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Population Genetics of SARS-CoV-2: Disentangling Effects of Sampling Bias and infection clusters

Genomics, Proteomics & Bioinformatics 2020年第6期18卷 640-647页

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 Beijing Institute of Genomics Chinese Academy of SciencesBeijing 100101China China National Center for Bioinformation Beijing 100101China University of Chinese Academy of Sciences Beijing 100049China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223China

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.

关键词： COVID-19 SARS-CoV-2 Phylogenetic divergence infection cluster Sampling bias

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