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

The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.04.976662 doi: bioRxiv preprint each window. To indicate the relative position of the mutations in the genome, we 1 8 0 selected the EPI ISL 402124 sequence as the reference genome. The alignment was then imported into DnaSP for haplotype analyses. Population BEAST using a Bayesian Markov chain Monte Carlo (MCMC) method with a strict 1 9 5 clock. In this study, the substitution rate was set as 0.92×10 -3 (95% CI, 1 9 6 0.33×10 -3 -1.46×10 -3 ) substitution/site/year based on the most recent estimation for 1 9 7 SARS-CoV-2 [25]. The other parameters were set as follows: extended Bayesian 1 9 8 skyline process, 10 million MCMC generations, sampling every 1,000 th iteration, the 1 9 9 initial 25% burn-in. Tracer was used to check the convergence of the MCMC analyses 2 0 0 (effective sample size [ESS] values >200). Convergence of the two independent 2 0 1 MCMC runs was assessed in Tracer, as was convergence of model parameter values 2 0 2 (ESS) to ensure ESS values >200. 2 0 3 author/funder. All rights reserved. No reuse allowed without permission.