Cited by 2,543SARS-CoV-2 and COVID-19 ResearchGenomics and Phylogenetic StudiesSARS-CoV-2 detection and testing

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A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

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Rambaut, Andrew, Holmes, Edward C., O’Toole, Áine, Hill, Verity, McCrone, John T., Ruis, Christopher, du Plessis, Louis, Pybus, Oliver G.·2020·Nature Microbiology

DOI 10.1038/s41564-020-0770-5PMC PMC7610519

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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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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: Rambaut, Andrew
Holmes, Edward C.
O’Toole, Áine
Hill, Verity
McCrone, John T.
Ruis, Christopher
du Plessis, Louis
Pybus, Oliver G.
Venue: Nature Microbiology
Publisher: Springer Science and Business Media LLC
Published: 2020-07-15
Volume: 5
Issue: 11
Pages: 1403-1407
ISSN: 2058-5276 (ISSN-L)
DOI: 10.1038/s41564-020-0770-5
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: www.springernature.com/gp/researchers/text-and-data-mining (tdm)
www.springernature.com/gp/researchers/text-and-data-mining (vor)
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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A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

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