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

To infer whether the retention of synonymous mutations is supported or hindered by natural selection, we further studied non-synonymous substitution rate (dN) and synonymous substitution rate (dS) in spike gene (Table 1) . Generally, positive (Darwinian) selection increases, but negative (purifying) selection decreases the ratios of non-synonymous to synonymous substitution rates (dN/dS). The results showed that both dN and dS of S gene of SARS-CoV-2 WIV04 versus Bat-SARr-CoV RaTG13 were the lowest among all typical coronaviruses, while those of SARS-CoV Tor2 versus bat SARS-like coronavirus WIV1 were the second lowest. When the ratio of dN to dS of spike gene is compared, all the tested dN/dS are less than 1, indicating that these non-synonymous mutations are harmful, and negative selection will reduce their retention speed. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.27.969006 doi: bioRxiv preprint Among them, dN/dS of spike gene of SARS-CoV-2 WIV04 versus that of Bat-SARr-CoV RaTG13 was 0.04, which was the lowest among all comparisons, reconfirming that the rate of synonymous mutation was increased between WIV04 and RaTG13 strains. Moreover, dN/dS rate of polyprotein (ORF1ab) and nucleocapsid (N) genes were similar with that of spike gene (Table S2 ).