The DOI matches its Crossref record; 16 of the 18 references it cites were found in a registry or an index.
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology
Open accessPublished version of a preprint
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
A novel coronavirus from patients with pneumonia in China, 2019
Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., Zhao, X., Huang, B., Shi, W., Lu, R., et al. (2020) · New England Journal of Medicine · doi:10.1056/nejmoa2001017 · Cited by 28,244
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
Katoh, K. (2002) · Nucleic Acids Research · doi:10.1093/nar/gkf436 · Cited by 17,027
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
Minh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M. D., von Haeseler, A., & Lanfear, R. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa015 · Cited by 16,873
Lu, R., Zhao, X., Li, J., Niu, P., Yang, B., Wu, H., Wang, W., Song, H., Huang, B., Zhu, N., et al. (2020) · The Lancet · doi:10.1016/s0140-6736(20)30251-8 · Cited by 11,907
Self-citationA new coronavirus associated with human respiratory disease in China
Wu, F., Zhao, S., Yu, B., Chen, Y.-M., Wang, W., Song, Z.-G., Hu, Y., Tao, Z.-W., Tian, J.-H., Pei, Y.-Y., et al. (2020) · Nature · doi:10.1038/s41586-020-2008-3 · Cited by 11,688
Self-citationUltrafast Approximation for Phylogenetic Bootstrap
Minh, B. Q., Nguyen, M. A. T., & von Haeseler, A. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst024 · Cited by 4,844
GISAID: Global initiative on sharing all influenza data – from vision to reality
Shu, Y., & McCauley, J. (2017) · Eurosurveillance · doi:10.2807/1560-7917.es.2017.22.13.30494 · Cited by 3,039
Yang, Z. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00160154 · Cited by 2,960
(1986) · Cited by 2,570
Smith, D. B., Bukh, J., KUIKEN, C. L., Muerhoff, A. S., Rice, C. M., Stapleton, J. T., & Peter Simmonds, K. (2013) · Hepatology · doi:10.1002/hep.26744 · Cited by 1,352
Cited by
Sorted by citations
SARS-CoV-2 variants, spike mutations and immune escape
Harvey, W. T., Carabelli, A. M., Jackson, B., Gupta, R. K., Thomson, E. C., Harrison, E. M., Ludden, C., Reeve, R., Rambaut, A., COVID-19 Genomics UK (COG-UK) Consortium, et al. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00573-0 · Cited by 3,528
Self-citationEstimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England
Davies, N. G., Abbott, S., Barnard, R. C., Jarvis, C. I., Kucharski, A. J., Munday, J. D., Pearson, C. A. B., Russell, T. W., Tully, D. C., Washburne, A. D., et al. (2021) · Science · doi:10.1126/science.abg3055 · Cited by 2,581
Detection of a SARS-CoV-2 variant of concern in South Africa
Tegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., Doolabh, D., Pillay, S., San, E. J., Msomi, N., et al. (2021) · Nature · doi:10.1038/s41586-021-03402-9 · Cited by 2,510
Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization
Planas, D., Veyer, D., Baidaliuk, A., Staropoli, I., Guivel-Benhassine, F., Rajah, M. M., Planchais, C., Porrot, F., Robillard, N., Puech, J., et al. (2021) · Nature · doi:10.1038/s41586-021-03777-9 · Cited by 1,992
Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
Viana, R. P. E. S., Moyo, S. M., Amoako, D. G., Tegally, H., Scheepers, C., Althaus, C. L., Anyaneji, U. J., Bester, P. A., Boni, M. F., Chand, M., et al. (2022) · Nature · doi:10.1038/s41586-022-04411-y · Cited by 1,678
Self-citation
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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
