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

Martin Hunt^{1

2

3

4}, Angie S Hinrichs⁵, Daniel Anderson¹, Lily Karim^{5

6}, Bethany L Dearlove⁷, Jeff Knaggs^{1

2

3

4}, Bede Constantinides^{2

4}, Philip W Fowler^{2

3

4}, Gillian Rodger^{2

4}, Teresa Street^{2

3}, Sheila Lumley^{2

8}, Hermione Webster^{2

4}, Theo Sanderson⁹, Christopher Ruis^{10

11}, Benjamin Kotzen¹², Nicola de Maio¹, Lucas N Amenga-Etego¹³, Dominic S Y Amuzu¹³, Martin Avaro¹⁴, Gordon A Awandare¹³, Reuben Ayivor-Djanie^{15

16}, Timothy Barkham¹⁷, Matthew Bashton¹⁸, Elizabeth M Batty^{19

20}, Yaw Bediako¹³, Denise De Belder²¹, Estefania Benedetti¹⁴, Andreas Bergthaler⁷, Stefan A Boers²², Josefina Campos²¹, Rosina Afua Ampomah Carr^{16

23}, Yuan Yi Constance Chen¹⁷, Facundo Cuba²¹, Maria Elena Dattero¹⁴, Wanwisa Dejnirattisai²⁴, Alexander Dilthey²⁵, Kwabena Obeng Duedu^{16

26}, Lukas Endler⁷, Ilka Engelmann²⁷, Ngiambudulu M Francisco²⁸, Jonas Fuchs²⁹, Etienne Z Gnimpieba³⁰, Soraya Groc³¹, Jones Gyamfi^{16

32}, Dennis Heemskerk²², Torsten Houwaart²⁵, Nei-Yuan Hsiao³³, Matthew Huska³⁴, Martin Hölzer³⁴, Arash Iranzadeh³⁵, Hanna Jarva³⁶, Chandima Jeewandara³⁷, Bani Jolly^{38

39}, Rageema Joseph³³, Ravi Kant^{40

41

42}, Karrie Ko Kwan Ki⁴³, Satu Kurkela³⁶, Maija Lappalainen³⁶, Marie Lataretu³⁴, Jacob Lemieux¹², Chang Liu^{44

45}, Gathsaurie Neelika Malavige³⁷, Tapfumanei Mashe⁴⁶, Juthathip Mongkolsapaya^{20

44

45}, Brigitte Montes³¹, Jose Arturo Molina Mora⁴⁷, Collins M Morang'a¹³, Bernard Mvula⁴⁸, Niranjan Nagarajan^{49

50}, Andrew Nelson⁵¹, Joyce M Ngoi¹³, Joana Paula da Paixão²⁸, Marcus Panning²⁹, Tomas Poklepovich²¹, Peter K Quashie¹³, Diyanath Ranasinghe³⁷, Mara Russo¹⁴, James Emmanuel San^{52

53}, Nicholas D Sanderson^{2

3}, Vinod Scaria^{39

54}, Gavin Screaton², October Michael Sessions⁵⁵, Tarja Sironen^{40

41}, Abay Sisay⁵⁶, Darren Smith¹⁸, Teemu Smura^{40

41}, Piyada Supasa^{44

45}, Chayaporn Suphavilai⁴⁹, Jeremy Swann², Houriiyah Tegally⁵⁷, Bryan Tegomoh^{58

59

60}, Olli Vapalahti^{40

41}, Andreas Walker⁶¹, Robert J Wilkinson^{9

62

63}, Carolyn Williamson³³, Xavier Zair⁵⁵; IMSSC Laboratory Network Consortium; Tulio de Oliveira^{57

64}, Timothy Ea Peto², Derrick Crook², Russell Corbett-Detig^{5

6}, Zamin Iqbal^{65

66}

Collaborators, Affiliations

Collaborators

Affiliations

¹ European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK.
² Nuffield Department of Medicine, University of Oxford, Oxford, UK.
³ National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK.
⁴ Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK.
⁵ Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
⁶ Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
⁷ Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria.
⁸ Department of Infectious Diseases and Microbiology, John Radcliffe Hospital, Oxford, UK.
⁹ Francis Crick Institute, London, UK.
¹⁰ Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK.
¹¹ Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
¹² Department of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
¹³ West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana.
¹⁴ Servicio de Virus Respiratorios, Instituto Nacional Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina.
¹⁵ Biomanufacturing Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy.
¹⁶ Department of Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana.
¹⁷ Tan Tock Seng Hospital, Singapore, Singapore.
¹⁸ The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK.
¹⁹ Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
²⁰ Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand.
²¹ Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina.
²² Center of Infectious Diseases, Medical Microbiology and Infection Control, Leiden University Medical Centre, Albinusdreef 2, Leiden, The Netherlands.
²³ Department of Computational Medicine and Bioinformatics, University of Michigan, Michigan, Ann Arbor, MI, USA.
²⁴ Division of Emerging Infectious Disease, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkoknoi, Thailand.
²⁵ Institute of Medical Microbiology and Hospital Hygiene, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
²⁶ College of Life Sciences, Birmingham City University, Birmingham, UK.
²⁷ Pathogenesis and Control of Chronic and Emerging Infections, Univ Montpellier, INSERM, Virology Laboratory, CHU Montpellier, Montpellier, France.
²⁸ Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola.
²⁹ Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
³⁰ Biomedical Engineering Department, University of South Dakota, Sioux Falls, SD, USA.
³¹ Virology Laboratory, CHU Montpellier, Montpellier, France.
³² School of Health and Life Sciences, Teesside University, Middlesbrough, UK.
³³ Divison of Medical Virology, University of Cape Town and National Health Laboratory Service, Cape Town, South Africa.
³⁴ Genome Competence Center (MF1), Robert Koch Institute, Nordufer 20, Berlin, Germany.
³⁵ Computational Biology Division, University of Cape Town, Cape Town, South Africa.
³⁶ HUS Diagnostic Center, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
³⁷ Institute of Allergology and Immunology, University of Sri Jayewardenepura, Gangodawila, Nugegoda, Sri Lanka.
³⁸ Karkinos Healthcare Private Limited (KHPL), Aurbis Business Parks, Bellandur, Bengaluru, India.
³⁹ Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
⁴⁰ Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.
⁴¹ Department of Virology, University of Helsinki, Helsinki, Finland.
⁴² Department of Tropical Parasitology, Institute of Maritime and Tropical Medicine, Medical University of Gdansk, Gdynia, Poland.
⁴³ Department of Microbiology, Singapore General Hospital, Singapore, Singapore.
⁴⁴ Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
⁴⁵ Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
⁴⁶ Health System Strengthening Unit, World Health Organisation, Harare, Zimbabwe.
⁴⁷ Centro de investigación en Enfermedades Tropicales & Facultad de Microbiologia, Universidad de Costa Rica, San José, Costa Rica.
⁴⁸ Public Health Institute of Malawi, Ministry of Health, Malawi, Malawi.
⁴⁹ Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
⁵⁰ Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
⁵¹ Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK.
⁵² Duke Human Vaccine Institute, Duke University, Durham, NC, England.
⁵³ University of KwaZulu Natal, Durban, South Africa.
⁵⁴ Vishwanath Cancer Care Foundation (VCCF), West Mumbai, India.
⁵⁵ Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.
⁵⁶ Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia.
⁵⁷ Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, Stellenbosch, South Africa.
⁵⁸ Centre de Coordination des Opérations d'Urgences de Santé Publique, Ministere de Sante Publique, Yaoundé, Cameroun.
⁵⁹ University of California, Berkeley, Berkeley, CA, USA.
⁶⁰ Nebraska Department of Health and Human Services, Lincoln, NE, USA.
⁶¹ Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
⁶² Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa.
⁶³ Imperial College London, London, UK.
⁶⁴ KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban, South Africa.
⁶⁵ European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK. zi245@bath.ac.uk.
⁶⁶ Milner Centre for Evolution, University of Bath, Bath, UK. zi245@bath.ac.uk.

PMID: 41663577
DOI: 10.1038/s41592-025-02947-1

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

Martin Hunt et al. Nat Methods. 2026.

. 2026 Feb 9.

doi: 10.1038/s41592-025-02947-1. Online ahead of print.

Authors

Collaborators

Affiliations

¹ European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK.
² Nuffield Department of Medicine, University of Oxford, Oxford, UK.
³ National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK.
⁴ Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK.
⁵ Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
⁶ Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
⁷ Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria.
⁸ Department of Infectious Diseases and Microbiology, John Radcliffe Hospital, Oxford, UK.
⁹ Francis Crick Institute, London, UK.
¹⁰ Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK.
¹¹ Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
¹² Department of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
¹³ West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana.
¹⁴ Servicio de Virus Respiratorios, Instituto Nacional Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina.
¹⁵ Biomanufacturing Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy.
¹⁶ Department of Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana.
¹⁷ Tan Tock Seng Hospital, Singapore, Singapore.
¹⁸ The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK.
¹⁹ Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
²⁰ Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand.
²¹ Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina.
²² Center of Infectious Diseases, Medical Microbiology and Infection Control, Leiden University Medical Centre, Albinusdreef 2, Leiden, The Netherlands.
²³ Department of Computational Medicine and Bioinformatics, University of Michigan, Michigan, Ann Arbor, MI, USA.
²⁴ Division of Emerging Infectious Disease, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkoknoi, Thailand.
²⁵ Institute of Medical Microbiology and Hospital Hygiene, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
²⁶ College of Life Sciences, Birmingham City University, Birmingham, UK.
²⁷ Pathogenesis and Control of Chronic and Emerging Infections, Univ Montpellier, INSERM, Virology Laboratory, CHU Montpellier, Montpellier, France.
²⁸ Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola.
²⁹ Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
³⁰ Biomedical Engineering Department, University of South Dakota, Sioux Falls, SD, USA.
³¹ Virology Laboratory, CHU Montpellier, Montpellier, France.
³² School of Health and Life Sciences, Teesside University, Middlesbrough, UK.
³³ Divison of Medical Virology, University of Cape Town and National Health Laboratory Service, Cape Town, South Africa.
³⁴ Genome Competence Center (MF1), Robert Koch Institute, Nordufer 20, Berlin, Germany.
³⁵ Computational Biology Division, University of Cape Town, Cape Town, South Africa.
³⁶ HUS Diagnostic Center, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
³⁷ Institute of Allergology and Immunology, University of Sri Jayewardenepura, Gangodawila, Nugegoda, Sri Lanka.
³⁸ Karkinos Healthcare Private Limited (KHPL), Aurbis Business Parks, Bellandur, Bengaluru, India.
³⁹ Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
⁴⁰ Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.
⁴¹ Department of Virology, University of Helsinki, Helsinki, Finland.
⁴² Department of Tropical Parasitology, Institute of Maritime and Tropical Medicine, Medical University of Gdansk, Gdynia, Poland.
⁴³ Department of Microbiology, Singapore General Hospital, Singapore, Singapore.
⁴⁴ Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
⁴⁵ Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
⁴⁶ Health System Strengthening Unit, World Health Organisation, Harare, Zimbabwe.
⁴⁷ Centro de investigación en Enfermedades Tropicales & Facultad de Microbiologia, Universidad de Costa Rica, San José, Costa Rica.
⁴⁸ Public Health Institute of Malawi, Ministry of Health, Malawi, Malawi.
⁴⁹ Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
⁵⁰ Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
⁵¹ Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK.
⁵² Duke Human Vaccine Institute, Duke University, Durham, NC, England.
⁵³ University of KwaZulu Natal, Durban, South Africa.
⁵⁴ Vishwanath Cancer Care Foundation (VCCF), West Mumbai, India.
⁵⁵ Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.
⁵⁶ Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia.
⁵⁷ Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, Stellenbosch, South Africa.
⁵⁸ Centre de Coordination des Opérations d'Urgences de Santé Publique, Ministere de Sante Publique, Yaoundé, Cameroun.
⁵⁹ University of California, Berkeley, Berkeley, CA, USA.
⁶⁰ Nebraska Department of Health and Human Services, Lincoln, NE, USA.
⁶¹ Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
⁶² Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa.
⁶³ Imperial College London, London, UK.
⁶⁴ KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban, South Africa.
⁶⁵ European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK. zi245@bath.ac.uk.
⁶⁶ Milner Centre for Evolution, University of Bath, Bath, UK. zi245@bath.ac.uk.

PMID: 41663577
DOI: 10.1038/s41592-025-02947-1

Abstract

The majority of SARS-CoV-2 genomes obtained during the pandemic were derived by amplifying overlapping windows of the genome ('tiled amplicons'), reconstructing their sequences and fitting them together. This leads to systematic errors in genomes unless the software is both aware of the amplicon scheme and of the error modes of amplicon sequencing. Additionally, over time, amplicon schemes need to be updated as new mutations in the virus interfere with the primer binding sites at the end of amplicons. Thus, waves of variants swept the world during the pandemic and were followed by waves of systematic errors in the genomes, which had significant impacts on the inferred phylogenetic tree.Here we reconstruct the genomes from all public data as of June 2024 using an assembly tool called Viridian ( https://github.com/iqbal-lab-org/viridian ), developed to rigorously process amplicon sequence data. With these high-quality consensus sequences we provide a global phylogenetic tree of 4,471,579 samples, viewable at https://viridian.taxonium.org . We provide simulation and empirical validation of the methodology, and quantify the improvement in the phylogeny.

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Conflict of interest statement

Competing interests: G. Screaton is on the GSK Vaccines Scientific Advisory Board, consults for AstraZeneca, and is a founding member of RQ Biotechnology. P. Fowler, D. Crook and Z. Iqbal have consulted for the Ellison Institute of Technology. B. Jolly is employed by Karkinos Healthcare Private Limited. The remaining authors declare no competing interests.

Update of

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.
Hunt M, Hinrichs AS, Anderson D, Karim L, Dearlove BL, Knaggs J, Constantinides B, Fowler PW, Rodger G, Street T, Lumley S, Webster H, Sanderson T, Ruis C, Kotzen B, de Maio N, Amenga-Etego LN, Amuzu DSY, Avaro M, Awandare GA, Ayivor-Djanie R, Barkham T, Bashton M, Batty EM, Bediako Y, De Belder D, Benedetti E, Bergthaler A, Boers SA, Campos J, Carr RAA, Chen YYC, Cuba F, Dattero ME, Dejnirattisai W, Dilthey A, Duedu KO, Endler L, Engelmann I, Francisco NM, Fuchs J, Gnimpieba EZ, Groc S, Gyamfi J, Heemskerk D, Houwaart T, Hsiao NY, Huska M, Hölzer M, Iranzadeh A, Jarva H, Jeewandara C, Jolly B, Joseph R, Kant R, Ki KKK, Kurkela S, Lappalainen M, Lataretu M, Lemieux J, Liu C, Malavige GN, Mashe T, Mongkolsapaya J, Montes B, Mora JAM, Morang'a CM, Mvula B, Nagarajan N, Nelson A, Ngoi JM, da Paixão JP, Panning M, Poklepovich T, Quashie PK, Ranasinghe D, Russo M, San JE, Sanderson ND, Scaria V, Screaton G, Sessions OM, Sironen T, Sisay A, Smith D, Smura T, Supasa P, Suphavilai C, Swann J, Tegally H, Tegomoh B, Vapalahti O, Walker A, Wilkinson RJ, Williamson C, Zair X; IMSSC2 Laboratory Network Consortium; de Oliveira T, Peto TE, Crook D, Corbett-Detig R, Iqbal Z. Hunt M, et al. bioRxiv [Preprint]. 2024 Nov 5:2024.04.29.591666. doi: 10.1101/2024.04.29.591666. bioRxiv. 2024. Update in: Nat Methods. 2026 Feb 9. doi: 10.1038/s41592-025-02947-1. PMID: 38746185 Free PMC article. Updated. Preprint.

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

Collaborators

Affiliations

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

Authors

Collaborators

Affiliations

Abstract

Conflict of interest statement

Update of

References

Grants and funding

LinkOut - more resources

Full Text Sources

Miscellaneous