Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.
Hunt Martin, Hinrichs Angie S, Anderson Daniel, Karim Lily, Dearlove Bethany L, Knaggs Jeff, Constantinides Bede, Fowler Philip W, Rodger Gillian, Street Teresa, Lumley Sheila, Webster Hermione, Sanderson Theo, Ruis Christopher, Kotzen Benjamin, de Maio Nicola, Amenga-Etego Lucas N, Amuzu Dominic S Y, Avaro Martin, Awandare Gordon A, Ayivor-Djanie Reuben, Barkham Timothy, Bashton Matthew, Batty Elizabeth M, Bediako Yaw, De Belder Denise, Benedetti Estefania, Bergthaler Andreas, Boers Stefan A, Campos Josefina, Carr Rosina Afua Ampomah, Chen Yuan Yi Constance, Cuba Facundo, Dattero Maria Elena, Dejnirattisai Wanwisa, Dilthey Alexander, Duedu Kwabena Obeng, Endler Lukas, Engelmann Ilka, Francisco Ngiambudulu M, Fuchs Jonas, Gnimpieba Etienne Z, Groc Soraya, Gyamfi Jones, Heemskerk Dennis, Houwaart Torsten, Hsiao Nei-Yuan, Huska Matthew, Hölzer Martin, Iranzadeh Arash, Jarva Hanna, Jeewandara Chandima, Jolly Bani, Joseph Rageema, Kant Ravi, Ki Karrie Ko Kwan, Kurkela Satu, Lappalainen Maija, Lataretu Marie, Lemieux Jacob, Liu Chang, Malavige Gathsaurie Neelika, Mashe Tapfumanei, Mongkolsapaya Juthathip, Montes Brigitte, Mora Jose Arturo Molina, Morang'a Collins M, Mvula Bernard, Nagarajan Niranjan, Nelson Andrew, Ngoi Joyce M, da Paixão Joana Paula, Panning Marcus, Poklepovich Tomas, Quashie Peter K, Ranasinghe Diyanath, Russo Mara, San James Emmanuel, Sanderson Nicholas D, Scaria Vinod, Screaton Gavin, Sessions October Michael, Sironen Tarja, Sisay Abay, Smith Darren, Smura Teemu, Supasa Piyada, Suphavilai Chayaporn, Swann Jeremy, Tegally Houriiyah, Tegomoh Bryan, Vapalahti Olli, Walker Andreas, Wilkinson Robert J, Williamson Carolyn, Zair Xavier, IMSSC Laboratory Network Consortium, de Oliveira Tulio, Peto Timothy Ea, Crook Derrick, Corbett-Detig Russell, Iqbal Zamin
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Аннотация
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.
Для цитирования: Hunt Martin, Hinrichs Angie S, Anderson Daniel, Karim Lily, Dearlove Bethany L, Knaggs Jeff, Constantinides Bede, Fowler Philip W, Rodger Gillian, Street Teresa, Lumley Sheila, Webster Hermione, Sanderson Theo, Ruis Christopher, Kotzen Benjamin, de Maio Nicola, Amenga-Etego Lucas N, Amuzu Dominic S Y, Avaro Martin, Awandare Gordon A, Ayivor-Djanie Reuben, Barkham Timothy, Bashton Matthew, Batty Elizabeth M, Bediako Yaw, De Belder Denise, Benedetti Estefania, Bergthaler Andreas, Boers Stefan A, Campos Josefina, Carr Rosina Afua Ampomah, Chen Yuan Yi Constance, Cuba Facundo, Dattero Maria Elena, Dejnirattisai Wanwisa, Dilthey Alexander, Duedu Kwabena Obeng, Endler Lukas, Engelmann Ilka, Francisco Ngiambudulu M, Fuchs Jonas, Gnimpieba Etienne Z, Groc Soraya, Gyamfi Jones, Heemskerk Dennis, Houwaart Torsten, Hsiao Nei-Yuan, Huska Matthew, Hölzer Martin, Iranzadeh Arash, Jarva Hanna, Jeewandara Chandima, Jolly Bani, Joseph Rageema, Kant Ravi, Ki Karrie Ko Kwan, Kurkela Satu, Lappalainen Maija, Lataretu Marie, Lemieux Jacob, Liu Chang, Malavige Gathsaurie Neelika, Mashe Tapfumanei, Mongkolsapaya Juthathip, Montes Brigitte, Mora Jose Arturo Molina, Morang'a Collins M, Mvula Bernard, Nagarajan Niranjan, Nelson Andrew, Ngoi Joyce M, da Paixão Joana Paula, Panning Marcus, Poklepovich Tomas, Quashie Peter K, Ranasinghe Diyanath, Russo Mara, San James Emmanuel, Sanderson Nicholas D, Scaria Vinod, Screaton Gavin, Sessions October Michael, Sironen Tarja, Sisay Abay, Smith Darren, Smura Teemu, Supasa Piyada, Suphavilai Chayaporn, Swann Jeremy, Tegally Houriiyah, Tegomoh Bryan, Vapalahti Olli, Walker Andreas, Wilkinson Robert J, Williamson Carolyn, Zair Xavier, IMSSC Laboratory Network Consortium, de Oliveira Tulio, Peto Timothy Ea, Crook Derrick, Corbett-Detig Russell, Iqbal Zamin. Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.. Nature methods. 2026. DOI: 10.1038/s41592-025-02947-1.
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