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

Abstract

The ongoing pandemic spread of a novel human coronavirus, SARS-COV-2, associated with severe pneumonia disease (COVID-19), has resulted in the generation 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. 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 declassifying virus lineages that become unobserved and hence are likely 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.

The proximal origin of SARS-CoV-2

“…Estimates of the timing of the most recent common ancestor of SARS-CoV-2 made with current sequence data point to emergence of the virus in late November 2019 to early December 2019 23 , compatible with the earliest retrospectively confirmed cases 24 . Hence, this scenario presumes a period of unrecognized transmission in humans between the initial zoonotic event and the acquisition of the polybasic cleavage site.…”

Evolving COVID-19 conundrum and its impact

“…Otherwise, the approach might generate a deduced network based on Hamming distance and a presumed cascade of mutational accumulations, leaving the conclusion uncorroborated by existing evidence. In fact, they are clustered within the lineages previously grouped by a maximum-likelihood method (6). It is tempting to assume that the A, B, and C groups were adapting to the local environment in specific geographical regions as the authors speculate.…”

Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission

“…Reactive screening of a further 18 ward F staff identified an additional three positive asymptomatic HCWs (Figure 4). Sequence analysis indicated that 6/9 samples from HCW who worked on ward F belonged to SARS-CoV-2 lineage B•1 (currently known to be circulating in at least 43 countries 20 ), with a further two that belonged to B1•7 and one that belonged to B2•1. This suggests more than two introductions of SARS-CoV-2 into the HCW population on ward F ( Figures S2-S3, Table S6).…”