R. and Dijkman, Ronald and Jores, Joerg and Benarafa, Charaf and Wentworth, David E. and Thiel, Volker and Beer, Martin},
    journal = {Nature},
    title = {{SARS-CoV-2} spike {D614G} change enhances replication and transmission.},
    year = {2021},
    abstract = {During the evolution of SARS-CoV-2 in humans a D614G substitution in the spike (S) protein emerged and became the predominant circulating variant (S-614G) of the COVID-19 pandemic . However, whether the increasing prevalence of the S-614G variant represents a fitness advantage that improves replication and/or transmission in humans or is merely due to founder effects remains elusive. Here, we generated isogenic SARS-CoV-2 variants and demonstrate that the S-614G variant has (i) enhanced binding to human host cell surface receptor angiotensin-converting enzyme 2 (ACE2), (ii) increased replication in primary human bronchial and nasal airway epithelial cultures as well as in a novel human ACE2 knock-in mouse model, and (iii) markedly increased replication and transmissibility in hamster and ferret models of SARS-CoV-2 infection. Collectively, our data show that while the S-614G substitution results in subtle increases in binding and replication in vitro, it provides a real competitive advantage in vivo, particularly during the transmission bottle neck, providing an explanation for the global predominance of S-614G variant among the SARS-CoV-2 viruses currently circulating.},
    doi = {10.1038/s41586-021-03361-1},
    pmid = {33636719},
    pubstate = {aheadofprint},
    }
  • [DOI] S. Deinhardt-Emmer, S. Böttcher, C. Häring, L. Giebeler, A. Henke, R. Zell, J. Jungwirth, P. M. Jordan, O. Werz, F. Hornung, C. Brandt, M. Marquet, A. S. Mosig, M. W. Pletz, M. Schacke, J. Rödel, R. Heller, S. Nietzsche, B. Löffler, and C. Ehrhardt, "SARS-CoV-2 causes severe epithelial inflammation and barrier dysfunction.," J Virol, 2021.
    [Bibtex]
    @Article{DeinhardtEmmer:21,
    author = {Deinhardt-Emmer, Stefanie and Böttcher, Sarah and Häring, Clio and Giebeler, Liane and Henke, Andreas and Zell, Roland and Jungwirth, Johannes and Jordan, Paul M. and Werz, Oliver and Hornung, Franziska and Brandt, Christian and Marquet, Mike and Mosig, Alexander S. and Pletz, Mathias W. and Schacke, Michael and Rödel, Jürgen and Heller, Regine and Nietzsche, Sandor and Löffler, Bettina and Ehrhardt, Christina},
    journal = {{J Virol}},
    title = {{SARS-CoV-2} causes severe epithelial inflammation and barrier dysfunction.},
    year = {2021},
    abstract = {Infections with SARS-CoV-2 can be asymptomatic, but they can also be accompanied by a variety of symptoms that result in mild to severe coronavirus disease-19 (COVID-19) and are sometimes associated with systemic symptoms. Although the viral infection originates in the respiratory system, it is unclear how the virus can overcome the alveolar barrier, which is observed in severe COVID-19 disease courses. To elucidate the viral effects on the barrier integrity and immune reactions, we used mono-cell culture systems and a complex human chip model composed of epithelial, endothelial, and mononuclear cells. Our data show that SARS-CoV-2 efficiently infected epithelial cells with high viral loads and inflammatory response, including interferon expression. By contrast, the adjacent endothelial layer was neither infected nor did it show productive virus replication or interferon release. With prolonged infection, both cell types were damaged, and the barrier function was deteriorated, allowing the viral particles to overbear. In our study, we demonstrate that although SARS-CoV-2 is dependent on the epithelium for efficient replication, the neighboring endothelial cells are affected, e.g., by the epithelial cytokines or components induced during infection, which further results in the damage of the epithelial/endothelial barrier function and viral dissemination. SARS-CoV-2 challenges healthcare systems and societies worldwide in unprecedented ways. Although numerous new studies have been conducted, research to better understand the molecular pathogen-host interactions are urgently needed. For this, experimental models have to be developed and adapted. In the present study we used mono cell-culture systems and we established a complex chip model, where epithelial and endothelial cells are cultured in close proximity. We demonstrate that epithelial cells can be infected with SARS-CoV-2, while the endothelium did not show any infection signs. Since SARS-CoV-2 is able to establish viremia, the link to thromboembolic events in severe COVID-19 courses is evident. However, whether the endothelial layer is damaged by the viral pathogens or whether other endothelial-independent homeostatic factors are induced by the virus is essential for understanding the disease development. Therefore, our study is important as it demonstrates that the endothelial layer could not be infected by SARS-CoV-2 in our experiments, but we were able to show the destruction of the epithelial-endothelial barrier in our chip model. From our experiments we can assume that virus-induced host factors disturbed the epithelial-endothelial barrier function and thereby promote viral spread.},
    doi = {10.1128/JVI.00110-21},
    pmid = {33637603},
    pubstate = {aheadofprint},
    }
  • [DOI] N. I. Vlachogiannis, K. Verrou, K. Stellos, P. P. Sfikakis, and D. Paraskevis, "The role of A-to-I RNA editing in infections by RNA viruses: possible implications for SARS-CoV-2 infection.," Clin Immunol, p. 108699, 2021.
    [Bibtex]
    @Article{Vlachogiannis:21,
    author = {Vlachogiannis, Nikolaos I. and Verrou, Kleio-Maria and Stellos, Konstantinos and Sfikakis, Petros P. and Paraskevis, Dimitrios},
    journal = {{Clin Immunol}},
    title = {The role of {A}-to-{I} {RNA} editing in infections by {RNA} viruses: Possible implications for {SARS-CoV-2} infection.},
    year = {2021},
    pages = {108699},
    abstract = {RNA editing is a fundamental biological process with 2 major forms, namely adenosine-to-inosine (A-to-I, recognized as A-to-G) and cytosine-to-uracil (C-to-U) deamination, mediated by ADAR and APOBEC enzyme families, respectively. A-to-I RNA editing has been shown to directly affect the genome/transcriptome of RNA viruses with significant repercussions for viral protein synthesis, proliferation and infectivity, while it also affects recognition of double-stranded RNAs by cytosolic receptors controlling the host innate immune response. Recent evidence suggests that RNA editing may be present in SARS-CoV-2 genome/transcriptome. The majority of mapped mutations in SARS-CoV-2 genome are A-to-G/U-to-C(opposite strand) and C-to-U/G-to-A(opposite strand) substitutions comprising potential ADAR-/APOBEC-mediated deamination events. A single nucleotide substitution can have dramatic effects on SARS-CoV-2 infectivity as shown by the D614G(A-to-G) substitution in the spike protein. Future studies utilizing serial sampling from patients with COVID-19 are warranted to delineate whether RNA editing affects viral replication and/or the host immune response to SARS-CoV-2.},
    doi = {10.1016/j.clim.2021.108699},
    keywords = {A-to-I RNA editing; Innate immunity; Mutations; SARS-CoV-2; Viral infections},
    pmid = {33639276},
    pubstate = {aheadofprint},
    }
  • [DOI] N. Marty, S. Saeng-Aroon, E. Heger, A. Thielen, M. Obermeier, N. Pfeifer, R. Kaiser, and T. Klimkait, "Adapting the geno2pheno[coreceptor] tool to HIV-1 subtype CRF01_AE by phenotypic validation using clinical isolates from South-East Asia.," J Clin Virol, vol. 136, p. 104755, 2021.
    [Bibtex]
    @Article{Marty:21,
    author = {Marty, Nina and Saeng-Aroon, Siriphan and Heger, Eva and Thielen, Alexander and Obermeier, Martin and Pfeifer, Nico and Kaiser, Rolf and Klimkait, Thomas},
    journal = {{J Clin Virol}},
    title = {Adapting the geno2pheno[coreceptor] tool to {HIV}-1 subtype {CRF01\_AE} by phenotypic validation using clinical isolates from {S}outh-{E}ast {A}sia.},
    year = {2021},
    pages = {104755},
    volume = {136},
    abstract = {Geno2pheno[coreceptor] is a widely used tool for the prediction of coreceptor usage (viral tropism) of HIV-1 samples. For HIV-1 CRF01_AE, a significant overcalling of X4-tropism is observed when using the standard settings of Geno2pheno[coreceptor]. The aim of this study was to provide the experimental backing for adaptations to the geno2pheno[coreceptor] algorithm in order to improve coreceptor usage predictions of clinical HIV-1 CRF01_AE isolates STUDY DESIGN: V3-sequences of 20 clinical HIV-1 subtype CRF01_AE samples were sequenced and analyzed by geno2pheno[coreceptor]. In parallel, coreceptor usage was determined for these samples by replicative phenotyping in human cells in the presence of specific X4- or R5-inhibitors. The sole introduction of the CRF01_AE V3 region into a full-length otherwise subtype B provirus failed to produce replication-competent viral progeny. A successive genome-replacement strategy revealed that also CRF01_AE derived gag and pol sequences are necessary to generate HIV genomes with sufficient replication competence. Subsequent phenotypic analysis confirmed overcalling of X4-tropism for CRF01_AE viruses using the current version and the standard cut-off at 10% false positive rate (FPR) of geno2pheno[coreceptor]. Lowering the FPR cut-off to 2.5% reduced the X4-overcalling in our sample collection, while still allowing a safe administration of Maraviroc (MCV). This study demonstrates the successful adjustment of geno2pheno[coreceptor] rules for subtype CRF01_AE. It also supports the unique strength of combining complementing methods, namely phenotyping and genotyping, for validating new bioinformatics tools prior to application in diagnostics.},
    doi = {10.1016/j.jcv.2021.104755},
    keywords = {Coreceptor; HIV-1; Phenotyping; Subtype CRF01_AE; Tropism; geno2pheno},
    pmid = {33639408},
    pubstate = {aheadofprint},
    }
  • [DOI] P. Vetter, S. Cordey, M. Schibler, L. Vieux, L. Despres, F. Laubscher, D. O. Andrey, R. Martischang, S. Harbarth, C. Cuvelier, M. Bekliz, I. Eckerle, C. Siegrist, A. M. Didierlaurent, C. S. Eberhardt, B. Meyer, and L. Kaiser, "Clinical, virological and immunological features of a mild case of SARS-CoV-2 re-infection," Clin Microbiol Infec, 2021.
    [Bibtex]
    @Article{Vetter:21,
    author = {Pauline Vetter and Samuel Cordey and Manuel Schibler and Laure Vieux and Lena Despres and Florian Laubscher and Diego O. Andrey and Romain Martischang and Stephan Harbarth and Cl{\'{e}}mence Cuvelier and Meriem Bekliz and Isabella Eckerle and Claire-Anne Siegrist and Arnaud M. Didierlaurent and Christiane S. Eberhardt and Benjamin Meyer and Laurent Kaiser},
    journal = {{Clin Microbiol Infec}},
    title = {Clinical, virological and immunological features of a mild case of {SARS}-{CoV}-2 re-infection},
    year = {2021},
    doi = {10.1016/j.cmi.2021.02.010},
    publisher = {Elsevier {BV}},
    }
  • [DOI] M. Grossegesse, A. Nitsche, L. Schaade, and J. Doellinger, "Application of spectral library prediction for parallel reaction monitoring of viral peptides," Proteomics, p. 2000226, 2021.
    [Bibtex]
    @Article{Grossegesse:21,
    author = {Marica Grossegesse and Andreas Nitsche and Lars Schaade and Joerg Doellinger},
    journal = {{Proteomics}},
    title = {Application of spectral library prediction for parallel reaction monitoring of viral peptides},
    year = {2021},
    pages = {2000226},
    doi = {10.1002/pmic.202000226},
    publisher = {Wiley},
    }
  • [DOI] J. A. H. Masoli, A. Jeffries, B. Temperton, C. Auckland, M. Michelsen, J. Warwick-Dugdale, R. Manley, A. Farbos, S. Ellard, B. Knight, C. Bewshea, C. Sambles, J. Harrison, B. Bunce, A. Carr, A. T. Hattersley, S. L. Michell, and D. J. Studholme, "Viral genetic sequencing identifies staff transmission of COVID-19 is important in a community hospital outbreak," medRxiv, 2021.
    [Bibtex]
    @Article{Masoli:21,
    author = {Jane A.H. Masoli and Aaron Jeffries and Ben Temperton and Cressida Auckland and Michelle Michelsen and Joanna Warwick-Dugdale and Robyn Manley and Audrey Farbos and Sian Ellard and Beatrice Knight and Claire Bewshea and Christine Sambles and James Harrison and Ben Bunce and Alexis Carr and Andrew T. Hattersley and Stephen Ll. Michell and David J. Studholme},
    journal = {{medRxiv}},
    title = {Viral genetic sequencing identifies staff transmission of {COVID}-19 is important in a community hospital outbreak},
    year = {2021},
    doi = {10.1101/2021.02.18.21250737},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] C. Wylezich, S. Calvelage, K. Schlottau, U. Ziegler, A. Pohlmann, D. Höper, and M. Beer, "Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including SARS-CoV-2," Microbiome, vol. 9, iss. 1, 2021.
    [Bibtex]
    @Article{Wylezich:21,
    author = {Claudia Wylezich and Sten Calvelage and Kore Schlottau and Ute Ziegler and Anne Pohlmann and Dirk Höper and Martin Beer},
    journal = {Microbiome},
    title = {Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including {SARS}-{CoV}-2},
    year = {2021},
    number = {1},
    volume = {9},
    doi = {10.1186/s40168-020-00973-z},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] C. Bahrs, A. Kimmig, S. Weis, J. Ankert, S. Hagel, J. Maschmann, A. Stallmach, A. Steiner, M. Bauer, W. Behringer, M. Baier, M. Kesselmeier, C. Richert, F. Zepf, M. Walter, A. Scherag, M. Kiehntopf, B. Löffler, and M. W. Pletz, "Prospective surveillance study in a 1,400-bed university hospital: COVID-19 exposure at home was the main risk factor for SARS-CoV-2 point seroprevalence among hospital staff," Transbound Emerg Dis, 2021.
    [Bibtex]
    @Article{Bahrs:21,
    author = {Christina Bahrs and Aurelia Kimmig and Sebastian Weis and Juliane Ankert and Stefan Hagel and Jens Maschmann and Andreas Stallmach and Andrea Steiner and Michael Bauer and Wilhelm Behringer and Michael Baier and Miriam Kesselmeier and Cora Richert and Florian Zepf and Martin Walter and Andr{\'{e}} Scherag and Michael Kiehntopf and Bettina Löffler and Mathias W. Pletz},
    journal = {{Transbound Emerg Dis}},
    title = {Prospective surveillance study in a 1,400-bed university hospital: {COVID}-19 exposure at home was the main risk factor for {SARS}-{CoV}-2 point seroprevalence among hospital staff},
    year = {2021},
    doi = {10.1111/tbed.14041},
    publisher = {Wiley},
    }
  • [DOI] A. M. Szemiel, A. Merits, R. J. Orton, O. MacLean, R. M. Pinto, A. Wickenhagen, G. Lieber, M. L. Turnbull, S. Wang, D. Mair, A. S. da Filipe, B. J. Willett, S. J. Wilson, A. H. Patel, E. C. Thomson, M. Palmarini, A. Kohl, and M. E. Stewart, "in vitro evolution of Remdesivir resistance reveals genome plasticity of SARS-CoV-2," bioRxiv, 2021.
    [Bibtex]
    @Article{Szemiel:21,
    author = {Agnieszka M. Szemiel and Andres Merits and Richard J. Orton and Oscar MacLean and Rute Maria Pinto and Arthur Wickenhagen and Gauthier Lieber and Matthew L. Turnbull and Sainan Wang and Daniel Mair and Ana da Silva Filipe and Brian J. Willett and Sam J. Wilson and Arvind H. Patel and Emma C. Thomson and Massimo Palmarini and Alain Kohl and Meredith E. Stewart},
    journal = {{bioRxiv}},
    title = {In vitro evolution of {R}emdesivir resistance reveals genome plasticity of {SARS}-{CoV}-2},
    year = {2021},
    doi = {10.1101/2021.02.01.429199},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] A. Pérez-Cataluña, Á. Chiner-Oms, E. Cuevas-Ferrando, A. Díaz-Reolid, I. Falcó, W. Randazzo, I. Girón-Guzmán, A. Allende, M. A. Bracho, I. Comas, and G. Sánchez, "Detection of genomic variants of SARS-CoV-2 circulating in wastewater by high-throughput sequencing," bioRxiv, 2021.
    [Bibtex]
    @Article{PerezCataluna:21,
    author = {Alba Pérez-Cataluña and {\'{A}}lvaro Chiner-Oms and Enric Cuevas-Ferrando and Azahara D{\'{\i}}az-Reolid and Irene Falc{\'{o}} and Walter Randazzo and In{\'{e}}s Gir{\'{o}}n-Guzm{\'{a}}n and Ana Allende and Mar{\'{\i}}a A. Bracho and I{\~{n}}aki Comas and Gloria S{\'{a}}nchez},
    journal = {{bioRxiv}},
    title = {Detection Of Genomic Variants Of {SARS}-{CoV}-2 Circulating In Wastewater By High-Throughput Sequencing},
    year = {2021},
    doi = {10.1101/2021.02.08.21251355},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] P. Lemey, N. Ruktanonchai, S. Hong, V. Colizza, C. Poletto, F. V. den Broeck, M. Gill, X. Ji, A. Levasseur, A. Sadilek, S. Lai, A. Tatem, G. Baele, M. Suchard, and S. Dellicour, "SARS-CoV-2 european resurgence foretold: interplay of introductions and persistence by leveraging genomic and mobility data," Research Square, 2021.
    [Bibtex]
    @Article{Lemey:21,
    author = {Philippe Lemey and Nick Ruktanonchai and Samuel Hong and Vittoria Colizza and Chiara Poletto and Frederik Van den Broeck and Mandev Gill and Xiang Ji and Anthony Levasseur and Adam Sadilek and Shengjie Lai and Andrew Tatem and Guy Baele and Marc Suchard and Simon Dellicour},
    journal = {{Research Square}},
    title = {{SARS}-{CoV}-2 European resurgence foretold: interplay of introductions and persistence by leveraging genomic and mobility data},
    year = {2021},
    doi = {10.21203/rs.3.rs-208849/v1},
    publisher = {Research Square},
    }
  • [DOI] E. Petter, O. Mor, N. Zuckerman, D. Oz-Levi, A. Younger, D. Aran, and Y. Erlich, "Initial real world evidence for lower viral load of individuals who have been vaccinated by BNT162b2," medRxiv, 2021.
    [Bibtex]
    @Article{Petter:21,
    author = {Ella Petter and Orna Mor and Neta Zuckerman and Danit Oz-Levi and Asaf Younger and Dvir Aran and Yaniv Erlich},
    journal = {{medRxiv}},
    title = {Initial real world evidence for lower viral load of individuals who have been vaccinated by {BNT}162b2},
    year = {2021},
    doi = {10.1101/2021.02.08.21251329},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. Ghafari, P. Simmonds, O. G. Pybus, and A. Katzourakis, "Prisoner of war dynamics explains the time-dependent pattern of substitution rates in viruses," bioRxiv, 2021.
    [Bibtex]
    @Article{Ghafari:21,
    author = {Mahan Ghafari and Peter Simmonds and Oliver G Pybus and Aris Katzourakis},
    journal = {{bioRxiv}},
    title = {Prisoner of War dynamics explains the time-dependent pattern of substitution rates in viruses},
    year = {2021},
    doi = {10.1101/2021.02.09.430479},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] D. A. Hoagland, R. Møller, S. A. Uhl, K. Oishi, J. Frere, I. Golynker, S. Horiuchi, M. Panis, D. Blanco-Melo, D. Sachs, K. Arkun, J. K. Lim, and B. R. tenOever, "Leveraging the antiviral type I interferon system as a first line of defense against SARS-CoV-2 pathogenicity.," Immunity, 2021.
    [Bibtex]
    @Article{Hoagland:21,
    author = {Hoagland, Daisy A. and Møller, Rasmus and Uhl, Skyler A. and Oishi, Kohei and Frere, Justin and Golynker, Ilona and Horiuchi, Shu and Panis, Maryline and Blanco-Melo, Daniel and Sachs, David and Arkun, Knarik and Lim, Jean K. and tenOever, Benjamin R.},
    journal = {Immunity},
    title = {Leveraging the antiviral type {I} interferon system as a first line of defense against {SARS-CoV-2} pathogenicity.},
    year = {2021},
    abstract = {The emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in significant global morbidity, mortality, and societal disruption. A better understanding of virus-host interactions may potentiate therapeutic insights toward limiting this infection. Here we investigated the dynamics of the systemic response to SARS-CoV-2 in hamsters by histological analysis and transcriptional profiling. Infection resulted in consistently high levels of virus in the upper and lower respiratory tracts and sporadic occurrence in other distal tissues. A longitudinal cohort revealed a wave of inflammation, including a type I interferon (IFN-I) response, that was evident in all tissues regardless of viral presence but was insufficient to prevent disease progression. Bolstering the antiviral response with intranasal administration of recombinant IFN-I reduced viral disease, prevented transmission, and lowered inflammation in vivo. This study defines the systemic host response to SARS-CoV-2 infection and supports use of intranasal IFN-I as an effective means of early treatment.},
    doi = {10.1016/j.immuni.2021.01.017},
    keywords = {COVID-19; IFN-I; cytokine; hamster; intranasal; mRNA-seq; pandemic; prophylactic; therapeutic; transcriptomics},
    pmid = {33577760},
    pubstate = {aheadofprint},
    }
  • [DOI] J. M. Bartoszewicz, A. Seidel, and B. Y. Renard, "Interpretable detection of novel human viruses from genome sequencing data.," NAR Genom Bioinform, vol. 3, p. lqab004, 2021.
    [Bibtex]
    @Article{Bartoszewicz:21a,
    author = {Bartoszewicz, Jakub M. and Seidel, Anja and Renard, Bernhard Y.},
    journal = {{NAR Genom Bioinform}},
    title = {Interpretable detection of novel human viruses from genome sequencing data.},
    year = {2021},
    pages = {lqab004},
    volume = {3},
    abstract = {Viruses evolve extremely quickly, so reliable methods for viral host prediction are necessary to safeguard biosecurity and biosafety alike. Novel human-infecting viruses are difficult to detect with standard bioinformatics workflows. Here, we predict whether a virus can infect humans directly from next-generation sequencing reads. We show that deep neural architectures significantly outperform both shallow machine learning and standard, homology-based algorithms, cutting the error rates in half and generalizing to taxonomic units distant from those presented during training. Further, we develop a suite of interpretability tools and show that it can be applied also to other models beyond the host prediction task. We propose a new approach for convolutional filter visualization to disentangle the information content of each nucleotide from its contribution to the final classification decision. Nucleotide-resolution maps of the learned associations between pathogen genomes and the infectious phenotype can be used to detect regions of interest in novel agents, for example, the SARS-CoV-2 coronavirus, unknown before it caused a COVID-19 pandemic in 2020. All methods presented here are implemented as easy-to-install packages not only enabling analysis of NGS datasets without requiring any deep learning skills, but also allowing advanced users to easily train and explain new models for genomics.},
    doi = {10.1093/nargab/lqab004},
    issue = {1},
    pmid = {33554119},
    pubstate = {epublish},
    }
  • [DOI] A. Ebinger, S. Fischer, and D. Höper, "A theoretical and generalized approach for the assessment of the sample-specific limit of detection for clinical metagenomics.," Comput Struct Biotechnol J, vol. 19, p. 732–742, 2021.
    [Bibtex]
    @Article{Ebinger:21,
    author = {Ebinger, Arnt and Fischer, Susanne and Höper, Dirk},
    journal = {{Comput Struct Biotechnol J}},
    title = {A theoretical and generalized approach for the assessment of the sample-specific limit of detection for clinical metagenomics.},
    year = {2021},
    pages = {732--742},
    volume = {19},
    abstract = {Metagenomics is a powerful tool to identify novel or unexpected pathogens, since it is generic and relatively unbiased. The limit of detection (LOD) is a critical parameter for the routine application of methods in the clinical diagnostic context. Although attempts for the determination of LODs for metagenomics next-generation sequencing (mNGS) have been made previously, these were only applicable for specific target species in defined samples matrices. Therefore, we developed and validated a generalized probability-based model to assess the sample-specific LOD of mNGS experiments (LOD ). Initial rarefaction analyses with datasets of Borna disease virus 1 human encephalitis cases revealed a stochastic behavior of virus read detection. Based on this, we transformed the Bernoulli formula to predict the minimal necessary dataset size to detect one virus read with a probability of 99%. We validated the formula with 30 datasets from diseased individuals, resulting in an accuracy of 99.1% and an average of 4.5 ± 0.4 viral reads found in the calculated minimal dataset size. We demonstrated by modeling the virus genome size, virus-, and total RNA-concentration that the main determinant of mNGS sensitivity is the virus-sample background ratio. The predicted LOD for the respective pathogenic virus in the datasets were congruent with the virus-concentration determined by RT-qPCR. Theoretical assumptions were further confirmed by correlation analysis of mNGS and RT-qPCR data from the samples of the analyzed datasets. This approach should guide standardization of mNGS application, due to the generalized concept of LOD .},
    doi = {10.1016/j.csbj.2020.12.040},
    keywords = {Bernoulli process; Detection limit; Metagenomics; Next-generation sequencing; Sensitivity; qPCR},
    pmid = {33552445},
    pubstate = {epublish},
    }
  • [DOI] J. Ratcliff and P. Simmonds, "Potential APOBEC-mediated RNA editing of the genomes of SARS-CoV-2 and other coronaviruses and its impact on their longer term evolution.," Virology, vol. 556, p. 62–72, 2021.
    [Bibtex]
    @Article{Ratcliff:21,
    author = {Ratcliff, Jeremy and Simmonds, Peter},
    journal = {Virology},
    title = {Potential {APOBEC}-mediated {RNA} editing of the genomes of {SARS-CoV-2} and other coronaviruses and its impact on their longer term evolution.},
    year = {2021},
    pages = {62--72},
    volume = {556},
    abstract = {Members of the APOBEC family of cytidine deaminases show antiviral activities in mammalian cells through lethal editing in the genomes of small DNA viruses, herpesviruses and retroviruses, and potentially those of RNA viruses such as coronaviruses. Consistent with the latter, APOBEC-like directional C→U transitions of genomic plus-strand RNA are greatly overrepresented in SARS-CoV-2 genome sequences of variants emerging during the COVID-19 pandemic. A C→U mutational process may leave evolutionary imprints on coronavirus genomes, including extensive homoplasy from editing and reversion at targeted sites and the occurrence of driven amino acid sequence changes in viral proteins. If sustained over longer periods, this process may account for the previously reported marked global depletion of C and excess of U bases in human seasonal coronavirus genomes. This review synthesizes the current knowledge on APOBEC evolution and function and the evidence of their role in APOBEC-mediated genome editing of SARS-CoV-2 and other coronaviruses.},
    doi = {10.1016/j.virol.2020.12.018},
    keywords = {APOBEC; Coronavirus; Innate immunity; SARS-CoV-2; Virus evolution},
    pmid = {33545556},
    pubstate = {aheadofprint},
    }
  • [DOI] S. Dellicour, M. S. Gill, N. R. Faria, A. Rambaut, O. G. Pybus, M. A. Suchard, and P. Lemey, "Relax, keep walking-a practical guide to continuous phylogeographic inference with BEAST.," Mol Biol Evol, 2021.
    [Bibtex]
    @Article{Dellicour:21,
    author = {Dellicour, Simon and Gill, Mandev S. and Faria, Nuno R. and Rambaut, Andrew and Pybus, Oliver G. and Suchard, Marc A. and Lemey, Philippe},
    journal = {{Mol Biol Evol}},
    title = {Relax, keep walking-a practical guide to continuous phylogeographic inference with {BEAST}.},
    year = {2021},
    abstract = {Spatially-explicit phylogeographic analyses can be performed with an inference framework that employs relaxed random walks to reconstruct phylogenetic dispersal histories in continuous space. This core model was first implemented ten years ago and has opened up new opportunities in the field of phylodynamics, allowing researchers to map and analyse the spatial dissemination of rapidly evolving pathogens. We here provide a detailed and step-by-step guide on how to set up, run, and interpret continuous phylogeographic analyses using the programs BEAUti, BEAST, Tracer, and TreeAnnotator.},
    doi = {10.1093/molbev/msab031},
    keywords = {BEAST; continuous phylogeography; relaxed random walk; viruses},
    pmid = {33528560},
    pubstate = {aheadofprint},
    }
  • [DOI] F. Stefaniak and J. M. Bujnicki, "AnnapuRNA: a scoring function for predicting RNA-small molecule binding poses.," PLoS Comput Biol, vol. 17, p. e1008309, 2021.
    [Bibtex]
    @Article{Stefaniak:21,
    author = {Stefaniak, Filip and Bujnicki, Janusz M.},
    journal = {{PLoS Comput Biol}},
    title = {{AnnapuRNA}: A scoring function for predicting {RNA}-small molecule binding poses.},
    year = {2021},
    pages = {e1008309},
    volume = {17},
    abstract = {RNA is considered as an attractive target for new small molecule drugs. Designing active compounds can be facilitated by computational modeling. Most of the available tools developed for these prediction purposes, such as molecular docking or scoring functions, are parametrized for protein targets. The performance of these methods, when applied to RNA-ligand systems, is insufficient. To overcome these problems, we developed AnnapuRNA, a new knowledge-based scoring function designed to evaluate RNA-ligand complex structures, generated by any computational docking method. We also evaluated three main factors that may influence the structure prediction, i.e., the starting conformer of a ligand, the docking program, and the scoring function used. We applied the AnnapuRNA method for a post-hoc study of the recently published structures of the FMN riboswitch. Software is available at https://github.com/filipspl/AnnapuRNA.},
    doi = {10.1371/journal.pcbi.1008309},
    issue = {2},
    pmid = {33524009},
    pubstate = {epublish},
    }
  • [DOI] F. Aubry, S. Jacobs, M. Darmuzey, S. Lequime, L. Delang, A. Fontaine, N. Jupatanakul, E. F. Miot, S. Dabo, C. Manet, X. Montagutelli, A. Baidaliuk, F. Gámbaro, E. Simon-Lorière, M. Gilsoul, C. M. Romero-Vivas, V. Cao-Lormeau, R. G. Jarman, C. T. Diagne, O. Faye, O. Faye, A. A. Sall, J. Neyts, L. Nguyen, S. J. F. Kaptein, and L. Lambrechts, "Recent african strains of Zika virus display higher transmissibility and fetal pathogenicity than Asian strains.," Nat Commun, vol. 12, p. 916, 2021.
    [Bibtex]
    @Article{Aubry:21,
    author = {Aubry, Fabien and Jacobs, Sofie and Darmuzey, Maïlis and Lequime, Sebastian and Delang, Leen and Fontaine, Albin and Jupatanakul, Natapong and Miot, Elliott F. and Dabo, Stéphanie and Manet, Caroline and Montagutelli, Xavier and Baidaliuk, Artem and Gámbaro, Fabiana and Simon-Lorière, Etienne and Gilsoul, Maxime and Romero-Vivas, Claudia M. and Cao-Lormeau, Van-Mai and Jarman, Richard G. and Diagne, Cheikh T. and Faye, Oumar and Faye, Ousmane and Sall, Amadou A. and Neyts, Johan and Nguyen, Laurent and Kaptein, Suzanne J. F. and Lambrechts, Louis},
    journal = {{Nat Commun}},
    title = {Recent African strains of {Zika} virus display higher transmissibility and fetal pathogenicity than {A}sian strains.},
    year = {2021},
    pages = {916},
    volume = {12},
    abstract = {The global emergence of Zika virus (ZIKV) revealed the unprecedented ability for a mosquito-borne virus to cause congenital birth defects. A puzzling aspect of ZIKV emergence is that all human outbreaks and birth defects to date have been exclusively associated with the Asian ZIKV lineage, despite a growing body of laboratory evidence pointing towards higher transmissibility and pathogenicity of the African ZIKV lineage. Whether this apparent paradox reflects the use of relatively old African ZIKV strains in most laboratory studies is unclear. Here, we experimentally compare seven low-passage ZIKV strains representing the recently circulating viral genetic diversity. We find that recent African ZIKV strains display higher transmissibility in mosquitoes and higher lethality in both adult and fetal mice than their Asian counterparts. We emphasize the high epidemic potential of African ZIKV strains and suggest that they could more easily go unnoticed by public health surveillance systems than Asian strains due to their propensity to cause fetal loss rather than birth defects.},
    doi = {10.1038/s41467-021-21199-z},
    issue = {1},
    pmid = {33568638},
    pubstate = {epublish},
    }
  • [DOI] T. Spicher, M. Delitz, A. B. de Schneider, and M. T. Wolfinger, "Dynamic molecular epidemiology reveals lineage-associated single-nucleotide variants that alter RNA structure in Chikungunya virus.," Genes, vol. 12, 2021.
    [Bibtex]
    @Article{Spicher:21,
    author = {Spicher, Thomas and Delitz, Markus and Schneider, Adriano de Bernardi and Wolfinger, Michael T.},
    journal = {Genes},
    title = {Dynamic Molecular Epidemiology Reveals Lineage-Associated Single-Nucleotide Variants That Alter {RNA} Structure in {C}hikungunya Virus.},
    year = {2021},
    volume = {12},
    abstract = {Chikungunya virus (CHIKV) is an emerging which causes millions of human infections every year. Outbreaks have been reported in Africa and Asia since the early 1950s, from three CHIKV lineages: West African, East Central South African, and Asian Urban. As new outbreaks occurred in the Americas, individual strains from the known lineages have evolved, creating new monophyletic groups that generated novel geographic-based lineages. Building on a recently updated phylogeny of CHIKV, we report here the availability of an interactive CHIKV phylodynamics dataset, which is based on more than 900 publicly available CHIKV genomes. We provide an interactive view of CHIKV molecular epidemiology built on Nextstrain, a web-based visualization framework for real-time tracking of pathogen evolution. CHIKV molecular epidemiology reveals single nucleotide variants that change the stability and fold of locally stable RNA structures. We propose alternative RNA structure formation in different CHIKV lineages by predicting more than a dozen RNA elements that are subject to perturbation of the structure ensemble upon variation of a single nucleotide.},
    doi = {10.3390/genes12020239},
    issue = {2},
    keywords = {Chikungunya virus; RNA structure; molecular epidemiology; mutation},
    pmid = {33567556},
    pubstate = {epublish},
    }
  • [DOI] A. Dastjerdi, D. J. Everest, H. Davies, D. Denk, and R. Zell, "A novel dicistrovirus in a captive red squirrel (Sciurus vulgaris)," J Gen Virol, 2021.
    [Bibtex]
    @Article{Dastjerdi:21,
    author = {Dastjerdi, Akbar and Everest, David J. and Davies, Hannah and Denk, Daniela and Zell, Roland},
    journal = {{J Gen Virol}},
    title = {A novel dicistrovirus in a captive red squirrel ({S}ciurus vulgaris)},
    year = {2021},
    abstract = {Dicistroviruses are single-stranded RNA viruses in the family . The viruses have mainly been detected in arthropods and are the cause of several devastating diseases in many of these species such as honeybees. Increasingly, dicistroviruses have also been detected in both mammalian and avian species in faeces, blood and liver, but with unconfirmed pathology. Here, we report a novel dicistrovirus detected in the intestinal content of a captive red squirrel with enteritis along with the disease history, pathology and genomic characterisation of the virus. Virus particle morphology resembled those of picornaviruses with a diameter of 28-32 nm but failed to be detected using a mammalian/avian pan viral microarray. Next-generation sequencing confirmed a dicistrovirus having a typical dicistrovirus genome organization, but with the polyprotein 1 being shorter by about 100 amino acids, compared to that of other dicistroviruses. Phylogenetic analysis of ORF1 and ORF2 sequences clustered the virus with two yet unassigned dicistroviruses detected in and a freshwater arthropod and likely to be designated to a new genus. Our data further highlights the ever-growing diversity of dicistroviruses, but the clinical significance of the virus in mammalian species and particularly red squirrels has yet to be established.},
    doi = {10.1099/jgv.0.001555},
    keywords = {dicistrovirus; enteritis; genomic organisation; phylogeny; red squirrel},
    pmid = {33565956},
    pubstate = {aheadofprint},
    }
  • [DOI] D. J. Baker, A. Aydin, T. Le-Viet, G. L. Kay, S. Rudder, L. de Oliveira Martins, A. P. Tedim, A. Kolyva, M. Diaz, N. Alikhan, L. Meadows, A. Bell, A. V. Gutierrez, A. J. Trotter, N. M. Thomson, R. Gilroy, L. Griffith, E. M. Adriaenssens, R. Stanley, I. G. Charles, N. Elumogo, J. Wain, R. Prakash, E. Meader, A. E. Mather, M. A. Webber, S. Dervisevic, A. J. Page, and J. O'Grady, "CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes.," Genome Med, vol. 13, p. 21, 2021.
    [Bibtex]
    @Article{Baker:21,
    author = {Baker, Dave J. and Aydin, Alp and Le-Viet, Thanh and Kay, Gemma L. and Rudder, Steven and de Oliveira Martins, Leonardo and Tedim, Ana P. and Kolyva, Anastasia and Diaz, Maria and Alikhan, Nabil-Fareed and Meadows, Lizzie and Bell, Andrew and Gutierrez, Ana Victoria and Trotter, Alexander J. and Thomson, Nicholas M. and Gilroy, Rachel and Griffith, Luke and Adriaenssens, Evelien M. and Stanley, Rachael and Charles, Ian G. and Elumogo, Ngozi and Wain, John and Prakash, Reenesh and Meader, Emma and Mather, Alison E. and Webber, Mark A. and Dervisevic, Samir and Page, Andrew J. and O'Grady, Justin},
    journal = {{Genome Med}},
    title = {{CoronaHiT}: high-throughput sequencing of {SARS-CoV-2} genomes.},
    year = {2021},
    pages = {21},
    volume = {13},
    abstract = {We present CoronaHiT, a platform and throughput flexible method for sequencing SARS-CoV-2 genomes (≤ 96 on MinION or > 96 on Illumina NextSeq) depending on changing requirements experienced during the pandemic. CoronaHiT uses transposase-based library preparation of ARTIC PCR products. Method performance was demonstrated by sequencing 2 plates containing 95 and 59 SARS-CoV-2 genomes on nanopore and Illumina platforms and comparing to the ARTIC LoCost nanopore method. Of the 154 samples sequenced using all 3 methods, ≥ 90% genome coverage was obtained for 64.3% using ARTIC LoCost, 71.4% using CoronaHiT-ONT and 76.6% using CoronaHiT-Illumina, with almost identical clustering on a maximum likelihood tree. This protocol will aid the rapid expansion of SARS-CoV-2 genome sequencing globally.},
    doi = {10.1186/s13073-021-00839-5},
    issue = {1},
    keywords = {ARTIC; Genetic; Genome; Multiplexing; NGS; Nanopore; SARS-CoV-2; Sequencing},
    pmid = {33563320},
    pubstate = {epublish},
    }
  • [DOI] R. Van Damme, M. Hölzer, A. Viehweger, B. Müller, E. Bongcam-Rudloff, and C. Brandt, "Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN).," PLoS Comput Biol, vol. 17, p. e1008716, 2021.
    [Bibtex]
    @Article{VanDamme:21,
    author = {Van Damme, Renaud and Hölzer, Martin and Viehweger, Adrian and Müller, Bettina and Bongcam-Rudloff, Erik and Brandt, Christian},
    journal = {{PLoS Comput Biol}},
    title = {Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis ({MUFFIN}).},
    year = {2021},
    pages = {e1008716},
    volume = {17},
    abstract = {Metagenomics has redefined many areas of microbiology. However, metagenome-assembled genomes (MAGs) are often fragmented, primarily when sequencing was performed with short reads. Recent long-read sequencing technologies promise to improve genome reconstruction. However, the integration of two different sequencing modalities makes downstream analyses complex. We, therefore, developed MUFFIN, a complete metagenomic workflow that uses short and long reads to produce high-quality bins and their annotations. The workflow is written by using Nextflow, a workflow orchestration software, to achieve high reproducibility and fast and straightforward use. This workflow also produces the taxonomic classification and KEGG pathways of the bins and can be further used for quantification and annotation by providing RNA-Seq data (optionally). We tested the workflow using twenty biogas reactor samples and assessed the capacity of MUFFIN to process and output relevant files needed to analyze the microbial community and their function. MUFFIN produces functional pathway predictions and, if provided de novo metatranscript annotations across the metagenomic sample and for each bin. MUFFIN is available on github under GNUv3 licence: https://github.com/RVanDamme/MUFFIN.},
    doi = {10.1371/journal.pcbi.1008716},
    issue = {2},
    pmid = {33561126},
    pubstate = {aheadofprint},
    }
  • [DOI] D. Bojkova, J. E. McGreig, K. McLaughlin, S. G. Masterson, M. Antczak, M. Widera, V. Krähling, S. Ciesek, M. N. Wass, M. Michaelis, and J. Cinatl, "Differentially conserved amino acid positions may reflect differences in SARS-CoV-2 and SARS-CoV behaviour.," Bioinformatics, 2021.
    [Bibtex]
    @Article{Bojkova:21,
    author = {Bojkova, Denisa and McGreig, Jake E. and McLaughlin, Katie-May and Masterson, Stuart G. and Antczak, Magdalena and Widera, Marek and Krähling, Verena and Ciesek, Sandra and Wass, Mark N. and Michaelis, Martin and Cinatl, Jindrich},
    journal = {{Bioinformatics}},
    title = {Differentially conserved amino acid positions may reflect differences in {SARS-CoV-2} and {SARS-CoV} behaviour.},
    year = {2021},
    abstract = {SARS-CoV-2 is a novel coronavirus currently causing a pandemic. Here, we performed a combined in-silico and cell culture comparison of SARS-CoV-2 and the closely related SARS-CoV. Many amino acid positions are differentially conserved between SARS-CoV-2 and SARS-CoV, which reflects the discrepancies in virus behaviour, i.e. more effective human-to-human transmission of SARS-CoV-2 and higher mortality associated with SARS-CoV. Variations in the S protein (mediates virus entry) were associated with differences in its interaction with ACE2 (cellular S receptor) and sensitivity to TMPRSS2 (enables virus entry via S cleavage) inhibition. Anti-ACE2 antibodies more strongly inhibited SARS-CoV than SARS-CoV-2 infection, probably due to a stronger SARS-CoV-2 S-ACE2 affinity relative to SARS-CoV S. Moreover, SARS-CoV-2 and SARS-CoV displayed differences in cell tropism. Cellular ACE2 and TMPRSS2 levels did not indicate susceptibility to SARS-CoV-2. In conclusion, we identified genomic variation between SARS-CoV-2 and SARS-CoV that may reflect the differences in their clinical and biological behaviour. Supplementary data are available at Bioinformatics online.},
    doi = {10.1093/bioinformatics/btab094},
    pmid = {33560365},
    pubstate = {aheadofprint},
    }
  • [DOI] S. S. Good, J. Westover, K. H. Jung, X. Zhou, A. Moussa, P. La Colla, G. Collu, B. Canard, and J. Sommadossi, "AT-527, a double prodrug of a guanosine nucleotide analog, is a potent inhibitor of SARS-CoV-2 in vitro and a promising oral antiviral for treatment of COVID-19.," Antimicrob Agents Chemother, 2021.
    [Bibtex]
    @Article{Good:21,
    author = {Good, Steven S. and Westover, Jonna and Jung, Kie Hoon and Zhou, Xiao-Jian and Moussa, Adel and La Colla, Paolo and Collu, Gabriella and Canard, Bruno and Sommadossi, Jean-Pierre},
    journal = {{Antimicrob Agents Chemother}},
    title = {{AT}-527, a double prodrug of a guanosine nucleotide analog, is a potent inhibitor of {SARS-CoV-2} in vitro and a promising oral antiviral for treatment of {COVID-19}.},
    year = {2021},
    abstract = {The impact of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of COVID-19, is global and unprecedented. Although remdesivir has recently been approved by the FDA to treat SARS-CoV-2 infection, no oral antiviral is available for outpatient treatment. AT-527, an orally administered double prodrug of a guanosine nucleotide analog, was previously shown to be highly efficacious and well tolerated in HCV-infected subjects. Here, we report the potent activity of AT-511, the free base of AT-527, against several coronaviruses, including SARS-CoV-2. In normal human airway epithelial cells, the concentration of AT-511 required to inhibit replication of SARS-CoV-2 by 90% (EC ) was 0.47 μM, very similar to its EC against HCoV-229E, HCoV-OC43 and SARS-CoV in Huh-7 cells. Little to no cytotoxicity was observed for AT-511 at concentrations up to 100 μM. Substantial levels of the active triphosphate metabolite AT-9010 were formed in normal human bronchial and nasal epithelial cells incubated with 10 μM AT-511 (698 ± 15 and 236 ± 14 μM, respectively), with a half-life of at least 38 h. Results from steady-state pharmacokinetic and tissue distribution studies of non-human primates administered oral doses of AT-527, as well as pharmacokinetic data from subjects given daily oral doses of AT-527, predict that twice daily oral doses of 550 mg AT-527 will produce AT-9010 trough concentrations in human lung that exceed the EC observed for the prodrug against SARS-CoV-2 replication. This suggests that AT-527 may be an effective treatment option for COVID-19.},
    doi = {10.1128/AAC.02479-20},
    pmid = {33558299},
    pubstate = {aheadofprint},
    }
  • [DOI] P. P. Mathkar, X. Chen, A. Sulovari, and D. Li, "Characterization of hepatitis B virus integrations identified in hepatocellular carcinoma genomes.," Viruses, vol. 13, 2021.
    [Bibtex]
    @Article{Mathkar:21,
    author = {Mathkar, Pranav P. and Chen, Xun and Sulovari, Arvis and Li, Dawei},
    journal = {Viruses},
    title = {Characterization of Hepatitis {B} Virus Integrations Identified in Hepatocellular Carcinoma Genomes.},
    year = {2021},
    volume = {13},
    abstract = {Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality. Almost half of HCC cases are associated with hepatitis B virus (HBV) infections, which often lead to HBV sequence integrations in the human genome. Accurate identification of HBV integration sites at a single nucleotide resolution is critical for developing a better understanding of the cancer genome landscape and of the disease itself. Here, we performed further analyses and characterization of HBV integrations identified by our recently reported VIcaller platform in recurrent or known HCC genes (such as , , and ) as well as non-recurrent cancer-related genes (such as , , and ). Our pathway enrichment analysis revealed multiple pathways involving the alcohol dehydrogenase 4 gene, such as the metabolism pathways of retinol, tyrosine, and fatty acid. Further analysis of the HBV integration sites revealed distinct patterns involving the integration upper breakpoints, integrated genome lengths, and integration allele fractions between tumor and normal tissues. Our analysis also implies that the VIcaller method has diagnostic potential through discovering novel clonal integrations in cancer-related genes. In conclusion, although VIcaller is a hypothesis free virome-wide approach, it can still be applied to accurately identify genome-wide integration events of a specific candidate virus and their integration allele fractions.},
    doi = {10.3390/v13020245},
    issue = {2},
    keywords = {VIcaller; hepatitis B virus (HBV); hepatocellular carcinoma (HCC); integration allele fraction; viral integration; virome-wide detection},
    pmid = {33557409},
    pubstate = {epublish},
    }
  • [DOI] A. Oulas, M. Zanti, M. Tomazou, M. Zachariou, G. Minadakis, M. M. Bourdakou, P. Pavlidis, and G. M. Spyrou, "Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains," PLoS One, vol. 16, iss. 1, p. e0238665, 2021.
    [Bibtex]
    @Article{Oulas:21,
    author = {Anastasis Oulas and Maria Zanti and Marios Tomazou and Margarita Zachariou and George Minadakis and Marilena M. Bourdakou and Pavlos Pavlidis and George M. Spyrou},
    journal = {{PLoS One}},
    title = {Generalized linear models provide a measure of virulence for specific mutations in {SARS}-{CoV}-2 strains},
    year = {2021},
    number = {1},
    pages = {e0238665},
    volume = {16},
    doi = {10.1371/journal.pone.0238665},
    editor = {Jean-Luc EPH Darlix},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] F. Briand, E. Niqueux, A. Schmitz, C. Martenot, M. Cherbonnel, P. Massin, F. Kerbrat, M. Chatel, C. Guillemoto, C. Guillou-Cloarec, K. Ogor, A. L. Prioux, C. Allée, V. Beven, E. Hirchaud, Y. Blanchard, A. Scoizec, S. L. Bouquin, N. Eterradossi, and B. Grasland, "Highly pathogenic avian influenza A(H5N8) virus spread by short- and long-range transmission, France, 2016–17," Emerg Infect Dis, vol. 27, iss. 2, p. 508–516, 2021.
    [Bibtex]
    @Article{Briand:21,
    author = {Fran{\c{c}}ois-Xavier Briand and Eric Niqueux and Audrey Schmitz and Claire Martenot and Martine Cherbonnel and Pascale Massin and Florian Kerbrat and Marina Chatel and Carole Guillemoto and Cecile Guillou-Cloarec and Katell Ogor and Aur{\'{e}}lie Le Prioux and Chantal All{\'{e}}e and V{\'{e}}ronique Beven and Edouard Hirchaud and Yannick Blanchard and Axelle Scoizec and Sophie Le Bouquin and Nicolas Eterradossi and B{\'{e}}atrice Grasland},
    journal = {{Emerg Infect Dis}},
    title = {Highly Pathogenic Avian Influenza {A(H5N8)} Virus Spread by Short- and Long-Range Transmission, {F}rance, 2016--17},
    year = {2021},
    number = {2},
    pages = {508--516},
    volume = {27},
    doi = {10.3201/eid2702.202920},
    publisher = {Centers for Disease Control and Prevention ({CDC})},
    }
  • [DOI] V. Sypsa, S. Roussos, D. Paraskevis, T. Lytras, S. Tsiodras, and A. Hatzakis, "Effects of social distancing measures during the first epidemic wave of Severe Acute Respiratory Syndrome infection, Greece," Emerg Infect Dis, vol. 27, iss. 2, p. 452–462, 2021.
    [Bibtex]
    @Article{Sypsa:21,
    author = {Vana Sypsa and Sotirios Roussos and Dimitrios Paraskevis and Theodore Lytras and Sotirios Tsiodras and Angelos Hatzakis},
    journal = {{Emerg Infect Dis}},
    title = {Effects of Social Distancing Measures during the First Epidemic Wave of {S}evere {A}cute {R}espiratory {S}yndrome Infection, {G}reece},
    year = {2021},
    number = {2},
    pages = {452--462},
    volume = {27},
    doi = {10.3201/eid2702.203412},
    publisher = {Centers for Disease Control and Prevention ({CDC})},
    }
  • [DOI] H. H. Buchholz, M. L. Michelsen, L. M. Bolaños, E. Browne, M. J. Allen, and B. Temperton, "Efficient dilution-to-extinction isolation of novel virus–host model systems for fastidious heterotrophic bacteria," ISME J, 2021.
    [Bibtex]
    @Article{Buchholz:21,
    author = {Holger H. Buchholz and Michelle L. Michelsen and Luis M. Bola{\~{n}}os and Emily Browne and Michael J. Allen and Ben Temperton},
    journal = {{ISME J}},
    title = {Efficient dilution-to-extinction isolation of novel virus{\textendash}host model systems for fastidious heterotrophic bacteria},
    year = {2021},
    doi = {10.1038/s41396-020-00872-z},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] G. Nouailles, E. Wyler, P. Pennitz, D. Postmus, D. Vladrimirova, J. Kazmierski, F. Pott, K. Dietert, M. Mülleder, V. Farztdinov, B. Obermayer, S. Wienhold, S. Andreotti, T. Hoefler, B. Sawitzki, C. Drosten, L. Sander, N. Suttorp, M. Ralser, D. Beule, A. Gruber, C. Goffinet, M. Landthaler, J. Trimpert, and M. Witzenrath, "Longitudinal omics in syrian hamsters integrated with human data unravel cellular effector responses to moderate COVID-19," Research Square, 2021.
    [Bibtex]
    @Article{Nouailles:21,
    author = {Nouailles, Geraldine and Wyler, Emanuel and Pennitz, Peter and Postmus, Dylan and Vladrimirova, Daria and Kazmierski, Julia and Pott, Fabian and Dietert, Kristina and Mülleder, Michael and Farztdinov, Vadim and Obermayer, Benedikt and Wienhold, Sandra-Maria and Andreotti, Sandro and Hoefler, Thomas and Sawitzki, Birgit and Drosten, Christian and Sander, Leif and Suttorp, Norbert and Ralser, Markus and Beule, Dieter and Gruber, Achim and Goffinet, Christine and Landthaler, Markus and Trimpert, Jakob and Witzenrath, Martin},
    journal = {{Research Square}},
    title = {Longitudinal omics in Syrian hamsters integrated with human data unravel cellular effector responses to moderate {COVID}-19},
    year = {2021},
    abstract = {In COVID-19, immune responses are key in determining disease severity. However, cellular mechanisms at the onset of inflammatory lung injury in SARS-CoV-2 infection, particularly involving endothelial cells, remain ill-defined. Using Syrian hamsters as model for moderate COVID-19, we conducted a detailed longitudinal analysis of systemic and pulmonary cellular responses, and corroborated it with datasets from COVID-19 patients. Monocyte-derived macrophages in lungs exerted the earliest and strongest transcriptional response to infection, including induction of pro-inflammatory genes, while epithelial cells showed weak activation. Without evidence for productive infection, endothelial cells reacted, depending on cell subtypes, by strong and early expression of anti-viral, pro-inflammatory, and T cell recruiting genes. Recruitment of cytotoxic T cells as well as emergence of IgM antibodies preceded viral clearance at day 5 post infection. Investigating SARS-CoV-2 infected Syrian hamsters can thus identify cell type-specific effector functions, provide detailed insights into pathomechanisms of COVID-19, and inform therapeutic strategies.},
    doi = {10.21203/rs.3.rs-148392/v1},
    url = {https://doi.org/10.21203/rs.3.rs-148392/v1},
    }
  • [DOI] V. Haage, A. Moreira-Soto, J. A. Sacks, V. Corman, C. Drosten, and F. Drexler, "Limited specificity of SARS-CoV-2 antigen-detecting rapid diagnostic tests at low temperatures," medRxiv, 2021.
    [Bibtex]
    @Article{Haage:21,
    author = {Verena Haage and Andres Moreira-Soto and Jilian A. Sacks and Victor Corman and Christian Drosten and Felix Drexler},
    journal = {{medRxiv}},
    title = {Limited specificity of {SARS}-{CoV}-2 antigen-detecting rapid diagnostic tests at low temperatures},
    year = {2021},
    doi = {10.1101/2021.02.01.21250904},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] C. Brandt, R. Spott, M. Hölzer, D. Kühnert, S. Fuchs, M. Lohde, M. Marquet, A. Viehweger, D. Rimek, and M. W. Pletz, "Molecular epidemiology of SARS-CoV-2 - a regional to global perspective," medRxiv, 2021.
    [Bibtex]
    @Article{Brandt:21,
    author = {Christian Brandt and Riccardo Spott and Martin Hölzer and Denise Kühnert and Stephan Fuchs and Mara Lohde and Mike Marquet and Adrian Viehweger and Dagmar Rimek and Mathias W. Pletz},
    journal = {{medRxiv}},
    title = {Molecular epidemiology of {SARS}-{CoV}-2 - a regional to global perspective},
    year = {2021},
    doi = {10.1101/2021.01.25.21250447},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] E. 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] C. B. F. Vogels, M. Breban, T. Alpert, M. E. Petrone, A. E. Watkins, E. B. Hodcroft, C. E. Mason, G. Khullar, J. Metti, J. T. Dudley, M. J. MacKay, M. Nash, J. Wang, C. Liu, P. Hui, S. Murphy, C. Neal, E. Laszlo, M. L. Landry, A. Muyombwe, R. Downing, J. Razeq, R. A. Neher, J. R. Fauver, and N. D. Grubaugh, "PCR assay to enhance global surveillance for SARS-CoV-2 variants of concern," medRxiv, 2021.
    [Bibtex]
    @Article{Vogels:21,
    author = {Chantal B.F. Vogels and Mallery Breban and Tara Alpert and Mary E. Petrone and Anne E. Watkins and Emma B. Hodcroft and Christopher E. Mason and Gaurav Khullar and Jessica Metti and Joel T. Dudley and Matthew J. MacKay and Megan Nash and Jianhui Wang and Chen Liu and Pei Hui and Steven Murphy and Caleb Neal and Eva Laszlo and Marie L. Landry and Anthony Muyombwe and Randy Downing and Jafar Razeq and Richard A. Neher and Joseph R. Fauver and Nathan D. Grubaugh},
    journal = {{medRxiv}},
    title = {{PCR} assay to enhance global surveillance for {SARS}-{CoV}-2 variants of concern},
    year = {2021},
    doi = {10.1101/2021.01.28.21250486},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] B. Tönshoff, B. Müller, R. Elling, H. Renk, P. Meissner, H. Hengel, S. F. Garbade, M. Kieser, K. Jeltsch, J. Grulich-Henn, J. Euler, M. Stich, K. Chobanyan-Jürgens, M. Zernickel, A. Janda, L. Wölfle, T. Stamminger, T. Iftner, T. Ganzenmueller, C. Schmitt, T. Görne, V. Laketa, S. Olberg, A. Plaszczyca, M. Cortese, R. Bartenschlager, C. Pape, R. Remme, D. Huzly, M. Panning, S. Weigang, S. Giese, K. Ciminski, J. Ankerhold, G. Kochs, M. Schwemmle, R. Handgretinger, C. M. Niemeyer, C. Engel, W. V. Kern, G. F. Hoffmann, A. R. Franz, P. Henneke, K. Debatin, and H. Kräusslich, "Prevalence of SARS-CoV-2 infection in children and their parents in Southwest Germany," JAMA Pediatr, 2021.
    [Bibtex]
    @Article{Toenshoff:21,
    author = {Burkhard Tönshoff and Barbara Müller and Roland Elling and Hanna Renk and Peter Meissner and Hartmut Hengel and Sven F. Garbade and Meinhard Kieser and Kathrin Jeltsch and Jürgen Grulich-Henn and Julia Euler and Maximilian Stich and Kristine Chobanyan-Jürgens and Maria Zernickel and Ale{\v{s}} Janda and Lena Wölfle and Thomas Stamminger and Thomas Iftner and Tina Ganzenmueller and Christian Schmitt and Tessa Görne and Vibor Laketa and Sylvia Olberg and Anna Plaszczyca and Mirko Cortese and Ralf Bartenschlager and Constantin Pape and Roman Remme and Daniela Huzly and Marcus Panning and Sebastian Weigang and Sebastian Giese and Kevin Ciminski and Jakob Ankerhold and Georg Kochs and Martin Schwemmle and Rupert Handgretinger and Charlotte M. Niemeyer and Corinna Engel and Winfried V. Kern and Georg Friedrich Hoffmann and Axel R. Franz and Philipp Henneke and Klaus-Michael Debatin and Hans-Georg Kräusslich},
    journal = {{JAMA Pediatr}},
    title = {Prevalence of {SARS}-{CoV}-2 Infection in Children and Their Parents in {S}outhwest {G}ermany},
    year = {2021},
    doi = {10.1001/jamapediatrics.2021.0001},
    publisher = {American Medical Association ({AMA})},
    }
  • [DOI] H. Slanina, R. Madhugiri, G. Bylapudi, K. Schultheiß, N. Karl, A. Gulyaeva, A. E. Gorbalenya, U. Linne, and J. Ziebuhr, "Coronavirus replication–transcription complex: Vital and selective NMPylation of a conserved site in nsp9 by the NiRAN-RdRp subunit," Proc Natl Acad Sci USA, vol. 118, iss. 6, p. e2022310118, 2021.
    [Bibtex]
    @Article{Slanina:21,
    author = {Heiko Slanina and Ramakanth Madhugiri and Ganesh Bylapudi and Karin Schulthei{\ss} and Nadja Karl and Anastasia Gulyaeva and Alexander E. Gorbalenya and Uwe Linne and John Ziebuhr},
    journal = {{Proc Natl Acad Sci USA}},
    title = {Coronavirus replication{\textendash}transcription complex: {V}ital and selective {NMPylation} of a conserved site in nsp9 by the {NiRAN}-{RdRp} subunit},
    year = {2021},
    number = {6},
    pages = {e2022310118},
    volume = {118},
    doi = {10.1073/pnas.2022310118},
    publisher = {Proceedings of the National Academy of Sciences},
    }
  • [DOI] S. Posada-Céspedes, D. Seifert, I. Topolsky, K. P. Jablonski, K. J. Metzner, and N. Beerenwinkel, "V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data," Bioinformatics, 2021.
    [Bibtex]
    @Article{PosadaCespedes:21,
    author = {Susana Posada-C{\'{e}}spedes and David Seifert and Ivan Topolsky and Kim Philipp Jablonski and Karin J Metzner and Niko Beerenwinkel},
    journal = {Bioinformatics},
    title = {V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data},
    year = {2021},
    doi = {10.1093/bioinformatics/btab015},
    editor = {Jinbo Xu},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] C. Simsek, V. M. Corman, H. U. Everling, A. N. Lukashev, A. Rasche, G. D. Maganga, T. Binger, D. Jansen, L. Beller, W. Deboutte, F. Gloza-Rausch, A. Seebens-Hoyer, S. Yordanov, A. Sylverken, S. Oppong, Y. A. Sarkodie, P. Vallo, E. M. Leroy, M. Bourgarel, K. C. Yinda, M. V. Ranst, C. Drosten, J. F. Drexler, and J. Matthijnssens, "At least seven distinct rotavirus genotype constellations in bats with evidence of reassortment and zoonotic transmissions," mBio, vol. 12, iss. 1, 2021.
    [Bibtex]
    @Article{Simsek:21,
    author = {Ceren Simsek and Victor Max Corman and Hermann Ulrich Everling and Alexander N. Lukashev and Andrea Rasche and Gael Darren Maganga and Tabea Binger and Daan Jansen and Leen Beller and Ward Deboutte and Florian Gloza-Rausch and Antje Seebens-Hoyer and Stoian Yordanov and Augustina Sylverken and Samuel Oppong and Yaw Adu Sarkodie and Peter Vallo and Eric M. Leroy and Mathieu Bourgarel and Kwe Claude Yinda and Marc Van Ranst and Christian Drosten and Jan Felix Drexler and Jelle Matthijnssens},
    journal = {{mBio}},
    title = {At Least Seven Distinct Rotavirus Genotype Constellations in Bats with Evidence of Reassortment and Zoonotic Transmissions},
    year = {2021},
    number = {1},
    volume = {12},
    doi = {10.1128/mbio.02755-20},
    editor = {John T. Patton},
    publisher = {American Society for Microbiology},
    }
  • [DOI] K. Jahn, D. Dreifuss, I. Topolsky, A. Kull, P. Ganesanandamoorthy, X. Fernandez-Cassi, C. Bänziger, E. Stachler, L. Fuhrmann, K. P. Jablonski, C. Chen, C. Aquino, T. Stadler, C. Ort, T. Kohn, T. R. Julian, and N. Beerenwinkel, "Detection of SARS-CoV-2 variants in Switzerland by genomic analysis of wastewater samples," medRxiv, 2021.
    [Bibtex]
    @Article{Jahn:21,
    author = {Katharina Jahn and David Dreifuss and Ivan Topolsky and Anina Kull and Pravin Ganesanandamoorthy and Xavier Fernandez-Cassi and Carola Bänziger and Elyse Stachler and Lara Fuhrmann and Kim Philipp Jablonski and Chaoran Chen and Catharine Aquino and Tanja Stadler and Christoph Ort and Tamar Kohn and Timothy R. Julian and Niko Beerenwinkel},
    journal = {{medRxiv}},
    title = {Detection of {SARS}-{CoV}-2 variants in {S}witzerland by genomic analysis of wastewater samples},
    year = {2021},
    doi = {10.1101/2021.01.08.21249379},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] S. J. Lycett, J. Hughes, M. P. McHugh, A. S. da Filipe, R. Dewar, L. Lu, T. Doherty, A. Shepherd, R. Inward, G. Rossi, D. Balaz, R. R. Kao, S. Rooke, S. Cotton, M. D. Gallagher, C. B. Lopez, Á. O'Toole, E. Scher, V. Hill, J. T. McCrone, R. M. Colquhoun, B. Jackson, T. C. Williams, K. A. Williamson, N. Johnson, K. Smollett, D. Mair, S. Carmichael, L. Tong, J. Nichols, K. Brunker, J. G. Shepherd, K. Li, E. Aranday-Cortes, Y. A. Parr, A. Broos, K. Nomikou, S. E. McDonald, M. Niebel, P. Asamaphan, I. Starinskij, N. Jesudason, R. Shah, V. B. Sreenu, T. Stanton, S. Shaaban, A. MacLean, M. Woolhouse, R. Gunson, K. Templeton, E. C. Thomson, A. Rambaut, M. T. G. Holden, and D. R. L. and, "Epidemic waves of COVID-19 in Scotland: a genomic perspective on the impact of the introduction and relaxation of lockdown on SARS-CoV-2," medRxiv, 2021.
    [Bibtex]
    @Article{Lycett:21,
    author = {Samantha J Lycett and Joseph Hughes and Martin P McHugh and Ana da Silva Filipe and Rebecca Dewar and Lu Lu and Thomas Doherty and Amy Shepherd and Rhys Inward and Gianluigi Rossi and Daniel Balaz and Rowland R Kao and Stefan Rooke and Seb Cotton and Michael D Gallagher and Carlos Balcazar Lopez and {\'{A}}ine O'Toole and Emily Scher and Verity Hill and John T McCrone and Rachel M Colquhoun and Ben Jackson and Thomas C Williams and Kathleen A Williamson and Natasha Johnson and Katherine Smollett and Daniel Mair and Stephen Carmichael and Lily Tong and Jenna Nichols and Kirstyn Brunker and James G Shepherd and Kathy Li and Elihu Aranday-Cortes and Yasmin A Parr and Alice Broos and Kyriaki Nomikou and Sarah E McDonald and Marc Niebel and Patawee Asamaphan and Igor Starinskij and Natasha Jesudason and Rajiv Shah and Vattipally B Sreenu and Tom Stanton and Sharif Shaaban and Alasdair MacLean and Mark Woolhouse and Rory Gunson and Kate Templeton and Emma C Thomson and Andrew Rambaut and Matthew T.G. Holden and David L Robertson and},
    journal = {{medRxiv}},
    title = {Epidemic waves of {COVID}-19 in {S}cotland: a genomic perspective on the impact of the introduction and relaxation of lockdown on {SARS}-{CoV}-2},
    year = {2021},
    doi = {10.1101/2021.01.08.20248677},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] S. Modha, D. L. Robertson, J. Hughes, and R. J. Orton, "Quantifying and cataloguing unknown sequences within human microbiomes," bioRxiv, 2021.
    [Bibtex]
    @Article{Modha:21,
    author = {Sejal Modha and David L. Robertson and Joseph Hughes and Richard J. Orton},
    journal = {{bioRxiv}},
    title = {Quantifying and cataloguing unknown sequences within human microbiomes},
    year = {2021},
    doi = {10.1101/2021.01.22.427751},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] S. Lytras, J. Hughes, W. Xia, X. Jiang, and D. L. Robertson, "Exploring the natural origins of SARS-CoV-2," bioRxiv, 2021.
    [Bibtex]
    @Article{Lytras:21,
    author = {Spyros Lytras and Joseph Hughes and Wei Xia and Xiaowei Jiang and David L Robertson},
    journal = {{bioRxiv}},
    title = {Exploring the natural origins of {SARS}-{CoV}-2},
    year = {2021},
    doi = {10.1101/2021.01.22.427830},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. Möckel, V. M. Corman, M. S. Stegemann, J. Hofmann, A. Stein, T. C. Jones, P. Gastmeier, J. Seybold, R. Offermann, U. Bachmann, T. Lindner, W. Bauer, C. Drosten, A. Rosen, and R. Somasundaram, "SARS-CoV-2 antigen rapid immunoassay for diagnosis of COVID-19 in the emergency department.," Biomarkers, p. 1–13, 2021.
    [Bibtex]
    @Article{Moeckel:21,
    author = {Möckel, Martin and Corman, Victor M. and Stegemann, Miriam S. and Hofmann, Jörg and Stein, Angela and Jones, Terry C. and Gastmeier, Petra and Seybold, Joachim and Offermann, Ralf and Bachmann, Ulrike and Lindner, Tobias and Bauer, Wolfgang and Drosten, Christian and Rosen, Alexander and Somasundaram, Rajan},
    journal = {{Biomarkers}},
    title = {{SARS-CoV-2} Antigen Rapid Immunoassay for Diagnosis of {COVID-19} in the Emergency Department.},
    year = {2021},
    pages = {1--13},
    abstract = {In the emergency department (ED) setting, rapid testing for SARS-CoV-2 is likely associated with advantages to patients and healthcare workers, for example enabling early but rationale use of limited isolation resources. Most recently, several SARS-CoV-2 rapid point-of-care antigen tests (AGTEST) became available. There is a growing need for data regarding their clinical utility and performance in the diagnosis of SARS-CoV-2 infection in the real life setting of 5 EDs. We implemented AGTEST (here: Roche/SD Biosensor) in all four adult and the one pediatric EDs at Charité - Universitätsmedizin Berlin in our diagnostic testing strategy. Test indication was limited to symptomatic suspected COVID-19 patients. Detailed written instructions on who to test were distributed and testing personnel were trained in proper specimen collection and handling. In each suspected COVID-19 patient, two sequential deep oro-nasopharyngeal swabs were obtained for viral tests. The first swab was collected for nucleic acid testing through SARS-CoV-2 Real-Time Reverse Transcriptase (rt)-PCR diagnostic panel (PCRTEST) in the central laboratory. The second swab was collected to perform the AGTEST. Analysis of routine data was prospectively planned and data were retrieved from the medical records after the inclusion period in the adult or pediatric ED. Diagnostic performance was calculated using the PCRTEST as reference standard. False negative and false positive AGTEST results were analyzed individually and compared with viral concentrations derived from the calibrated PCRTEST. We included n = 483 patients including n= 202 from the pediatric ED. N = 10 patients had to be excluded due to missing data and finally n = 473 patients were analyzed. In the adult cohort, the sensitivity of the AGTEST was 75.3 (95%CI: 65.8/83.4)% and the specificity was 100 (95%CI: 98.4/100)% with a SARS-CoV-2 prevalence of 32.8%; the positive predictive value was 100 (95%CI: 95.7/100)% and the negative predictive value 89.2 (95%CI: 84.5/93.9)%. In the pediatric cohort the sensitivity was 72.0 (95%CI: 53.3/86.7)%, the specificity was 99.4 (95%CI:97.3/99.9)% with a prevalence of 12.4%; the positive predictive value was 94.7 (95%CI: 78.3/99.7)% and the negative predictive value was 96.2 (95%CI:92.7/98.3)%.Thus, n = 22 adult and n = 7 pediatric patients showed false negative AGTEST results and only one false positive AGTEST occurred, in the pediatric cohort. Calculated viral concentrations from the rt-PCR lay between 3.16 and 9.51 log10 RNA copies/mL buffer. All false negative patients in the adult ED cohort, who had confirmed symptom onset at least seven days earlier had less than 5x 10^5 RNA copies/mL buffer. We conclude that the use of AGTEST among symptomatic patients in the emergency setting is useful for the early identification of COVID-19, but patients who test negative require confirmation by PCRTEST and must stay isolated until this result becomes available. Adult patients with a false negative AGTEST and symptom onset at least one week earlier have typically a low SARS-CoV-2 RNA concentration and likely pass the infectious period.},
    doi = {10.1080/1354750X.2021.1876769},
    pmid = {33455451},
    pubstate = {aheadofprint},
    }
  • [DOI] A. Osterman, H. Baldauf, M. Eletreby, J. M. Wettengel, S. Q. Afridi, T. Fuchs, E. Holzmann, A. Maier, J. Döring, N. Grzimek-Koschewa, M. Muenchhoff, U. Protzer, L. Kaderali, and O. T. Keppler, "Evaluation of two rapid antigen tests to detect SARS-CoV-2 in a hospital setting.," Med Microbiol Immunol, 2021.
    [Bibtex]
    @Article{Osterman:21,
    author = {Osterman, Andreas and Baldauf, Hanna-Mari and Eletreby, Marwa and Wettengel, Jochen M. and Afridi, Suliman Q. and Fuchs, Thimo and Holzmann, Elena and Maier, Anton and Döring, Johanna and Grzimek-Koschewa, Natascha and Muenchhoff, Maximilian and Protzer, Ulrike and Kaderali, Lars and Keppler, Oliver T.},
    journal = {{Med Microbiol Immunol}},
    title = {Evaluation of two rapid antigen tests to detect {SARS-CoV-2} in a hospital setting.},
    year = {2021},
    abstract = {Successful containment strategies for the SARS-CoV-2 pandemic will depend on reliable diagnostic assays. Point-of-care antigen tests (POCT) may provide an alternative to time-consuming PCR tests to rapidly screen for acute infections on site. Here, we evaluated two SARS-CoV-2 antigen tests: the STANDARD™ F COVID-19 Ag FIA (FIA) and the SARS-CoV-2 Rapid Antigen Test (RAT). For diagnostic assessment, we used a large set of PCR-positive and PCR-negative respiratory swabs from asymptomatic and symptomatic patients and health care workers in the setting of two University Hospitals in Munich, Germany, i.e. emergency rooms, patient care units or employee test centers. For FIA, overall clinical sensitivity and specificity were 45.4% (n = 381) and 97.8% (n = 360), respectively, and for RAT, 50.3% (n = 445) and 97.7% (n = 386), respectively. For primary diagnosis of asymptomatic and symptomatic individuals, diagnostic sensitivities were 60.9% (FIA) (n = 189) and 64.5% (RAT) (n = 256). This questions these tests' utility for the reliable detection of acute SARS-CoV-2-infected individuals, in particular in high-risk settings. We support the proposal that convincing high-quality outcome data on the impact of false-negative and false-positive antigen test results need to be obtained in a POCT setting. Moreover, the efficacy of alternative testing strategies to complement PCR assays must be evaluated by independent laboratories, prior to widespread implementation in national and international test strategies.},
    doi = {10.1007/s00430-020-00698-8},
    keywords = {COVID-19 point-of-care; Diagnostic test; SARS-CoV-2 antigen test; Sensitivity; Specificity},
    pmid = {33452927},
    pubstate = {aheadofprint},
    }
  • [DOI] M. Bárcena, C. O. Barnes, M. Beck, P. J. Bjorkman, B. Canard, G. F. Gao, Y. Gao, R. Hilgenfeld, G. Hummer, A. Patwardhan, G. Santoni, E. O. Saphire, C. Schaffitzel, S. L. Schendel, J. L. Smith, A. Thorn, D. Veesler, P. Zhang, and Q. Zhou, "Structural biology in the fight against COVID-19.," Nat Struct Mol Biol, vol. 28, p. 2–7, 2021.
    [Bibtex]
    @Article{Barcena:21,
    author = {Bárcena, Montserrat and Barnes, Christopher O. and Beck, Martin and Bjorkman, Pamela J. and Canard, Bruno and Gao, George F. and Gao, Yunyun and Hilgenfeld, Rolf and Hummer, Gerhard and Patwardhan, Ardan and Santoni, Gianluca and Saphire, Erica Ollmann and Schaffitzel, Christiane and Schendel, Sharon L. and Smith, Janet L. and Thorn, Andrea and Veesler, David and Zhang, Peijun and Zhou, Qiang},
    journal = {{Nat Struct Mol Biol}},
    title = {Structural biology in the fight against {COVID-19}.},
    year = {2021},
    pages = {2--7},
    volume = {28},
    doi = {10.1038/s41594-020-00544-8},
    issue = {1},
    keywords = {Computational Biology, methods; Cryoelectron Microscopy, methods; Databases, Protein; Epitopes, chemistry, immunology; Host-Pathogen Interactions; Humans; Linoleic Acid, chemistry, metabolism, pharmacology; Molecular Biology, methods; SARS-CoV-2, chemistry, genetics, pathogenicity; Spike Glycoprotein, Coronavirus, chemistry, metabolism; Viral Proteins, chemistry, metabolism; Viral Vaccines, immunology, pharmacology; Virus Replication, physiology},
    pmid = {33437043},
    pubstate = {ppublish},
    }
  • [DOI] D. A. Hofmaenner, P. D. Wendel Garcia, B. Duvnjak, B. Chakrakodi, J. D. Maier, M. Huber, J. Huder, A. Wolfensberger, P. W. Schreiber, R. A. Schuepbach, A. S. Zinkernagel, P. K. Buehler, S. D. Brugger, and COVID-19 ICU-Research Group Zurich, "Bacterial but no SARS-CoV-2 contamination after terminal disinfection of tertiary care intensive care units treating COVID-19 patients.," Antimicrob Resist Infect Control, vol. 10, p. 11, 2021.
    [Bibtex]
    @Article{Hofmaenner:21,
    author = {Hofmaenner, Daniel A. and Wendel Garcia, Pedro David and Duvnjak, Branko and Chakrakodi, Bhavya and Maier, Julian D. and Huber, Michael and Huder, Jon and Wolfensberger, Aline and Schreiber, Peter W. and Schuepbach, Reto A. and Zinkernagel, Annelies S. and Buehler, Philipp K. and Brugger, Silvio D. and {COVID-19 ICU-Research Group Zurich}},
    journal = {{Antimicrob Resist Infect Control}},
    title = {Bacterial but no {SARS-CoV-2} contamination after terminal disinfection of tertiary care intensive care units treating {COVID-19} patients.},
    year = {2021},
    pages = {11},
    volume = {10},
    abstract = {In intensive care units (ICUs) treating patients with Coronavirus disease 2019 (COVID-19) invasive ventilation poses a high risk for aerosol and droplet formation. Surface contamination of severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) or bacteria can result in nosocomial transmission. Two tertiary care COVID-19 intensive care units treating 53 patients for 870 patient days were sampled after terminal cleaning and preparation for regular use to treat non-COVID-19 patients. A total of 176 swabs were sampled of defined locations covering both ICUs. No SARS-CoV-2 ribonucleic acid (RNA) was detected. Gram-negative bacterial contamination was mainly linked to sinks and siphons. Skin flora was isolated from most swabbed areas and Enterococcus faecium was detected on two keyboards. After basic cleaning with standard disinfection measures no remaining SARS-CoV-2 RNA was detected. Bacterial contamination was low and mainly localised in sinks and siphons.},
    doi = {10.1186/s13756-021-00885-z},
    investigator = {Bartussek, Jan and Buehler, Phillip and Heuberger, Dorothea Monika and Hilty, Matthias Peter and Hofmänner, Daniel Andrea and Maibach, Martina and Andreas, Schuepbach Reto and Wendel Garcia, Pedro David},
    issue = {1},
    keywords = {Aerosols, analysis; Bacteria, classification, genetics, growth & development, isolation & purification; COVID-19, therapy, virology; Cross Infection, microbiology, prevention & control, virology; Disinfection, methods; Equipment Contamination, statistics & numerical data; Female; Humans; Intensive Care Units, statistics & numerical data; Male; Middle Aged; SARS-CoV-2, genetics, isolation & purification, physiology; Tertiary Healthcare, statistics & numerical data; Disinfection; Hospital epidemiology; Hydrogen peroxide nebulisation; ICU; Nosocomial infection; SARS-CoV-2},
    pmid = {33436105},
    pubstate = {epublish},
    }
  • [DOI] U. Teichgräber, A. Malouhi, M. Ingwersen, R. Neumann, M. Reljic, S. Deinhardt-Emmer, B. Löffler, W. Behringer, J. Lewejohann, A. Stallmach, and P. Reuken, "Ruling out COVID-19 by chest CT at emergency admission when prevalence is low: the prospective, observational SCOUT study.," Respir Res, vol. 22, p. 13, 2021.
    [Bibtex]
    @Article{Teichgraeber:21,
    author = {Teichgräber, Ulf and Malouhi, Amer and Ingwersen, Maja and Neumann, Rotraud and Reljic, Marina and Deinhardt-Emmer, Stefanie and Löffler, Bettina and Behringer, Wilhelm and Lewejohann, Jan-Christoph and Stallmach, Andreas and Reuken, Philipp},
    journal = {{Respir Res}},
    title = {Ruling out {COVID-19} by chest {CT} at emergency admission when prevalence is low: the prospective, observational {SCOUT} study.},
    year = {2021},
    pages = {13},
    volume = {22},
    abstract = {It is essential to avoid admission of patients with undetected corona virus disease 2019 (COVID-19) to hospitals' general wards. Even repeated negative reverse transcription polymerase chain reaction (RT-PCR) results do not rule-out COVID-19 with certainty. The study aimed to evaluate a rule-out strategy for COVID-19 using chest computed tomography (CT) in adults being admitted to the emergency department and suspected of COVID-19. In this prospective, single centre, diagnostic accuracy cohort study, consecutive adults (≥ 18 years) presenting with symptoms consistent with COVID-19 or previous contact to infected individuals, admitted to the emergency department and supposed to be referred to general ward were included in March and April 2020. All participants underwent low-dose chest CT. RT-PCR- and specific antibody tests were used as reference standard. Main outcome measures were sensitivity and specificity of chest CT. Predictive values were calculated based on the theorem of Bayes using Fagan's nomogram. Of 165 participants (56.4% male, 71 ± 16 years) included in the study, the diagnosis of COVID-19 was confirmed with RT-PCR and AB tests in 13 participants (prevalence 7.9%). Sensitivity and specificity of chest CT were 84.6% (95% confidence interval [CI], 54.6-98.1) and 94.7% (95% CI, 89.9-97.7), respectively. Positive and negative likelihood ratio of chest CT were 16.1 (95% CI, 7.9-32.8) and 0.16 (95% CI, 0.05-0.58) and positive and negative predictive value were 57.9% (95% CI, 40.3-73.7) and 98.6% (95% CI, 95.3-99.6), respectively. At a low prevalence of COVID-19, chest CT could be used as a complement to repeated RT-PCR testing for early COVID-19 exclusion in adults with suspected infection before referral to hospital's general wards. Trial registration ClinicalTrials.gov: NCT04357938 April 22, 2020.},
    doi = {10.1186/s12931-020-01611-w},
    issue = {1},
    keywords = {Aged; Aged, 80 and over; COVID-19, blood, diagnostic imaging, epidemiology; Cohort Studies; Emergency Service, Hospital, trends; Female; Germany, epidemiology; Humans; Male; Middle Aged; Patient Admission, trends; Prevalence; Prospective Studies; Quarantine, methods, trends; Tomography, X-Ray Computed, methods, trends; COVID-19; Computed tomography; Prevalence; Reverse transcriptase polymerase chain reaction; Sensitivity and specificity; Severe acute respiratory syndrome coronavirus 2},
    pmid = {33435973},
    pubstate = {epublish},
    }
  • [DOI] I. P. Trougakos, K. Stamatelopoulos, E. Terpos, O. E. Tsitsilonis, E. Aivalioti, D. Paraskevis, E. Kastritis, G. N. Pavlakis, and M. A. Dimopoulos, "Insights to SARS-CoV-2 life cycle, pathophysiology, and rationalized treatments that target COVID-19 clinical complications.," J Biomed Sci, vol. 28, p. 9, 2021.
    [Bibtex]
    @Article{Trougakos:21,
    author = {Trougakos, Ioannis P. and Stamatelopoulos, Kimon and Terpos, Evangelos and Tsitsilonis, Ourania E. and Aivalioti, Evmorfia and Paraskevis, Dimitrios and Kastritis, Efstathios and Pavlakis, George N. and Dimopoulos, Meletios A.},
    journal = {{J Biomed Sci}},
    title = {Insights to {SARS-CoV-2} life cycle, pathophysiology, and rationalized treatments that target {COVID-19} clinical complications.},
    year = {2021},
    pages = {9},
    volume = {28},
    abstract = {Gaining further insights into SARS-CoV-2 routes of infection and the underlying pathobiology of COVID-19 will support the design of rational treatments targeting the life cycle of the virus and/or the adverse effects (e.g., multi-organ collapse) that are triggered by COVID-19-mediated adult respiratory distress syndrome (ARDS) and/or other pathologies. COVID-19 is a two-phase disease being marked by (phase 1) increased virus transmission and infection rates due to the wide expression of the main infection-related ACE2, TMPRSS2 and CTSB/L human genes in tissues of the respiratory and gastrointestinal tract, as well as by (phase 2) host- and probably sex- and/or age-specific uncontrolled inflammatory immune responses which drive hyper-cytokinemia, aggressive inflammation and (due to broad organotropism of SARS-CoV-2) collateral tissue damage and systemic failure likely because of imbalanced ACE/ANGII/AT1R and ACE2/ANG(1-7)/MASR axes signaling. Here we discuss SARS-CoV-2 life cycle and a number of approaches aiming to suppress viral infection rates or propagation; increase virus antigen presentation in order to activate a robust and durable adaptive immune response from the host, and/or mitigate the ARDS-related "cytokine storm" and collateral tissue damage that triggers the severe life-threatening complications of COVID-19.},
    doi = {10.1186/s12929-020-00703-5},
    issue = {1},
    keywords = {COVID-19, complications, drug therapy, physiopathology, virology; Humans; Life Cycle Stages; SARS-CoV-2, isolation & purification, physiology; ACE2; ARDS; COVID-19; SARS-CoV-2; TMPRSS2},
    pmid = {33435929},
    pubstate = {epublish},
    }
  • [DOI] C. M. Crava, F. S. Varghese, E. Pischedda, R. Halbach, U. Palatini, M. Marconcini, L. Gasmi, S. Redmond, Y. Afrane, D. Ayala, C. Paupy, R. Carballar-Lejarazu, P. Miesen, R. P. van Rij, and M. Bonizzoni, "Population genomics in the arboviral vector Aedes aegypti reveals the genomic architecture and evolution of endogenous viral elements.," Mol Ecol, 2021.
    [Bibtex]
    @Article{Crava:21,
    author = {Crava, Cristina M. and Varghese, Finny S. and Pischedda, Elisa and Halbach, Rebecca and Palatini, Umberto and Marconcini, Michele and Gasmi, Leila and Redmond, Seth and Afrane, Yaw and Ayala, Diego and Paupy, Christophe and Carballar-Lejarazu, Rebeca and Miesen, Pascal and van Rij, Ronald P. and Bonizzoni, Mariangela},
    journal = {{Mol Ecol}},
    title = {Population genomics in the arboviral vector {A}edes aegypti reveals the genomic architecture and evolution of endogenous viral elements.},
    year = {2021},
    abstract = {Horizontal gene transfer from viruses to eukaryotic cells is a pervasive phenomenon. Somatic viral integrations are linked to persistent viral infection whereas integrations into germline cells are maintained in host genomes by vertical transmission and may be co-opted for host functions. In the arboviral vector Aedes aegypti, an endogenous viral element from a non-retroviral RNA virus (nrEVE) was shown to produce PIWI-interacting RNAs (piRNAs) to limit infection with a cognate virus. Thus, nrEVEs may constitute a heritable, sequence-specific mechanism for antiviral immunity, analogous to piRNA-mediated silencing of transposable elements. Here, we intersect population genomics and evolutionary approaches to analyze the genomic architecture of nrEVEs in Ae. aegypti. We conducted a genome-wide screen for adaptive nrEVEs and searched for novel population-specific nrEVEs in the genomes of eighty individual wild-caught mosquitoes from five geographical populations. We show a dynamic landscape of nrEVEs in mosquito genomes and identified five novel nrEVEs derived from two currently circulating viruses, providing evidence of the environmental-dependent modification of a piRNA cluster. Overall, our results show that virus endogenization events are complex events with only few nrEVEs contributing to adaptive evolution in Ae. aegypti.},
    doi = {10.1111/mec.15798},
    keywords = {Aedes aegypti ; endogenous viral elements; mosquito genomes; piRNA cluster},
    pmid = {33432714},
    pubstate = {aheadofprint},
    }
  • [DOI] S. R. Vaidya, S. M. Kasibhatla, M. B. Kamble, A. Munivenkatappa, N. S. Kumbhar, M. M. Jayaswamy, M. R. Ramtirthkar, M. M. Kale, and U. Kulkarni-Kale, "Genetic and antigenic characterization of wild type rubella viruses isolated from India.," Vaccine, 2021.
    [Bibtex]
    @Article{Vaidya21,
    author = {Vaidya, Sunil R. and Kasibhatla, Sunitha M. and Kamble, Madhukar B. and Munivenkatappa, Ashok and Kumbhar, Neelakshi S. and Jayaswamy, Manjunatha M. and Ramtirthkar, Mukund R. and Kale, Mohan M. and Kulkarni-Kale, Urmila},
    journal = {Vaccine},
    title = {Genetic and antigenic characterization of wild type rubella viruses isolated from {I}ndia.},
    year = {2021},
    abstract = {Rubella, is a contagious disease caused by Rubella virus (RuV) that manifests as fever with skin-rashes in children and adults along with complications in pregnant women. WHO-SEAR has set a target for Rubella elimination by 2023. This is the first report of antigenic characterization and genome sequencing of nine RuVs sampled during 1992, 2007-9, and 2015-17 from four Indian states. Comparative analysis of Indian RuVs (2B) with that of global isolates and vaccine strain RA 27/3 (1a) revealed that the observed mutations in structural proteins have no major impact on the 3D structure, function and antigenicity. Indian RuVs formed three major clusters (Pune-1992, Kannur-2009 and Chitradurg-2007) in genome-based phylogeny of global isolates. Neutralizing antibody titers in a panel of serum samples from measles negative cases were significantly higher to the vaccine strain compared to a wild-type 2B isolate (Kannur) with concordance of 91.9%, thereby substantiating the use of current vaccines.},
    doi = {10.1016/j.vaccine.2020.12.063},
    keywords = {Complete genome; Epitopes; Indian rubella virus isolates; Neutralization test; Rubella vaccine strain; Rubella virus bioinformatics},
    pmid = {33423836},
    pubstate = {aheadofprint},
    }
  • [DOI] C. Müller, W. Obermann, N. Karl, H. Wendel, G. Taroncher-Oldenburg, S. Pleschka, R. K. Hartmann, A. Grünweller, and J. Ziebuhr, "The rocaglate CR-31-B (-) inhibits SARS-CoV-2 replication at non-cytotoxic, low nanomolar concentrations in vitro and ex vivo.," Antiviral Res, vol. 186, p. 105012, 2021.
    [Bibtex]
    @Article{Mueller:21,
    author = {Müller, Christin and Obermann, Wiebke and Karl, Nadja and Wendel, Hans-Guido and Taroncher-Oldenburg, Gaspar and Pleschka, Stephan and Hartmann, Roland K. and Grünweller, Arnold and Ziebuhr, John},
    journal = {{Antiviral Res}},
    title = {The rocaglate {CR-31-B} (-) inhibits {SARS-CoV-2} replication at non-cytotoxic, low nanomolar concentrations in vitro and ex vivo.},
    year = {2021},
    pages = {105012},
    volume = {186},
    abstract = {Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of COVID-19, a severe respiratory disease with varying clinical presentations and outcomes, and responsible for a major pandemic that started in early 2020. With no vaccines or effective antiviral treatments available, the quest for novel therapeutic solutions remains an urgent priority. Rocaglates, a class of plant-derived cyclopenta[b]benzofurans, exhibit broad-spectrum antiviral activity against multiple RNA viruses including coronaviruses. Specifically, rocaglates inhibit eukaryotic initiation factor 4A (eIF4A)-dependent mRNA translation initiation, resulting in strongly reduced viral RNA translation. Here, we assessed the antiviral activity of the synthetic rocaglate CR-31-B (-) against SARS-CoV-2 using both in vitro and ex vivo cell culture models. In Vero E6 cells, CR-31-B (-) inhibited SARS-CoV-2 replication with an EC of ~1.8 nM. In primary human airway epithelial cells, CR-31-B (-) reduced viral titers to undetectable levels at a concentration of 100 nM. Reduced virus reproduction was accompanied by substantially reduced viral protein accumulation and replication/transcription complex formation. The data reveal a potent anti-SARS-CoV-2 activity by CR-31-B (-), corroborating previous results obtained for other coronaviruses and supporting the idea that rocaglates may be used in first-line antiviral intervention strategies against novel and emerging RNA virus outbreaks.},
    doi = {10.1016/j.antiviral.2021.105012},
    keywords = {Antiviral activity; COVID-19; Rocaglate; SARS-CoV-2; Translation initiation; eIF4A},
    pmid = {33422611},
    pubstate = {aheadofprint},
    }
  • [DOI] E. Criscuolo, R. A. Diotti, R. Ferrarese, C. Alippi, G. Viscardi, C. Signorelli, N. Mancini, M. Clementi, and N. Clementi, "Fast inactivation of SARS-CoV-2 by UV-C and ozone exposure on different materials.," Emerg Microbes Infect, p. 1–18, 2021.
    [Bibtex]
    @Article{Criscuolo:21,
    author = {Criscuolo, Elena and Diotti, Roberta A. and Ferrarese, Roberto and Alippi, Cesare and Viscardi, Gabriele and Signorelli, Carlo and Mancini, Nicasio and Clementi, Massimo and Clementi, Nicola},
    journal = {{Emerg Microbes Infect}},
    title = {Fast inactivation of {SARS-CoV-2} by {UV-C} and ozone exposure on different materials.},
    year = {2021},
    pages = {1--18},
    doi = {10.1080/22221751.2021.1872354},
    keywords = {SARS-CoV-2; UV-C; contact transmission; inactivation; ozone},
    pmid = {33399524},
    pubstate = {aheadofprint},
    }
  • [DOI] T. Tu, B. Zehnder, B. Qu, and S. Urban, "De novo synthesis of hepatitis B virus nucleocapsids is dispensable for the maintenance and transcriptional regulation of cccDNA," JHEP Rep, vol. 3, p. 100195, 2021.
    [Bibtex]
    @Article{Tu21,
    author = {Tu, Thomas and Zehnder, Benno and Qu, Bingqian and Urban, Stephan},
    journal = {{JHEP Rep}},
    title = {{D}e novo synthesis of hepatitis {B} virus nucleocapsids is dispensable for the maintenance and transcriptional regulation of {cccDNA}},
    year = {2021},
    pages = {100195},
    volume = {3},
    abstract = {Chronic HBV infection cannot be cured by current therapeutics owing to their limited ability to reduce covalently closed circular (ccc)DNA levels in the livers of infected individuals. Therefore, greater understanding of the molecular determinants of cccDNA formation and persistence is required. One key issue is the extent to which nucleocapsid-mediated replenishment (reimport) contributes to cccDNA levels in an infected hepatocyte. We engineered an infectious HBV mutant with a genome encoding a stop codon at position T67 in the HBV core open reading frame (ΔHBc HBV). Importantly, ΔHBc HBV virions cannot initiate nucleocapsid synthesis upon infection. Long-term HBV infection markers were followed for up for 9 weeks in HepG2-NTCP cells (A3 clone) and HBV DNA was quantified using a newly-developed, highly-precise PCR assay (cccDNA inversion quantitative PCR). ΔHBc and wild-type (WT) HBV resulted in comparable expression of HBV surface antigen (HBsAg), which could be blocked using the entry inhibitor Myrcludex B, confirming infection via the receptor sodium taurocholate cotransporting polypeptide (NTCP). In primary human hepatocytes, Huh7-NTCP, HepG2-NTCP, and HepaRG-NTCP cells, comparable copy numbers of cccDNA were formed. cccDNA levels, transcription of viral RNA, and HBsAg secretion remained comparably stable in WT and ΔHBc HBV-infected cells for at least 9 weeks. Our results imply that synthesised HBc plays a minor role in transcriptional regulation of cccDNA. Importantly, we show that initially-formed cccDNA is stable in hepatocytes without requiring continuous replenishment in infection systems and contribution from DNA-containing nucleocapsids is not required. Thus, short-term therapeutic targeting of capsid-reimport is likely an inefficient strategy in eliminating cccDNA in chronically infected hepatocytes. The hepatitis B virus can maintain itself in the liver for a patient's lifetime, causing liver injury and cancer. We have clarified exactly how it maintains itself in an infected cell. This now means we have a better idea at how to target the virus and cure a chronic infection.},
    doi = {10.1016/j.jhepr.2020.100195},
    issue = {1},
    keywords = {ALT, alanine aminotransferase; Antivirals; Bulevirtide; CIs, capsid inhibitors; Capsid inhibitors; Core protein; Covalently closed circular DNA; DHBV, duck hepatitis B virus; HBV DNA integration; HBV persistence; HBV, hepatitis B virus; HBcAg; HBsAg, hepatitis B virus surface antigen; Hepcludex; Myrcludex B; NC, naked capsids; NTCP, sodium taurocholate cotransporting polypeptide; NUCs, nucleos(t)ide analogues; ORF, open reading frame; PEG, polyethylene glycol; PHH, primary human hepatocytes; SN, supernatant; VP, virions; WT, wild-type; cccDNA, covalently closed circular DNA; dpi, days post inoculation; mge, multiplicity of genomic equivalent; pgRNA, pregenomic RNA; rcDNA, relaxed circular DNA; vge, viral genome equivalents},
    pmid = {33385130},
    pubstate = {epublish},
    }
  • [DOI] T. Toptan, L. Eckermann, A. E. Pfeiffer, S. Hoehl, S. Ciesek, C. Drosten, and V. M. Corman, "Evaluation of a SARS-CoV-2 rapid antigen test: potential to help reduce community spread?," J Clin Virol, vol. 135, p. 104713, 2021.
    [Bibtex]
    @Article{Toptan:21,
    author = {Tuna Toptan and Lisa Eckermann and Annika E. Pfeiffer and Sebastian Hoehl and Sandra Ciesek and Christian Drosten and Victor M. Corman},
    title = {Evaluation of a {SARS}-{CoV}-2 rapid antigen test: Potential to help reduce community spread?},
    journal = {{J Clin Virol}},
    year = {2021},
    volume = {135},
    pages = {104713},
    doi = {10.1016/j.jcv.2020.104713},
    publisher = {Elsevier {BV}},
    }
  • [DOI] A. Pérez-Cataluña, E. Cuevas-Ferrando, W. Randazzo, I. Falcó, A. Allende, and G. Sánchez, "Comparing analytical methods to detect SARS-CoV-2 in wastewater," Sci Total Environ, vol. 758, p. 143870, 2021.
    [Bibtex]
    @Article{Perez-Cataluna:21,
    author = {Alba Pérez-Cataluña and Enric Cuevas-Ferrando and Walter Randazzo and Irene Falc{\'{o}} and Ana Allende and Gloria Sánchez},
    journal = {{Sci Total Environ}},
    title = {Comparing analytical methods to detect {SARS}-{CoV}-2 in wastewater},
    year = {2021},
    pages = {143870},
    volume = {758},
    doi = {10.1016/j.scitotenv.2020.143870},
    publisher = {Elsevier {BV}},
    }

2020

  • [DOI] Z. Deng, A. Dhingra, A. Fritz, J. Götting, P. C. Münch, L. Steinbrück, T. F. Schulz, T. Ganzenmüller, and A. C. McHardy, "Evaluating assembly and variant calling software for strain-resolved analysis of large DNA viruses," Brief Bioinform, vol. 22, iss. 3, 2020.
    [Bibtex]
    @Article{Deng:20,
    author = {Zhi-Luo Deng and Akshay Dhingra and Adrian Fritz and Jasper Götting and Philipp C Münch and Lars Steinbrück and Thomas F Schulz and Tina Ganzenmüller and Alice C McHardy},
    journal = {{Brief Bioinform}},
    title = {Evaluating assembly and variant calling software for strain-resolved analysis of large {DNA} viruses},
    year = {2020},
    number = {3},
    volume = {22},
    doi = {10.1093/bib/bbaa123},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] U. Ashraf, C. Benoit-Pilven, V. Navratil, C. Ligneau, G. Fournier, S. Munier, O. Sismeiro, J. Coppée, V. Lacroix, and N. Naffakh, "Influenza virus infection induces widespread alterations of host cell splicing.," NAR Genom Bioinform, vol. 2, p. lqaa095, 2020.
    [Bibtex]
    @Article{Ashraf:20,
    author = {Ashraf, Usama and Benoit-Pilven, Clara and Navratil, Vincent and Ligneau, Cécile and Fournier, Guillaume and Munier, Sandie and Sismeiro, Odile and Coppée, Jean-Yves and Lacroix, Vincent and Naffakh, Nadia},
    journal = {{NAR Genom Bioinform}},
    title = {Influenza virus infection induces widespread alterations of host cell splicing.},
    year = {2020},
    pages = {lqaa095},
    volume = {2},
    abstract = {Influenza A viruses (IAVs) use diverse mechanisms to interfere with cellular gene expression. Although many RNA-seq studies have documented IAV-induced changes in host mRNA abundance, few were designed to allow an accurate quantification of changes in host mRNA splicing. Here, we show that IAV infection of human lung cells induces widespread alterations of cellular splicing, with an overall increase in exon inclusion and decrease in intron retention. Over half of the mRNAs that show differential splicing undergo no significant changes in abundance or in their 3' end termination site, suggesting that IAVs can specifically manipulate cellular splicing. Among a randomly selected subset of 21 IAV-sensitive alternative splicing events, most are specific to IAV infection as they are not observed upon infection with VSV, induction of interferon expression or induction of an osmotic stress. Finally, the analysis of splicing changes in RED-depleted cells reveals a limited but significant overlap with the splicing changes in IAV-infected cells. This observation suggests that hijacking of RED by IAVs to promote splicing of the abundant viral NS1 mRNAs could partially divert RED from its target mRNAs. All our RNA-seq datasets and analyses are made accessible for browsing through a user-friendly Shiny interface (http://virhostnet.prabi.fr:3838/shinyapps/flu-splicing or https://github.com/cbenoitp/flu-splicing).},
    doi = {10.1093/nargab/lqaa095},
    issue = {4},
    pmid = {33575639},
    pubstate = {epublish},
    }
  • [DOI] S. Schlickeiser, T. Schwarz, S. Steiner, K. Wittke, N. Al Besher, O. Meyer, U. Kalus, A. Pruß, F. Kurth, T. Zoller, M. Witzenrath, L. E. Sander, M. A. Müller, C. Scheibenbogen, H. Volk, C. Drosten, V. M. Corman, and L. G. Hanitsch, "Disease severity, fever, age, and sex correlate with SARS-CoV-2 neutralizing antibody responses.," Front Immunol, vol. 11, p. 628971, 2020.
    [Bibtex]
    @Article{Schlickeiser:20,
    author = {Schlickeiser, Stephan and Schwarz, Tatjana and Steiner, Sophie and Wittke, Kirsten and Al Besher, Nabeel and Meyer, Oliver and Kalus, Ulrich and Pruß, Axel and Kurth, Florian and Zoller, Thomas and Witzenrath, Martin and Sander, Leif Erik and Müller, Marcel A. and Scheibenbogen, Carmen and Volk, Hans-Dieter and Drosten, Christian and Corman, Victor M. and Hanitsch, Leif G.},
    journal = {{Front Immunol}},
    title = {Disease Severity, Fever, Age, and Sex Correlate With {SARS-CoV-2} Neutralizing Antibody Responses.},
    year = {2020},
    pages = {628971},
    volume = {11},
    abstract = {Clinical trials on the use of COVID-19 convalescent plasma remain inconclusive. While data on safety is increasingly available, evidence for efficacy is still sparse. Subgroup analyses hint to a dose-response relationship between convalescent plasma neutralizing antibody levels and mortality. In particular, patients with primary and secondary antibody deficiency might benefit from this approach. However, testing of neutralizing antibodies is limited to specialized biosafety level 3 laboratories and is a time- and labor-intense procedure. In this single center study of 206 COVID-19 convalescent patients, clinical data, results of commercially available ELISA testing of SARS-CoV-2 spike-IgG and -IgA, and levels of neutralizing antibodies, determined by plaque reduction neutralization testing (PRNT), were analyzed. At a medium time point of 58 days after symptom onset, only 12.6% of potential plasma donors showed high levels of neutralizing antibodies (PRNT50 ≥ 1:320). Multivariable proportional odds logistic regression analysis revealed need for hospitalization due to COVID-19 (odds ratio 6.87; -value 0.0004) and fever (odds ratio 3.00; -value 0.0001) as leading factors affecting levels of SARS-CoV-2 neutralizing antibody titers in convalescent plasma donors. Using penalized estimation, a predictive proportional odds logistic regression model including the most important variables hospitalization, fever, age, sex, and anosmia or dysgeusia was developed. The predictive discrimination for PRNT50 ≥ 1:320 was reasonably good with AUC: 0.86 (with 95% CI: 0.79-0.92). Combining clinical and ELISA-based pre-screening, assessment of neutralizing antibodies could be spared in 75% of potential donors with a maximal loss of 10% of true positives (PRNT50 ≥ 1:320).},
    doi = {10.3389/fimmu.2020.628971},
    keywords = {COVID-19; SARS-CoV-2; SARS-CoV-2 neutralizing antibody; antibody deficiency; convalescent plasma; coronavirus disease 2019; immunodeficiency; plaque reduction neutralization test},
    pmid = {33584731},
    pubstate = {epublish},
    }
  • [DOI] V. Puller, P. Sagulenko, and R. A. Neher, "Efficient inference, potential, and limitations of site-specific substitution models.," Virus Evol, vol. 6, p. veaa066, 2020.
    [Bibtex]
    @Article{Puller:20,
    author = {Puller, Vadim and Sagulenko, Pavel and Neher, Richard A.},
    journal = {{Virus Evol}},
    title = {Efficient inference, potential, and limitations of site-specific substitution models.},
    year = {2020},
    pages = {veaa066},
    volume = {6},
    abstract = {Natural selection imposes a complex filter on which variants persist in a population resulting in evolutionary patterns that vary greatly along the genome. Some sites evolve close to neutrally, while others are highly conserved, allow only specific states, or only change in concert with other sites. On one hand, such constraints on sequence evolution can be to infer biological function, one the other hand they need to be accounted for in phylogenetic reconstruction. Phylogenetic models often account for this complexity by partitioning sites into a small number of discrete classes with different rates and/or state preferences. Appropriate model complexity is typically determined by model selection procedures. Here, we present an efficient algorithm to estimate more complex models that allow for different preferences at every site and explore the accuracy at which such models can be estimated from simulated data. Our iterative approximate maximum likelihood scheme uses information in the data efficiently and accurately estimates site-specific preferences from large data sets with moderately diverged sequences and known topology. However, the joint estimation of site-specific rates, and site-specific preferences, and phylogenetic branch length can suffer from identifiability problems, while ignoring variation in preferences across sites results in branch length underestimates. Site-specific preferences estimated from large HIV alignments show qualitative concordance with intra-host estimates of fitness costs. Analysis of these substitution models suggests near saturation of divergence after a few hundred years. Such saturation can explain the inability to infer deep divergence times of HIV and SIVs using molecular clock approaches and time-dependent rate estimates.},
    doi = {10.1093/ve/veaa066},
    issue = {2},
    keywords = {algorithms; fitness landscapes; phylogenetics},
    pmid = {33343922},
    pubstate = {epublish},
    }
  • [DOI] L. van der Hoek, "SARS-CoV-2 re-infections: lessons from other coronaviruses," Med, vol. 1, iss. 1, p. 23–28, 2020.
    [Bibtex]
    @Article{Hoek:20,
    author = {Lia van der Hoek},
    journal = {Med},
    title = {{SARS}-{CoV}-2 Re-infections: Lessons from Other Coronaviruses},
    year = {2020},
    number = {1},
    pages = {23--28},
    volume = {1},
    doi = {10.1016/j.medj.2020.12.005},
    publisher = {Elsevier {BV}},
    }
  • [DOI] S. Kuchi, Q. Gu, M. Palmarini, S. J. Wilson, and D. L. Robertson, "Meta-analysis of virus-induced host gene expression reveals unique signatures of immune dysregulation induced by SARS-CoV-2," bioRxiv, 2020.
    [Bibtex]
    @Article{Kuchi:20,
    author = {Srikeerthana Kuchi and Quan Gu and Massimo Palmarini and Sam J Wilson and David L Robertson},
    journal = {{bioRxiv}},
    title = {Meta-analysis of virus-induced host gene expression reveals unique signatures of immune dysregulation induced by {SARS}-{CoV}-2},
    year = {2020},
    doi = {10.1101/2020.12.29.424739},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] D. Paraskevis, E. Kostaki, N. Alygizakis, N. S. Thomaidis, C. Cartalis, S. Tsiodras, and M. A. Dimopoulos, "A review of the impact of weather and climate variables to COVID-19: in the absence of public health measures high temperatures cannot probably mitigate outbreaks.," Sci Total Environ, vol. 768, p. 144578, 2020.
    [Bibtex]
    @Article{Paraskevis:20a,
    author = {Paraskevis, Dimitrios and Kostaki, Evangelia-Georgia and Alygizakis, Nikiforos and Thomaidis, Nikolaos S. and Cartalis, Constantinos and Tsiodras, Sotirios and Dimopoulos, Meletios Athanasios},
    journal = {{Sci Total Environ}},
    title = {A review of the impact of weather and climate variables to {COVID-19}: In the absence of public health measures high temperatures cannot probably mitigate outbreaks.},
    year = {2020},
    pages = {144578},
    volume = {768},
    abstract = {The new severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) pandemic was first recognized at the end of 2019 and has caused one of the most serious global public health crises in the last years. In this paper, we review current literature on the effect of weather (temperature, humidity, precipitation, wind, etc.) and climate (temperature as an essential climate variable, solar radiation in the ultraviolet, sunshine duration) variables on SARS-CoV-2 and discuss their impact to the COVID-19 pandemic; the review also refers to respective effect of urban parameters and air pollution. Most studies suggest that a negative correlation exists between ambient temperature and humidity on the one hand and the number of COVID-19 cases on the other, while there have been studies which support the absence of any correlation or even a positive one. The urban environment and specifically the air ventilation rate, as well as air pollution, can probably affect, also, the transmission dynamics and the case fatality rate of COVID-19. Due to the inherent limitations in previously published studies, it remains unclear if the magnitude of the effect of temperature or humidity on COVID-19 is confounded by the public health measures implemented widely during the first pandemic wave. The effect of weather and climate variables, as suggested previously for other viruses, cannot be excluded, however, under the conditions of the first pandemic wave, it might be difficult to be uncovered. The increase in the number of cases observed during summertime in the Northern hemisphere, and especially in countries with high average ambient temperatures, demonstrates that weather and climate variables, in the absence of public health interventions, cannot mitigate the resurgence of COVID-19 outbreaks.},
    doi = {10.1016/j.scitotenv.2020.144578},
    keywords = {Air pollution; Climate and weather variables; Outbreak; Pandemic; Public health interventions; SARS-CoV-2; Urban environment},
    pmid = {33450689},
    pubstate = {aheadofprint},
    }
  • [DOI] A. Pérez-Cataluña, E. Cuevas-Ferrando, W. Randazzo, and G. Sánchez, "Bias of library preparation for virome characterization in untreated and treated wastewaters.," The science of the total environment, vol. 767, p. 144589, 2020.
    [Bibtex]
    @Article{PerezCataluna20,
    author = {Pérez-Cataluña, Alba and Cuevas-Ferrando, Enric and Randazzo, Walter and Sánchez, Gloria},
    journal = {The Science of the total environment},
    title = {Bias of library preparation for virome characterization in untreated and treated wastewaters.},
    year = {2020},
    pages = {144589},
    volume = {767},
    abstract = {The use of metagenomics for virome characterization and its implementation for wastewater analyses, including wastewater-based epidemiology, has increased in the last years. However, the lack of standardized methods can led to highly different results. The aim of this work was to analyze virome profiles in upstream and downstream wastewater samples collected from four wastewater treatment plants (WWTPs) using two different library preparation kits. Viral particles were enriched from wastewater concentrates using a filtration and nuclease digestion procedure prior to total nucleic acid (NA) extraction. Sequencing was performed using the ScriptSeq v2 RNA-Seq (LS) and the NEBNext Ultra II RNA (NB) library preparation kits. Cleaned reads and contigs were annotated using a curated in-house database composed by reads assigned to viruses at NCBI. Significant differences in viral families and in the ratio of detection were shown between the two library kits used. The use of LS library showed Virgaviridae, Microviridae and Siphoviridae as the most abundant families; while Ackermannviridae and Helleviridae were highly represented within the NB library. Additionally, the two sequencing libraries produced outcomes that differed in the detection of viral indicators. These results highlighted the importance of library selection for studying viruses in untreated and treated wastewater. Our results underline the need for further studies to elucidate the influence of sequencing procedures in virome profiles in wastewater matrices in order to improve the knowledge of the virome in the water environment.},
    doi = {10.1016/j.scitotenv.2020.144589},
    keywords = {Enteric viruses; Metagenomics; Viability RT-qPCR; Wastewater},
    pmid = {33422963},
    pubstate = {aheadofprint},
    }
  • [DOI] A. A. Gulyaeva and A. E. Gorbalenya, "A nidovirus perspective on SARS-CoV-2.," Biochem Biophys Res Commun, 2020.
    [Bibtex]
    @Article{Gulyaeva20a,
    author = {Gulyaeva, Anastasia A. and Gorbalenya, Alexander E.},
    journal = {{Biochem Biophys Res Commun}},
    title = {A nidovirus perspective on {SARS}-{CoV}-2.},
    year = {2020},
    abstract = {Two pandemics of respiratory distress diseases associated with zoonotic introductions of the species Severe acute respiratory syndrome-related coronavirus in the human population during 21st century raised unprecedented interest in coronavirus research and assigned it unseen urgency. The two viruses responsible for the outbreaks, SARS-CoV and SARS-CoV-2, respectively, are in the spotlight, and SARS-CoV-2 is the focus of the current fast-paced research. Its foundation was laid down by studies of many corona- and related viruses that collectively form the vast order Nidovirales. Comparative genomics of nidoviruses played a key role in this advancement over more than 30 years. It facilitated the transfer of knowledge from characterized to newly identified viruses, including SARS-CoV and SARS-CoV-2, as well as contributed to the dissection of the nidovirus proteome and identification of patterns of variations between different taxonomic groups, from species to families. This review revisits selected cases of protein conservation and variation that define nidoviruses, illustrates the remarkable plasticity of the proteome during nidovirus adaptation, and asks questions at the interface of the proteome and processes that are vital for nidovirus reproduction and could inform the ongoing research of SARS-CoV-2.},
    doi = {10.1016/j.bbrc.2020.11.015},
    keywords = {Comparative genomics; Coronaviruses; Evolution; Nidoviruses; Proteome},
    pmid = {33413979},
    pubstate = {aheadofprint},
    }
  • [DOI] O. M. Allicock, N. Sahadeo, P. Lemey, A. J. Auguste, M. A. Suchard, A. Rambaut, and C. V. F. Carrington, "Determinants of dengue virus dispersal in the Americas.," Virus Evol, vol. 6, p. veaa074, 2020.
    [Bibtex]
    @Article{Allicock20,
    author = {Allicock, Orchid M. and Sahadeo, Nikita and Lemey, Philippe and Auguste, Albert J. and Suchard, Marc A. and Rambaut, Andrew and Carrington, Christine V. F.},
    journal = {{Virus Evol}},
    title = {Determinants of dengue virus dispersal in the {A}mericas.},
    year = {2020},
    pages = {veaa074},
    volume = {6},
    abstract = {Dengue viruses (DENVs) are classified into four serotypes, each of which contains multiple genotypes. DENV genotypes introduced into the Americas over the past five decades have exhibited different rates and patterns of spatial dispersal. In order to understand factors underlying these patterns, we utilized a statistical framework that allows for the integration of ecological, socioeconomic, and air transport mobility data as predictors of viral diffusion while inferring the phylogeographic history. Predictors describing spatial diffusion based on several covariates were compared using a generalized linear model approach, where the support for each scenario and its contribution is estimated simultaneously from the data set. Although different predictors were identified for different serotypes, our analysis suggests that overall diffusion of DENV-1, -2, and -3 in the Americas was associated with airline traffic. The other significant predictors included human population size, the geographical distance between countries and between urban centers and the density of people living in urban environments.},
    doi = {10.1093/ve/veaa074},
    issue = {2},
    keywords = {Bayesian phylogeography; dengue virus; hypothesis testing; spatial diffusion},
    pmid = {33408877},
    pubstate = {epublish},
    }
  • [DOI] A. Brinkmann, C. Kohl, A. Radonić, P. W. Dabrowski, K. Mühldorfer, A. Nitsche, G. Wibbelt, and A. Kurth, "First detection of bat-borne Issyk-Kul virus in Europe," Sci Rep, vol. 10, iss. 1, 2020.
    [Bibtex]
    @Article{Brinkmann20a,
    author = {Annika Brinkmann and Claudia Kohl and Aleksandar Radonić and Piotr Wojtek Dabrowski and Kristin Mühldorfer and Andreas Nitsche and Gudrun Wibbelt and Andreas Kurth},
    journal = {{Sci Rep}},
    title = {First detection of bat-borne {I}ssyk-{K}ul virus in {E}urope},
    year = {2020},
    number = {1},
    volume = {10},
    doi = {10.1038/s41598-020-79468-8},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] H. Blake, J. Corner, C. Cirelli, J. Hassard, L. Briggs, J. M. Daly, M. Bennett, J. G. Chappell, L. Fairclough, P. C. McClure, A. Tarr, P. Tighe, A. Favier, W. Irving, and J. Ball, "Perceptions and experiences of the University of Nottingham pilot SARS-CoV-2 asymptomatic testing service: a mixed-methods study.," Int J Environ Res Public Health, vol. 18, 2020.
    [Bibtex]
    @Article{Blake20,
    author = {Blake, Holly and Corner, Jessica and Cirelli, Cecilia and Hassard, Juliet and Briggs, Lydia and Daly, Janet M. and Bennett, Malcolm and Chappell, Joseph G. and Fairclough, Lucy and McClure, C. Patrick and Tarr, Alexander and Tighe, Patrick and Favier, Alex and Irving, William and Ball, Jonathan},
    journal = {{Int J Environ Res Public Health}},
    title = {Perceptions and Experiences of the {U}niversity of {N}ottingham Pilot {SARS-CoV-2} Asymptomatic Testing Service: A Mixed-Methods Study.},
    year = {2020},
    volume = {18},
    abstract = {We aimed to explore student and staff perceptions and experiences of a pilot SARS-CoV-2 asymptomatic testing service (P-ATS) in a UK university campus setting. This was a mixed-method study comprised of an online survey, and thematic analysis of qualitative data from interviews and focus groups conducted at the mid-point and end of the 12-week P-ATS programme. Ninety-nine students (84.8% female, 70% first year; 93.9% P-ATS participants) completed an online survey, 41 individuals attended interviews or focus groups, including 31 students (21 first year; 10 final year) and 10 staff. All types of testing and logistics were highly acceptable ( : swab, saliva; : finger prick) and 94.9% would participate again. Reported adherence to weekly virus testing was high (92.4% completed ≥6 tests; 70.8% submitted all 10 swabs; 89.2% completed ≥1 saliva sample) and 76.9% submitted ≥3 blood samples. Students tested to "keep campus safe", "contribute to national efforts to control COVID-19", and "protect others". In total, 31.3% had high anxiety as measured by the Generalized Anxiety Disorder scale (GAD-7) (27.1% of first year). Students with lower levels of anxiety and greater satisfaction with university communications around P-ATS were more likely to adhere to virus and antibody tests. Increased adherence to testing was associated with higher perceived risk of COVID-19 to self and others. Qualitative findings revealed 5 themes and 13 sub-themes: "emotional responses to COVID-19", "university life during COVID-19", "influences on testing participation", "testing physical and logistical factors" and "testing effects on mental wellbeing". Asymptomatic COVID-19 testing (SARS-CoV-2 virus/antibodies) is highly acceptable to students and staff in a university campus setting. Clear communications and strategies to reduce anxiety are likely to be important for testing uptake and adherence. Strategies are needed to facilitate social connections and mitigate the mental health impacts of COVID-19 and self-isolation.},
    doi = {10.3390/ijerph18010188},
    issue = {1},
    keywords = {Asymptomatic Infections; COVID-19, diagnosis, psychology; COVID-19 Testing; Female; Humans; Male; Specimen Handling; Surveys and Questionnaires; United Kingdom; Universities; Young Adult; COVID-19; SARS-CoV-2; coronavirus; disease outbreaks; health promotion; students; virus; young people},
    pmid = {33383781},
    pubstate = {epublish},
    }
  • [DOI] S. Lequime, J. Dehecq, S. Matheus, F. de Laval, L. Almeras, S. Briolant, and A. Fontaine, "Modeling intra-mosquito dynamics of Zika virus and its dose-dependence confirms the low epidemic potential of Aedes albopictus," PLoS Pathog, vol. 16, iss. 12, p. e1009068, 2020.
    [Bibtex]
    @Article{Lequime20a,
    author = {Sebastian Lequime and Jean-S{\'{e}}bastien Dehecq and S{\'{e}}verine Matheus and Franck de Laval and Lionel Almeras and S{\'{e}}bastien Briolant and Albin Fontaine},
    journal = {{PLoS Pathog}},
    title = {Modeling intra-mosquito dynamics of {Z}ika virus and its dose-dependence confirms the low epidemic potential of {A}edes albopictus},
    year = {2020},
    number = {12},
    pages = {e1009068},
    volume = {16},
    doi = {10.1371/journal.ppat.1009068},
    editor = {Elizabeth Ann McGraw},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] S. Trump, S. Lukassen, M. S. Anker, R. L. Chua, J. Liebig, L. Thürmann, V. M. Corman, M. Binder, J. Loske, C. Klasa, T. Krieger, B. P. Hennig, M. Messingschlager, F. Pott, J. Kazmierski, S. Twardziok, J. P. Albrecht, J. Eils, S. Hadzibegovic, A. Lena, B. Heidecker, T. Bürgel, J. Steinfeldt, C. Goffinet, F. Kurth, M. Witzenrath, M. T. Völker, S. D. Müller, U. G. Liebert, N. Ishaque, L. Kaderali, L. Sander, C. Drosten, S. Laudi, R. Eils, C. Conrad, U. Landmesser, and I. Lehmann, "Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19.," Nat Biotechnol, 2020.
    [Bibtex]
    @Article{Trump20,
    author = {Trump, Saskia and Lukassen, Soeren and Anker, Markus S. and Chua, Robert Lorenz and Liebig, Johannes and Thürmann, Loreen and Corman, Victor Max and Binder, Marco and Loske, Jennifer and Klasa, Christina and Krieger, Teresa and Hennig, Bianca P. and Messingschlager, Marey and Pott, Fabian and Kazmierski, Julia and Twardziok, Sven and Albrecht, Jan Philipp and Eils, Jürgen and Hadzibegovic, Sara and Lena, Alessia and Heidecker, Bettina and Bürgel, Thore and Steinfeldt, Jakob and Goffinet, Christine and Kurth, Florian and Witzenrath, Martin and Völker, Maria Theresa and Müller, Sarah Dorothea and Liebert, Uwe Gerd and Ishaque, Naveed and Kaderali, Lars and Sander, Leif-Erik and Drosten, Christian and Laudi, Sven and Eils, Roland and Conrad, Christian and Landmesser, Ulf and Lehmann, Irina},
    journal = {{Nat Biotechnol}},
    title = {Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with {COVID}-19.},
    year = {2020},
    abstract = {In coronavirus disease 2019 (COVID-19), hypertension and cardiovascular diseases are major risk factors for critical disease progression. However, the underlying causes and the effects of the main anti-hypertensive therapies-angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs)-remain unclear. Combining clinical data (n = 144) and single-cell sequencing data of airway samples (n = 48) with in vitro experiments, we observed a distinct inflammatory predisposition of immune cells in patients with hypertension that correlated with critical COVID-19 progression. ACEI treatment was associated with dampened COVID-19-related hyperinflammation and with increased cell intrinsic antiviral responses, whereas ARB treatment related to enhanced epithelial-immune cell interactions. Macrophages and neutrophils of patients with hypertension, in particular under ARB treatment, exhibited higher expression of the pro-inflammatory cytokines CCL3 and CCL4 and the chemokine receptor CCR1. Although the limited size of our cohort does not allow us to establish clinical efficacy, our data suggest that the clinical benefits of ACEI treatment in patients with COVID-19 who have hypertension warrant further investigation.},
    doi = {10.1038/s41587-020-00796-1},
    pmid = {33361824},
    pubstate = {aheadofprint},
    }
  • [DOI] J. Nkengasong, A. Iwasaki, C. Victora, J. Oh, G. F. Gao, A. Agrawal, C. Drosten, C. Söderberg-Naucler, E. López-Collazo, A. M. Pollock, A. Viola, and M. Baker, "The global response to the COVID-19 pandemic.," Med (NY), vol. 1, p. 3–8, 2020.
    [Bibtex]
    @Article{Nkengasong20,
    author = {Nkengasong, John and Iwasaki, Akiko and Victora, Cesar and Oh, Juhwan and Gao, George F. and Agrawal, Anurag and Drosten, Christian and Söderberg-Naucler, Cecilia and López-Collazo, Eduardo and Pollock, Allyson M. and Viola, Antonella and Baker, Michael},
    journal = {{Med (NY)}},
    title = {The Global Response to the {COVID-19} Pandemic.},
    year = {2020},
    pages = {3--8},
    volume = {1},
    abstract = {Global approaches towards pandemic control range from strict lockdowns to minimal restrictions. We asked experts worldwide about the lessons learned from their countries' response. Their voices converge on the importance of scientifically guided interventions to limit the spread of SARS-CoV-2 and its impact on human health.},
    doi = {10.1016/j.medj.2020.12.003},
    issue = {1},
    pmid = {33363282},
    pubstate = {ppublish},
    }
  • [DOI] S. Peter, P. Dittrich, and B. Ibrahim, "Structure and hierarchy of SARS-CoV-2 infection dynamics models revealed by reaction network analysis.," Viruses, vol. 13, 2020.
    [Bibtex]
    @Article{Peter20,
    author = {Peter, Stephan and Dittrich, Peter and Ibrahim, Bashar},
    journal = {Viruses},
    title = {Structure and Hierarchy of {SARS-CoV-2} Infection Dynamics Models Revealed by Reaction Network Analysis.},
    year = {2020},
    volume = {13},
    abstract = {This work provides a mathematical technique for analyzing and comparing infection dynamics models with respect to their potential long-term behavior, resulting in a hierarchy integrating all models. We apply our technique to coupled ordinary and partial differential equation models of SARS-CoV-2 infection dynamics operating on different scales, that is, within a single organism and between several hosts. The structure of a model is assessed by the theory of chemical organizations, not requiring quantitative kinetic information. We present the Hasse diagrams of organizations for the twelve virus models analyzed within this study. For comparing models, each organization is characterized by the types of species it contains. For this, each species is mapped to one out of four types, representing uninfected, infected, immune system, and bacterial species, respectively. Subsequently, we can integrate these results with those of our former work on Influenza-A virus resulting in a single joint hierarchy of 24 models. It appears that the SARS-CoV-2 models are simpler with respect to their long term behavior and thus display a simpler hierarchy with little dependencies compared to the Influenza-A models. Our results can support further development towards more complex SARS-CoV-2 models targeting the higher levels of the hierarchy.},
    doi = {10.3390/v13010014},
    issue = {1},
    keywords = {COVID-19, virology; Host-Pathogen Interactions; Humans; Influenza A virus; Influenza, Human, virology; Models, Biological; Models, Theoretical; SARS-CoV-2; Covid-19; ODEs; PDEs; SARS-CoV-2; between hosts; chemical organization theory; corona; reaction networks analysis; virus dynamics modeling; within hosts},
    pmid = {33374824},
    pubstate = {epublish},
    }
  • [DOI] A. Strömer, R. Rose, M. Schäfer, F. Schön, A. Vollersen, T. Lorentz, H. Fickenscher, and A. Krumbholz, "Performance of a point-of-care test for the rapid detection of SARS-CoV-2 antigen.," Microorganisms, vol. 9, 2020.
    [Bibtex]
    @Article{Stroemer20,
    author = {Strömer, Annabelle and Rose, Ruben and Schäfer, Miriam and Schön, Frieda and Vollersen, Anna and Lorentz, Thomas and Fickenscher, Helmut and Krumbholz, Andi},
    journal = {Microorganisms},
    title = {Performance of a Point-of-Care Test for the Rapid Detection of {SARS-CoV-2} Antigen.},
    year = {2020},
    volume = {9},
    abstract = {The rapid detection of infections caused by the (SARS-CoV-2) is necessary in the ongoing pandemic. Antigen-specific point-of-care tests (POCT) may be useful for this purpose. Here, such a POCT (SARS-CoV-2 NADAL COVID-19 Ag) was compared to a laboratory-developed triplex real-time polymerase chain reaction (RT-PCR) designed for the detection of viral nucleoprotein gene and two control targets. This RT-PCR served as a reference to investigate POCT sensitivity by re-testing upper respiratory tract (URT) samples ( = 124) exhibiting different SARS-CoV-2 loads in terms of RT-PCR threshold cycle (Ct) values. The optical intensities of the antigen bands were compared to the Ct values of the RT-PCR. The infectivity of various virus loads was estimated by inoculating Vero cells with URT samples ( = 64, Ct 17-34). POCT sensitivity varied from 100% (Ct < 25) to 73.1% (Ct ≤ 30); higher SARS-CoV-2 loads correlated with higher band intensities. All samples with a Ct > 30 were negative; among SARS-CoV-2 free samples ( = 10) no false-positives were detected. A head-to-head comparison with another POCT (Abbott, Panbio™ COVID-19 Ag Rapid Test) yielded similar results. Isolation of SARS-CoV-2 in cell-culture was successful up to a Ct value of 29. The POCT reliably detects high SARS-CoV-2 loads and rapidly identifies infectious individuals.},
    doi = {10.3390/microorganisms9010058},
    issue = {1},
    keywords = {COVID-19; PCR; POCT; antigen; comparison; diagnostic},
    pmid = {33379279},
    pubstate = {epublish},
    }
  • [DOI] B. Morel, P. Barbera, L. Czech, B. Bettisworth, L. Hübner, S. Lutteropp, D. Serdari, E. Kostaki, I. Mamais, A. M. Kozlov, P. Pavlidis, D. Paraskevis, and A. Stamatakis, "Phylogenetic analysis of SARS-CoV-2 data is difficult," Mol Biol Evol, 2020.
    [Bibtex]
    @Article{Morel:20,
    author = {Benoit Morel and Pierre Barbera and Lucas Czech and Ben Bettisworth and Lukas Hübner and Sarah Lutteropp and Dora Serdari and Evangelia-Georgia Kostaki and Ioannis Mamais and Alexey M Kozlov and Pavlos Pavlidis and Dimitrios Paraskevis and Alexandros Stamatakis},
    title = {Phylogenetic analysis of {SARS}-{CoV}-2 data is difficult},
    journal = {{Mol Biol Evol}},
    year = {2020},
    doi = {10.1093/molbev/msaa314},
    editor = {Harmit Malik},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] K. P. Szillat, D. Höper, M. Beer, and P. König, "Full-genome sequencing of German rabbit haemorrhagic disease virus uncovers recombination between RHDV (GI.2) and EBHSV (GII.1)," Virus Evol, vol. 6, iss. 2, 2020.
    [Bibtex]
    @Article{Szillat:20,
    author = {Kevin P Szillat and Dirk Höper and Martin Beer and Patricia König},
    title = {Full-genome sequencing of {G}erman rabbit haemorrhagic disease virus uncovers recombination between {RHDV} ({GI}.2) and {EBHSV} ({GII}.1)},
    journal = {{Virus Evol}},
    year = {2020},
    volume = {6},
    number = {2},
    doi = {10.1093/ve/veaa080},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] C. P. Shannon, T. M. Blimkie, R. Ben-Othman, N. Gladish, N. Amenyogbe, S. Drissler, R. D. Edgar, Q. Chan, M. Krajden, L. J. Foster, M. S. Kobor, W. W. Mohn, R. R. Brinkman, K. L. Cao, R. H. Scheuermann, S. J. Tebbutt, R. E. W. Hancock, W. C. Koff, T. R. Kollmann, M. Sadarangani, and A. H. Lee, "Multi-omic data integration allows baseline immune signatures to predict hepatitis B vaccine response in a small cohort," Front Immunol, vol. 11, 2020.
    [Bibtex]
    @Article{Shannon:20b,
    author = {Casey P. Shannon and Travis M. Blimkie and Rym Ben-Othman and Nicole Gladish and Nelly Amenyogbe and Sibyl Drissler and Rachel D. Edgar and Queenie Chan and Mel Krajden and Leonard J. Foster and Michael S. Kobor and William W. Mohn and Ryan R. Brinkman and Kim-Anh Le Cao and Richard H. Scheuermann and Scott J. Tebbutt and Robert E.W. Hancock and Wayne C. Koff and Tobias R. Kollmann and Manish Sadarangani and Amy Huei-Yi Lee},
    title = {Multi-Omic Data Integration Allows Baseline Immune Signatures to Predict Hepatitis {B} Vaccine Response in a Small Cohort},
    journal = {{Front Immunol}},
    year = {2020},
    volume = {11},
    doi = {10.3389/fimmu.2020.578801},
    publisher = {Frontiers Media {SA}},
    }
  • [DOI] P. Simmonds, S. Williams, and H. Harvala, "Understanding the outcomes of COVID-19 – does the current model of an acute respiratory infection really fit?," J Gen Virol, 2020.
    [Bibtex]
    @Article{Simmonds:20,
    author = {Peter Simmonds and Sarah Williams and Heli Harvala},
    title = {Understanding the outcomes of {COVID}-19 {\textendash} does the current model of an acute respiratory infection really fit?},
    journal = {{J Gen Virol}},
    year = {2020},
    doi = {10.1099/jgv.0.001545},
    publisher = {Microbiology Society},
    }
  • [DOI] J. Wolff, S. A. E. Rahman, J. King, M. El-Beskawy, A. Pohlmann, M. Beer, and B. Hoffmann, "Establishment of a challenge model for sheeppox virus infection," Microorganisms, vol. 8, iss. 12, p. 2001, 2020.
    [Bibtex]
    @Article{Wolff:20,
    author = {Janika Wolff and Sahar Abd El Rahman and Jacqueline King and Mohamed El-Beskawy and Anne Pohlmann and Martin Beer and Bernd Hoffmann},
    title = {Establishment of a Challenge Model for Sheeppox Virus Infection},
    journal = {Microorganisms},
    year = {2020},
    volume = {8},
    number = {12},
    pages = {2001},
    doi = {10.3390/microorganisms8122001},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] A. S. da Filipe, J. G. Shepherd, T. Williams, J. Hughes, E. Aranday-Cortes, P. Asamaphan, S. Ashraf, C. Balcazar, K. Brunker, A. Campbell, S. Carmichael, C. Davis, R. Dewar, M. D. Gallagher, R. Gunson, V. Hill, A. Ho, B. Jackson, E. James, N. Jesudason, N. Johnson, C. M. E. Leitch, K. Li, A. MacLean, D. Mair, D. A. McAllister, J. T. McCrone, S. E. McDonald, M. P. McHugh, K. A. Morris, J. Nichols, M. Niebel, K. Nomikou, R. J. Orton, Á. O'Toole, M. Palmarini, B. J. Parcell, Y. A. Parr, A. Rambaut, S. Rooke, S. Shaaban, R. Shah, J. B. Singer, K. Smollett, I. Starinskij, L. Tong, V. B. Sreenu, E. Wastnedge, M. T. G. Holden, D. L. Robertson, K. Templeton, and E. C. Thomson, "Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland," Nat Microbiol, vol. 6, iss. 1, p. 112–122, 2020.
    [Bibtex]
    @Article{SilvaFilipe:20,
    author = {Ana da Silva Filipe and James G. Shepherd and Thomas Williams and Joseph Hughes and Elihu Aranday-Cortes and Patawee Asamaphan and Shirin Ashraf and Carlos Balcazar and Kirstyn Brunker and Alasdair Campbell and Stephen Carmichael and Chris Davis and Rebecca Dewar and Michael D. Gallagher and Rory Gunson and Verity Hill and Antonia Ho and Ben Jackson and Edward James and Natasha Jesudason and Natasha Johnson and E. Carol McWilliam Leitch and Kathy Li and Alasdair MacLean and Daniel Mair and David A. McAllister and John T. McCrone and Sarah E. McDonald and Martin P. McHugh and A. Keith Morris and Jenna Nichols and Marc Niebel and Kyriaki Nomikou and Richard J. Orton and {\'{A}}ine O'Toole and Massimo Palmarini and Benjamin J. Parcell and Yasmin A. Parr and Andrew Rambaut and Stefan Rooke and Sharif Shaaban and Rajiv Shah and Joshua B. Singer and Katherine Smollett and Igor Starinskij and Lily Tong and Vattipally B. Sreenu and Elizabeth Wastnedge and Matthew T. G. Holden and David L. Robertson and Kate Templeton and Emma C. Thomson},
    title = {Genomic epidemiology reveals multiple introductions of {SARS}-{CoV}-2 from mainland {E}urope into {S}cotland},
    journal = {{Nat Microbiol}},
    year = {2020},
    volume = {6},
    number = {1},
    pages = {112--122},
    doi = {10.1038/s41564-020-00838-z},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] N. Schmidt, C. A. Lareau, H. Keshishian, S. Ganskih, C. Schneider, T. Hennig, R. Melanson, S. Werner, Y. Wei, M. Zimmer, J. Ade, L. Kirschner, S. Zielinski, L. Dölken, E. S. Lander, N. Caliskan, U. Fischer, J. Vogel, S. A. Carr, J. Bodem, and M. Munschauer, "The SARS-CoV-2 RNA–protein interactome in infected human cells," Nat Microbiol, 2020.
    [Bibtex]
    @Article{Schmidt:20,
    author = {Nora Schmidt and Caleb A. Lareau and Hasmik Keshishian and Sabina Ganskih and Cornelius Schneider and Thomas Hennig and Randy Melanson and Simone Werner and Yuanjie Wei and Matthias Zimmer and Jens Ade and Luisa Kirschner and Sebastian Zielinski and Lars Dölken and Eric S. Lander and Neva Caliskan and Utz Fischer and Jörg Vogel and Steven A. Carr and Jochen Bodem and Mathias Munschauer},
    title = {The {SARS}-{CoV}-2 {RNA}{\textendash}protein interactome in infected human cells},
    journal = {{Nat Microbiol}},
    year = {2020},
    doi = {10.1038/s41564-020-00846-z},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] A. Michelitsch, D. Hoffmann, K. Wernike, and M. Beer, "Occurrence of antibodies against SARS-CoV-2 in the domestic cat population of Germany," Vaccines, vol. 8, iss. 4, p. 772, 2020.
    [Bibtex]
    @Article{Michelitsch:20,
    author = {Anna Michelitsch and Donata Hoffmann and Kerstin Wernike and Martin Beer},
    title = {Occurrence of Antibodies against {SARS}-{CoV}-2 in the Domestic Cat Population of {G}ermany},
    journal = {Vaccines},
    year = {2020},
    volume = {8},
    number = {4},
    pages = {772},
    doi = {10.3390/vaccines8040772},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] G. Nouailles, E. Wyler, P. Pennitz, D. Postmus, D. Vladimirova, J. Kazmierski, F. Pott, K. Dietert, M. Mülleder, V. Farztdinov, B. Obermayer, S. Wienhold, S. Andreotti, T. Höfler, B. Sawitzki, C. Drosten, L. E. Sander, N. Suttorp, M. Ralser, D. Beule, A. D. Gruber, C. Goffinet, M. Landthaler, J. Trimpert, and M. Witzenrath, "Longitudinal omics in Syrian hamsters integrated with human data unravel complexity of moderate immune responses to SARS-CoV-2," bioRxiv, 2020.
    [Bibtex]
    @Article{Nouailles:20,
    author = {Geraldine Nouailles and Emanuel Wyler and Peter Pennitz and Dylan Postmus and Daria Vladimirova and Julia Kazmierski and Fabian Pott and Kristina Dietert and Michael Mülleder and Vadim Farztdinov and Benedikt Obermayer and Sandra-Maria Wienhold and Sandro Andreotti and Thomas Höfler and Birgit Sawitzki and Christian Drosten and Leif Erik Sander and Norbert Suttorp and Markus Ralser and Dieter Beule and Achim Dieter Gruber and Christine Goffinet and Markus Landthaler and Jakob Trimpert and Martin Witzenrath},
    title = {Longitudinal omics in {S}yrian hamsters integrated with human data unravel complexity of moderate immune responses to {SARS}-{CoV}-2},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.12.18.423524},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] R. Weersma, R. Gacesa, A. Kurilshikov, A. V. Vila, T. Sinha, M. Klaassen, L. Bolte, S. Andreu-Sanchez, L. Chen, V. Collij, S. Hu, J. Dekens, V. Lenters, J. Björk, C. J. Swarte, M. Swertz, B. H. Jansen, J. Gelderloos-Arends, M. Hofker, R. Vermeuelen, S. Sanna, H. Harmsen, C. Wijmenga, J. Fu, and A. Zhernakova, "The Dutch Microbiome Project defines factors that shape the healthy gut microbiome," Research Square, 2020.
    [Bibtex]
    @Article{Weersma:20,
    author = {Rinse Weersma and Ranko Gacesa and Alexander Kurilshikov and Arnau Vich Vila and Trishla Sinha and Marjolein Klaassen and Laura Bolte and Sergio Andreu-Sanchez and Lianmin Chen and Valerie Collij and Shixian Hu and Jackie Dekens and Virissa Lenters and Johannes Björk and J. Casper Swarte and Morris Swertz and B. H. Jansen and Jody Gelderloos-Arends and Marten Hofker and Roel Vermeuelen and Serena Sanna and Hermie Harmsen and Cisca Wijmenga and Jingyuan Fu and Alexandra Zhernakova},
    title = {The {D}utch {M}icrobiome {P}roject defines factors that shape the healthy gut microbiome},
    journal = {{Research Square}},
    year = {2020},
    doi = {10.21203/rs.3.rs-117376/v1},
    publisher = {Research Square},
    }
  • [DOI] M. Kohls, M. Kircher, J. Krepel, P. Liebig, and K. Jung, "Estimating the distribution of viral taxa in next-generation sequencing data using artificial neural networks," Research Square, 2020.
    [Bibtex]
    @Article{Kohls:20,
    author = {Moritz Kohls and Magdalena Kircher and Jessica Krepel and Pamela Liebig and Klaus Jung},
    title = {Estimating the Distribution of Viral Taxa in Next-generation Sequencing data using Artificial Neural Networks},
    journal = {{Research Square}},
    year = {2020},
    doi = {10.21203/rs.3.rs-127809/v1},
    publisher = {Research Square},
    }
  • [DOI] E. Kostaki, S. Limnaios, S. Roussos, M. Psichogiou, G. K. Nikolopoulos, S. R. Friedman, A. Antoniadou, M. Chini, A. Hatzakis, V. Sypsa, G. Magiorkinis, C. Seguin-Devaux, and D. Paraskevis, "Validation of molecular clock inferred HIV infection ages: evidence for accurate estimation of infection dates," medRxiv, 2020.
    [Bibtex]
    @Article{Kostaki:20,
    author = {Evangelia-Georgia Kostaki and Stefanos Limnaios and Sotirios Roussos and Mina Psichogiou and Georgios K. Nikolopoulos and Samuel R. Friedman and Anastasia Antoniadou and Maria Chini and Angelos Hatzakis and Vana Sypsa and Gkikas Magiorkinis and Carole Seguin-Devaux and Dimitrios Paraskevis},
    title = {Validation of molecular clock inferred {HIV} infection ages: evidence for accurate estimation of infection dates},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.12.11.20247601},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] E. Karakike, E. J. Giamarellos-Bourboulis, M. Kyprianou, C. Fleischmann-Struzek, M. W. Pletz, M. G. Netea, K. Reinhart, and E. Kyriazopoulou, "COVID-19 as cause of viral sepsis: a systematic review and meta-analysis," medRxiv, 2020.
    [Bibtex]
    @Article{Karakike:20,
    author = {Eleni Karakike and Evangelos J. Giamarellos-Bourboulis and Miltiades Kyprianou and Carolin Fleischmann-Struzek and Mathias W. Pletz and Mihai G. Netea and Konrad Reinhart and Evdoxia Kyriazopoulou},
    title = {{COVID}-19 as cause of viral sepsis: A Systematic Review and Meta-Analysis},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.12.02.20242354},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. Zafferani, C. Haddad, L. Luo, J. Davila-Calderon, L. Yuan-Chiu, C. S. Mugisha, A. G. Monaghan, A. A. Kennedy, J. D. Yesselman, R. J. Gifford, A. W. Tai, S. B. Kutluay, M. Li, G. Brewer, B. S. Tolbert, and A. E. Hargrove, "Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures," bioRxiv, 2020.
    [Bibtex]
    @Article{Zafferani:20,
    author = {Martina Zafferani and Christina Haddad and Le Luo and Jesse Davila-Calderon and Liang Yuan-Chiu and Christian Shema Mugisha and Adeline G. Monaghan and Andrew A. Kennedy and Joseph D. Yesselman and Robert J. Gifford and Andrew W. Tai and Sebla B. Kutluay and Mei-Ling Li and Gary Brewer and Blanton S. Tolbert and Amanda E. Hargrove},
    journal = {{bioRxiv}},
    title = {Amilorides inhibit {SARS}-{CoV}-2 replication in vitro by targeting {RNA} structures},
    year = {2020},
    doi = {10.1101/2020.12.05.409821},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] M. Huber, P. W. Schreiber, T. Scheier, A. Audigé, R. Buonomano, A. Rudiger, D. L. Braun, G. Eich, D. Keller, B. Hasse, C. Berger, A. Manrique, H. F. Günthard, J. Böni, and A. Trkola, "Large parallel screen of saliva and nasopharyngeal swabs in a test center setting proofs utility of saliva as alternate specimen for SARS-CoV-2 detection by RT-PCR," medRxiv, 2020.
    [Bibtex]
    @Article{Huber:20,
    author = {Michael Huber and Peter W. Schreiber and Thomas Scheier and Annette Audig{\'{e}} and Roberto Buonomano and Alain Rudiger and Dominique L. Braun and Gerhard Eich and Dagmar Keller and Barbara Hasse and Christoph Berger and Amapola Manrique and Huldrych F. Günthard and Jürg Böni and Alexandra Trkola},
    title = {Large parallel screen of saliva and nasopharyngeal swabs in a test center setting proofs utility of saliva as alternate specimen for {SARS}-{CoV}-2 detection by {RT}-{PCR}},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.12.01.20241778},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] B. Bartolini, M. Rueca, C. E. M. Gruber, F. Messina, E. Giombini, G. Ippolito, M. R. Capobianchi, and A. D. Caro, "The newly introduced SARS-CoV-2 variant A222V is rapidly spreading in Lazio region, Italy," medRxiv, 2020.
    [Bibtex]
    @Article{Bartolini:20a,
    author = {Barbara Bartolini and Martina Rueca and Cesare Ernesto Maria Gruber and Francesco Messina and Emanuela Giombini and Giuseppe Ippolito and Maria Rosaria Capobianchi and Antonino Di Caro},
    title = {The newly introduced {SARS}-{CoV}-2 variant {A222V} is rapidly spreading in {L}azio region, {I}taly},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.11.28.20237016},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] J. S. Huisman, J. Scire, D. C. Angst, R. A. Neher, S. Bonhoeffer, and T. Stadler, "Estimation and worldwide monitoring of the effective reproductive number of SARS-CoV-2," medRxiv, 2020.
    [Bibtex]
    @Article{Huisman:20,
    author = {Jana S. Huisman and J{\'{e}}r{\'{e}}mie Scire and Daniel C. Angst and Richard A. Neher and Sebastian Bonhoeffer and Tanja Stadler},
    title = {Estimation and worldwide monitoring of the effective reproductive number of {SARS}-{CoV}-2},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.11.26.20239368},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] W. J. D. Ouwendijk, D. P. Depledge, L. Rajbhandari, T. L. Rovis, S. Jonjic, J. Breuer, A. Venkatesan, G. M. G. M. Verjans, and T. Sadaoka, "Varicella-zoster virus VLT-ORF63 fusion transcript induces broad viral gene expression during reactivation from neuronal latency," Nat Commun, vol. 11, iss. 1, 2020.
    [Bibtex]
    @Article{Ouwendijk:20,
    author = {Werner J. D. Ouwendijk and Daniel P. Depledge and Labchan Rajbhandari and Tihana Lenac Rovis and Stipan Jonjic and Judith Breuer and Arun Venkatesan and Georges M. G. M. Verjans and Tomohiko Sadaoka},
    title = {Varicella-zoster virus {VLT}-{ORF}63 fusion transcript induces broad viral gene expression during reactivation from neuronal latency},
    journal = {{Nat Commun}},
    year = {2020},
    volume = {11},
    number = {1},
    doi = {10.1038/s41467-020-20031-4},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] A. K. Lindner, O. Nikolai, F. Kausch, M. Wintel, F. Hommes, M. Gertler, L. J. Krüger, M. Gaeddert, F. Tobian, F. Lainati, L. Köppel, J. Seybold, V. M. Corman, C. Drosten, J. Hofmann, J. A. Sacks, F. P. Mockenhaupt, and C. M. Denkinger, "Head-to-head comparison of SARS-CoV-2 antigen-detecting rapid test with self-collected anterior nasal swab versus professional-collected nasopharyngeal swab.," Eur Respir J, 2020.
    [Bibtex]
    @Article{Lindner:20,
    author = {Lindner, Andreas K and Nikolai, Olga and Kausch, Franka and Wintel, Mia and Hommes, Franziska and Gertler, Maximilian and Krüger, Lisa J and Gaeddert, Mary and Tobian, Frank and Lainati, Federica and Köppel, Lisa and Seybold, Joachim and Corman, Victor M and Drosten, Christian and Hofmann, Jörg and Sacks, Jilian A and Mockenhaupt, Frank P and Denkinger, Claudia M},
    title = {Head-to-head comparison of {SARS-CoV-2} antigen-detecting rapid test with self-collected anterior nasal swab versus professional-collected nasopharyngeal swab.},
    journal = {{Eur Respir J}},
    year = {2020},
    doi = {10.1183/13993003.03961-2020},
    pmid = {33303544},
    }
  • [DOI] X. Chen and D. Li, "Sequencing facility and DNA source associated patterns of virus-mappable reads in whole-genome sequencing data," Genomics, 2020.
    [Bibtex]
    @Article{Chen:20,
    author = {Xun Chen and Dawei Li},
    title = {Sequencing facility and {DNA} source associated patterns of virus-mappable reads in whole-genome sequencing data},
    journal = {Genomics},
    year = {2020},
    doi = {10.1016/j.ygeno.2020.12.004},
    publisher = {Elsevier {BV}},
    }
  • [DOI] M. I. Andersson, C. V. Arancibia-Carcamo, K. Auckland, K. J. Baillie, E. Barnes, T. Beneke, S. Bibi, T. Brooks, M. Carroll, D. Crook, K. Dingle, C. Dold, L. O. Downs, L. Dunn, D. W. Eyre, J. G. Jaramillo, H. Harvala, S. Hoosdally, S. Ijaz, T. James, W. James, K. Jeffery, A. Justice, P. Klenerman, J. C. Knight, M. Knight, X. Liu, S. F. Lumley, P. C. Matthews, A. L. McNaughton, A. J. Mentzer, J. Mongkolsapaya, S. Oakley, M. S. Oliveira, T. Peto, R. J. Ploeg, J. Ratcliff, M. J. Robbins, D. J. Roberts, J. Rudkin, R. A. Russell, G. Screaton, M. G. Semple, D. Skelly, P. Simmonds, N. Stoesser, L. Turtle, S. Wareing, and M. Zambon, "SARS-CoV-2 RNA detected in blood products from patients with COVID-19 is not associated with infectious virus," Wellcome Open Res, vol. 5, p. 181, 2020.
    [Bibtex]
    @Article{Andersson:20,
    author = {Monique I. Andersson and Carolina V. Arancibia-Carcamo and Kathryn Auckland and J. Kenneth Baillie and Eleanor Barnes and Tom Beneke and Sagida Bibi and Tim Brooks and Miles Carroll and Derrick Crook and Kate Dingle and Christina Dold and Louise O. Downs and Laura Dunn and David W. Eyre and Javier Gilbert Jaramillo and Heli Harvala and Sarah Hoosdally and Samreen Ijaz and Tim James and William James and Katie Jeffery and Anita Justice and Paul Klenerman and Julian C. Knight and Michael Knight and Xu Liu and Sheila F. Lumley and Philippa C. Matthews and Anna L. McNaughton and Alexander J. Mentzer and Juthathip Mongkolsapaya and Sarah Oakley and Marta S. Oliveira and Timothy Peto and Rutger J. Ploeg and Jeremy Ratcliff and Melanie J. Robbins and David J. Roberts and Justine Rudkin and Rebecca A. Russell and Gavin Screaton and Malcolm G. Semple and Donal Skelly and Peter Simmonds and Nicole Stoesser and Lance Turtle and Susan Wareing and Maria Zambon},
    title = {{SARS}-{CoV}-2 {RNA} detected in blood products from patients with {COVID}-19 is not associated with infectious virus},
    journal = {{Wellcome Open Res}},
    year = {2020},
    volume = {5},
    pages = {181},
    doi = {10.12688/wellcomeopenres.16002.2},
    publisher = {F1000 Research Ltd},
    }
  • [DOI] F. Hufsky, N. Beerenwinkel, I. M. Meyer, S. Roux, G. M. Cook, C. M. Kinsella, K. Lamkiewicz, M. Marquet, D. F. Nieuwenhuijse, I. Olendraite, S. Paraskevopoulou, F. Young, R. Dijkman, B. Ibrahim, J. Kelly, P. Le Mercier, M. Marz, A. Ramette, and V. Thiel, "The International Virus Bioinformatics Meeting 2020.," Viruses, vol. 12, 2020.
    [Bibtex]
    @Article{Hufsky:20a,
    author = {Hufsky, Franziska and Beerenwinkel, Niko and Meyer, Irmtraud M and Roux, Simon and Cook, Georgia May and Kinsella, Cormac M and Lamkiewicz, Kevin and Marquet, Mike and Nieuwenhuijse, David F and Olendraite, Ingrida and Paraskevopoulou, Sofia and Young, Francesca and Dijkman, Ronald and Ibrahim, Bashar and Kelly, Jenna and Le Mercier, Philippe and Marz, Manja and Ramette, Alban and Thiel, Volker},
    title = {{T}he {I}nternational {V}irus {B}ioinformatics {M}eeting 2020.},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    abstract = {The International Virus Bioinformatics Meeting 2020 was originally planned to take place in Bern, Switzerland, in March 2020. However, the COVID-19 pandemic put a spoke in the wheel of almost all conferences to be held in 2020. After moving the conference to 8-9 October 2020, we got hit by the second wave and finally decided at short notice to go fully online. On the other hand, the pandemic has made us even more aware of the importance of accelerating research in viral bioinformatics. Advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks. The International Virus Bioinformatics Meeting 2020 has attracted approximately 120 experts in virology and bioinformatics from all over the world to join the two-day virtual meeting. Despite concerns being raised that virtual meetings lack possibilities for face-to-face discussion, the participants from this small community created a highly interactive scientific environment, engaging in lively and inspiring discussions and suggesting new research directions and questions. The meeting featured five invited and twelve contributed talks, on the four main topics: (1) proteome and RNAome of RNA viruses, (2) viral metagenomics and ecology, (3) virus evolution and classification and (4) viral infections and immunology. Further, the meeting featured 20 oral poster presentations, all of which focused on specific areas of virus bioinformatics. This report summarizes the main research findings and highlights presented at the meeting.},
    doi = {10.3390/v12121398},
    issue = {12},
    keywords = {COVID-19; genome evolution; identification; metagenomics; software; viral diversity; viral taxonomy; virology; virome; virus bioinformatics},
    pmid = {33291220},
    }
  • [DOI] G. Cantelli, G. Cochrane, C. Brooksbank, E. McDonagh, P. Flicek, J. McEntyre, E. Birney, and R. Apweiler, "The European Bioinformatics Institute: empowering cooperation in response to a global health crisis," Nucleic Acids Res, 2020.
    [Bibtex]
    @Article{Cantelli:20,
    author = {Gaia Cantelli and Guy Cochrane and Cath Brooksbank and Ellen McDonagh and Paul Flicek and Johanna McEntyre and Ewan Birney and Rolf Apweiler},
    title = {The {E}uropean {B}ioinformatics {I}nstitute: empowering cooperation in response to a global health crisis},
    journal = {{Nucleic Acids Res}},
    year = {2020},
    doi = {10.1093/nar/gkaa1077},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] A. M. Price, K. E. Hayer, A. B. R. McIntyre, N. S. Gokhale, J. S. Abebe, A. D. N. Fera, C. E. Mason, S. M. Horner, A. C. Wilson, D. P. Depledge, and M. D. Weitzman, "Direct RNA sequencing reveals m6A modifications on adenovirus RNA are necessary for efficient splicing," Nat Commun, vol. 11, iss. 1, 2020.
    [Bibtex]
    @Article{Price:20,
    author = {Alexander M. Price and Katharina E. Hayer and Alexa B. R. McIntyre and Nandan S. Gokhale and Jonathan S. Abebe and Ashley N. Della Fera and Christopher E. Mason and Stacy M. Horner and Angus C. Wilson and Daniel P. Depledge and Matthew D. Weitzman},
    title = {Direct {RNA} sequencing reveals {m6A} modifications on adenovirus {RNA} are necessary for efficient splicing},
    journal = {{Nat Commun}},
    year = {2020},
    volume = {11},
    number = {1},
    doi = {10.1038/s41467-020-19787-6},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] C. Santos-Hövener, H. K. Neuhauser, A. S. Rosario, M. Busch, M. Schlaud, R. Hoffmann, A. Gößwald, C. Koschollek, J. Hoebel, J. Allen, A. Haack-Erdmann, S. Brockmann, T. Ziese, A. Nitsche, J. Michel, S. Haller, H. Wilking, O. Hamouda, V. M. Corman, C. Drosten, L. Schaade, L. H. Wieler, and T. L. and, "Serology- and PCR-based cumulative incidence of SARS-CoV-2 infection in adults in a successfully contained early hotspot (CoMoLo study), Germany, May to June 2020," Euro Surveill, vol. 25, iss. 47, 2020.
    [Bibtex]
    @Article{Santos-Hövener:20,
    author = {Claudia Santos-Hövener and Hannelore K Neuhauser and Angelika Schaffrath Rosario and Markus Busch and Martin Schlaud and Robert Hoffmann and Antje Gö{\ss}wald and Carmen Koschollek and Jens Hoebel and Jennifer Allen and Antje Haack-Erdmann and Stefan Brockmann and Thomas Ziese and Andreas Nitsche and Janine Michel and Sebastian Haller and Hendrik Wilking and Osamah Hamouda and Victor M Corman and Christian Drosten and Lars Schaade and Lothar H Wieler and Thomas Lampert and},
    title = {Serology- and {PCR}-based cumulative incidence of {SARS}-{CoV}-2 infection in adults in a successfully contained early hotspot ({CoMoLo} study), {G}ermany, {M}ay to {J}une 2020},
    journal = {{Euro Surveill}},
    year = {2020},
    volume = {25},
    number = {47},
    doi = {10.2807/1560-7917.es.2020.25.47.2001752},
    publisher = {European Centre for Disease Control and Prevention ({ECDC})},
    }
  • [DOI] F. Husain-Syed, I. Vadász, J. Wilhelm, H. Walmrath, W. Seeger, H. Birk, B. Jennert, H. Dietrich, S. Herold, J. Trauth, K. Tello, M. Sander, R. E. Morty, H. Slanina, C. G. Schüttler, J. Ziebuhr, S. Kassoumeh, C. Ronco, F. Ferrari, K. Warnatz, K. Stahl, B. Seeliger, M. M. Hoeper, T. Welte, and S. David, "Immunoglobulin deficiency as an indicator of disease severity in patients with COVID-19," Am J Physiol Lung Cell Mol Physiol, 2020.
    [Bibtex]
    @Article{Husain-Syed:20,
    author = {Faeq Husain-Syed and Istv{\'{a}}n Vad{\'{a}}sz and Jochen Wilhelm and Hans-Dieter Walmrath and Werner Seeger and Horst-Walter Birk and Birgit Jennert and Hartmut Dietrich and Susanne Herold and Janina Trauth and Khodr Tello and Michael Sander and Rory E. Morty and Heiko Slanina and Christian G. Schüttler and John Ziebuhr and Shadi Kassoumeh and Claudio Ronco and Fiorenza Ferrari and Klaus Warnatz and Klaus Stahl and Benjamin Seeliger and Marius M. Hoeper and Tobias Welte and Sascha David},
    title = {Immunoglobulin Deficiency as an Indicator of Disease Severity in Patients with {COVID}-19},
    journal = {{Am J Physiol Lung Cell Mol Physiol}},
    year = {2020},
    doi = {10.1152/ajplung.00359.2020},
    publisher = {American Physiological Society},
    }
  • [DOI] S. Duchene, L. Featherstone, M. Haritopoulou-Sinanidou, A. Rambaut, P. Lemey, and G. Baele, "Temporal signal and the phylodynamic threshold of SARS-CoV-2," Virus Evol, vol. 6, iss. 2, 2020.
    [Bibtex]
    @Article{Duchene:20,
    author = {Sebastian Duchene and Leo Featherstone and Melina Haritopoulou-Sinanidou and Andrew Rambaut and Philippe Lemey and Guy Baele},
    title = {Temporal signal and the phylodynamic threshold of {SARS}-{CoV}-2},
    journal = {{Virus Evol}},
    year = {2020},
    volume = {6},
    number = {2},
    doi = {10.1093/ve/veaa061},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] N. Alygizakis, A. N. Markou, N. I. Rousis, A. Galani, M. Avgeris, P. G. Adamopoulos, A. Scorilas, E. S. Lianidou, D. Paraskevis, S. Tsiodras, A. Tsakris, M. Dimopoulos, and N. S. Thomaidis, "Analytical methodologies for the detection of SARS-CoV-2 in wastewater: protocols and future perspectives," Trends Analyt Chem, p. 116125, 2020.
    [Bibtex]
    @Article{Alygizakis:20,
    author = {Nikiforos Alygizakis and Athina N. Markou and Nikolaos I. Rousis and Aikaterini Galani and Margaritis Avgeris and Panagiotis G. Adamopoulos and Andreas Scorilas and Evi S. Lianidou and Dimitrios Paraskevis and Sotirios Tsiodras and Athanassios Tsakris and Meletios-Athanasios Dimopoulos and Nikolaos S. Thomaidis},
    title = {Analytical methodologies for the detection of {SARS}-{CoV}-2 in wastewater: Protocols and future perspectives},
    journal = {{Trends Analyt Chem}},
    year = {2020},
    pages = {116125},
    doi = {10.1016/j.trac.2020.116125},
    publisher = {Elsevier {BV}},
    }
  • [DOI] T. Schlesinger, B. Weißbrich, F. Wedekink, Q. Notz, J. Herrmann, M. Krone, M. Sitter, B. Schmid, M. Kredel, J. Stumpner, L. Dölken, J. Wischhusen, P. Kranke, P. Meybohm, and C. Lotz, "Biodistribution and serologic response in SARS-CoV-2 induced ARDS: a cohort study," PLoS One, vol. 15, iss. 11, p. e0242917, 2020.
    [Bibtex]
    @Article{Schlesinger:20,
    author = {Tobias Schlesinger and Benedikt Wei{\ss}brich and Florian Wedekink and Quirin Notz and Johannes Herrmann and Manuel Krone and Magdalena Sitter and Benedikt Schmid and Markus Kredel and Jan Stumpner and Lars Dölken and Jörg Wischhusen and Peter Kranke and Patrick Meybohm and Christopher Lotz},
    title = {Biodistribution and serologic response in {SARS}-{CoV}-2 induced {ARDS}: A cohort study},
    journal = {{PLoS One}},
    year = {2020},
    volume = {15},
    number = {11},
    pages = {e0242917},
    doi = {10.1371/journal.pone.0242917},
    editor = {Francesco Di Gennaro},
    publisher = {Public Library of Science ({PLoS})},
    }
  • [DOI] S. Gryseels, L. D. Bruyn, R. Gyselings, S. Calvignac-Spencer, F. H. Leendertz, and H. Leirs, "Risk of human-to-wildlife transmission of SARS-CoV-2," Mamm Rev, 2020.
    [Bibtex]
    @Article{Gryseels:20a,
    author = {Sophie Gryseels and Luc De Bruyn and Ralf Gyselings and S{\'{e}}bastien Calvignac-Spencer and Fabian H. Leendertz and Herwig Leirs},
    title = {Risk of human-to-wildlife transmission of {SARS}-{CoV}-2},
    journal = {{Mamm Rev}},
    year = {2020},
    doi = {10.1111/mam.12225},
    publisher = {Wiley},
    }
  • [DOI] A. Popa, J. Genger, M. D. Nicholson, T. Penz, D. Schmid, S. W. Aberle, B. Agerer, A. Lercher, L. Endler, H. Colaço, M. Smyth, M. Schuster, M. L. Grau, F. Martínez-Jiménez, O. Pich, W. Borena, E. Pawelka, Z. Keszei, M. Senekowitsch, J. Laine, J. H. Aberle, M. Redlberger-Fritz, M. Karolyi, A. Zoufaly, S. Maritschnik, M. Borkovec, P. Hufnagl, M. Nairz, G. Weiss, M. T. Wolfinger, D. von Laer, G. Superti-Furga, N. Lopez-Bigas, E. Puchhammer-Stöckl, F. Allerberger, F. Michor, C. Bock, and A. Bergthaler, "Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2," Sci Transl Med, p. eabe2555, 2020.
    [Bibtex]
    @Article{Popa:20,
    author = {Alexandra Popa and Jakob-Wendelin Genger and Michael D. Nicholson and Thomas Penz and Daniela Schmid and Stephan W. Aberle and Benedikt Agerer and Alexander Lercher and Lukas Endler and Henrique Cola{\c{c}}o and Mark Smyth and Michael Schuster and Miguel L. Grau and Francisco Mart{\'{\i}}nez-Jim{\'{e}}nez and Oriol Pich and Wegene Borena and Erich Pawelka and Zsofia Keszei and Martin Senekowitsch and Jan Laine and Judith H. Aberle and Monika Redlberger-Fritz and Mario Karolyi and Alexander Zoufaly and Sabine Maritschnik and Martin Borkovec and Peter Hufnagl and Manfred Nairz and Günter Weiss and Michael T. Wolfinger and Dorothee von Laer and Giulio Superti-Furga and Nuria Lopez-Bigas and Elisabeth Puchhammer-Stöckl and Franz Allerberger and Franziska Michor and Christoph Bock and Andreas Bergthaler},
    title = {Genomic epidemiology of superspreading events in {A}ustria reveals mutational dynamics and transmission properties of {SARS}-{CoV}-2},
    journal = {{Sci Transl Med}},
    year = {2020},
    pages = {eabe2555},
    doi = {10.1126/scitranslmed.abe2555},
    publisher = {American Association for the Advancement of Science ({AAAS})},
    }
  • [DOI] V. Feuillet, B. Canard, and A. Trautmann, "Combining antivirals and immunomodulators to fight COVID-19," Trends Immunol, 2020.
    [Bibtex]
    @Article{Feuillet:20,
    author = {Vincent Feuillet and Bruno Canard and Alain Trautmann},
    title = {Combining Antivirals and Immunomodulators to Fight {COVID}-19},
    journal = {{Trends Immunol}},
    year = {2020},
    doi = {10.1016/j.it.2020.11.003},
    publisher = {Elsevier {BV}},
    }
  • [DOI] X. F. López-Labrador, J. R. Brown, N. Fischer, H. Harvala, S. V. Boheemen, O. Cinek, A. Sayiner, T. V. Madsen, E. Auvinen, V. Kufner, M. Huber, C. Rodriguez, M. Jonges, M. Hönemann, P. Susi, H. Sousa, P. E. Klapper, A. Pérez-Cataluña, M. Hernandez, R. Molenkamp, L. van der Hoek, R. Schuurman, N. Couto, K. Leuzinger, P. Simmonds, M. Beer, D. Höper, S. Kamminga, M. C. W. Feltkamp, J. Rodríguez-Díaz, E. Keyaerts, X. C. Nielsen, E. Puchhammer-Stöckl, A. C. M. Kroes, J. Buesa, J. Breuer, E. C. J. Claas, and J. J. C. de Vries, "Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: wet lab procedure," J Clin Virol, vol. 134, p. 104691, 2020.
    [Bibtex]
    @Article{Lopez-Labrador:20,
    author = {F. Xavier L{\'{o}}pez-Labrador and Julianne R. Brown and Nicole Fischer and Heli Harvala and Sander Van Boheemen and Ondrej Cinek and Arzu Sayiner and Tina Vasehus Madsen and Eeva Auvinen and Verena Kufner and Michael Huber and Christophe Rodriguez and Marcel Jonges and Mario Hönemann and Petri Susi and Hugo Sousa and Paul E. Klapper and Alba Pérez-Cataluña and Marta Hernandez and Richard Molenkamp and Lia van der Hoek and Rob Schuurman and Natacha Couto and Karoline Leuzinger and Peter Simmonds and Martin Beer and Dirk Höper and Sergio Kamminga and Mariet C.W. Feltkamp and Jes{\'{u}}s Rodr{\'{\i}}guez-D{\'{\i}}az and Els Keyaerts and Xiaohui Chen Nielsen and Elisabeth Puchhammer-Stöckl and Aloys C.M. Kroes and Javier Buesa and Judy Breuer and Eric C.J. Claas and Jutte J.C. de Vries},
    title = {Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part {I}: Wet lab procedure},
    journal = {{J Clin Virol}},
    year = {2020},
    volume = {134},
    pages = {104691},
    doi = {10.1016/j.jcv.2020.104691},
    publisher = {Elsevier {BV}},
    }
  • [DOI] A. Brinkmann, A. R. V. Souza, J. Esparza, A. Nitsche, and C. R. Damaso, "Re-assembly of nineteenth-century smallpox vaccine genomes reveals the contemporaneous use of horsepox and horsepox-related viruses in the USA," Genome Biol, vol. 21, iss. 1, 2020.
    [Bibtex]
    @Article{Brinkmann:20,
    author = {Annika Brinkmann and Aline R. V. Souza and Jos{\'{e}} Esparza and Andreas Nitsche and Clarissa R. Damaso},
    title = {Re-assembly of nineteenth-century smallpox vaccine genomes reveals the contemporaneous use of horsepox and horsepox-related viruses in the {USA}},
    journal = {{Genome Biol}},
    year = {2020},
    volume = {21},
    number = {1},
    doi = {10.1186/s13059-020-02202-0},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] E. Volz, V. Hill, J. T. McCrone, A. Price, D. Jorgensen, Á. O'Toole, J. Southgate, R. Johnson, B. Jackson, F. F. Nascimento, S. M. Rey, S. M. Nicholls, R. M. Colquhoun, A. S. da Filipe, J. Shepherd, D. J. Pascall, R. Shah, N. Jesudason, K. Li, R. Jarrett, N. Pacchiarini, M. Bull, L. Geidelberg, I. Siveroni, I. Goodfellow, N. J. Loman, O. G. Pybus, D. L. Robertson, E. C. Thomson, A. Rambaut, T. R. Connor, C. Koshy, E. Wise, N. Cortes, J. Lynch, S. Kidd, M. Mori, D. J. Fairley, T. Curran, J. P. McKenna, H. Adams, C. Fraser, T. Golubchik, D. Bonsall, C. Moore, S. L. Caddy, F. A. Khokhar, M. Wantoch, N. Reynolds, B. Warne, J. Maksimovic, K. Spellman, K. McCluggage, M. John, R. Beer, S. Afifi, S. Morgan, A. Marchbank, A. Price, C. Kitchen, H. Gulliver, I. Merrick, J. Southgate, M. Guest, R. Munn, T. Workman, T. R. Connor, W. Fuller, C. Bresner, L. B. Snell, T. Charalampous, G. Nebbia, R. Batra, J. Edgeworth, S. C. Robson, A. Beckett, K. F. Loveson, D. M. Aanensen, A. P. 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Young, J. Allan, J. Loh, P. A. Randell, A. Cox, P. Madona, A. Holmes, F. Bolt, J. Price, S. Mookerjee, A. Rowan, G. P. Taylor, M. Ragonnet-Cronin, F. F. Nascimento, D. Jorgensen, I. Siveroni, R. Johnson, O. Boyd, L. Geidelberg, E. M. Volz, K. Brunker, K. L. Smollett, N. J. Loman, J. Quick, C. McMurray, J. Stockton, S. Nicholls, W. Rowe, R. Poplawski, R. T. Martinez-Nunez, J. Mason, T. I. Robinson, E. O. textquotesingle, J. Watts, C. Breen, A. Cowell, C. Ludden, G. Sluga, N. W. Machin, S. S. Y. Ahmad, R. P. George, F. Halstead, V. Sivaprakasam, E. C. Thomson, J. G. Shepherd, P. Asamaphan, M. O. Niebel, K. K. Li, R. N. Shah, N. G. Jesudason, Y. A. Parr, L. Tong, A. Broos, D. Mair, J. Nichols, S. N. Carmichael, K. Nomikou, E. Aranday-Cortes, N. Johnson, I. Starinskij, A. S. da Filipe, D. L. Robertson, R. J. Orton, J. Hughes, S. Vattipally, J. B. Singer, A. D. Hale, L. R. Macfarlane-Smith, K. L. Harper, Y. Taha, B. A. I. Payne, S. Burton-Fanning, S. Waugh, J. Collins, G. Eltringham, K. E. 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    [Bibtex]
    @Article{Volz:20,
    author = {Erik Volz and Verity Hill and John T. McCrone and Anna Price and David Jorgensen and {\'{A}}ine O'Toole and Joel Southgate and Robert Johnson and Ben Jackson and Fabricia F. Nascimento and Sara M. Rey and Samuel M. Nicholls and Rachel M. Colquhoun and Ana da Silva Filipe and James Shepherd and David J. Pascall and Rajiv Shah and Natasha Jesudason and Kathy Li and Ruth Jarrett and Nicole Pacchiarini and Matthew Bull and Lily Geidelberg and Igor Siveroni and Ian Goodfellow and Nicholas J. Loman and Oliver G. Pybus and David L. Robertson and Emma C. Thomson and Andrew Rambaut and Thomas R. Connor and Cherian Koshy and Emma Wise and Nick Cortes and Jessica Lynch and Stephen Kidd and Matilde Mori and Derek J. Fairley and Tanya Curran and James P. McKenna and Helen Adams and Christophe Fraser and Tanya Golubchik and David Bonsall and Catrin Moore and Sarah L. Caddy and Fahad A. Khokhar and Michelle Wantoch and Nicola Reynolds and Ben Warne and Joshua Maksimovic and Karla Spellman and Kathryn McCluggage and Michaela John and Robert Beer and Safiah Afifi and Sian Morgan and Angela Marchbank and Anna Price and Christine Kitchen and Huw Gulliver and Ian Merrick and Joel Southgate and Martyn Guest and Robert Munn and Trudy Workman and Thomas R. Connor and William Fuller and Catherine Bresner and Luke B. Snell and Themoula Charalampous and Gaia Nebbia and Rahul Batra and Jonathan Edgeworth and Samuel C. Robson and Angela Beckett and Katie F. Loveson and David M. Aanensen and Anthony P. Underwood and Corin A. Yeats and Khalil Abudahab and Ben E.W. Taylor and Mirko Menegazzo and Gemma Clark and Wendy Smith and Manjinder Khakh and Vicki M. Fleming and Michelle M. Lister and Hannah C. Howson-Wells and Louise Berry and Tim Boswell and Amelia Joseph and Iona Willingham and Paul Bird and Thomas Helmer and Karlie Fallon and Christopher Holmes and Julian Tang and Veena Raviprakash and Sharon Campbell and Nicola Sheriff and Matthew W. Loose and Nadine Holmes and Christopher Moore and Matthew Carlile and Victoria Wright and Fei Sang and Johnny Debebe and Francesc Coll and Adrian W. Signell and Gilberto Betancor and Harry D. Wilson and Theresa Feltwell and Charlotte J. Houldcroft and Sahar Eldirdiri and Anita Kenyon and Thomas Davis and Oliver Pybus and Louis du Plessis and Alex Zarebski and Jayna Raghwani and Moritz Kraemer and Sarah Francois and Stephen Attwood and Tetyana Vasylyeva and M. Estee Torok and William L. Hamilton and Ian G. Goodfellow and Grant Hall and Aminu S. Jahun and Yasmin Chaudhry and Myra Hosmillo and Malte L. Pinckert and Iliana Georgana and Anna Yakovleva and Luke W. Meredith and Samuel Moses and Hannah Lowe and Felicity Ryan and Chloe L. Fisher and Ali R. Awan and John Boyes and Judith Breuer and Kathryn Ann Harris and Julianne Rose Brown and Divya Shah and Laura Atkinson and Jack C.D. Lee and Adela Alcolea-Medina and Nathan Moore and Nicholas Cortes and Rebecca Williams and Michael R. Chapman and Lisa J. Levett and Judith Heaney and Darren L. Smith and Matthew Bashton and Gregory R. Young and John Allan and Joshua Loh and Paul A. Randell and Alison Cox and Pinglawathee Madona and Alison Holmes and Frances Bolt and James Price and Siddharth Mookerjee and Aileen Rowan and Graham P. Taylor and Manon Ragonnet-Cronin and Fabricia F. Nascimento and David Jorgensen and Igor Siveroni and Rob Johnson and Olivia Boyd and Lily Geidelberg and Erik M. Volz and Kirstyn Brunker and Katherine L. Smollett and Nicholas J. Loman and Joshua Quick and Claire McMurray and Joanne Stockton and Sam Nicholls and Will Rowe and Radoslaw Poplawski and Rocio T. Martinez-Nunez and Jenifer Mason and Trevor I. Robinson and Elaine O{\textquotesingle}Toole and Joanne Watts and Cassie Breen and Angela Cowell and Catherine Ludden and Graciela Sluga and Nicholas W. Machin and Shazaad S.Y. Ahmad and Ryan P. George and Fenella Halstead and Venkat Sivaprakasam and Emma C. Thomson and James G. Shepherd and Patawee Asamaphan and Marc O. Niebel and Kathy K. Li and Rajiv N. Shah and Natasha G. Jesudason and Yasmin A. Parr and Lily Tong and Alice Broos and Daniel Mair and Jenna Nichols and Stephen N. Carmichael and Kyriaki Nomikou and Elihu Aranday-Cortes and Natasha Johnson and Igor Starinskij and Ana da Silva Filipe and David L. Robertson and Richard J. Orton and Joseph Hughes and Sreenu Vattipally and Joshua B. Singer and Antony D. Hale and Louissa R. Macfarlane-Smith and Katherine L. Harper and Yusri Taha and Brendan A.I. Payne and Shirelle Burton-Fanning and Sheila Waugh and Jennifer Collins and Gary Eltringham and Kate E. Templeton and Martin P. McHugh and Rebecca Dewar and Elizabeth Wastenge and Samir Dervisevic and Rachael Stanley and Reenesh Prakash and Claire Stuart and Ngozi Elumogo and Dheeraj K. Sethi and Emma J. Meader and Lindsay J. Coupland and Will Potter and Clive Graham and Edward Barton and Debra Padgett and Garren Scott and Emma Swindells and Jane Greenaway and Andrew Nelson and Wen C. Yew and Paola C. Resende Silva and Monique Andersson and Robert Shaw and Timothy Peto and Anita Justice and David Eyre and Derrick Crooke and Sarah Hoosdally and Tim J. Sloan and Nichola Duckworth and Sarah Walsh and Anoop J. Chauhan and Sharon Glaysher and Kelly Bicknell and Sarah Wyllie and Ethan Butcher and Scott Elliott and Allyson Lloyd and Robert Impey and Nick Levene and Lynn Monaghan and Declan T. Bradley and Elias Allara and Clare Pearson and Peter Muir and Ian B. Vipond and Richard Hopes and Hannah M. Pymont and Stephanie Hutchings and Martin D. Curran and Surendra Parmar and Angie Lackenby and Tamyo Mbisa and Steven Platt and Shahjahan Miah and David Bibby and Carmen Manso and Jonathan Hubb and Meera Chand and Gavin Dabrera and Mary Ramsay and Daniel Bradshaw and Alicia Thornton and Richard Myers and Ulf Schaefer and Natalie Groves and Eileen Gallagher and David Lee and David Williams and Nicholas Ellaby and Ian Harrison and Hassan Hartman and Nikos Manesis and Vineet Patel and Chloe Bishop and Vicki Chalker and Husam Osman and Andrew Bosworth and Esther Robinson and Matthew T.G. Holden and Sharif Shaaban and Alec Birchley and Alexander Adams and Alisha Davies and Amy Gaskin and Amy Plimmer and Bree Gatica-Wilcox and Caoimhe McKerr and Catherine Moore and Chris Williams and David Heyburn and Elen De Lacy and Ember Hilvers and Fatima Downing and Giri Shankar and Hannah Jones and Hibo Asad and Jason Coombes and Joanne Watkins and Johnathan M. Evans and Laia Fina and Laura Gifford and Lauren Gilbert and Lee Graham and Malorie Perry and Mari Morgan and Matthew Bull and Michelle Cronin and Nicole Pacchiarini and Noel Craine and Rachel Jones and Robin Howe and Sally Corden and Sara Rey and Sara Kumziene-Summerhayes and Sarah Taylor and Simon Cottrell and Sophie Jones and Sue Edwards and Justin O'Grady and Andrew J. Page and John Wain and Mark A. Webber and Alison E. Mather and David J. Baker and Steven Rudder and Muhammad Yasir and Nicholas M. Thomson and Alp Aydin and Ana P. Tedim and Gemma L. Kay and Alexander J. Trotter and Rachel A.J. Gilroy and Nabil-Fareed Alikhan and Leonardo de Oliveira Martins and Thanh Le-Viet and Lizzie Meadows and Anastasia Kolyva and Maria Diaz and Andrew Bell and Ana Victoria Gutierrez and Ian G. Charles and Evelien M. Adriaenssens and Robert A. Kingsley and Anna Casey and David A. Simpson and Zoltan Molnar and Thomas Thompson and Erwan Acheson and Jane A.H. Masoli and Bridget A. Knight and Andrew Hattersley and Sian Ellard and Cressida Auckland and Tabitha W. Mahungu and Dianne Irish-Tavares and Tanzina Haque and Yann Bourgeois and Garry P. Scarlett and David G. Partridge and Mohammad Raza and Cariad Evans and Kate Johnson and Steven Liggett and Paul Baker and Sarah Essex and Ronan A. Lyons and Laura G. Caller and Sergi Castellano and Rachel J. Williams and Mark Kristiansen and Sunando Roy and Charlotte A. Williams and Patricia L. Dyal and Helena J. Tutill and Yasmin N. Panchbhaya and Leysa M. Forrest and Paola Niola and Jacqueline Findlay and Tony T. Brooks and Artemis Gavriil and Lamia Mestek-Boukhibar and Sam Weeks and Sarojini Pandey and Lisa Berry and Katie Jones and Alex Richter and Andrew Beggs and Colin P. Smith and Giselda Bucca and Andrew R. Hesketh and Ewan M. Harrison and Sharon J. Peacock and Sophie Palmer and Carol M. Churcher and Katherine L. Bellis and Sophia T. Girgis and Plamena Naydenova and Beth Blane and Sushmita Sridhar and Chris Ruis and Sally Forrest and Claire Cormie and Harmeet K. Gill and Joana Dias and Ellen E. Higginson and Mailis Maes and Jamie Young and Leanne M. Kermack and Nazreen F. Hadjirin and Dinesh Aggarwal and Luke Griffith and Tracey Swingler and Rose K. Davidson and Andrew Rambaut and Thomas Williams and Carlos E. Balcazar and Michael D. Gallagher and {\'{A}}ine O{\textquotesingle}Toole and Stefan Rooke and Ben Jackson and Rachel Colquhoun and Jordan Ashworth and Verity Hill and J.T. McCrone and Emily Scher and Xiaoyu Yu and Kathleen A. Williamson and Thomas D. Stanton and Stephen L. Michell and Claire M. Bewshea and Ben Temperton and Michelle L. Michelsen and Joanna Warwick-Dugdale and Robin Manley and Audrey Farbos and James W. Harrison and Christine M. Sambles and David J. Studholme and Aaron R. Jeffries and Alistair C. Darby and Julian A. Hiscox and Steve Paterson and Miren Iturriza-Gomara and Kathryn A. Jackson and Anita O. Lucaci and Edith E. Vamos and Margaret Hughes and Lucille Rainbow and Richard Eccles and Charlotte Nelson and Mark Whitehead and Lance Turtle and Sam T. Haldenby and Richard Gregory and Matthew Gemmell and Dominic Kwiatkowski and Thushan I. de Silva and Nikki Smith and Adrienn Angyal and Benjamin B. Lindsey and Danielle C. Groves and Luke R. Green and Dennis Wang and Timothy M. Freeman and Matthew D. Parker and Alexander J. Keeley and Paul J. Parsons and Rachel M. Tucker and Rebecca Brown and Matthew Wyles and Chrystala Constantinidou and Meera Unnikrishnan and Sascha Ott and Jeffrey K.J. Cheng and Hannah E. Bridgewater and Lucy R. Frost and Grace Taylor-Joyce and Richard Stark and Laura Baxter and Mohammad T. Alam and Paul E. Brown and Patrick C. McClure and Joseph G. Chappell and Theocharis Tsoleridis and Jonathan Ball and Dimitris Gramatopoulos and David Buck and John A. Todd and Angie Green and Amy Trebes and George MacIntyre-Cockett and Mariateresa de Cesare and Cordelia Langford and Alex Alderton and Roberto Amato and Sonia Goncalves and David K. Jackson and Ian Johnston and John Sillitoe and Steve Palmer and Mara Lawniczak and Matt Berriman and John Danesh and Rich Livett and Lesley Shirley and Ben Farr and Mike Quail and Scott Thurston and Naomi Park and Emma Betteridge and Danni Weldon and Scott Goodwin and Rachel Nelson and Charlotte Beaver and Laura Letchford and David A. Jackson and Luke Foulser and Liz McMinn and Liam Prestwood and Sally Kay and Leanne Kane and Matthew J. Dorman and Inigo Martincorena and Christoph Puethe and Jon-Paul Keatley and Gerry Tonkin-Hill and Christen Smith and Dorota Jamrozy and Mathew A. Beale and Minal Patel and Cristina Ariani and Michael Spencer-Chapman and Eleanor Drury and Stephanie Lo and Shavanthi Rajatileka and Carol Scott and Keith James and Sarah K. Buddenborg and Duncan J. Berger and Gaurang Patel and Maria V. Garcia-Casado and Thomas Dibling and Samantha McGuigan and Hazel A. Rogers and Adam D. Hunter and Emily Souster and Alexandra S. Neaverson},
    title = {Evaluating the Effects of {SARS}-{CoV}-2 Spike Mutation {D614G} on Transmissibility and Pathogenicity},
    journal = {Cell},
    year = {2020},
    doi = {10.1016/j.cell.2020.11.020},
    publisher = {Elsevier {BV}},
    }
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    [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}},
    }
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    [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}},
    }
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    [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}},
    }
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    [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})},
    }
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    [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}},
    }
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    [Bibtex]
    @Article{Rastogi:20,
    author = {Meghana Rastogi and Neha Pandey and Astha Shukla and Sunit K. Singh},
    title = {{SARS} coronavirus 2: from genome to infectome},
    journal = {{Respir Res}},
    year = {2020},
    volume = {21},
    number = {1},
    doi = {10.1186/s12931-020-01581-z},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] L. Sanchez-Felipe, T. Vercruysse, S. Sharma, J. Ma, V. Lemmens, D. V. Looveren, M. P. A. Javarappa, R. Boudewijns, B. Malengier-Devlies, L. Liesenborghs, S. J. F. Kaptein, C. D. Keyzer, L. Bervoets, S. Debaveye, M. Rasulova, L. Seldeslachts, L. Li, S. Jansen, M. B. Yakass, B. E. Verstrepen, K. P. Böszörményi, G. Kiemenyi-Kayere, N. van Driel, O. Quaye, X. Zhang, S. ter Horst, N. Mishra, W. Deboutte, J. Matthijnssens, L. Coelmont, C. Vandermeulen, E. Heylen, V. Vergote, D. Schols, Z. Wang, W. Bogers, T. Kuiken, E. Verschoor, C. Cawthorne, K. V. Laere, G. Opdenakker, G. V. Velde, B. Weynand, D. E. Teuwen, P. Matthys, J. Neyts, H. J. Thibaut, and K. Dallmeier, "A single-dose live-attenuated YF17D-vectored SARS-CoV-2 vaccine candidate," Nature, 2020.
    [Bibtex]
    @Article{Sanchez-Felipe:20,
    author = {Lorena Sanchez-Felipe and Thomas Vercruysse and Sapna Sharma and Ji Ma and Viktor Lemmens and Dominique Van Looveren and Mahadesh Prasad Arkalagud Javarappa and Robbert Boudewijns and Bert Malengier-Devlies and Laurens Liesenborghs and Suzanne J. F. Kaptein and Carolien De Keyzer and Lindsey Bervoets and Sarah Debaveye and Madina Rasulova and Laura Seldeslachts and Li-Hsin Li and Sander Jansen and Michael Bright Yakass and Babs E. Verstrepen and Kinga P. Böszörm{\'{e}}nyi and Gwendoline Kiemenyi-Kayere and Nikki van Driel and Osbourne Quaye and Xin Zhang and Sebastiaan ter Horst and Niraj Mishra and Ward Deboutte and Jelle Matthijnssens and Lotte Coelmont and Corinne Vandermeulen and Elisabeth Heylen and Valentijn Vergote and Dominique Schols and Zhongde Wang and Willy Bogers and Thijs Kuiken and Ernst Verschoor and Christopher Cawthorne and Koen Van Laere and Ghislain Opdenakker and Greetje Vande Velde and Birgit Weynand and Dirk E. Teuwen and Patrick Matthys and Johan Neyts and Hendrik Jan Thibaut and Kai Dallmeier},
    title = {A single-dose live-attenuated {YF17D}-vectored {SARS}-{CoV}-2 vaccine candidate},
    journal = {Nature},
    year = {2020},
    doi = {10.1038/s41586-020-3035-9},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] O. Ziv, J. Price, L. Shalamova, T. Kamenova, I. Goodfellow, F. Weber, and E. A. Miska, "The short- and long-range RNA-RNA interactome of SARS-CoV-2," Mol Cell, 2020.
    [Bibtex]
    @Article{Ziv:20,
    author = {Omer Ziv and Jonathan Price and Lyudmila Shalamova and Tsveta Kamenova and Ian Goodfellow and Friedemann Weber and Eric A. Miska},
    title = {The Short- and Long-Range {RNA}-{RNA} Interactome of {SARS}-{CoV}-2},
    journal = {{Mol Cell}},
    year = {2020},
    doi = {10.1016/j.molcel.2020.11.004},
    publisher = {Elsevier {BV}},
    }
  • [DOI] J. Meinhardt, J. Radke, C. Dittmayer, J. Franz, C. Thomas, R. Mothes, M. Laue, J. Schneider, S. Brünink, S. Greuel, M. Lehmann, O. Hassan, T. Aschman, E. Schumann, R. L. Chua, C. Conrad, R. Eils, W. Stenzel, M. Windgassen, L. Rößler, H. Goebel, H. R. Gelderblom, H. Martin, A. Nitsche, W. J. Schulz-Schaeffer, S. Hakroush, M. S. Winkler, B. Tampe, F. Scheibe, P. Körtvélyessy, D. Reinhold, B. Siegmund, A. A. Kühl, S. Elezkurtaj, D. Horst, L. Oesterhelweg, M. Tsokos, B. Ingold-Heppner, C. Stadelmann, C. Drosten, V. M. Corman, H. Radbruch, and F. L. Heppner, "Olfactory transmucosal SARS-CoV-2 invasion as a port of central nervous system entry in individuals with COVID-19," Nat Neurosci, 2020.
    [Bibtex]
    @Article{Meinhardt:20,
    author = {Jenny Meinhardt and Josefine Radke and Carsten Dittmayer and Jonas Franz and Carolina Thomas and Ronja Mothes and Michael Laue and Julia Schneider and Sebastian Brünink and Selina Greuel and Malte Lehmann and Olga Hassan and Tom Aschman and Elisa Schumann and Robert Lorenz Chua and Christian Conrad and Roland Eils and Werner Stenzel and Marc Windgassen and Larissa Rö{\ss}ler and Hans-Hilmar Goebel and Hans R. Gelderblom and Hubert Martin and Andreas Nitsche and Walter J. Schulz-Schaeffer and Samy Hakroush and Martin S. Winkler and Björn Tampe and Franziska Scheibe and P{\'{e}}ter Körtv{\'{e}}lyessy and Dirk Reinhold and Britta Siegmund and Anja A. Kühl and Sefer Elezkurtaj and David Horst and Lars Oesterhelweg and Michael Tsokos and Barbara Ingold-Heppner and Christine Stadelmann and Christian Drosten and Victor Max Corman and Helena Radbruch and Frank L. Heppner},
    title = {Olfactory transmucosal {SARS}-{CoV}-2 invasion as a port of central nervous system entry in individuals with {COVID}-19},
    journal = {{Nat Neurosci}},
    year = {2020},
    doi = {10.1038/s41593-020-00758-5},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] D. W. Hawman, G. Ahlén, S. K. Appelberg, K. Meade-White, P. W. Hanley, D. Scott, V. Monteil, S. Devignot, A. Okumura, F. Weber, H. Feldmann, M. Sällberg, and A. Mirazimi, "A DNA-based vaccine protects against Crimean-Congo haemorrhagic fever virus disease in a Cynomolgus macaque model," Nat Microbiol, 2020.
    [Bibtex]
    @Article{Hawman:20,
    author = {David W. Hawman and Gustaf Ahl{\'{e}}n and K. Sofia Appelberg and Kimberly Meade-White and Patrick W. Hanley and Dana Scott and Vanessa Monteil and Stephanie Devignot and Atsushi Okumura and Friedemann Weber and Heinz Feldmann and Matti Sällberg and Ali Mirazimi},
    title = {A {DNA}-based vaccine protects against {C}rimean-{C}ongo haemorrhagic fever virus disease in a {C}ynomolgus macaque model},
    journal = {{Nat Microbiol}},
    year = {2020},
    doi = {10.1038/s41564-020-00815-6},
    publisher = {Springer Science and Business Media {LLC}},
    }
  • [DOI] C. Hörner, C. Schürmann, A. Auste, A. Ebenig, S. Muraleedharan, K. H. Dinnon, T. Scholz, M. Herrmann, B. S. Schnierle, R. S. Baric, and M. D. Mühlebach, "A highly immunogenic and effective measles virus-based Th1-biased COVID-19 vaccine," Proc Natl Acad Sci USA, p. 202014468, 2020.
    [Bibtex]
    @Article{Hörner:20,
    author = {Cindy Hörner and Christoph Schürmann and Arne Auste and Aileen Ebenig and Samada Muraleedharan and Kenneth H. Dinnon and Tatjana Scholz and Maike Herrmann and Barbara S. Schnierle and Ralph S. Baric and Michael D. Mühlebach},
    title = {A highly immunogenic and effective measles virus-based {T}h1-biased {COVID}-19 vaccine},
    journal = {{Proc Natl Acad Sci USA}},
    year = {2020},
    pages = {202014468},
    doi = {10.1073/pnas.2014468117},
    publisher = {Proceedings of the National Academy of Sciences},
    }
  • [DOI] M. Holwerda, P. V'kovski, M. Wider, V. Thiel, and R. Dijkman, "Identification of an antiviral compound from the pandemic response box that efficiently inhibits SARS-CoV-2 infection in vitro," Microorganisms, vol. 8, iss. 12, p. 1872, 2020.
    [Bibtex]
    @Article{Holwerda:20,
    author = {Melle Holwerda and Philip V'kovski and Manon Wider and Volker Thiel and Ronald Dijkman},
    title = {Identification of an Antiviral Compound from the Pandemic Response Box that Efficiently Inhibits {SARS}-{CoV}-2 Infection In Vitro},
    journal = {Microorganisms},
    year = {2020},
    volume = {8},
    number = {12},
    pages = {1872},
    doi = {10.3390/microorganisms8121872},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] D. M. Brown, Y. Zhang, and R. H. Scheuermann, "Epidemiology and sequence-based evolutionary analysis of circulating non-polio enteroviruses," Microorganisms, vol. 8, iss. 12, p. 1856, 2020.
    [Bibtex]
    @Article{Brown:20,
    author = {David M. Brown and Yun Zhang and Richard H. Scheuermann},
    title = {Epidemiology and Sequence-Based Evolutionary Analysis of Circulating Non-Polio Enteroviruses},
    journal = {Microorganisms},
    year = {2020},
    volume = {8},
    number = {12},
    pages = {1856},
    doi = {10.3390/microorganisms8121856},
    publisher = {{MDPI} {AG}},
    }
  • [DOI] R. Ben-Othman, B. Cai, A. C. Liu, N. Varankovich, D. He, T. M. Blimkie, A. H. Lee, E. E. Gill, M. Novotny, B. Aevermann, S. Drissler, C. P. Shannon, S. McCann, K. Marty, G. Bjornson, R. D. Edgar, D. T. S. Lin, N. Gladish, J. Maclsaac, N. Amenyogbe, Q. Chan, A. Llibre, J. Collin, E. Landais, K. Le, S. M. Reiss, W. C. Koff, C. Havenar-Daughton, M. Heran, B. Sangha, D. Walt, M. Krajden, S. Crotty, D. Sok, B. Briney, D. R. Burton, D. Duffy, L. J. Foster, W. W. Mohn, M. S. Kobor, S. J. Tebbutt, R. R. Brinkman, R. H. Scheuermann, R. E. W. Hancock, T. R. Kollmann, and M. Sadarangani, "Systems biology methods applied to blood and tissue for a comprehensive analysis of immune response to hepatitis B vaccine in adults," Frontiers in immunology, vol. 11, 2020.
    [Bibtex]
    @Article{Ben-Othman:20,
    author = {Rym Ben-Othman and Bing Cai and Aaron C. Liu and Natallia Varankovich and Daniel He and Travis M. Blimkie and Amy H. Lee and Erin E. Gill and Mark Novotny and Brian Aevermann and Sibyl Drissler and Casey P. Shannon and Sarah McCann and Kim Marty and Gordean Bjornson and Rachel D. Edgar and David Tse Shen Lin and Nicole Gladish and Julia Maclsaac and Nelly Amenyogbe and Queenie Chan and Alba Llibre and Joyce Collin and Elise Landais and Khoa Le and Samantha M. Reiss and Wayne C. Koff and Colin Havenar-Daughton and Manraj Heran and Bippan Sangha and David Walt and Mel Krajden and Shane Crotty and Devin Sok and Bryan Briney and Dennis R. Burton and Darragh Duffy and Leonard J. Foster and William W. Mohn and Michael S. Kobor and Scott J. Tebbutt and Ryan R. Brinkman and Richard H. Scheuermann and Robert E. W. Hancock and Tobias R. Kollmann and Manish Sadarangani},
    title = {Systems Biology Methods Applied to Blood and Tissue for a Comprehensive Analysis of Immune Response to Hepatitis {B} Vaccine in Adults},
    journal = {Frontiers in Immunology},
    year = {2020},
    volume = {11},
    doi = {10.3389/fimmu.2020.580373},
    publisher = {Frontiers Media {SA}},
    }
  • [DOI] F. L. Nobrega, H. Walinga, B. E. Dutilh, and S. J. J. Brouns, "Prophages are associated with extensive CRISPR–cas auto-immunity," Nucleic Acids Res, 2020.
    [Bibtex]
    @Article{Nobrega:20,
    author = {Franklin L Nobrega and Hielke Walinga and Bas E Dutilh and Stan J J Brouns},
    title = {Prophages are associated with extensive {CRISPR}{\textendash}Cas auto-immunity},
    journal = {{Nucleic Acids Res}},
    year = {2020},
    doi = {10.1093/nar/gkaa1071},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] S. Weis, A. Scherag, M. Baier, M. Kiehntopf, T. Kamradt, S. Kolanos, J. Ankert, S. Glöckner, O. Makarewicz, S. Hagel, C. Bahrs, A. Kimmig, H. Proquitté, J. Guerra, D. Rimek, B. Löffler, M. W. Pletz, T. Hotz, P. Enders, R. Koch, S. Mai, M. Ullrich, C. Richert, C. Eibner, B. Meinung, K. Stötzer, J. Köhler, H. Cipowicz, C. Pinkwart, M. Bauer, P. Dickmann, A. Licht, J. Scholz, W. Wetzker, A. Hartung, D. Weiss, L. Thieme, G. Hanf, C. Schnizer, J. Müller, J. Kosenkow, F. Röstel, N. Andreas, R. Marquardt, S. Deinhardt-Emmer, and S. Kuhn, "Antibody response using six different serological assays in a completely PCR-tested community after a COVID-19 outbreak - the CoNAN study," Clin Microbiol Infect, 2020.
    [Bibtex]
    @Article{Weis:20,
    author = {Sebastian Weis and Andr{\'{e}} Scherag and Michael Baier and Michael Kiehntopf and Thomas Kamradt and Steffi Kolanos and Juliane Ankert and Stefan Glöckner and Oliwia Makarewicz and Stefan Hagel and Christina Bahrs and Aurelia Kimmig and Hans Proquitt{\'{e}} and Joel Guerra and Dagmar Rimek and Bettina Löffler and Mathias W. Pletz and Thomas Hotz and Petra Enders and Renate Koch and Steffen Mai and Matthias Ullrich and Cora Richert and Cornelius Eibner and Bettina Meinung and Kay Stötzer and Julia Köhler and Hans Cipowicz and Christine Pinkwart and Michael Bauer and Petra Dickmann and Annika Licht and Juliane Scholz and Wibke Wetzker and Anita Hartung and Daniel Weiss and Lara Thieme and Gabi Hanf and Clara Schnizer and Jasmin Müller and Jennifer Kosenkow and Franziska Röstel and Nico Andreas and Raphaela Marquardt and Stefanie Deinhardt-Emmer and Sebastian Kuhn},
    title = {Antibody response using six different serological assays in a completely {PCR}-tested community after a {COVID}-19 outbreak - The {CoNAN} study},
    journal = {{Clin Microbiol Infect}},
    year = {2020},
    doi = {10.1016/j.cmi.2020.11.009},
    publisher = {Elsevier {BV}},
    }
  • [DOI] I. Kalvari, E. P. Nawrocki, N. Ontiveros-Palacios, J. Argasinska, K. Lamkiewicz, M. Marz, S. Griffiths-Jones, C. Toffano-Nioche, D. Gautheret, Z. Weinberg, E. Rivas, S. R. Eddy, R. Finn, A. Bateman, and A. I. Petrov, "Rfam 14: expanded coverage of metagenomic, viral and microRNA families," Nucleic Acids Res, 2020.
    [Bibtex]
    @Article{Kalvari:20,
    author = {Ioanna Kalvari and Eric P Nawrocki and Nancy Ontiveros-Palacios and Joanna Argasinska and Kevin Lamkiewicz and Manja Marz and Sam Griffiths-Jones and Claire Toffano-Nioche and Daniel Gautheret and Zasha Weinberg and Elena Rivas and Sean R Eddy and Robert~D Finn and Alex Bateman and Anton I Petrov},
    title = {Rfam 14: expanded coverage of metagenomic, viral and {microRNA} families},
    journal = {{Nucleic Acids Res}},
    year = {2020},
    doi = {10.1093/nar/gkaa1047},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] L. Novelli, F. Motta, A. Ceribelli, G. M. Guidelli, N. Luciano, N. Isailovic, M. Vecellio, M. Caprioli, N. Clementi, M. Clementi, N. Mancini, C. Selmi, and M. D. Santis, "A case of psoriatic arthritis triggered by SARS-CoV-2 infection," Rheumatology, 2020.
    [Bibtex]
    @Article{Novelli:20,
    author = {Lucia Novelli and Francesca Motta and Angela Ceribelli and Giacomo M Guidelli and Nicoletta Luciano and Natasa Isailovic and Matteo Vecellio and Marta Caprioli and Nicola Clementi and Massimo Clementi and Nicasio Mancini and Carlo Selmi and Maria De Santis},
    title = {A case of psoriatic arthritis triggered by {SARS}-{CoV}-2 infection},
    journal = {Rheumatology},
    year = {2020},
    doi = {10.1093/rheumatology/keaa691},
    publisher = {Oxford University Press ({OUP})},
    }
  • [DOI] P. A. Reuken, M. Wüst, B. Löffler, M. Bauer, and A. Stallmach, "Letter: SARS-CoV-2-induced gastrointestinal inflammation.," Aliment Pharmacol Ther, vol. 52, p. 1748–1749, 2020.
    [Bibtex]
    @Article{Reuken:20,
    author = {Reuken, Philipp A and Wüst, Michaela and Löffler, Bettina and Bauer, Michael and Stallmach, Andreas},
    title = {Letter: {SARS-CoV-2}-induced gastrointestinal inflammation.},
    journal = {{Aliment Pharmacol Ther}},
    year = {2020},
    volume = {52},
    pages = {1748--1749},
    doi = {10.1111/apt.16087},
    issue = {11-12},
    pmid = {33205881},
    }
  • [DOI] R. Boudewijns, H. J. Thibaut, S. J. F. Kaptein, R. Li, V. Vergote, L. Seldeslachts, J. Van Weyenbergh, C. De Keyzer, L. Bervoets, S. Sharma, L. Liesenborghs, J. Ma, S. Jansen, D. Van Looveren, T. Vercruysse, X. Wang, D. Jochmans, E. Martens, K. Roose, D. De Vlieger, B. Schepens, T. Van Buyten, S. Jacobs, Y. Liu, J. Martí-Carreras, B. Vanmechelen, T. Wawina-Bokalanga, L. Delang, J. Rocha-Pereira, L. Coelmont, W. Chiu, P. Leyssen, E. Heylen, D. Schols, L. Wang, L. Close, J. Matthijnssens, M. Van Ranst, V. Compernolle, G. Schramm, K. Van Laere, X. Saelens, N. Callewaert, G. Opdenakker, P. Maes, B. Weynand, C. Cawthorne, G. Vande Velde, Z. Wang, J. Neyts, and K. Dallmeier, "STAT2 signaling restricts viral dissemination but drives severe pneumonia in SARS-CoV-2 infected hamsters.," Nat Commun, vol. 11, p. 5838, 2020.
    [Bibtex]
    @Article{Boudewijns:20,
    author = {Boudewijns, Robbert and Thibaut, Hendrik Jan and Kaptein, Suzanne J F and Li, Rong and Vergote, Valentijn and Seldeslachts, Laura and Van Weyenbergh, Johan and De Keyzer, Carolien and Bervoets, Lindsey and Sharma, Sapna and Liesenborghs, Laurens and Ma, Ji and Jansen, Sander and Van Looveren, Dominique and Vercruysse, Thomas and Wang, Xinyu and Jochmans, Dirk and Martens, Erik and Roose, Kenny and De Vlieger, Dorien and Schepens, Bert and Van Buyten, Tina and Jacobs, Sofie and Liu, Yanan and Martí-Carreras, Joan and Vanmechelen, Bert and Wawina-Bokalanga, Tony and Delang, Leen and Rocha-Pereira, Joana and Coelmont, Lotte and Chiu, Winston and Leyssen, Pieter and Heylen, Elisabeth and Schols, Dominique and Wang, Lanjiao and Close, Lila and Matthijnssens, Jelle and Van Ranst, Marc and Compernolle, Veerle and Schramm, Georg and Van Laere, Koen and Saelens, Xavier and Callewaert, Nico and Opdenakker, Ghislain and Maes, Piet and Weynand, Birgit and Cawthorne, Christopher and Vande Velde, Greetje and Wang, Zhongde and Neyts, Johan and Dallmeier, Kai},
    title = {{STAT2} signaling restricts viral dissemination but drives severe pneumonia in {SARS-CoV-2} infected hamsters.},
    journal = {{Nat Commun}},
    year = {2020},
    volume = {11},
    pages = {5838},
    abstract = {Emergence of SARS-CoV-2 causing COVID-19 has resulted in hundreds of thousands of deaths. In search for key targets of effective therapeutics, robust animal models mimicking COVID-19 in humans are urgently needed. Here, we show that Syrian hamsters, in contrast to mice, are highly permissive to SARS-CoV-2 and develop bronchopneumonia and strong inflammatory responses in the lungs with neutrophil infiltration and edema, further confirmed as consolidations visualized by micro-CT alike in clinical practice. Moreover, we identify an exuberant innate immune response as key player in pathogenesis, in which STAT2 signaling plays a dual role, driving severe lung injury on the one hand, yet restricting systemic virus dissemination on the other. Our results reveal the importance of STAT2-dependent interferon responses in the pathogenesis and virus control during SARS-CoV-2 infection and may help rationalizing new strategies for the treatment of COVID-19 patients.},
    doi = {10.1038/s41467-020-19684-y},
    issue = {1},
    pmid = {33203860},
    }
  • [DOI] K. Wernike, A. Aebischer, A. Michelitsch, D. Hoffmann, C. Freuling, A. Balkema-Buschmann, A. Graaf, T. Müller, N. Osterrieder, M. Rissmann, D. Rubbenstroth, J. Schön, C. Schulz, J. Trimpert, L. Ulrich, A. Volz, T. C. Mettenleiter, and M. Beer, "Multi-species ELISA for the detection of antibodies against SARS-CoV-2 in animals," Transbound Emerg Dis, 2020.
    [Bibtex]
    @Article{Wernike:20b,
    author = {Kerstin Wernike and Andrea Aebischer and Anna Michelitsch and Donata Hoffmann and Conrad Freuling and Anne Balkema-Buschmann and Annika Graaf and Thomas Müller and Nikolaus Osterrieder and Melanie Rissmann and Dennis Rubbenstroth and Jacob Schön and Claudia Schulz and Jakob Trimpert and Lorenz Ulrich and Asisa Volz and Thomas C. Mettenleiter and Martin Beer},
    title = {Multi-species {ELISA} for the detection of antibodies against {SARS}-{CoV}-2 in animals},
    journal = {{Transbound Emerg Dis}},
    year = {2020},
    doi = {10.1111/tbed.13926},
    publisher = {Wiley},
    }
  • M. Gultom, M. Licheri, L. Laloli, M. Wider, M. Straessle, S. Steiner, A. Kratzel, T. T. N. Thao, H. Stalder, J. Portmann, and others, "Susceptibility of well-differentiated airway epithelial cell cultures from domestic and wildlife animals to SARS-CoV-2," bioRxiv, 2020.
    [Bibtex]
    @Article{Gultom:20,
    author = {Gultom, Mitra and Licheri, Matthias and Laloli, Laura and Wider, Manon and Straessle, Marina and Steiner, Silvio and Kratzel, Annika and Thao, Tran Thi Nhu and Stalder, Hanspeter and Portmann, Jasmine and others},
    title = {Susceptibility of well-differentiated airway epithelial cell cultures from domestic and wildlife animals to {SARS-CoV-2}},
    journal = {{bioRxiv}},
    year = {2020},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] S. Lytras, G. Arriagada, and R. J. Gifford, "Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes," bioRxiv, 2020.
    [Bibtex]
    @Article{Lytras:20a,
    author = {Spyros Lytras and Gloria Arriagada and Robert J. Gifford},
    title = {Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.11.02.364562},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] W. V. der Toorn, D. Oh, D. Bourquain, J. Michel, E. Krause, A. Nitsche, and M. V. K. and, "COVIDStrategyCalculator: a standalone software to assess testing- and quarantine strategies for incoming travelers, contact person management and de-isolation," medRxiv, 2020.
    [Bibtex]
    @Article{Toorn:20,
    author = {Wiep Van der Toorn and Djin-Ye Oh and Daniel Bourquain and Janine Michel and Eva Krause and Andreas Nitsche and Max Von Kleist and},
    title = {{COVIDStrategyCalculator}: A standalone software to assess testing- and quarantine strategies for incoming travelers, contact person management and de-isolation},
    journal = {{medRxiv}},
    year = {2020},
    doi = {10.1101/2020.11.18.20233825},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] A. C. Gregory, K. Gerhardt, Z. Zhong, B. Bolduc, B. Temperton, K. T. Konstantinidis, and M. B. Sullivan, "MetaPop: a pipeline for macro- and micro-diversity analyses and visualization of microbial and viral metagenome-derived populations," bioRxiv, 2020.
    [Bibtex]
    @Article{Gregory:20,
    author = {Ann C. Gregory and Kenji Gerhardt and Zhi-Ping Zhong and Benjamin Bolduc and Ben Temperton and Konstantinos T. Konstantinidis and Matthew B. Sullivan},
    title = {{MetaPop}: A pipeline for macro- and micro-diversity analyses and visualization of microbial and viral metagenome-derived populations},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.11.01.363960},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] P. Vetter, C. S. Eberhardt, B. Meyer, P. A. M. Murillo, G. Torriani, F. Pigny, S. Lemeille, S. Cordey, F. Laubscher, D. Vu, A. Calame, M. Schibler, F. Jacquerioz, G. Blanchard-Rohner, C. Siegrist, L. Kaiser, A. M. Didierlaurent, and I. Eckerle, "Daily viral kinetics and innate and adaptive immune response assessment in COVID-19: a case series," mSphere, vol. 5, iss. 6, 2020.
    [Bibtex]
    @Article{Vetter:20,
    author = {Pauline Vetter and Christiane S. Eberhardt and Benjamin Meyer and Paola Andrea Martinez Murillo and Giulia Torriani and Fiona Pigny and Sylvain Lemeille and Samuel Cordey and Florian Laubscher and Diem-Lan Vu and Adrien Calame and Manuel Schibler and Frederique Jacquerioz and G{\'{e}}raldine Blanchard-Rohner and Claire-Anne Siegrist and Laurent Kaiser and Arnaud M. Didierlaurent and Isabella Eckerle},
    title = {Daily Viral Kinetics and Innate and Adaptive Immune Response Assessment in {COVID}-19: a Case Series},
    journal = {{mSphere}},
    year = {2020},
    volume = {5},
    number = {6},
    doi = {10.1128/msphere.00827-20},
    editor = {Christina F. Spiropoulou},
    publisher = {American Society for Microbiology},
    }
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    @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})},
    }
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    @Article{Mirzaei:20b,
    author = {Mohammadali Khan Mirzaei and Li Deng},
    title = {Sustainable Microbiome: a symphony orchestrated by synthetic phages},
    journal = {{Microb Biotechnol}},
    year = {2020},
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    publisher = {Wiley},
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    title = {Genome-wide mapping of {SARS}-{CoV}-2 {RNA} structures identifies therapeutically-relevant elements},
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    @Article{Glebe:20,
    author = {Dieter Glebe and Nora Goldmann and Chris Lauber and Stefan Seitz},
    title = {{HBV} evolution and genetic variability: impact on prevention, treatment and development of antivirals},
    journal = {{Antiviral Res}},
    year = {2020},
    pages = {104973},
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    @Article{Howe:20,
    author = {Kevin L Howe and Premanand Achuthan and James Allen and Jamie Allen and Jorge Alvarez-Jarreta and M Ridwan Amode and Irina M Armean and Andrey G Azov and Ruth Bennett and Jyothish Bhai and Konstantinos Billis and Sanjay Boddu and Mehrnaz Charkhchi and Carla Cummins and Luca Da~Rin~Fioretto and Claire Davidson and Kamalkumar Dodiya and Bilal El~Houdaigui and Reham Fatima and Astrid Gall and Carlos Garcia~Giron and Tiago Grego and Cristina Guijarro-Clarke and Leanne Haggerty and Anmol Hemrom and Thibaut Hourlier and Osagie G Izuogu and Thomas Juettemann and Vinay Kaikala and Mike Kay and Ilias Lavidas and Tuan Le and Diana Lemos and Jose Gonzalez~Martinez and Jos{\'{e}} Carlos Marug{\'{a}}n and Thomas Maurel and Aoife C McMahon and Shamika Mohanan and Benjamin Moore and Matthieu Muffato and Denye N Oheh and Dimitrios Paraschas and Anne Parker and Andrew Parton and Irina Prosovetskaia and Manoj P Sakthivel and Ahamed~I~Abdul Salam and Bianca M Schmitt and Helen Schuilenburg and Dan Sheppard and Emily Steed and Michal Szpak and Marek Szuba and Kieron Taylor and Anja Thormann and Glen Threadgold and Brandon Walts and Andrea Winterbottom and Marc Chakiachvili and Ameya Chaubal and Nishadi De~Silva and Bethany Flint and Adam Frankish and Sarah E Hunt and Garth R IIsley and Nick Langridge and Jane E Loveland and Fergal J Martin and Jonathan M Mudge and Joanella Morales and Emily Perry and Magali Ruffier and John Tate and David Thybert and Stephen J Trevanion and Fiona Cunningham and Andrew D Yates and Daniel R Zerbino and Paul Flicek},
    title = {Ensembl 2021},
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    @Article{Gleizes:20,
    author = {Anne Gleizes and Florian Laubscher and Nicolas Guex and Christian Iseli and Thomas Junier and Samuel Cordey and Jacques Fellay and Ioannis Xenarios and Laurent Kaiser and Philippe {Le Mercier}},
    title = {Virosaurus A Reference to Explore and Capture Virus Genetic Diversity},
    journal = {Viruses},
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    @Article{Carlisle:20,
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    title = {{HCV} Genetic Diversity Can Be Used to Infer Infection Recency and Time since Infection},
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    year = {2020},
    volume = {12},
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    title = {Aprotinin Inhibits {SARS}-{CoV}-2 Replication},
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    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},
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    title = {Dissecting Herpes Simplex Virus 1-Induced Host Shutoff at the {RNA} Level},
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    title = {First isolation, in vivo and genomic characterization of zoonotic variegated squirrel {B}ornavirus 1 ({VSBV}-1) isolates},
    journal = {{Emerg Microbes Infect}},
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    journal = {{PLoS Comput Biol}},
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    title = {Aerosol persistence in relation to possible transmission of {SARS}-{CoV}-2},
    journal = {{Phys Fluids}},
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    author = {Simon Dellicour and Sebastian Lequime and Bram Vrancken and Mandev S. Gill and Paul Bastide and Karthik Gangavarapu and Nathaniel L. Matteson and Yi Tan and Louis du Plessis and Alexander A. Fisher and Martha I. Nelson and Marius Gilbert and Marc A. Suchard and Kristian G. Andersen and Nathan D. Grubaugh and Oliver G. Pybus and Philippe Lemey},
    title = {Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework},
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    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},
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    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}},
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    title = {From Orphan Phage to a Proposed New Family{\textendash}The Diversity of {N4}-Like Viruses},
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    title = {Stability of the Virome in Lab- and Field-Collected {A}edes albopictus Mosquitoes across Different Developmental Stages and Possible Core Viruses in the Publicly Available Virome Data of {A}edes Mosquitoes},
    journal = {{mSystems}},
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    title = {Effect of antiviral therapy on the outcomes of mechanically ventilated patients with herpes simplex virus detected in the respiratory tract: a systematic review and meta-analysis},
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    title = {Physiologic {RNA} Targets and Refined Sequence Specificity of Coronavirus {EndoU}},
    journal = {{RNA}},
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    title = {Accommodating individual travel history and unsampled diversity in {B}ayesian phylogeographic inference of {SARS}-{CoV}-2},
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    title = {Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses},
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    @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},
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    doi = {10.3201/eid2612.203799},
    publisher = {Centers for Disease Control and Prevention ({CDC})},
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    @Article{Bennett:20,
    author = {Andrew J. Bennett and Adrian C. Paskey and Arnt Ebinger and Florian Pfaff and Grit Priemer and Dirk Höper and Angele Breithaupt and Elisa Heuser and Rainer G. Ulrich and Jens H. Kuhn and Kimberly A. Bishop-Lilly and Martin Beer and Tony L. Goldberg},
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    volume = {586},
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    author = {Shirley E. Braspenning and Tomohiko Sadaoka and Judith Breuer and Georges M. G. M. Verjans and Werner J. D. Ouwendijk and Daniel P. Depledge},
    title = {Decoding the Architecture of the Varicella-Zoster Virus Transcriptome},
    journal = {{mBio}},
    year = {2020},
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    @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},
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    pages = {200287},
    doi = {10.1183/16000617.0287-2020},
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    @Article{Ciminski:20a,
    author = {Kevin Ciminski and Geoffrey P. Chase and Martin Beer and Martin Schwemmle},
    title = {Influenza {A} Viruses: Understanding Human Host Determinants},
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    title = {Laser spectroscopic technique for direct identification of a single virus {I}: {FASTER} {CARS}},
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    title = {Viral variant visualizer ({VVV}): A novel bioinformatic tool for rapid and simple visualization of viral genetic diversity},
    journal = {{Virus Res}},
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    @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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    @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},
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    year = {2020},
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    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}},
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    @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},
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    publisher = {Cold Spring Harbor Laboratory},
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    @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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    @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{Walker:20,
    author = {Peter J. Walker and Stuart G. Siddell and Elliot J. Lefkowitz and Arcady R. Mushegian and Evelien M. Adriaenssens and Donald M. Dempsey and Bas E. Dutilh and Bal{\'{a}}zs Harrach and Robert L. Harrison and R. Curtis Hendrickson and Sandra Junglen and Nick J. Knowles and Andrew M. Kropinski and Mart Krupovic and Jens H. Kuhn and Max Nibert and Richard J. Orton and Luisa Rubino and Sead Sabanadzovic and Peter Simmonds and Donald B. Smith and Arvind Varsani and Francisco Murilo Zerbini and Andrew J. Davison},
    title = {Changes to virus taxonomy and the Statutes ratified by the {I}nternational {C}ommittee on {T}axonomy of {V}iruses (2020)},
    journal = {{Arch Virol}},
    year = {2020},
    doi = {10.1007/s00705-020-04752-x},
    publisher = {Springer Science and Business Media {LLC}},
    }
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    [Bibtex]
    @Article{Jordan-Paiz:20,
    author = {Ana Jordan-Paiz and Maria Nevot and Kevin Lamkiewicz and Marie Lataretu and Sandra Franco and Manja Marz and Miguel Angel Martinez},
    title = {{HIV}-1 lethality and loss of {E}nv protein expression induced by single synonymous substitutions in the virus genome intronic splicing silencer},
    journal = {{J Virol}},
    year = {2020},
    doi = {10.1128/jvi.01108-20},
    publisher = {American Society for Microbiology},
    }
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    @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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    @Article{Jonge:20,
    author = {Patrick A. de Jonge and F.A. Bastiaan von Meijenfeldt and Ana Rita Costa and Franklin L. Nobrega and Stan J.J. Brouns and Bas E. Dutilh},
    title = {Adsorption Sequencing as a Rapid Method to Link Environmental Bacteriophages to Hosts},
    journal = {{iScience}},
    year = {2020},
    volume = {23},
    number = {9},
    pages = {101439},
    doi = {10.1016/j.isci.2020.101439},
    publisher = {Elsevier {BV}},
    }
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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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    @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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    @Article{Zanella:20,
    author = {Marie-C{\'{e}}line Zanella and Samuel Cordey and Laurent Kaiser},
    title = {Beyond Cytomegalovirus and Epstein-Barr Virus: a Review of Viruses Composing the Blood Virome of Solid Organ Transplant and Hematopoietic Stem Cell Transplant Recipients},
    journal = {{Clin Microbiol Rev}},
    year = {2020},
    volume = {33},
    number = {4},
    doi = {10.1128/cmr.00027-20},
    publisher = {American Society for Microbiology},
    }
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    @Article{Palatini:20,
    author = {Umberto Palatini and Reem A. Masri and Luciano V. Cosme and Sergey Koren and Fran{\c{c}}oise Thibaud-Nissen and James K. Biedler and Flavia Krsticevic and J. Spencer Johnston and Rebecca Halbach and Jacob E. Crawford and Igor Antoshechkin and Anna-Bella Failloux and Elisa Pischedda and Michele Marconcini and Jay Ghurye and Arang Rhie and Atashi Sharma and Dmitry A. Karagodin and Jeremy Jenrette and Stephanie Gamez and Pascal Miesen and Patrick Masterson and Adalgisa Caccone and Maria V. Sharakhova and Zhijian Tu and Philippos A. Papathanos and Ronald P. Van Rij and Omar S. Akbari and Jeffrey Powell and Adam M. Phillippy and Mariangela Bonizzoni},
    title = {Improved reference genome of the arboviral vector {A}edes albopictus},
    journal = {{Genome Biol}},
    year = {2020},
    volume = {21},
    number = {1},
    doi = {10.1186/s13059-020-02141-w},
    publisher = {Springer Science and Business Media {LLC}},
    }
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    @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},
    doi = {10.1007/s11192-020-03591-6},
    publisher = {Springer Science and Business Media {LLC}},
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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},
    doi = {10.1007/978-1-0716-0900-2_13},
    }
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    @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}},
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    @Article{King:20,
    author = {Jacqueline King and Timm Harder and Martin Beer and Anne Pohlmann},
    title = {Rapid multiplex {MinION} nanopore sequencing workflow for Influenza {A} viruses},
    journal = {{BMC Infect Dis}},
    year = {2020},
    volume = {20},
    number = {1},
    doi = {10.1186/s12879-020-05367-y},
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    @Article{Bach:20,
    author = {Simone Bach and Jana-Christin Demper and Nadine Biedenkopf and Stephan Becker and Roland K. Hartmann},
    title = {{RNA} secondary structure at the transcription start site influences {EBOV} transcription initiation and replication in a length- and stability-dependent manner},
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    doi = {10.1080/15476286.2020.1818459},
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    @Article{Abrantes:20,
    author = {Joana Abrantes and Cl{\'{e}}ment Droillard and Ana M. Lopes and Evelyne Lemaitre and Pierrick Lucas and Yannick Blanchard and St{\'{e}}phane Marchandeau and Pedro J. Esteves and Ghislaine Le Gall-Recul{\'{e}}},
    title = {Recombination at the emergence of the pathogenic rabbit haemorrhagic disease virus Lagovirus europaeus/{GI}.2},
    journal = {Scientific Reports},
    year = {2020},
    volume = {10},
    number = {1},
    doi = {10.1038/s41598-020-71303-4},
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  • A. Tehel, T. Streicher, S. Tragust, and R. J. Paxton, "Experimental infection of bumblebees with honeybee-associated viruses: no direct fitness costs but potential future threats to novel wild bee hosts," R Soc Open Sci, vol. 7, iss. 7, p. 200480, 2020.
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    @Article{Tehel:20,
    author = {Tehel, Anja and Streicher, Tabea and Tragust, Simon and Paxton, Robert J},
    title = {Experimental infection of bumblebees with honeybee-associated viruses: no direct fitness costs but potential future threats to novel wild bee hosts},
    journal = {{R Soc Open Sci}},
    year = {2020},
    volume = {7},
    number = {7},
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    publisher = {The Royal Society},
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    @Article{Balvert:20,
    author = {Marleen Balvert and Xiao Luo and Ernestina Hauptfeld and Alexander Schönhuth and Bas E Dutilh},
    title = {{OGRE}: {O}verlap {G}raph-based metagenomic {R}ead clust{E}ring},
    journal = {Bioinformatics},
    year = {2020},
    doi = {10.1093/bioinformatics/btaa760},
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    }
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    @Article{Mecate-Zambrano:20,
    author = {Angeles Mecate-Zambrano and Swathi Sukumar and Guiscard Seebohm and Kevin Ciminski and Andr{\'{e}} Schreiber and Darisuren Anhlan and Lilo Greune and Ludmilla Wixler and Stephanie Grothe and Nora Caroline Stein and M. Alexander Schmidt and Klaus Langer and Martin Schwemmle and Tianlai Shi and Stephan Ludwig and Yvonne Boergeling},
    title = {Discrete spatio-temporal regulation of tyrosine phosphorylation directs influenza {A} virus {M1} protein towards its function in virion assembly},
    journal = {{PLoS Pathog}},
    year = {2020},
    volume = {16},
    number = {8},
    pages = {e1008775},
    doi = {10.1371/journal.ppat.1008775},
    editor = {Beatriz M. Fontoura},
    publisher = {Public Library of Science ({PLoS})},
    }
  • K. Schubert, E. D. Karousis, A. Jomaa, A. Scaiola, B. Echeverria, L. Gurzeler, M. Leibundgut, V. Thiel, O. Mühlemann, and N. Ban, "SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation," Nat Struct Mol Biol, p. 1–8, 2020.
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    @Article{Schubert:20,
    author = {Schubert, Katharina and Karousis, Evangelos D and Jomaa, Ahmad and Scaiola, Alain and Echeverria, Blanca and Gurzeler, Lukas-Adrian and Leibundgut, Marc and Thiel, Volker and M{\"u}hlemann, Oliver and Ban, Nenad},
    title = {{SARS}-{CoV}-2 {Nsp1} binds the ribosomal {mRNA} channel to inhibit translation},
    journal = {{Nat Struct Mol Biol}},
    year = {2020},
    pages = {1--8},
    publisher = {Nature Publishing Group},
    }
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    @Article{Rahman:20,
    author = {Sahar Abd El Rahman and Bernd Hoffmann and Reham Karam and Mohamed El-Beskawy and Mohammed F. Hamed and Leonie F. Forth and Dirk Höper and Michael Eschbaumer},
    title = {Sequence Analysis of {E}gyptian Foot-and-Mouth Disease Virus Field and Vaccine Strains: Intertypic Recombination and Evidence for Accidental Release of Virulent Virus},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    number = {9},
    pages = {990},
    doi = {10.3390/v12090990},
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    @Article{Duchene:20a,
    author = {Sebastian Duchene and Philippe Lemey and Tanja Stadler and Simon Y W Ho and David A Duchene and Vijaykrishna Dhanasekaran and Guy Baele},
    title = {Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations},
    journal = {Molecular Biology and Evolution},
    year = {2020},
    doi = {10.1093/molbev/msaa163},
    editor = {Keith Crandall},
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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},
    number = {1},
    doi = {10.1038/s41467-020-18463-z},
    publisher = {Springer Science and Business Media {LLC}},
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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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    [Bibtex]
    @Article{Konno:20,
    author = {Yoriyuki Konno and Izumi Kimura and Keiya Uriu and Masaya Fukushi and Takashi Irie and Yoshio Koyanagi and Daniel Sauter and Robert J. Gifford and So Nakagawa and Kei Sato},
    title = {{SARS}-{CoV}-2 {ORF}3b Is a Potent Interferon Antagonist Whose Activity Is Increased by a Naturally Occurring Elongation Variant},
    journal = {{Cell Rep}},
    year = {2020},
    volume = {32},
    number = {12},
    pages = {108185},
    doi = {10.1016/j.celrep.2020.108185},
    publisher = {Elsevier {BV}},
    }
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    @Article{Kinsella:20,
    author = {Cormac M. Kinsella and Aldert Bart and Martin Deijs and Patricia Broekhuizen and Joanna Kaczorowska and Maarten F. Jebbink and Tom van Gool and Matthew Cotten and Lia van der Hoek},
    title = {{E}ntamoeba and {G}iardia parasites implicated as hosts of {CRESS} viruses},
    journal = {{Nat Commun}},
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    title = {{SAR} of novel benzamides and isoindolines, designed as {SARS}-{CoV} protease inhibitors {\textendash} effective against {SARS}-{CoV}-2},
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    title = {Field-based sciences must transform in response to {COVID}-19},
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    @Article{Baele:20,
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    journal = {{Wellcome Open Res}},
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    @Article{Almansour:20,
    author = {Iman Almansour},
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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},
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    @Article{Rossi:20,
    author = {Alessandro Rossi and Laura Treu and Stefano Toppo and Henrike Zschach and Stefano Campanaro and Bas E. Dutilh},
    title = {Evolutionary Study of the cr{A}ssphage Virus at Gene Level},
    journal = {Viruses},
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    title = {{CIAlign} - A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments},
    journal = {{bioRxiv}},
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    title = {Antisense oligonucleotides target a nearly invariant structural element from the {SARS}-{CoV}-2 genome and drive {RNA} degradation},
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    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},
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    title = {Rabies mortality and morbidity associated with animal bites in {A}frica: {A} case for {I}ntegrated {R}abies {D}iseases {S}urveillance, {P}revention and {C}ontrol -- {A} {S}coping review},
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    @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},
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    title = {At least seven distinct rotavirus genotype constellations in bats with evidence of reassortment and zoonotic transmissions},
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    @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}},
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    @Article{Gilroy:20,
    author = {Rachel Gilroy and Anuradha Ravi and Maria Getino and Isabella Pursley and Daniel Horton and Nabil-Fareed Alikhan and David Baker and Karim Gharbi and Neil Hall and Mick Watson and Evelien M. Adriaenssens and Ebenezer Foster-Nyarko and Sheikh Jarju and Arss Secka and Martin Antonio and Aharon Oren and Roy Chaudhuri and Falk Hildebrand and Mark Pallen},
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    @Article{Meyer:20,
    author = {Fernando Meyer and Till-Robin Lesker and David Koslicki and Adrian Fritz and Alexey Gurevich and Aaron E. Darling and Alexander Sczyrba and Andreas Bremges and Alice C. McHardy},
    title = {Tutorial: Assessing metagenomics software with the {CAMI} benchmarking toolkit},
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    @Article{Hölzer:20,
    author = {Martin Hölzer and Manja Marz},
    title = {{PoSeiDon}: a Nextflow pipeline for the detection of evolutionary recombination events and positive selection},
    journal = {Bioinformatics},
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    @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},
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    @Article{Meister:20,
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    title = {Virucidal efficacy of different oral rinses against {SARS}-{CoV}-2},
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    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},
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    @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},
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    publisher = {{MDPI} {AG}},
    }
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    [Bibtex]
    @Article{Henritzi:20,
    author = {Dinah Henritzi and Philipp Peter Petric and Nicola Sarah Lewis and Annika Graaf and Alberto Pessia and Elke Starick and Angele Breithaupt and Günter Strebelow and Christine Luttermann and Larissa Mareike Kristin Parker and Charlotte Schröder and Bärbel Hammerschmidt and Georg Herrler and Elisabeth gro{\ss}e Beilage and Daniel Stadlbauer and Viviana Simon and Florian Krammer and Silke Wacheck and Stefan Pesch and Martin Schwemmle and Martin Beer and Timm Clemens Harder},
    title = {Surveillance of {E}uropean Domestic Pig Populations Identifies an Emerging Reservoir of Potentially Zoonotic Swine Influenza {A} Viruses},
    journal = {{Cell Host Microbe}},
    year = {2020},
    doi = {10.1016/j.chom.2020.07.006},
    publisher = {Elsevier {BV}},
    }
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    @InCollection{Leonetti:20,
    author = {Paola Leonetti and Pascal Miesen and Ronald P. van Rij and Vitantonio Pantaleo},
    title = {Viral and subviral derived small {RNAs} as pathogenic determinants in plants and insects},
    booktitle = {{Adv Virus Res}},
    publisher = {Elsevier},
    year = {2020},
    pages = {1--36},
    doi = {10.1016/bs.aivir.2020.04.001},
    }
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    @Article{Papageorgiou:20,
    author = {Nicolas Papageorgiou and Maria Spiliopoulou and Thi-Hong Van Nguyen and Afroditi Vaitsopoulou and Elsie Yekwa Laban and Karine Alvarez and Irene Margiolaki and Bruno Canard and Fran{\c{c}}ois Ferron},
    title = {Brothers in Arms: Structure, Assembly and Function of {A}renaviridae Nucleoprotein},
    journal = {Viruses},
    year = {2020},
    volume = {12},
    number = {7},
    pages = {772},
    doi = {10.3390/v12070772},
    publisher = {{MDPI} {AG}},
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    @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{Overholt:20,
    author = {Will A. Overholt and Martin Hölzer and Patricia Geesink and Celia Diezel and Manja Marz and Kirsten Küsel},
    title = {Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome-assembled genomes from a complex aquifer system},
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    @Article{Blome:20,
    author = {Sandra Blome and Kati Franzke and Martin Beer},
    title = {African swine fever -- A review of current knowledge},
    journal = {{Virus Res}},
    year = {2020},
    volume = {287},
    pages = {198099},
    doi = {10.1016/j.virusres.2020.198099},
    publisher = {Elsevier {BV}},
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    title = {Combined Prophylactic and Therapeutic Use Maximizes Hydroxychloroquine Anti-{SARS}-{CoV}-2 Effects in vitro},
    journal = {{Front Microbiol}},
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    @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},
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    @Article{Lycett:20,
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    title = {Genesis and spread of multiple reassortants during the 2016/2017 {H5} avian influenza epidemic in {E}urasia},
    journal = {{Proc Natl Acad Sci USA}},
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    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}},
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    @Article{Loessner:20,
    author = {Holger Loessner and Insea Schlattmeier and Marie Anders-Maurer and Isabelle Bekeredjian-Ding and Christine Rohde and Johannes Wittmann and Cornelia Pokalyuk and Oleg Krut and Christel Kamp},
    title = {Kinetic Fingerprinting Links Bacteria-Phage Interactions with Emergent Dynamics: Rapid Depletion of {K}lebsiella pneumoniae Indicates Phage Synergy},
    journal = {Antibiotics},
    year = {2020},
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    [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}},
    }
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    @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},
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    journal = {Viruses},
    year = {2020},
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    @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},
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    [Bibtex]
    @Article{Fisher:20,
    author = {Alexander A Fisher and Xiang Ji and Zhenyu Zhang and Philippe Lemey and Marc A Suchard},
    title = {Relaxed Random Walks at Scale},
    journal = {{Syst Biol}},
    year = {2020},
    doi = {10.1093/sysbio/syaa056},
    publisher = {Oxford University Press ({OUP})},
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    @Article{Marquet:20,
    author = {Mike Marquet and Martin Hölzer and Mathias W. Pletz and Adrian Viehweger and Oliwia Makarewicz and Ralf Ehricht and Christian Brandt},
    title = {What the {P}hage: A scalable workflow for the identification and analysis of phage sequences},
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    @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}},
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    @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},
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    @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}},
    }
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    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}},
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    @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},
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    @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},
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    @Article{Caputo:20,
    author = {Valeria Caputo and Roberta Antonia Diotti and Enzo Boeri and Hamid Hasson and Michela Sampaolo and Elena Criscuolo and Sabrina Bagaglio and Emanuela Messina and Caterina Uberti-Foppa and Matteo Castelli and Roberto Burioni and Nicasio Mancini and Massimo Clementi and Nicola Clementi},
    title = {Detection of low-level {HCV} variants in {DAA} treated patients: comparison amongst three different {NGS} data analysis protocols},
    journal = {{Virol J}},
    year = {2020},
    volume = {17},
    number = {1},
    doi = {10.1186/s12985-020-01381-3},
    publisher = {Springer Science and Business Media {LLC}},
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    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})},
    }
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    @Article{Suzuki:20,
    author = {Yasutsugu Suzuki and Artem Baidaliuk and Pascal Miesen and Lionel Frangeul and Anna B. Crist and Sarah H. Merkling and Albin Fontaine and Sebastian Lequime and Isabelle Moltini-Conclois and Herv{\'{e}} Blanc and Ronald P. van Rij and Louis Lambrechts and Maria-Carla Saleh},
    title = {Non-retroviral Endogenous Viral Element Limits Cognate Virus Replication in {Aedes} aegypti Ovaries},
    journal = {{Curr Biol}},
    year = {2020},
    doi = {10.1016/j.cub.2020.06.057},
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    @Article{Piro:20,
    author = {Vitor C Piro and Temesgen H Dadi and Enrico Seiler and Knut Reinert and Bernhard Y Renard},
    title = {{ganon}: precise metagenomics classification against large and up-to-date sets of reference sequences},
    journal = {Bioinformatics},
    year = {2020},
    volume = {36},
    number = {Supplement\_1},
    pages = {i12--i20},
    doi = {10.1093/bioinformatics/btaa458},
    publisher = {Oxford University Press ({OUP})},
    }
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    @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},
    }
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    @Article{Foglierini:20,
    author = {Mathilde Foglierini and Leontios Pappas and Antonio Lanzavecchia and Davide Corti and Laurent Perez},
    title = {{AncesTree}: An interactive immunoglobulin lineage tree visualizer},
    journal = {{PLoS Comput Biol}},
    year = {2020},
    volume = {16},
    number = {7},
    pages = {e1007731},
    doi = {10.1371/journal.pcbi.1007731},
    editor = {Mihaela Pertea},
    publisher = {Public Library of Science ({PLoS})},
    }
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    @Article{Mirzaei:20a,
    author = {Mohammadali Khan Mirzaei and Jinling Xue and Rita Costa and Jinlong Ru and Sarah Schulz and Zofia E. Taranu and Li Deng},
    title = {Challenges of Studying the Human Virome {\textendash} Relevant Emerging Technologies},
    journal = {{Trends Microbiol}},
    year = {2020},
    doi = {10.1016/j.tim.2020.05.021},
    publisher = {Elsevier {BV}},
    }
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    @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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    @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},
    publisher = {Centers for Disease Control and Prevention ({CDC})},
    }
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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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    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},
    volume = {18},
    pages = {191},
    doi = {10.1186/s12916-020-01636-4},
    publisher = {Springer Science and Business Media {LLC}},
    }
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    [Bibtex]
    @Article{Muenchhoff:20,
    author = {Maximilian Muenchhoff and Helga Mairhofer and Hans Nitschko and Natascha Grzimek-Koschewa and Dieter Hoffmann and Annemarie Berger and Holger Rabenau and Marek Widera and Nikolaus Ackermann and Regina Konrad and Sabine Zange and Alexander Graf and Stefan Krebs and Helmut Blum and Andreas Sing and Bernhard Liebl and Roman Wölfel and Sandra Ciesek and Christian Drosten and Ulrike Protzer and Stephan Boehm and Oliver T Keppler},
    title = {Multicentre comparison of quantitative {PCR}-based assays to detect {SARS}-{CoV}-2, {G}ermany, {M}arch 2020},
    journal = {{Euro Surveill}},
    year = {2020},
    volume = {25},
    number = {24},
    pages = {2001057},
    doi = {10.2807/1560-7917.es.2020.25.24.2001057},
    publisher = {European Centre for Disease Control and Prevention ({ECDC})},
    }
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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},
    journal = {{bioRxiv}},
    year = {2020},
    doi = {10.1101/2020.06.22.165464},
    publisher = {Cold Spring Harbor Laboratory},
    }
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    [Bibtex]
    @Article{Kurth:20,
    author = {Florian Kurth and Maria Roennefarth and Charlotte Thibeault and Victor M. Corman and Holger Müller-Redetzky and Mirja Mittermaier and Christoph Ruwwe-Glösenkamp and Katrin M. Heim and Alexander Krannich and Saskia Zvorc and Sein Schmidt and Lucie Kretzler and Chantip Dang-Heine and Matthias Rose and Michael Hummel and Andreas Hocke and Ralf H. Hübner and Bastian Opitz and Marcus A. Mall and Jobst Röhmel and Ulf Landmesser and Burkert Pieske and Samuel Knauss and Matthias Endres and Joachim Spranger and Frank P. Mockenhaupt and Frank Tacke and Sascha Treskatsch and Stefan Angermair and Britta Siegmund and Claudia Spies and Steffen Weber-Carstens and Kai-Uwe Eckardt and Dirk Schürmann and Alexander Uhrig and Miriam S. Stegemann and Thomas Zoller and Christian Drosten and Norbert Suttorp and Martin Witzenrath and Stefan Hippenstiel and Christof von Kalle and Leif Erik Sander},
    title = {Studying the pathophysiology of coronavirus disease 2019: a protocol for the {B}erlin prospective {COVID}-19 patient cohort ({Pa}-{COVID}-19)},
    journal = {Infection},
    year = {2020},
    doi = {10.1007/s15010-020-01464-x},
    publisher = {Springer Science and Business Media {LLC}},
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    @Article{Penzes:20,
    author = {Judit J. P{\'{e}}nzes and Maria Söderlund-Venermo and Marta Canuti and Anna Maria Eis-Hübinger and Joseph Hughes and Susan F. Cotmore and Bal{\'{a}}zs Harrach},
    title = {Reorganizing the family {P}arvoviridae: a revised taxonomy independent of the canonical approach based on host association},
    journal = {{Arch Virol}},
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    @Article{Broggi:20,
    author = {Achille Broggi and Sreya Ghosh and Benedetta Sposito and Roberto Spreafico and Fabio Balzarini and Antonino Lo Cascio and Nicola Clementi and Maria De Santis and Nicasio Mancini and Francesca Granucci and Ivan Zanoni},
    title = {Type {III} interferons disrupt the lung epithelial barrier upon viral recognition},
    journal = {Science},
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    @Article{Perot:20,
    author = {Philippe P{\'{e}}rot and Franck Bielle and Thomas Bigot and Vincent Foulongne and Karine Bollor{\'{e}} and Delphine Chr{\'{e}}tien and Patricia Gil and Seraf{\'{\i}}n Guti{\'{e}}rrez and Gr{\'{e}}gory L'Ambert and Karima Mokhtari and Jan Hellert and Marie Flamand and Carole Tamietti and Muriel Coulpier and Anne Huard de Verneuil and Sarah Temmam and Th{\'{e}}r{\`{e}}se Couderc and Edouard De Sousa Cunha and Susana Boluda and Isabelle Plu and Marie Bernadette Delisle and Fabrice Bonneville and David Brassat and Claire Fieschi and Marion Malphettes and Charles Duyckaerts and Bertrand Mathon and Sophie Demeret and Danielle Seilhean and Marc Eloit},
    title = {Identification of {Umbre} Orthobunyavirus as a Novel Zoonotic Virus Responsible for Lethal Encephalitis in 2 {French} Patients with Hypogammaglobulinemia},
    journal = {{Clin Infect Dis}},
    year = {2020},
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    @Article{SilvaCandido:20,
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    title = {Evolution and epidemic spread of {SARS}-{CoV}-2 in {Brazil}},
    journal = {{medRxiv}},
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    journal = {{iScience}},
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    title = {Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection},
    journal = {Cell},
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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}},
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    title = {Measles virus and rinderpest virus divergence dated to the sixth century {BCE}},
    journal = {Science},
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    title = {Pitfalls in {SARS}-{CoV}-2 {PCR} diagnostics},
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    title = {An analysis of {SARS}-{CoV}-2 viral load by patient age},
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    @Article{Cespedes:20,
    author = {Susana Posada-Cespedes and David Seifert and Ivan Topolsky and Karin J Metzner and Niko Beerenwinkel},
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    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},
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    publisher = {Cold Spring Harbor Laboratory},
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    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},
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    @Article{Young:20,
    author = {Francesca Young and Simon Rogers and David L. Robertson},
    title = {Predicting host taxonomic information from viral genomes: A comparison of feature representations},
    journal = {{PLoS Comput Biol}},
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    @Article{Vandamme:20,
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    journal = {Nature},
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    title = {Gradients do grow on trees: a linear-time $\mathcal{O}$({N})-dimensional gradient for statistical phylogenetics},
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    title = {{SARS}-{CoV}-2 Phylogenetic Analysis, {L}azio Region, {I}taly, {F}ebruary--{M}arch 2020},
    journal = {{Emerg Infect Dis}},
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    @Article{Randazzo:20a,
    author = {Walter Randazzo and Gloria Sánchez},
    journal = {{J Appl Microbiol}},
    title = {Hepatitis {A} infections from food},
    year = {2020},
    doi = {10.1111/jam.14727},
    publisher = {Wiley},
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    title = {Temperature-dependent surface stability of {SARS}-{CoV}-2},
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    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}},
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    @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},
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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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    author = {Maximilian Collatz and Florian Mock and Martin Hölzer and Emanuel Barth and Konrad Sachse and Manja Marz},
    title = {{EpiDope}: {A Deep} neural network for linear {B}-cell epitope prediction},
    journal = {{bioRxiv}},
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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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    @Article{Worobey:20,
    author = {Michael Worobey and Jonathan Pekar and Brendan B. Larsen and Martha I. Nelson and Verity Hill and Jeffrey B. Joy and Andrew Rambaut and Marc A. Suchard and Joel O. Wertheim and Philippe Lemey},
    title = {The emergence of {SARS}-{CoV}-2 in {Europe} and the {US}},
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    @Article{MacLean:20,
    author = {Oscar A. MacLean and Spyros Lytras and Joshua B. Singer and Steven Weaver and Sergei L. Kosakovsky Pond and David L. Robertson},
    title = {Evidence of significant natural selection in the evolution of {SARS}-{CoV}-2 in bats, not humans},
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    @Article{Grant:20,
    author = {Heather E Grant and Emma B Hodcroft and Deogratius Ssemwanga and John M Kitayimbwa and Gonzalo Yebra and Luis Roger Esquivel Gomez and Dan Frampton and Astrid Gall and Paul Kellam and Tulio de Oliveira and Nicholas Bbosa and Rebecca N Nsubuga and Freddie Kibengo and Tsz Ho Kwan and Samantha Lycett and Rowland Kao and David L Robertson and Oliver Ratmann and Christophe Fraser and Deenan Pillay and Pontiano Kaleebu and Andrew J Leigh Brown},
    title = {Pervasive and non-random recombination in near full-length {HIV} genomes from {U}ganda},
    journal = {{Virus Evol}},
    year = {2020},
    volume = {6},
    number = {1},
    pages = {veaa004},
    doi = {10.1093/ve/veaa004},
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    @Article{Faye:20,
    author = {Oumar Faye and Maria de Lourdes Monteiro and Bram Vrancken and Matthieu Prot and Sebastian Lequime and Maryam Diarra and Oumar Ndiaye and Tomas Valdez and Sandra Tavarez and Jessica Ramos and Silv{\^{a}}nia da Veiga Leal and Cecilio Pires and Antonio Moreira and Maria Filomena Tavares and Linete Fernandes and Jorge Noel Barreto and Maria do C{\'{e}}u Teixeira and Maria da Luz de Lima Mendon{\c{c}}a and Carolina Cardoso da Silva Leite Gomes and Mariano Salazar Castellon and Laurence Ma and Fr{\'{e}}d{\'{e}}ric Lemoine and Fabiana G{\'{a}}mbaro-Roglia and D{\'{e}}borah Delaune and Gamou Fall and Ibrahima Soc{\'{e}} Fall and Mamadou Diop and Anavaj Sakuntabhai and Cheikh Loucoubar and Philippe Lemey and Edward C. Holmes and Ousmane Faye and Amadou Alpha Sall and Etienne Simon-Loriere},
    title = {Genomic Epidemiology of 2015{\textendash}2016 {Zika} Virus Outbreak in {Cape} {Verde}},
    journal = {{Emerg. Infect. Dis.}},
    year = {2020},
    volume = {26},
    number = {6},
    pages = {1084--1090},
    doi = {10.3201/eid2606.190928},
    publisher = {Centers for Disease Control and Prevention ({CDC})},
    }
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    @Article{Gryseels:20,
    author = {Sophie Gryseels and Thomas D. Watts and Jean-Marie Kabongo Mpolesha and Brendan B. Larsen and Philippe Lemey and Jean-Jacques Muyembe-Tamfum and Dirk E. Teuwen and Michael Worobey},
    title = {A near full-length {HIV}-1 genome from 1966 recovered from formalin-fixed paraffin-embedded tissue},
    journal = {{Proc Natl Acad Sci USA}},
    year = {2020},
    volume = {117},
    number = {22},
    pages = {12222--12229},
    doi = {10.1073/pnas.1913682117},
    publisher = {Proceedings of the National Academy of Sciences},
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    @Article{Kemenesi:20,
    author = {G{\'{a}}bor Kemenesi and L{\'{a}}szl{\'{o}} Kornya and G{\'{a}}bor Endre T{\'{o}}th and Korn{\'{e}}lia Kurucz and Safia Zeghbib and Bal{\'{a}}zs A. Somogyi and Viktor Zöldi and P{\'{e}}ter Urb{\'{a}}n and R{\'{o}}bert Herczeg and Ferenc Jakab},
    title = {Nursing homes and the elderly regarding the {COVID}-19 pandemic: situation report from {H}ungary},
    journal = {{GeroScience}},
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    doi = {10.1007/s11357-020-00195-z},
    publisher = {Springer Science and Business Media {LLC}},
    }
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    @Article{Randazzo:20,
    author = {Walter Randazzo and Pilar Truchado and Enric Cuevas-Ferrando and Pedro Sim{\'{o}}n and Ana Allende and Gloria Sánchez},
    journal = {{Water Res}},
    title = {{SARS}-{CoV}-2 {RNA} in wastewater anticipated {COVID}-19 occurrence in a low prevalence area},
    year = {2020},
    pages = {115942},
    volume = {181},
    doi = {10.1016/j.watres.2020.115942},
    publisher = {Elsevier {BV}},
    }
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    @Article{Böhmer:20,
    author = {Merle M Böhmer and Udo Buchholz and Victor M Corman and Martin Hoch and Katharina Katz and Durdica V Marosevic and Stefanie Böhm and Tom Woudenberg and Nikolaus Ackermann and Regina Konrad and Ute Eberle and Bianca Treis and Alexandra Dangel and Katja Bengs and Volker Fingerle and Anja Berger and Stefan Hörmansdorfer and Siegfried Ippisch and Bernd Wicklein and Andreas Grahl and Kirsten Pörtner and Nadine Muller and Nadine Zeitlmann and T Sonia Boender and Wei Cai and Andreas Reich and Maria an der Heiden and Ute Rexroth and Osamah Hamouda and Julia Schneider and Talitha Veith and Barbara Mühlemann and Roman Wölfel and Markus Antwerpen and Mathias Walter and Ulrike Protzer and Bernhard Liebl and Walter Haas and Andreas Sing and Christian Drosten and Andreas Zapf},
    title = {Investigation of a {COVID}-19 outbreak in {G}ermany resulting from a single travel-associated primary case: a case series},
    journal = {{Lancet Infect Dis}},
    year = {2020},
    doi = {10.1016/s1473-3099(20)30314-5},
    publisher = {Elsevier {BV}},
    }
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    @Article{Farkas:20,
    author = {Kata Farkas and David I. Walker and Evelien M. Adriaenssens and James E. McDonald and Luke S. Hillary and Shelagh K. Malham and Davey L. Jones},
    title = {Viral indicators for tracking domestic wastewater contamination in the aquatic environment},
    journal = {{Water Res}},
    year = {2020},
    volume = {181},
    pages = {115926},
    doi = {10.1016/j.watres.2020.115926},
    publisher = {Elsevier {BV}},
    }
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    @Article{Zitzmann:20,
    author = {Carolin Zitzmann and Bianca Schmid and Alessia Ruggieri and Alan S. Perelson and Marco Binder and Ralf Bartenschlager and Lars Kaderali},
    title = {A Coupled Mathematical Model of the Intracellular Replication of Dengue Virus and the Host Cell Immune Response to Infection},
    journal = {{Front Microbiol}},
    year = {2020},
    volume = {11},
    pages = {725},
    doi = {10.3389/fmicb.2020.00725},
    publisher = {Frontiers Media {SA}},
    }
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    @Article{He:20,
    author = {Wan-Ting He and Xiang Ji and Wei He and Simon Dellicour and Shilei Wang and Gairu Li and Letian Zhang and Marius Gilbert and Henan Zhu and Gang Xing and Michael Veit and Zhen Huang and Guan-Zhu Han and Yaowei Huang and Marc A Suchard and Guy Baele and Philippe Lemey and Shuo Su},
    title = {Genomic epidemiology, evolution, and transmission dynamics of porcine deltacoronavirus},
    journal = {{Mol Biol Evol}},
    year = {2020},
    pages = {msaa117},
    doi = {10.1093/molbev/msaa117},
    editor = {Sergei Kosakovsky Pond},
    publisher = {Oxford University Press ({OUP})},
    }
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    @Article{Maganga:20,
    author = {Gael Darren Maganga and Anaïs Pinto and Illich Manfred Mombo and Mankomra Madjitobaye and Antoine Mitte Mbeang Beyeme and Larson Boundenga and Meriadeg Ar Gouilh and Nadine N'Dilimabaka and Jan Felix Drexler and Christian Drosten and Eric Maurice Leroy},
    title = {Genetic diversity and ecology of coronaviruses hosted by cave-dwelling bats in {G}abon},
    journal = {{Sci Rep}},
    year = {2020},
    volume = {10},
    pages = {7314},
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    publisher = {Springer Science and Business Media {LLC}},
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    @Article{Groenke:20,
    author = {Nicole Groenke and Jakob Trimpert and Sophie Merz and Andel{\'{e}} M. Conradie and Emanuel Wyler and Hongwei Zhang and Orsalia-Georgia Hazapis and Sebastian Rausch and Markus Landthaler and Nikolaus Osterrieder and Dusan Kunec},
    title = {Mechanism of Virus Attenuation by Codon Pair Deoptimization},
    journal = {{Cell Rep}},
    year = {2020},
    volume = {31},
    number = {4},
    pages = {107586},
    doi = {10.1016/j.celrep.2020.107586},
    publisher = {Elsevier {BV}},
    }
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    @Article{Pascall:20,
    author = {David J. Pascall and Kyriaki Nomikou and Emmanuel Br{\'{e}}ard and Stephan Zientara and Ana da Silva Filipe and Bernd Hoffmann and Maude Jacquot and Joshua B. Singer and Kris De Clercq and Anette B{\o}tner and Corinne Sailleau and Cyril Viarouge and Carrie Batten and Giantonella Puggioni and Ciriaco Ligios and Giovanni Savini and Piet A. van Rijn and Peter P. C. Mertens and Roman Biek and Massimo Palmarini},
    title = {"{F}rozen evolution" of an {RNA} virus suggests accidental release as a potential cause of arbovirus re-emergence},
    journal = {{PLoS Biol}},
    year = {2020},
    volume = {18},
    number = {4},
    pages = {e3000673},
    doi = {10.1371/journal.pbio.3000673},
    editor = {Andrew Fraser Read},
    publisher = {Public Library of Science ({PLoS})},
    }