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; IMSSC Laboratory Network Consortium; Tulio de Oliveira; Timothy E.A. Peto; Derrick Crook; Russell Corbett-Detig; Zamin Iqbal

doi:10.1038/s41592-025-02947-1

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. AwandareReuben 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, IMSSC Laboratory Network Consortium, Tulio de Oliveira, Timothy E.A. Peto, Derrick Crook, Russell Corbett-Detig, Zamin Iqbal^*

^*Corresponding author for this work

School of Geography and Natural Sciences

Research output: Contribution to journal › Article › peer-review

1 Citation (Scopus)

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.

Original language	English
Pages (from-to)	653-662
Number of pages	10
Journal	Nature Methods
Volume	23
Issue number	3
Early online date	9 Feb 2026
DOIs	https://doi.org/10.1038/s41592-025-02947-1
Publication status	Published - 1 Mar 2026

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

COVID-19/virology
Genome, Viral
Humans
Pandemics
Phylogeny
SARS-CoV-2/genetics
Software

Access to Document

10.1038/s41592-025-02947-1Licence: CC BY

s41592-025-02947-1 (1)Final published version, 2.85 MBLicence: CC BY

Cite this

Hunt, M., Hinrichs, A. S., Anderson, D., Karim, L., Dearlove, B. L., Knaggs, J., Constantinides, B., Fowler, P. W., Rodger, G., Street, T., Lumley, S., Webster, H., Sanderson, T., Ruis, C., Kotzen, B., de Maio, N., Amenga-Etego, L. N., Amuzu, D. S. Y., Avaro, M., ... Iqbal, Z. (2026). Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny. Nature Methods, 23(3), 653-662. https://doi.org/10.1038/s41592-025-02947-1

@article{2f3d564a6e134156b4a4148d87c55b50,

title = "Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny",

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

year = "2026",

month = mar,

day = "1",

doi = "10.1038/s41592-025-02947-1",

language = "English",

volume = "23",

pages = "653--662",

journal = "Nature Methods",

issn = "1548-7091",

publisher = "Nature Research",

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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, N-Y, 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, IMSSC Laboratory Network Consortium, de Oliveira, T, Peto, TEA, Crook, D, Corbett-Detig, R & Iqbal, Z 2026, 'Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny', Nature Methods, vol. 23, no. 3, pp. 653-662. https://doi.org/10.1038/s41592-025-02947-1

TY - JOUR

T1 - Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny

AU - Hunt, Martin

AU - Hinrichs, Angie S.

AU - Anderson, Daniel

AU - Karim, Lily

AU - Dearlove, Bethany L.

AU - Knaggs, Jeff

AU - Constantinides, Bede

AU - Fowler, Philip W.

AU - Rodger, Gillian

AU - Street, Teresa

AU - Lumley, Sheila

AU - Webster, Hermione

AU - Sanderson, Theo

AU - Ruis, Christopher

AU - Kotzen, Benjamin

AU - de Maio, Nicola

AU - Amenga-Etego, Lucas N.

AU - Amuzu, Dominic S. Y.

AU - Avaro, Martin

AU - Awandare, Gordon A.

AU - Ayivor-Djanie, Reuben

AU - Barkham, Timothy

AU - Bashton, Matthew

AU - Batty, Elizabeth M.

AU - Bediako, Yaw

AU - De Belder, Denise

AU - Benedetti, Estefania

AU - Bergthaler, Andreas

AU - Boers, Stefan A.

AU - Campos, Josefina

AU - Carr, Rosina Afua Ampomah

AU - Chen, Yuan Yi Constance

AU - Cuba, Facundo

AU - Dattero, Maria Elena

AU - Dejnirattisai, Wanwisa

AU - Dilthey, Alexander

AU - Duedu, Kwabena Obeng

AU - Endler, Lukas

AU - Engelmann, Ilka

AU - Francisco, Ngiambudulu M.

AU - Fuchs, Jonas

AU - Gnimpieba, Etienne Z.

AU - Groc, Soraya

AU - Gyamfi, Jones

AU - Heemskerk, Dennis

AU - Houwaart, Torsten

AU - Hsiao, Nei-Yuan

AU - Huska, Matthew

AU - Hölzer, Martin

AU - Iranzadeh, Arash

AU - Jarva, Hanna

AU - Jeewandara, Chandima

AU - Jolly, Bani

AU - Joseph, Rageema

AU - Kant, Ravi

AU - Ki, Karrie Ko Kwan

AU - Kurkela, Satu

AU - Lappalainen, Maija

AU - Lataretu, Marie

AU - Lemieux, Jacob

AU - Liu, Chang

AU - Malavige, Gathsaurie Neelika

AU - Mashe, Tapfumanei

AU - Mongkolsapaya, Juthathip

AU - Montes, Brigitte

AU - Mora, Jose Arturo Molina

AU - Morang’a, Collins M.

AU - Mvula, Bernard

AU - Nagarajan, Niranjan

AU - Nelson, Andrew

AU - Ngoi, Joyce M.

AU - da Paixão, Joana Paula

AU - Panning, Marcus

AU - Poklepovich, Tomas

AU - Quashie, Peter K.

AU - Ranasinghe, Diyanath

AU - Russo, Mara

AU - San, James Emmanuel

AU - Sanderson, Nicholas D.

AU - Scaria, Vinod

AU - Screaton, Gavin

AU - Sessions, October Michael

AU - Sironen, Tarja

AU - Sisay, Abay

AU - Smith, Darren

AU - Smura, Teemu

AU - Supasa, Piyada

AU - Suphavilai, Chayaporn

AU - Swann, Jeremy

AU - Tegally, Houriiyah

AU - Tegomoh, Bryan

AU - Vapalahti, Olli

AU - Walker, Andreas

AU - Wilkinson, Robert J.

AU - Williamson, Carolyn

AU - Zair, Xavier

AU - IMSSC Laboratory Network Consortium

AU - de Oliveira, Tulio

AU - Peto, Timothy E.A.

AU - Crook, Derrick

AU - Corbett-Detig, Russell

AU - Iqbal, Zamin

PY - 2026/3/1

Y1 - 2026/3/1

N2 - 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.

AB - 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.

KW - COVID-19/virology

KW - Genome, Viral

KW - Humans

KW - Pandemics

KW - Phylogeny

KW - SARS-CoV-2/genetics

KW - Software

UR - https://www.scopus.com/pages/publications/105029877354

U2 - 10.1038/s41592-025-02947-1

DO - 10.1038/s41592-025-02947-1

M3 - Article

C2 - 41663577

SN - 1548-7091

VL - 23

SP - 653

EP - 662

JO - Nature Methods

JF - Nature Methods

IS - 3

ER -

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

Abstract

UN SDGs

Keywords

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