Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

The SARS-CoV-2 genome occupies a unique place in infection biology - it is the most highly sequenced genome on earth (making up over 20% of public sequencing datasets) with fine scale information on sampling date and geography, and has been subject to unprecedented intense analysis. As a result, these phylogenetic data are an incredibly valuable resource for science and public health. However, the vast majority of the data was sequenced by tiling amplicons across the full genome, with amplicon schemes that changed over the pandemic as mutations in the viral genome interacted with primer binding sites. In combination with the disparate set of genome assembly workflows and lack of consistent quality control (QC) processes, the current genomes have many systematic errors that have evolved with the virus and amplicon schemes. These errors have significant impacts on the phylogeny, and therefore over the last few years, many thousands of hours of researchers time has been spent in "eyeballing" trees, looking for artefacts, and then patching the tree. Given the huge value of this dataset, we therefore set out to reprocess the complete set of public raw sequence data in a rigorous amplicon-aware manner, and build a cleaner phylogeny. Here we provide a global tree of 4,471,579 samples, built from a consistently assembled set of high quality consensus sequences from all available public data as of June 2024, viewable at https://viridian.taxonium.org. Each genome was constructed using a novel assembly tool called Viridian (https://github.com/iqbal-lab-org/viridian), developed specifically to process amplicon sequence data, eliminating artefactual errors and mask the genome at low quality positions. We provide simulation and empirical validation of the methodology, and quantify the improvement in the phylogeny. We hope the tree, consensus sequences and Viridian will be a valuable resource for researchers.

Authors 92

1. Martin Hunt

   European Bioinformatics Institute · John Radcliffe Hospital · University of Oxford · NIHR Oxford Biomedical Research Centre

   Affiliation as printed

   European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK

   Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK

   National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK

   Nuffield Department of Medicine, University of Oxford, Oxford, UK

2. Angie S. Hinrichs

   University of California, Santa Cruz

   Affiliation as printed

   Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA

3. Lily Karim

   University of California, Santa Cruz

   Affiliation as printed

   Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA

   Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA

4. Bethany L. Dearlove

   Medical University of Vienna

   Affiliation as printed

   Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna 1090, Austria

5. Jeff Knaggs

   European Bioinformatics Institute · John Radcliffe Hospital · University of Oxford · NIHR Oxford Biomedical Research Centre

   Affiliation as printed

   European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK

   Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK

   National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK

   Nuffield Department of Medicine, University of Oxford, Oxford, UK

6. Bede Constantinides

   University of Oxford

   Affiliation as printed

   Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK

   Nuffield Department of Medicine, University of Oxford, Oxford, UK

7. Philip William Fowler

   John Radcliffe Hospital · University of Oxford · NIHR Oxford Biomedical Research Centre

   Affiliation as printed

   Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK

   National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK

   Nuffield Department of Medicine, University of Oxford, Oxford, UK

8. Gillian Rodger

   University of Oxford

   Affiliation as printed

   Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK

   Nuffield Department of Medicine, University of Oxford, Oxford, UK

9. Teresa L. Street

   John Radcliffe Hospital · University of Oxford · NIHR Oxford Biomedical Research Centre

   Affiliation as printed

   National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK

   Nuffield Department of Medicine, University of Oxford, Oxford, UK

10. Sheila Lumley

    John Radcliffe Hospital · University of Oxford

    Affiliation as printed

    Department of Infectious Diseases and Microbiology, John Radcliffe Hospital, Oxford, UK

    Nuffield Department of Medicine, University of Oxford, Oxford, UK

11. Hermione J. Webster

    University of Oxford

    Affiliation as printed

    Nuffield Department of Medicine, University of Oxford, Oxford, UK

12. Theo Sanderson

    The Francis Crick Institute

    Affiliation as printed

    Francis Crick Institute, London, UK

13. Christopher Ruis

    University of Cambridge

    Affiliation as printed

    Department of Veterinary Medicine, University of Cambridge, Cambridge, UK

    Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK

14. Ben Kotzen

    European Bioinformatics Institute · Massachusetts General Hospital

    Affiliation as printed

    Department of Infectious Diseases, Massachusetts General Hospital., Boston, Massachusetts, USA

    European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK

15. Nicola De Maio

    European Bioinformatics Institute · University of Ghana · West African Centre for Cell Biology of Infectious Pathogens

    Affiliation as printed

    European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK

    West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana

16. Lucas Naam-Kayagre Amenga-Etego

    University of Ghana · West African Centre for Cell Biology of Infectious Pathogens

    Affiliation as printed

    West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana

17. Dominic S. Y. Amuzu

    University of Ghana · Administración Nacional de Laboratorios e Institutos de Salud · West African Centre for Cell Biology of Infectious Pathogens

    Affiliation as printed

    West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana

    Servicio de Virus Respiratorios, Instituto Nacional Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina

18. Martín Avaro

    University of Ghana · Administración Nacional de Laboratorios e Institutos de Salud · West African Centre for Cell Biology of Infectious Pathogens

    Affiliation as printed

    Servicio de Virus Respiratorios, Instituto Nacional Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina

    West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana

19. Gordon A. Awandare

    University of Ghana · University of Health and Allied Sciences · West African Centre for Cell Biology of Infectious Pathogens · International Centre for Genetic Engineering and Biotechnology

    Affiliation as printed

    West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana

    Department of Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana

    Laboratory for Medical Biotechnology and Biomanufacturing, International Centre for Genetic Engineering and Biotechnology, Tristie, Italy

20. Reuben Ayivor-Djanie

    University of Health and Allied Sciences · Northumbria University · International Centre for Genetic Engineering and Biotechnology

    Affiliation as printed

    Department of Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana

    Laboratory for Medical Biotechnology and Biomanufacturing, International Centre for Genetic Engineering and Biotechnology, Tristie, Italy

    The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK

21. Matthew Bashton

    University of Ghana · Northumbria University · West African Centre for Cell Biology of Infectious Pathogens

    Affiliation as printed

    The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK

    West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana

22. Elizabeth M. Batty

    University of Oxford · Administración Nacional de Laboratorios e Institutos de Salud · Mahidol Oxford Tropical Medicine Research Unit

    Affiliation as printed

    Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK

    Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand

    Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina

23. Yaw Bediako

    University of Ghana · Administración Nacional de Laboratorios e Institutos de Salud · West African Centre for Cell Biology of Infectious Pathogens

    Affiliation as printed

    West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana

    Servicio de Virus Respiratorios, Instituto Nacional Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina

24. Denise De Belder

    Administración Nacional de Laboratorios e Institutos de Salud · Medical University of Vienna

    Affiliation as printed

    Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina

    Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna 1090, Austria

25. Estefanía Benedetti Aachen Dept. Medical Microbiology

    Leiden University Medical Center · Administración Nacional de Laboratorios e Institutos de Salud

    Affiliation as printed

    Servicio de Virus Respiratorios, Instituto Nacional Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina

    Dept. Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands

26. Andreas Bergthaler

    Administración Nacional de Laboratorios e Institutos de Salud · Medical University of Vienna

    Affiliation as printed

    Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna 1090, Austria

    Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina

27. Stefan A. Boers Aachen Dept. Medical Microbiology

    University of Health and Allied Sciences · University of Michigan · Leiden University Medical Center

    Affiliation as printed

    Dept. Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands

    Department of Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana

    Department of Computational Medicine and Bioinformatics, University of Michigan, Michigan, Ann Arbor, MI, USA

28. Josefina Campos

    Administración Nacional de Laboratorios e Institutos de Salud

    Affiliation as printed

    Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina

29. Rosina Afua Ampomah Carr

    University of Health and Allied Sciences · University of Michigan · Administración Nacional de Laboratorios e Institutos de Salud

    Affiliation as printed

    Department of Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana

    Department of Computational Medicine and Bioinformatics, University of Michigan, Michigan, Ann Arbor, MI, USA

    Servicio de Virus Respiratorios, Instituto Nacional Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina

30. Facundo Cuba

    Düsseldorf University Hospital · Administración Nacional de Laboratorios e Institutos de Salud · Heinrich Heine University Düsseldorf

    Affiliation as printed

    Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina

    Institute of Medical Microbiology and Hospital Hygiene, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany

31. María Elena Dattero

    Birmingham City University · University of Health and Allied Sciences · Administración Nacional de Laboratorios e Institutos de Salud

    Affiliation as printed

    Servicio de Virus Respiratorios, Instituto Nacional Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina

    College of Life Sciences, Birmingham City University, Birmingham, UK

    Department of Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana

32. Wanwisa Dejnirattisai

    Siriraj Hospital · Mahidol University · Medical University of Vienna

    Affiliation as printed

    Division of Emerging Infectious Disease, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkoknoi, Bangkok 10700, Thailand

    Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna 1090, Austria

33. Alexander Dilthey

    Inserm · Université de Montpellier · Düsseldorf University Hospital · Centre Hospitalier Universitaire de Montpellier · Établissement Français du Sang · Pathogenesis and Control of Chronic and Emerging Infections · Heinrich Heine University Düsseldorf

    Affiliation as printed

    Institute of Medical Microbiology and Hospital Hygiene, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany

    Pathogenesis and Control of Chronic and Emerging Infections, Univ Montpellier, INSERM, Etablissement Français du Sang, Virology Laboratory, CHU Montpellier, Montpellier, France

34. Kwabena Obeng Duedu

    Birmingham City University · University of Health and Allied Sciences · Instituto Nacional de Investigação em Saúde

    Affiliation as printed

    College of Life Sciences, Birmingham City University, Birmingham, UK

    Department of Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana

    Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola

35. Lukas Endler

    University of Freiburg · University Medical Center Freiburg · Medical University of Vienna

    Affiliation as printed

    Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna 1090, Austria

    Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany

36. Ilka Engelmann

    Inserm · University of South Dakota · Université de Montpellier · Centre Hospitalier Universitaire de Montpellier · Établissement Français du Sang · Pathogenesis and Control of Chronic and Emerging Infections

    Affiliation as printed

    Pathogenesis and Control of Chronic and Emerging Infections, Univ Montpellier, INSERM, Etablissement Français du Sang, Virology Laboratory, CHU Montpellier, Montpellier, France

    Biomedical Engineering Department, University of South Dakota, Sioux Falls, SD 57107

37. Ngiambudulu M. Francisco

    Centre Hospitalier Universitaire de Montpellier · Instituto Nacional de Investigação em Saúde

    Affiliation as printed

    Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola

    Virology Laboratory, CHU Montpellier, Montpellier, France

38. Jonas Fuchs

    University of Freiburg · University of Health and Allied Sciences · University Medical Center Freiburg · Teesside University

    Affiliation as printed

    Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany

    Department of Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana

    School of Health and Life Sciences, Teesside University, Middlesbrough, UK

39. Etienne Z. Gnimpiéba Aachen Dept. Medical Microbiology

    University of South Dakota · Leiden University Medical Center

    Affiliation as printed

    Biomedical Engineering Department, University of South Dakota, Sioux Falls, SD 57107

    Dept. Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands

40. Soraya Groc

    Düsseldorf University Hospital · Centre Hospitalier Universitaire de Montpellier · Heinrich Heine University Düsseldorf

    Affiliation as printed

    Virology Laboratory, CHU Montpellier, Montpellier, France

    Institute of Medical Microbiology and Hospital Hygiene, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany

41. Jones Gyamfi

    National Health Laboratory Service · University of Cape Town · University of Health and Allied Sciences · Teesside University

    Affiliation as printed

    Department of Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana

    School of Health and Life Sciences, Teesside University, Middlesbrough, UK

    Divison of Medical Virology, University of Cape Town and National Health Laboratory Service

42. Dennis Heemskerk Aachen Dept. Medical Microbiology

    Robert Koch Institute · Leiden University Medical Center

    Affiliation as printed

    Dept. Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands

    Genome Competence Center (MF1), Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany

43. Torsten Houwaart

    Robert Koch Institute · Düsseldorf University Hospital · Heinrich Heine University Düsseldorf

    Affiliation as printed

    Institute of Medical Microbiology and Hospital Hygiene, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany

    Genome Competence Center (MF1), Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany

44. Marvin Hsiao

    National Health Laboratory Service · University of Cape Town

    Affiliation as printed

    Divison of Medical Virology, University of Cape Town and National Health Laboratory Service

    Computational Biology Division, University of Cape Town

45. Matthew R. Huska

    University of Helsinki · Robert Koch Institute · Helsinki University Hospital · Hospital District of Helsinki and Uusimaa

    Affiliation as printed

    Genome Competence Center (MF1), Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany

    HUS Diagnostic Center, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland

46. Martin Hölzer

    University of Sri Jayewardenepura · Robert Koch Institute

    Affiliation as printed

    Genome Competence Center (MF1), Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany

    Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka

47. Arash Iranzadeh

    University of Cape Town · Academy of Scientific and Innovative Research

    Affiliation as printed

    Computational Biology Division, University of Cape Town

    Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India

    Karkinos Healthcare Private Limited (KHPL), Aurbis Business Parks, Bellandur, Bengaluru, Karnataka, 560103, India

48. Hanna Jarva

    University of Helsinki · University of Cape Town · Helsinki University Hospital · Hospital District of Helsinki and Uusimaa

    Affiliation as printed

    HUS Diagnostic Center, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland

    Computational Biology Division, University of Cape Town

49. Chandima Jeewandara

    University of Helsinki · University of Sri Jayewardenepura · Gdańsk Medical University

    Affiliation as printed

    Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka

    Department of Tropical Parasitology, Institute of Maritime and Tropical Medicine, Medical University of Gdansk, 81-519 Gdynia, Poland

    Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland

    Department of Virology, University of Helsinki, 00014 Helsinki, Finland

50. Bani Jolly

    Singapore General Hospital · Academy of Scientific and Innovative Research

    Affiliation as printed

    Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India

    Karkinos Healthcare Private Limited (KHPL), Aurbis Business Parks, Bellandur, Bengaluru, Karnataka, 560103, India

    Department of Microbiology, Singapore General Hospital, Singapore

51. Rageema Joseph

    University of Helsinki · University of Cape Town · Helsinki University Hospital · Hospital District of Helsinki and Uusimaa

    Affiliation as printed

    Computational Biology Division, University of Cape Town

    HUS Diagnostic Center, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland

52. Ravi Kant

    University of Helsinki · Helsinki University Hospital · Hospital District of Helsinki and Uusimaa · Gdańsk Medical University

    Affiliation as printed

    Department of Tropical Parasitology, Institute of Maritime and Tropical Medicine, Medical University of Gdansk, 81-519 Gdynia, Poland

    Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland

    Department of Virology, University of Helsinki, 00014 Helsinki, Finland

    HUS Diagnostic Center, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland

53. Karrie Kwan Ki Ko

    Singapore General Hospital · Robert Koch Institute

    Affiliation as printed

    Department of Microbiology, Singapore General Hospital, Singapore

    Genome Competence Center (MF1), Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany

54. Satu Kurkela

    Centre for Human Genetics · University of Helsinki · Helsinki University Hospital · University of Oxford · Hospital District of Helsinki and Uusimaa

    Affiliation as printed

    HUS Diagnostic Center, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland

    Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK

    Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK

55. Maija Lappalainen

    University of Helsinki · University of Sri Jayewardenepura · Helsinki University Hospital · Hospital District of Helsinki and Uusimaa

    Affiliation as printed

    HUS Diagnostic Center, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland

    Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka

56. Marie Lataretu

    Robert Koch Institute · World Health Organization - Zimbabwe

    Affiliation as printed

    Genome Competence Center (MF1), Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany

    Health System Strengthening Unit, World Health Organisation, Harare, Zimbabwe

57. Chang Liu

    Centre for Human Genetics · University of Oxford · Centre Hospitalier Universitaire de Montpellier

    Affiliation as printed

    Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK

    Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK

    Virology Laboratory, CHU Montpellier, Montpellier, France

58. Gathsaurie Neelika Malavige

    University of Sri Jayewardenepura · Universidad de Costa Rica

    Affiliation as printed

    Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka

    Centro de investigación en Enfermedades Tropicales & Facultad de Microbiología, Universidad de Costa Rica, Costa Rica

59. Tapfumanei Mashe

    University of Ghana · World Health Organization - Zimbabwe · West African Centre for Cell Biology of Infectious Pathogens

    Affiliation as printed

    Health System Strengthening Unit, World Health Organisation, Harare, Zimbabwe

    West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana

60. Juthathip Mongkolsapaya

    Centre for Human Genetics · University of Oxford · Public Health Institute of Malawi · Mahidol Oxford Tropical Medicine Research Unit · Ministry of Health

    Affiliation as printed

    Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK

    Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand

    Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK

    Public Health Institute of Malawi, Ministry of Health, Malawi

61. Brigitte Montès

    Agency for Science, Technology and Research · National University of Singapore · Centre Hospitalier Universitaire de Montpellier · Genome Institute of Singapore

    Affiliation as printed

    Virology Laboratory, CHU Montpellier, Montpellier, France

    Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore

    Yong Loo Lin School of Medicine, National University of Singapore, Singapore

62. José Arturo Molina-Mora

    Universidad de Costa Rica · Northumbria University

    Affiliation as printed

    Centro de investigación en Enfermedades Tropicales & Facultad de Microbiología, Universidad de Costa Rica, Costa Rica

    Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK

63. Bernard Mvula

    Public Health Institute of Malawi · Ministry of Health · Instituto Nacional de Investigação em Saúde

    Affiliation as printed

    Public Health Institute of Malawi, Ministry of Health, Malawi

    Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola

64. Niranjan Nagarajan

    Agency for Science, Technology and Research · University of Freiburg · National University of Singapore · University Medical Center Freiburg · Genome Institute of Singapore

    Affiliation as printed

    Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore

    Yong Loo Lin School of Medicine, National University of Singapore, Singapore

    Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany

65. Andrew Nelson

    Northumbria University · Administración Nacional de Laboratorios e Institutos de Salud

    Affiliation as printed

    Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK

    Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina

66. Joyce Mwongeli Ngoi

    University of Ghana · West African Centre for Cell Biology of Infectious Pathogens

    Affiliation as printed

    West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana

67. Joana Paixão

    University of Sri Jayewardenepura · Instituto Nacional de Investigação em Saúde

    Affiliation as printed

    Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola

    Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka

68. Marcus Panning

    University of Freiburg · University Medical Center Freiburg · Administración Nacional de Laboratorios e Institutos de Salud

    Affiliation as printed

    Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany

    Servicio de Virus Respiratorios, Instituto Nacional Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina

69. Tomás Poklépovich

    Duke University · Administración Nacional de Laboratorios e Institutos de Salud · University of KwaZulu-Natal

    Affiliation as printed

    Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina

    Duke Human Vaccine Institute, Duke University, Durham, NC 27710

    University of KwaZulu Natal, Durban, South Africa, 4001

70. Peter K. Quashie

    University of Ghana · John Radcliffe Hospital · University of Oxford · NIHR Oxford Biomedical Research Centre · West African Centre for Cell Biology of Infectious Pathogens

    Affiliation as printed

    West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana

    National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK

    Nuffield Department of Medicine, University of Oxford, Oxford, UK

71. Mara Russo

    University of Oxford · Administración Nacional de Laboratorios e Institutos de Salud

    Affiliation as printed

    Servicio de Virus Respiratorios, Instituto Nacional Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina

    Nuffield Department of Medicine, University of Oxford, Oxford, UK

72. James Emmanuel San

    University of Helsinki · Duke University · University of KwaZulu-Natal

    Affiliation as printed

    Duke Human Vaccine Institute, Duke University, Durham, NC 27710

    University of KwaZulu Natal, Durban, South Africa, 4001

    Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland

    Department of Virology, University of Helsinki, 00014 Helsinki, Finland

73. Nicholas D. Sanderson

    John Radcliffe Hospital · University of Oxford · NIHR Oxford Biomedical Research Centre · Addis Ababa University

    Affiliation as printed

    National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK

    Nuffield Department of Medicine, University of Oxford, Oxford, UK

    Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia

74. Vinod Scaria

    Northumbria University · Academy of Scientific and Innovative Research

    Affiliation as printed

    Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India

    Vishwanath Cancer Care Foundation (VCCF), Neelkanth Business Park Kirol Village, West Mumbai, Maharashtra, 400086, India

    The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK

75. Gavin Robert Screaton

    University of Helsinki · University of Oxford

    Affiliation as printed

    Nuffield Department of Medicine, University of Oxford, Oxford, UK

    Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland

    Department of Virology, University of Helsinki, 00014 Helsinki, Finland

76. Tarja A. Sironen

    Agency for Science, Technology and Research · University of Helsinki · Genome Institute of Singapore

    Affiliation as printed

    Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland

    Department of Virology, University of Helsinki, 00014 Helsinki, Finland

    Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore

77. Abay Sisay

    University of Oxford · Addis Ababa University

    Affiliation as printed

    Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia

    Nuffield Department of Medicine, University of Oxford, Oxford, UK

78. Darren Smith

    Stellenbosch University · Northumbria University

    Affiliation as printed

    The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK

    Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa

79. Teemu Smura

    Nebraska Department of Health and Human Services · University of Helsinki · Ministry of Public Health · University of California, Berkeley

    Affiliation as printed

    Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland

    Department of Virology, University of Helsinki, 00014 Helsinki, Finland

    Centre de Coordination des Opérations d'Urgences de Santé Publique, Ministere de Sante Publique, Cameroun

    Nebraska Department of Health and Human Services, Lincoln, Nebraska, USA

    University of California, Berkeley, Berkeley, California, USA

80. Piyada Supasa

    Centre for Human Genetics · University of Helsinki · University of Oxford

    Affiliation as printed

    Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK

    Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK

    Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland

    Department of Virology, University of Helsinki, 00014 Helsinki, Finland

81. Chayaporn Suphavilai

    Agency for Science, Technology and Research · Düsseldorf University Hospital · Heinrich Heine University Düsseldorf · Genome Institute of Singapore

    Affiliation as printed

    Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore

    Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany

82. Jeremy Swann

    University of Cape Town · The Francis Crick Institute · University of Oxford · Wellcome Centre for Infectious Diseases Research in Africa · Imperial College London

    Affiliation as printed

    Nuffield Department of Medicine, University of Oxford, Oxford, UK

    Centre for Infectious Diseases Research in Africa, University of Cape Town

    Francis Crick Institute, London, UK

    Imperial College London, UK

83. Houriiyah Tegally

    University of Cape Town · Stellenbosch University

    Affiliation as printed

    Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa

    Computational Biology Division, University of Cape Town

84. Bryan Tegomoh

    Nebraska Department of Health and Human Services · Stellenbosch University · Ministry of Public Health · University of KwaZulu-Natal · University of California, Berkeley

    Affiliation as printed

    Centre de Coordination des Opérations d'Urgences de Santé Publique, Ministere de Sante Publique, Cameroun

    Nebraska Department of Health and Human Services, Lincoln, Nebraska, USA

    University of California, Berkeley, Berkeley, California, USA

    Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa

    KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, South Africa

85. Olli P. Vapalahti

    University of Helsinki · University of Oxford

    Affiliation as printed

    Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland

    Department of Virology, University of Helsinki, 00014 Helsinki, Finland

    Nuffield Department of Medicine, University of Oxford, Oxford, UK

86. Andreas Walker

    University of Oxford · Düsseldorf University Hospital · Heinrich Heine University Düsseldorf

    Affiliation as printed

    Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany

    Nuffield Department of Medicine, University of Oxford, Oxford, UK

87. Robert John Wilkinson

    University of Cape Town · University of California, Santa Cruz · The Francis Crick Institute · Wellcome Centre for Infectious Diseases Research in Africa · Imperial College London

    Affiliation as printed

    Centre for Infectious Diseases Research in Africa, University of Cape Town

    Francis Crick Institute, London, UK

    Imperial College London, UK

    Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA

    Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA

88. Carolyn E. Williamson

    European Bioinformatics Institute · University of Cape Town · University of Bath

    Affiliation as printed

    Computational Biology Division, University of Cape Town

    European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK

    Milner Centre for Evolution, University of Bath, UK

89. Túlio de Oliveira

    Stellenbosch University · University of KwaZulu-Natal

    Affiliation as printed

    Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa

    KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, South Africa

90. Tim Peto

    University of Oxford

    Affiliation as printed

    Nuffield Department of Medicine, University of Oxford, Oxford, UK

91. Derrick W. Crook

    University of Oxford

    Affiliation as printed

    Nuffield Department of Medicine, University of Oxford, Oxford, UK

92. Russell B Corbett-Detig

    University of California, Santa Cruz

    Affiliation as printed

    Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA

    Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA