Abstract: Microsatellites were crucial in the control of SARS-CoV-2 genomic expression, population genetic evolution and host immunity interaction. The NCBI database and microsatellite analysis systems were utilized in this study to screen and test the correlation between the number of different microsatellites and genetic characteristics in the original strain and variants of SARS-CoV-2, as well as to investigate the microsatellite features affecting the genetic diversity of SARS-CoV-2. By bioinformatics analysis, the whole-genome sequence database of SARS-CoV-2 was constructed, and information on the genetic characteristics, microsatellite numbers and relative position distribution characteristics of microsatellites in the sequence database were collected; correlation analysis between the number of various microsatellites and one-sample Wilcoxon signed-rank non-parametric tests were performed by biostatistical analysis. The findings revealed that the quantity, proportion, and relative distributing features of various microsatellites in the original strain and SARS-CoV-2 variants (except Lambda and Omicron) were comparable. The proportion of microsatellites with 2 nucleotide repeats (77%～78%), 3 motif repeats (22%～23%), and 6 bp full-length (73%) were relatively high, and the microsatellite density of ORF3a (0.48/100 bp), E (0.44/100 bp), and N (0.40/100 bp) coding regions were also high. The total average number of microsatellites was negatively correlated with the base content (r: –0.799 6, P: 0.009 7), whereas no significant correlation with the number of base substitutions. This study enriched the research on the genetic diversity as well as the evolutionary mechanism of SARS-CoV-2 in the field of molecular biology and provided new ideas for the prevention and control of the corona virus disease 2019 pandemic.
Key words: SARS-CoV-2; microsatellites; genetic diversity; base content bias; population genetic evolution
（Acta Laser Biology Sinica, 2023, 32(3): 208-216）