Molecular evolutionary characteristics of SARS-CoV-2 emerging in the United States


Posted: 2021-09-10 19:00:00
J Med Virol . 2021 Sep 10. doi: 10.1002/jmv.27331. Online ahead of print. Affiliations Expand Affiliations 1 National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, 201306, China. 2 Department of Developmental Biology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China. 3 School of Physical Education & Health Care, East China Normal University, Shanghai, 200241, China. 4 Central South University Xiangya Public Health School, Changsha, 410078, P.R.China. 5 College of Mathematics and Information Engineering, Jiaxing University, Jiaxing, 314033, P.R. China. Item in Clipboard Shihang Wang et al. J Med Virol. 2021. Show details Display options Display options Format J Med Virol . 2021 Sep 10. doi: 10.1002/jmv.27331. Online ahead of print. Affiliations 1 National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, 201306, China. 2 Department of Developmental Biology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China. 3 School of Physical Education & Health Care, East China Normal University, Shanghai, 200241, China. 4 Central South University Xiangya Public Health School, Changsha, 410078, P.R.China. 5 College of Mathematics and Information Engineering, Jiaxing University, Jiaxing, 314033, P.R. China. Item in Clipboard CiteDisplay options Display options Format 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. Keywords: Bioinformatics; Molecular evolution; SARS-CoV-2; Spike protein. This article is protected by copyright. All rights reserved. [x] Cite Copy Format: Send To [x]

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バイオクイックニュース日本語版
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