Pathology

Virus

Disease

Coronavirus disease 2019 (COVID-19)

Infectious disease (medical specialty)

Biology

Codon usage bias

Gene

Nonsynonymous substitution

Synonymous substitution

Genome

Molecular evolution

Virology

Whole genome sequencing

Silent mutation

Coronavirus

Mutation

Missense mutation

Genetics

Medicine

Mutation rate

Journal of Medical Virology

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, 1875 SARS-CoV-2 whole genome sequences and the sequence coding spike protein (S gene) sampled from the United States were used for 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 the S gene. The results showed that the nucleotide mutation rate of the whole genome was 6.677 × 10

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