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

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.

Fig. 1

Maximum likelihood phylogeny of globally sampled sequences of SARS-CoV-2 downloaded from the GISAID database (http://gisaid.org) on May 18^th 2020. Five representative genomes are included from each of the defined lineages. The largest lineages that are defined by our proposed nomenclature system are highlighted with coloured areas and labelled on the right. The remaining lineages defined by the nomenclature system are denoted by triangles. The scale bar represents the number of nucleotide changes within the coding region of the genome.