Abstract

The ongoing pandemic spread of a novel human coronavirus, SARS-COV-2, 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. 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 de-labelling virus lineages that become unobserved and hence are likely 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.

Rights

This content is not covered by the Open Government Licence. Please see source record or item for information on rights and permissions.

Cite as

Rambaut, A., Holmes, E., O'Toole, Á., Hill, V., McCrone, J., Ruis, C., du Plessis, L. & Pybus, O. 2020, 'A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology', Nature Microbiology, 5, pp. 1403-1407. https://doi.org/10.1038/s41564-020-0770-5

Downloadable citations

Download HTML citationHTML Download BIB citationBIB Download RIS citationRIS
Last updated: 30 September 2022
Was this page helpful?