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@article{Hunt:2026:10.1038/s41592-025-02947-1,
author = {Hunt, M and Hinrichs, AS and Anderson, D and Karim, L and Dearlove, BL and Knaggs, J and Constantinides, B and Fowler, PW and Rodger, G and Street, T and Lumley, S and Webster, H and Sanderson, T and Ruis, C and Kotzen, B and de, Maio N and Amenga-Etego, LN and Amuzu, DSY and Avaro, M and Awandare, GA and Ayivor-Djanie, R and Barkham, T and Bashton, M and Batty, EM and Bediako, Y and De, Belder D and Benedetti, E and Bergthaler, A and Boers, SA and Campos, J and Carr, RAA and Chen, YYC and Cuba, F and Dattero, ME and Dejnirattisai, W and Dilthey, A and Duedu, KO and Endler, L and Engelmann, I and Francisco, NM and Fuchs, J and Gnimpieba, EZ and Groc, S and Gyamfi, J and Heemskerk, D and Houwaart, T and Hsiao, N-Y and Huska, M and Hölzer, M and Iranzadeh, A and Jarva, H and Jeewandara, C and Jolly, B and Joseph, R and Kant, R and Ki, KKK and Kurkela, S and Lappalainen, M and Lataretu, M and Lemieux, J and Liu, C and Malavige, GN and Mashe, T and Mongkolsapaya, J and Montes, B and Mora, },
doi = {10.1038/s41592-025-02947-1},
journal = {Nat Methods},
title = {Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.},
url = {http://dx.doi.org/10.1038/s41592-025-02947-1},
year = {2026}
}
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TY  - JOUR
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.
AU  - Hunt,M
AU  - Hinrichs,AS
AU  - Anderson,D
AU  - Karim,L
AU  - Dearlove,BL
AU  - Knaggs,J
AU  - Constantinides,B
AU  - Fowler,PW
AU  - Rodger,G
AU  - Street,T
AU  - Lumley,S
AU  - Webster,H
AU  - Sanderson,T
AU  - Ruis,C
AU  - Kotzen,B
AU  - de,Maio N
AU  - Amenga-Etego,LN
AU  - Amuzu,DSY
AU  - Avaro,M
AU  - Awandare,GA
AU  - Ayivor-Djanie,R
AU  - Barkham,T
AU  - Bashton,M
AU  - Batty,EM
AU  - Bediako,Y
AU  - De,Belder D
AU  - Benedetti,E
AU  - Bergthaler,A
AU  - Boers,SA
AU  - Campos,J
AU  - Carr,RAA
AU  - Chen,YYC
AU  - Cuba,F
AU  - Dattero,ME
AU  - Dejnirattisai,W
AU  - Dilthey,A
AU  - Duedu,KO
AU  - Endler,L
AU  - Engelmann,I
AU  - Francisco,NM
AU  - Fuchs,J
AU  - Gnimpieba,EZ
AU  - Groc,S
AU  - Gyamfi,J
AU  - Heemskerk,D
AU  - Houwaart,T
AU  - Hsiao,N-Y
AU  - Huska,M
AU  - Hölzer,M
AU  - Iranzadeh,A
AU  - Jarva,H
AU  - Jeewandara,C
AU  - Jolly,B
AU  - Joseph,R
AU  - Kant,R
AU  - Ki,KKK
AU  - Kurkela,S
AU  - Lappalainen,M
AU  - Lataretu,M
AU  - Lemieux,J
AU  - Liu,C
AU  - Malavige,GN
AU  - Mashe,T
AU  - Mongkolsapaya,J
AU  - Montes,B
AU  - Mora,JAM
AU  - Morang'a,CM
AU  - Mvula,B
AU  - Nagarajan,N
AU  - Nelson,A
AU  - Ngoi,JM
AU  - da,Paixão JP
AU  - Panning,M
AU  - Poklepovich,T
AU  - Quashie,PK
AU  - Ranasinghe,D
AU  - Russo,M
AU  - San,JE
AU  - Sanderson,ND
AU  - Scaria,V
AU  - Screaton,G
AU  - Sessions,OM
AU  - Sironen,T
AU  - Sisay,A
AU  - Smith,D
AU  - Smura,T
AU  - Supasa,P
AU  - Suphavilai,C
AU  - Swann,J
AU  - Tegally,H
AU  - Tegomoh,B
AU  - Vapalahti,O
AU  - Walker,A
AU  - Wilkinson,RJ
AU  - Williamson,C
AU  - Zair,X
AU  - IMSSC,Laboratory Network Consortium
AU  - de,Oliveira T
AU  - Peto,TE
AU  - Crook,D
AU  - Corbett-Detig,R
AU  - Iqbal,Z
DO  - 10.1038/s41592-025-02947-1
PY  - 2026///
TI  - Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.
T2  - Nat Methods
UR  - http://dx.doi.org/10.1038/s41592-025-02947-1
UR  - https://www.ncbi.nlm.nih.gov/pubmed/41663577
ER  -
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