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

Martin Hunt; Angie S. Hinrichs; Daniel Anderson; Lily Karim; Bethany L Dearlove; Jeff Knaggs; Bede Constantinides; Philip W. Fowler; Gillian Rodger; Teresa Street; Sheila Lumley; Hermione Webster; Theo Sanderson; Christopher Ruis; Benjamin Kotzen; Nicola de Maio; Lucas N. Amenga-Etego; Dominic S. Y. Amuzu; Martin Avaro; Gordon A. Awandare; Reuben Ayivor-Djanie; Timothy Barkham; Matthew Bashton; Elizabeth M Batty; Yaw Bediako; Denise De Belder; Estefania Benedetti; Andreas Bergthaler; Stefan A. Boers; Josefina Campos; Rosina Afua Ampomah Carr; Yuan Yi Constance Chen; Facundo Cuba; Maria Elena Dattero; Wanwisa Dejnirattisai; Alexander Dilthey; Kwabena Obeng Duedu; Lukas Endler; Ilka Engelmann; Ngiambudulu M. Francisco; Jonas Fuchs; Etienne Z. Gnimpieba; Soraya Groc; Jones Gyamfi; Dennis Heemskerk; Torsten Houwaart; Nei-yuan Hsiao; Matthew Huska; Martin Hölzer; Arash Iranzadeh; Hanna Jarva; Chandima Jeewandara; Bani Jolly; Rageema Joseph; Ravi Kant; Karrie Ko Kwan Ki; Satu Kurkela; Maija Lappalainen; Marie Lataretu; Jacob Lemieux; Chang Liu; Gathsaurie Neelika Malavige; Tapfumanei Mashe; Juthathip Mongkolsapaya; Brigitte Montes; Jose Arturo Molina Mora; Collins M. Morang’a; Bernard Mvula; Niranjan Nagarajan; Andrew Nelson; Joyce M. Ngoi; Joana Paula da Paixão; Marcus Panning; Tomas Poklepovich; Peter K. Quashie; Diyanath Ranasinghe; Mara Russo; James Emmanuel San; Nicholas D. Sanderson; Vinod Scaria; Gavin Screaton; October Michael Sessions; Tarja Sironen; Abay Sisay; Darren Smith; Teemu Smura; Piyada Supasa; Chayaporn Suphavilai; Jeremy Swann; Houriiyah Tegally; Bryan Tegomoh; Olli Vapalahti; Andreas Walker; Robert J Wilkinson; Carolyn Williamson; Xavier Zair; Tulio de Oliveira; Timothy EA Peto; Derrick Crook; Russell Corbett-Detig; IMSSC2 Laboratory Network Consortium; Zamin Iqbal

doi:10.1101/2024.04.29.591666

Prépublication

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

Martin Hunt, Angie S. Hinrichs, Daniel Anderson, Lily Karim, Bethany L Dearlove, Jeff Knaggs, Bede Constantinides, Philip W. Fowler, Gillian Rodger, Teresa Street, …

bioRxiv

Cold Spring Harbor Laboratory, 1.3

05/11/2024

DOI: https://doi.org/10.1101/2024.04.29.591666

PMID: 38746185

Résumé

Bioinformatics

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.

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Détails

Titre: Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny
Créateurs - sans rôle: Martin Hunt - Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford
Angie S. Hinrichs - Genomics Institute, University of California
Daniel Anderson - European Molecular Biology Laboratory – European Bioinformatics Institute
Lily Karim - Department of Biomolecular Engineering, University of California
Bethany L Dearlove - Medical University of Vienna
Jeff Knaggs - Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford
Bede Constantinides - Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford
Philip W. Fowler - Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford
Gillian Rodger - Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford
Teresa Street - National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital
Sheila Lumley - Department of Infectious Diseases and Microbiology, John Radcliffe Hospital
Hermione Webster - Nuffield Department of Medicine, University of Oxford
Theo Sanderson - Francis Crick Institute
Christopher Ruis - Department of Veterinary Medicine, University of Cambridge
Benjamin Kotzen - Department of Infectious Diseases, Massachusetts General Hospital
Nicola de Maio - European Bioinformatics Institute
Lucas N. Amenga-Etego - West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana
Dominic S. Y. Amuzu - West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana
Martin Avaro - Servicio de Virus Respiratorios, Instituto Nacional Enfermedades Infecciosas
Gordon A. Awandare - University of Ghana
Reuben Ayivor-Djanie - University of Health and Allied Sciences
Timothy Barkham - Tan Tock Seng Hospital
Matthew Bashton - The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University
Elizabeth M Batty - Mahidol-Oxford Tropical Medicine Research Unit
Yaw Bediako - West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana
Denise De Belder - Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS “Dr. Carlos G. Malbŕan”
Estefania Benedetti - Servicio de Virus Respiratorios, Instituto Nacional Enfermedades Infecciosas
Andreas Bergthaler - Medical University of Vienna
Stefan A. Boers - Dept. Medical Microbiology, Leiden University Medical Center
Josefina Campos - Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS “Dr. Carlos G. Malbŕan”
Rosina Afua Ampomah Carr - Department of Computational Medicine and Bioinformatics, University of Michigan
Yuan Yi Constance Chen - Tan Tock Seng Hospital
Facundo Cuba - Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS “Dr. Carlos G. Malbŕan”
Maria Elena Dattero - Servicio de Virus Respiratorios, Instituto Nacional Enfermedades Infecciosas
Wanwisa Dejnirattisai - Division of Emerging Infectious Disease, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University
Alexander Dilthey - Institute of Medical Microbiology and Hospital Hygiene, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf
Kwabena Obeng Duedu - College of Life Sciences, Birmingham City University
Lukas Endler - Medical University of Vienna
Ilka Engelmann - Pathogenesis and Control of Chronic and Emerging Infections, Univ Montpellier, INSERM, Etablissement Franҫais du Sang, Virology Laboratory
Ngiambudulu M. Francisco - Grupo de Investigaҫão Microbiana e Imunológica, Instituto Nacional de Investigaҫão em Saúde (National Institute for Health Research)
Jonas Fuchs - Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg
Etienne Z. Gnimpieba - Biomedical Engineering Department, University of South Dakota
Soraya Groc - Virology Laboratory
Jones Gyamfi - School of Health and Life Sciences, Teesside University
Dennis Heemskerk - Dept. Medical Microbiology, Leiden University Medical Center
Torsten Houwaart - Institute of Medical Microbiology and Hospital Hygiene, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf
Nei-yuan Hsiao - Divison of Medical Virology, University of Cape Town and National Health Laboratory Service
Matthew Huska - Genome Competence Center (MF1), Robert Koch Institute
Martin Hölzer - Robert Koch Institute
Arash Iranzadeh - Computational Biology Division, University of Cape Town
Hanna Jarva - HUS Diagnostic Center, Clinical Microbiology, University of Helsinki and Helsinki University Hospital
Chandima Jeewandara - Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura
Bani Jolly - Academy of Scientific and Innovative Research (AcSIR)
Rageema Joseph - Computational Biology Division, University of Cape Town
Ravi Kant - Department of Tropical Parasitology, Institute of Maritime and Tropical Medicine, Medical University of Gdansk
Karrie Ko Kwan Ki - Department of Microbiology, Singapore General Hospital
Satu Kurkela - HUS Diagnostic Center, Clinical Microbiology, University of Helsinki and Helsinki University Hospital
Maija Lappalainen - HUS Diagnostic Center, Clinical Microbiology, University of Helsinki and Helsinki University Hospital
Marie Lataretu - Genome Competence Center (MF1), Robert Koch Institute
Jacob Lemieux - Department of Infectious Diseases, Massachusetts General Hospital
Chang Liu - Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford
Gathsaurie Neelika Malavige - Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura
Tapfumanei Mashe - Health System Strengthening Unit, World Health Organisation
Juthathip Mongkolsapaya - Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford
Brigitte Montes - Virology Laboratory
Jose Arturo Molina Mora - Centro de investigación en Enfermedades Tropicales & Facultad de Microbiología, Universidad de Costa Rica
Collins M. Morang’a - West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana
Bernard Mvula - Public Health Institute of Malawi, Ministry of Health
Niranjan Nagarajan - Yong Loo Lin School of Medicine, National University of Singapore
Andrew Nelson - Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University
Joyce M. Ngoi - University of Ghana
Joana Paula da Paixão - Grupo de Investigaҫão Microbiana e Imunológica, Instituto Nacional de Investigaҫão em Saúde (National Institute for Health Research)
Marcus Panning - Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg
Tomas Poklepovich - Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS “Dr. Carlos G. Malbŕan”
Peter K. Quashie - West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana
Diyanath Ranasinghe - Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura
Mara Russo - Servicio de Virus Respiratorios, Instituto Nacional Enfermedades Infecciosas
James Emmanuel San - University of KwaZulu Natal
Nicholas D. Sanderson - National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital
Vinod Scaria - Vishwanath Cancer Care Foundation (VCCF), Neelkanth Business Park Kirol Village
Gavin Screaton - Nuffield Department of Medicine, University of Oxford
October Michael Sessions - Saw Swee Hock School of Public Health
Tarja Sironen - University of Helsinki
Abay Sisay - Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University
Darren Smith - The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University
Teemu Smura - University of Helsinki
Piyada Supasa - Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford
Chayaporn Suphavilai - Genome Institute of Singapore, Agency for Science, Technology and Research (ASTAR)
Jeremy Swann - Nuffield Department of Medicine, University of Oxford
Houriiyah Tegally - Centre for Epidemic Response and Innovation (CERI), Stellenbosch University
Bryan Tegomoh - Nebraska Department of Health and Human Services
Olli Vapalahti - Department of Virology, University of Helsinki
Andreas Walker - Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf
Robert J Wilkinson - Imperial College London
Carolyn Williamson - Computational Biology Division, University of Cape Town
Xavier Zair - Saw Swee Hock School of Public Health
Tulio de Oliveira - University of KwaZulu-Natal
Timothy EA Peto - Nuffield Department of Medicine, University of Oxford
Derrick Crook - University of Oxford
Russell Corbett-Detig - Department of Biomolecular Engineering, University of California
IMSSC2 Laboratory Network Consortium
Zamin Iqbal - Milner Centre for Evolution, University of Bath
Détails de publication: bioRxiv
Éditeur: Cold Spring Harbor Laboratory
Édition: 1.3
Nombre de pages: 35
Identifiants: 99148136609311
Unité académique: Pathogenesis and Control of Chronic and Emerging Infections - PCCEI
Langue: English
Type de ressource: Preprint