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

• Published in: Nature microbiology Vol. 5; no. 11; pp. 1403 - 1407
• Main Authors: Rambaut, Andrew, Holmes, Edward C., O’Toole, Áine, Hill, Verity, McCrone, John T., Ruis, Christopher, du Plessis, Louis, Pybus, Oliver G.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.11.2020; Nature Publishing Group
• Subjects: 45; 631/114/1386; 631/114/739; 631/181/757; 631/326/596/2554; 631/326/596/4130; Betacoronavirus - genetics; Betacoronavirus - isolation & purification; Biomedical and Life Sciences; Coronavirus Infections - epidemiology; Coronavirus Infections - virology; Coronaviruses; COVID-19; Decision making; Disease transmission; Epidemiology; Genome, Viral; Genomes; Genotype; Humans; Infectious Diseases; Life Sciences; Medical Microbiology; Microbiology; Molecular Epidemiology; Nomenclature; Pandemics; Parasitology; Phylogenetics; Phylogeny; Pneumonia, Viral - epidemiology; Pneumonia, Viral - virology; SARS-CoV-2; Severe acute respiratory syndrome coronavirus 2; Virology
• ISSN: 2058-5276; 2058-5276
• DOI: 10.1038/s41564-020-0770-5

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. The authors propose a nomenclature of SARS-CoV-2 lineages to assist research on epidemiology and decision-making during the COVID-19 pandemic. This nomenclature is based on the SARS-CoV-2 phylogeny and designed to provide a real-time bird’s-eye view of the diversity of the hundreds of thousands of genome sequences collected worldwide. The authors develop a set of rules to produce a hierarchical four-level nomenclature of labels that is flexible and dynamic.