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

Some of these principles are, necessarily, specific to the COVID-19 pandemic, reflecting the new normal of large-scale real-time generation of virus genome sequences. The nomenclature system is not intended to represent every evolutionary change in SARS-CoV-2, as these will number many thousand by the end of the pandemic. Instead, the focus is on genetic changes associated with important epidemiological and biological events. Fortunately, because of the early sampling and genome sequencing of COVID-19 cases in China, especially in Hubei province, it appears that the "root sequence" of SARS-CoV-2 is known. Many of the genomes from the earliest sampled cases are genetically identical and hence also likely identical to the most recent common ancestor of all sampled viruses. This occurrence is different to previous viruses and epidemics and provides some advantages for the development of a rational and scalable classification scheme. Specifically, setting the "reference sequence" to be the "root sequence" forms a natural starting point, as direct comparisons in the number and position of mutations can be made with respect to the root sequence.