Journal article
Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny
- Abstract:
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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.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
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- Publisher copy:
- 10.1038/s41592-025-02947-1
Authors
- Publisher:
- Springer Nature
- Journal:
- Nature Methods More from this journal
- Publication date:
- 2026-02-09
- Acceptance date:
- 2025-08-27
- DOI:
- EISSN:
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1548-7105
- ISSN:
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1548-7091
- Language:
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English
- Keywords:
- Pubs id:
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2284602
- Local pid:
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pubs:2284602
- Deposit date:
-
2025-08-28
- ARK identifier:
Terms of use
- Copyright holder:
- Hunt et al
- Copyright date:
- 2026
- Rights statement:
- © The Author(s) 2025. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
- Licence:
- CC Attribution (CC BY)
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