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

While we regard this proposed nomenclature as practical and robust, it is important to recognise that phylogenetic inference carries statistical uncertainty and much of the available genome data is noisy, with incomplete genome coverage and errors arising from the amplification and sequencing processes. We have proposed a genome coverage threshold for proposing new lineages (see above), and we further suggest that sequences are not ascribed a lineage designation unless the genome coverage of that sequence exceeds 70% of the coding region. As noted above, when SARS-CoV-2 genetic diversity is low during the early pandemic period, there will be a direct association between lineage assignation and the presence of particular sets of mutations (with respect to the root sequence). This should help with the development of algorithmic genome labelling approaches. This task will become more complex, but still tractable, as SARS-CoV-2 genetic diversity accumulates, increasing the chance of both homoplasies and reverse mutations. Classification algorithms based on . 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 It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the .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 analysing patterns of mutations may be practical if they are frequently cross-checked and validated against phylogenetic estimations.