Comparative genomic analysis revealed specific mutation pattern between human coronavirus SARS-CoV-2 and Bat-SARSr-CoV RaTG13

Longxian Lv; Gaolei Li; Jinhui Chen; Xinle Liang; Yudong Li

The newly identified SARS-CoV-2 strain WIV04 genome sequence was closely related with Bat-SARSr-CoV RaTG13 and Bat-SL-CoVZC45, which was collected from host Rhinolophus affinis (5) . Compared with RaTG13 genome, many nucleotide substitutions are observed, but there are only five small inserts and deletions (indels) mutations, and the largest insert segment in WIV04 genome was " CGGCGGGCACGT " sequence, which is located near the boundary of S1 and S2 regions of spike protein. Interestingly, only synonymous mutation are observed near this insertion sequence (Fig. 1 , panel C). Compared with Bat-SL-CoVZC45 genome, this insert segment is detected as well, but non-synonymous mutations are also observed around it. Then, we further compared the proportion of synonymous mutations in spike gene between WIV04 and RaTG13 or Bat-SL-CoVZC45. The ratio of nucleotide substitutions (263 NT) to amino acid substitutions (29 AA) was 9.07 from WIV04 to RaTG13, which was significantly higher than the ratio (3.91, 864/221) from WIV04 to Bat-SL-CoVZC45 (p < 0.05) (Fig. 2) . Moreover, we also observed that the synonymous mutations increased in whole genome level between WIV04 and RaTG13 than that between WIV04 and Bat-SL-CoVZC45.