Comprehensive evolution and molecular characteristics of a large number of SARS-CoV-2 genomes reveal its epidemic trends

Bai, Yunmeng; Jiang, Dawei; Lon, Jerome R.; Chen, Xiaoshi; Hu, Meiling; Lin, Shudai; Chen, Zixi; Wang, Xiaoning; Meng, Yuhuan; Du, Hongli

Objectives To further reveal the phylogenetic evolution and molecular characteristics of the whole genome of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) based on a large number of genomes and provide a basis for the prevention and treatment of SARS-CoV-2. Methods Various evolution analysis methods were employed. Results The estimated ratio of the rates of non-synonymous to synonymous changes (Ka/Ks) of SARS-CoV-2 was 1.008 or 1.094 based on 622 or 3624 SARS-CoV-2 genomes and 9 key specific sites of highly linkage and four major haplotypes H1, H2, H3 and H4 were found. The results of Ka/Ks, detected population size and development trends of each major haplotype showed H3 and H4 subgroups were going through a purify evolution and almost disappeared after detection, indicating they might have existed for a long time. H1 and H2 subgroups were going through a near neutral or neutral evolution and globally increased with time, and the frequency of H1 was generally high in Europe and correlated to death rate (r>0.37), suggesting these two haplotypes might relate to infectivity or pathogenicity of SARS-CoV-2. Conclusions Several key specific sites and haplotypes related to infectivity or pathogenicity of SARS-CoV-2 as well as the possible earlier origin time and place of SARS-CoV-2 were indicated based on evolution and epidemiology of 16373 SARS-CoV-2 genomes.