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

Andrew Rambaut, Edward C. Holmes, Áine O'Toole, Verity Hill, JT McCrone, Christopher Ruis, Louis du Plessis, Oliver G. Pybus

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

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.
Original languageEnglish
Pages (from-to)1403-1407
Number of pages5
JournalNature Microbiology
Early online date15 Jul 2020
Publication statusPublished - 1 Nov 2020


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