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

Andrew Rambaut; Edward C Holmes; Verity Hill; Aine OToole; John McCrone; Chris Ruis; Louis du Plessis; Oliver Pybus

Such systems are useful for discussing epidemiology and transmission when the number of taxonomic labels remains roughly constant through time; this is the case for slowly evolving pathogens (e.g. many bacteria) and for rapidly evolving viruses with low rates of lineage turnover (e.g. HIV and HCV). In contrast, some rapidly evolving viruses such as influenza A are characterised by high rates of lineage turnover, so that the genetic diversity circulating in any particular year largely emerges out of and replaces the diversity present in the preceding few years. For human seasonal influenza, this behaviour is the result of strong natural selection among competing lineages. In such circumstances a more explicitly phylogenetic classification system is used; for example, avian influenza viruses are classified into 'subtypes', 'clades' and 'higher order clades' according to several quantitative criteria (WHO/OIE/FAO H5N1 Evolution Working Group 2012). Such a system can provide a convenient way to refer to the emergence of new (and potentially antigenically distinct) variants and is suitable for the process of selecting the component viruses for the regularly updated influenza vaccine. A similar approach to tracking antigenic diversity may be needed to inform SARS-CoV-2 vaccine design efforts. While useful, we recognise that dynamic nomenclature systems based on genetic distance thresholds have the potential to over-accumulate cumbersome lineage names.