J Med Virol. 2021 Sep 10. doi: 10.1002/jmv.27331. Online ahead of print.
ABSTRACT
SARS-CoV-2 is a newly discovered beta coronavirus at the end of 2019, which is highly pathogenic and poses a serious threat to human health. In this paper, 1,875 SARS-CoV-2 whole genome sequences and the sequence coding spike protein (S gene) sampled from the United States were used for the bioinformatics analysis to study the molecular evolutionary characteristics of its genome and spike protein. The MCMC method was used to calculate the evolution rate of the whole genome sequence and the nucleotide mutation rate of S gene. The results showed that the nucleotide mutation rate of the whole genome was 6.677×10-4 substitution per site per year, and the nucleotide mutation rate of S gene was 8.066×10-4 substitution per site per year, which was at a medium level compared with other RNA viruses. Our findings confirmed the scientific hypothesis that the rate of evolution of the virus gradually decreases over time. We also found 13 statistically significant positive selection sites in SARS-CoV-2 genome. In addition, the results showed that there were 101 non-synonymous mutation sites in the amino acid sequence of S protein, including seven putative harmful mutation sites. This paper preliminarily clarified the evolutionary characteristics of SARS-CoV-2 in the United States, providing a scientific basis for future surveillance and prevention of virus variants. This article is protected by copyright. All rights reserved.
PMID:34506640 | DOI:10.1002/jmv.27331
