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A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology
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Abstract
The ongoing pandemic spread of a new human coronavirus, SARS-CoV-2, which is associated with severe pneumonia/disease (COVID-19), has resulted in the generation of tens of thousands of virus genome sequences. The rate of genome generation is unprecedented, yet there is currently no coherent nor accepted scheme for naming the expanding phylogenetic diversity of SARS-CoV-2. Here, we present a rational and dynamic virus nomenclature that uses a phylogenetic framework to identify those lineages that contribute most to active spread. Our system is made tractable by constraining the number and depth of hierarchical lineage labels and by flagging and delabelling virus lineages that become unobserved and hence are probably inactive. By focusing on active virus lineages and those spreading to new locations, this nomenclature will assist in tracking and understanding the patterns and determinants of the global spread of SARS-CoV-2.
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“The B.1.617 lineage, which is divided into three sublineages according to the PANGO classification 12 , derives from the B.1 lineage (D614G).”
From Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization (2021) · cites this paper as [12]
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Metadata
- Authors
- Rambaut, A., Holmes, E. C., O’Toole, Á., Hill, V., McCrone, J. T., Ruis, C., du Plessis, L., & Pybus, O. G.
- Affiliations
- University of Edinburgh (GB)
- The University of Sydney (AU)
- University of Cambridge (GB)
- University of Oxford (GB)
- Corresponding author
- Rambaut, Andrew
- Holmes, Edward C.
- Pybus, Oliver G.
- ORCID
- Venue
- Nature Microbiology
- Published
- 2020-07-15
- Volume
- 5
- Issue
- 11
- Pages
- 1403-1407
- ISSN
- 2058-5276 (ISSN-L)
- PMC
- PMC7610519
- OpenAlex
- W3043124965
- Cited by
- 2,543
- References
- 18
- Citations by year
- 2026: 86 · 2025: 141 · 2024: 235 · 2023: 365 · 2022: 700 · 2021: 851 · 2020: 163
- FWCI
- 68.76
- Type
- journal article
- Language
- en
- Update notices
- addendum (2021-01-29)
- Open access
- bronze
- doi.org
- Licence
- Locations
- Nature Microbiology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
- The Sydney eScholarship Repository (The University of Sydney) (submittedVersion)
- Funders
- Wellcome Trust (206298/Z/17/Z-ARTIC, FP7/2007–2013, Z/17/Z, 206298/Z/17/Z, 206298, 725422-ReservoirDOCS)
- European Commission (725422, 725422-RESERVOIRDOCS, 2007–2013, FP7 2007-2013, HORIZON2020, FP7/2007, COVID-19)
- Australian Research Council (FL170100022)
- FP7 Ideas: European Research Council (614725)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 detection and testing
- Keywords
- SARS-CoV-2, COVID-19 pandemic, virus nomenclature, phylogenetic lineages, genomic epidemiology
- MeSH terms
- Betacoronavirus, COVID-19, SARS-CoV-2, Genotype, Humans, Phylogeny, Pneumonia, Viral, Genome, Viral, Molecular Epidemiology, Coronavirus Infections, Pandemics
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