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Xu Xuanyu found that there is a clear positive choice for the amino acid sequence of S protein of SARS-CoV-2.
Molecular Evolution and Variation Characteristics of SARS-CoV-2 Spike Protein
Abstacts:SARS-CoV-2 is a new type of β-coronavirus newly discovered at the end of 2019, which is highly pathogenic and poses a serious threat to human health. In this paper, through the bioinformatics analysis of the new virus, the molecular evolution and mutation of its spike protein are studied. Using 213 SARS-CoV-2 samples obtained from the United States, the evolution rate of the whole genome sequence and spike protein sequence was analyzed by MCMC method, and it was found that the evolution rate of the whole genome was higher than that of the spike protein region. Compared with previous studies, the results obtained are lower in evolution rate. Because it is highly similar to the sequences of various bat SARS-like coronaviruses and SARS-CoV in GenBank, we established their phylogenetic tree to study the selective evolution of SARS-CoV-2 spike protein. According to the research results, there is a clear positive selection in the spike protein of SARS-CoV-2, and 12 statistically significant positive selection sites were found, of which 3 are located in the receptor binding domain of the spike protein. In addition, sequence alignment results show that multiple non-synonymous mutation sites have appeared in 213 SARS-CoV-2 samples. According to sequence homology and amino acid physical properties, there are mutations that can cause the structure and function of spike protein.
