Abstract
Here we aim to describe early mutational events across samples from publicly available SARS-CoV-2 sequences from the sequence read archive and GenBank repositories. Up until 27 March 2020, we downloaded 50 illumina datasets, mostly from China, USA (WA State) and Australia (VIC). A total of 30 datasets (60%) contain at least a single founder mutation and most of the variants are missense (over 63%). Five-point mutations with clonal (founder) effect were found in USA next-generation sequencing samples. Sequencing samples from North America in GenBank (22 April 2020) present this signature with up to 39% allele frequencies among samples (n = 1,359). Australian variant signatures were more diverse than USA samples, but still, clonal events were found in these samples. Mutations in the helicase, encoded by the ORF1ab gene in SARS-CoV-2 were predominant, among others, suggesting that these regions are actively evolving. Finally, we firmly urge that primer sets for diagnosis be carefully designed, since rapidly occurring variants would affect the performance of the reverse transcribed quantitative PCR (RT-qPCR) based viral testing.
Highlights
The COVID-19 pandemic caused by a novel 2019 SARS coronavirus, known as SARS-CoV-2, is rapidly evolving worldwide, surpassing the 8000 total cases of 2002-2004 SARS coronavirus outbreak (SARS-CoV-1) after one month of the initially identified case on December 31, 2019, in Wuhan city, China (Wilder-Smith et al 2020)
One of the striking genomic features of this novel virus is the presence of a novel furin-like cleavage site in the S-protein of the virus, which differs from SARS-CoV-1 and may have implications for the life cycle and pathogenicity of the novel virus (Coutard et al 2020; Wu et al 2020a)
We reveal the early mutational events in small samples from mainly two geographically unrelated populations (Washington, USA, and Victoria, Australia) and we compared these results with variants observed in submitted GenBank sequences in NCBI viral portal, from different countries
Summary
The COVID-19 pandemic caused by a novel 2019 SARS coronavirus, known as SARS-CoV-2, is rapidly evolving worldwide, surpassing the 8000 total cases of 2002-2004 SARS coronavirus outbreak (SARS-CoV-1) after one month of the initially identified case on December 31, 2019, in Wuhan city, China (Wilder-Smith et al 2020). As SARS-CoV-2 is human-to-human transmitted, it is a threat to the global population. It is critical to understand SARS-CoV-2 characteristics to deal with this ongoing pandemic and to develop future treatments. SARS-CoV2 virus is an enveloped, positive-stranded RNA virus with a large genome (29.9 kb) belonging to the family Coronaviridae, order Nidovirales (de Wit et al 2016). One of the striking genomic features of this novel virus is the presence of a novel furin-like cleavage site in the S-protein of the virus, which differs from SARS-CoV-1 and may have implications for the life cycle and pathogenicity of the novel virus (Coutard et al 2020; Wu et al 2020a). It was suggested that SARS-CoV-2 is a close relative of the RaTG13 bat-derived coronavirus
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