Coronavirus Analysis

https://github.com/galaxyproject/SARS-CoV-2 Haplotype analyses were conducted on the alignment of coding regions using DnaSP. Evolutionary analysis of haplotypes used NETWORK. Population size changes were estimated using both DnaSP and Arlequin genome sequences were aligned using MAFFT,18 then the alignment was manually checked using Geneious (Biomatters, New Zealand). The alignment was then imported into DnaSP19 for haplotype analyses. Population size changes were estimated based on a constant population size hypothesis using DnaSP, in combination with neutrality tests (Tajima’s D and Fu’s Fs). We also used Arlequin20 to test the sudden population expansion hypothesis and to calculate the expansion parameter tau (τ) if sudden population expansion is not rejected. We used the formula t=τ/2u to estimate the time since expansion (in days). In the formula, u is the cumulative substitution rate per year (for the genome sequence, so we used the formula u = μk to calculate it, where μ is the substitution rate per site per year, and k is the genome sequence length (29,358 bp for the CDS matrix). In this study, the substitution rate was set as 0·92×10 3 (95% CI, 0·33×10 3 1·46×10 3) substitution/site/year based on the most recent estimation for SARS CoV 2.21 A median joining network of haplotypes was generated by the NETWORK program22 with bat RaTG13 CoV as the outgroup. Phylogenomic analyses of haplotypes were performed using IQ TREE23. We conducted likelihood mapping and SH like approximate likelihood ratio tests to assess the phylogenetic information and branch supports,