Abstract
Four signature groups of frequently occurred single-nucleotide variants (SNVs) were identified in over twenty-eight thousand high-quality and high-coverage SARS-CoV-2 complete genome sequences, representing different viral strains. Some SNVs predominated but were mutually exclusively presented in patients from different countries and areas. These major SNV signatures exhibited distinguishable evolution patterns over time. A few hundred patients were detected with multiple viral strain-representing mutations simultaneously, which may stand for possible co-infection or potential homogenous recombination of SARS-CoV-2 in environment or within the viral host. Interestingly nucleotide substitutions among SARS-CoV-2 genomes tended to switch between bat RaTG13 coronavirus sequence and Wuhan-Hu-1 genome, indicating the higher genetic instability or tolerance of mutations on those sites or suggesting that major viral strains might exist between Wuhan-Hu-1 and RaTG13 coronavirus.
Highlights
A novel betacoronavirus SARS-CoV-2 (Viruses CSGotICoTo, 2020) causing human coronavirus disease 2019 (COVID-19) was first reported in Wuhan, Hubei China in December 2019 (Wu et al, 2020a; Zhou et al, 2020; Zhu et al, 2020)
Comparing with four bat coronavirus genomes, we found that alternations of nucleotides on SARS-CoV-2 genome tend to occur at the same sites where bat coronavirus sequences were different from Wuhan-Hu-1
We further investigated protein structure alternations caused by the amino acid (AA) changes due to high-frequent non-synonymous single-nucleotide variants (SNVs)
Summary
A novel betacoronavirus SARS-CoV-2 (Viruses CSGotICoTo, 2020) causing human coronavirus disease 2019 (COVID-19) was first reported in Wuhan, Hubei China in December 2019 (Wu et al, 2020a; Zhou et al, 2020; Zhu et al, 2020). The pandemic of SARS-CoV2 has infected more than 12 million people over 180 countries and areas around the world with a death over a half million as of July 9, 2020 (Dong et al, 2020). Much effort has been devoted by scientists all over the world to understand the features of SARS-CoV2, the viral genome variations. Viral genomic mutations play a key role in propagation of SARS-COV-2
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