Genome-wide data inferring the evolution and population demography of the novel pneumonia coronavirus (SARS-CoV-2)

Bin Fang; Linlin Liu; Xiao Yu; Xiang Li; Guojun Ye; Juan Xu; Ling Zhang; Faxian Zhan; Guiming Liu; Tao Pan; Yilin Shu; Yongzhong Jiang

On this analysis technique, to precisely decode the evolutionary history of 1 5 9 SARS-CoV-2, the genome EPI ISL 402131 (bat-RaTG13-CoV) from GISAID was 1 6 0 also included as the outgroup following the previous study [25] , because it is the 1 6 1 closest sister betacoronavirus to SARS-CoV-2.3. The 136 complete genome 1 6 2 sequences of SARS-CoV-2 and an outgroup (bat-RaTG13-CoV) were aligned using 1 6 3 MAFFT then the alignment was manually checked using Geneious. For probing the 1 6 4 haplotypes relationships among localities, the Network v.4.6.1 (Fluxus Technology, 1 6 5 Suffolk, UK) was used to construct the minimum-spanning network based on the full 1 6 6 median-joining algorithm [26] . During the alignment, 10 genomes containing 1 6 7 ambiguous sites or "N" bases or more degenerated bases were excluded in this study 1 6 8 (Table S1 ). In addition, 4 genome sequences (EPI ISL 409067, EPI ISL 412981, EPI 1 6 9 ISL 407071 and EPI ISL 408489) with one degenerated base were included, which 1 7 0 were divided into two sequences without degenerated base. For ensuring the accuracy 1 7 1 of this analysis, the 5'UTR and 3'UTR contain missing and ambiguous sites of both 1 7 2 regions were excluded in the following alignment analyses. DnaSP v.5.10 [27] was 1 7 3 used to convert the relevant format. Population genetic indices in was estimated in 1 7 4