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

During the early phase of the pandemic, it will be possible to unambiguously assign a genome to a lineage through the presence/absence of particular sets of mutations. However, a central component of a useful nomenclature system is that it focuses on those virus lineages that contribute most to global transmission and genetic diversity. Hence, rather than naming every new possible lineage, classification should focus on those that have exhibited onward spread in the population, particularly those that have seeded an epidemic in a new location. For example, the large epidemic in Lombardy, northern Italy, thought to have begun in early . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.17.046086 doi: bioRxiv preprint February (Zehender et al. 2020) , has since been disseminated to other locations in northern Europe and elsewhere.