Population Genetics of SARS-CoV-2: Disentangling Effects of Sampling Bias and Infection Clusters

作     者：Qi Liu Shilei Zhao Cheng-Min Shi Shuhui Song Sihui Zhu Yankai Su Wenming Zhao Mingkun Li Yiming Bao Yongbiao Xue Hua Chen Qi Liu;Shilei Zhao;Cheng-Min Shi;Shuhui Song;Sihui Zhu;Yankai Su;Wenming Zhao;Mingkun Li;Yiming Bao;Yongbiao Xue;Hua Chen

作者机构：Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China China National Center for BioinformationBeijing 100101China University of Chinese Academy of SciencesBeijing 100049China Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunming 650223China 

出 版 物：《Genomics, Proteomics & Bioinformatics》 (基因组蛋白质组与生物信息学报（英文版）)

年 卷 期：2020年第18卷第6期

页      面：640-647页

核心收录：

学科分类：1007[医学-药学(可授医学、理学学位)] 100705[医学-微生物与生化药学] 1001[医学-基础医学(可授医学、理学学位)] 100103[医学-病原生物学] 10[医学] 

基　　金：This study was supported by the National Key R&D Program of China(Grant No.2020YFC0847000) the National Natural Science Foundation of China(Grant Nos.31571370,91731302,and 31772435) 

主　　题：COVID-19 SARS-CoV-2 Phylogenetic divergence Infection cluster Sampling bias 

摘      要：A novel RNA virus,the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),is responsible for the ongoing outbreak of coronavirus disease 2019(COVID-19).Population genetic analysis could be useful for investigating the origin and evolutionary dynamics of ***,due to extensive sampling bias and existence of infection clusters during the epidemic spread,direct applications of existing approaches can lead to biased parameter estimations and data *** this study,we first present robust estimator for the time to the most recent common ancestor(TMRCA)and the mutation rate,and then apply the approach to analyze 12,909 genomic sequences of *** mutation rate is inferred to be 8.69×10^(−4) per site per year with a 95%confidence interval(CI)of[8.61×10^(−4),8.77×10^(−4)],and the TMRCA of the samples inferred to be Nov 28,2019 with a 95%CI of[Oct 20,2019,Dec 9,2019].The results indicate that COVID-19 might originate earlier than and outside of Wuhan Seafood *** further demonstrate that genetic polymorphism patterns,including the enrichment of specific haplotypes and the temporal allele frequency trajectories generated from infection clusters,are similar to those caused by evolutionary forces such as natural *** results show that population genetic methods need to be developed to efficiently detangle the effects of sampling bias and infection clusters to gain insights into the evolutionary mechanism of *** for implementing VirusMuT can be downloaded at https://***/biocode/tools/BT007081.