{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,16]],"date-time":"2024-09-16T10:00:38Z","timestamp":1726480838342},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,5,14]],"date-time":"2024-05-14T00:00:00Z","timestamp":1715644800000},"content-version":"vor","delay-in-days":1402,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2020,7,12]],"date-time":"2020-07-12T00:00:00Z","timestamp":1594512000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2020,7,2]],"date-time":"2020-07-02T00:00:00Z","timestamp":1593648000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"publisher","award":["2020YFC0847000"],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31571370","91731302","31772435"],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002855","name":"Ministry of Science and Technology of the People's Republic of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002855","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2020,12,1]]},"abstract":"Abstract<\/jats:title>\n 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 COVID-19. However, 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 misinterpretation. In 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 SARS-CoV-2. The mutation rate is inferred to be 8.69 \u00d7 10\u22124 per site per year with a 95% confidence interval (CI) of [8.61 \u00d7 10\u22124, 8.77 \u00d7 10\u22124], 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 Market. We 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 selection. Our 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 SARS-CoV-2. Software for implementing VirusMuT can be downloaded at https:\/\/bigd.big.ac.cn\/biocode\/tools\/BT007081.<\/jats:p>","DOI":"10.1016\/j.gpb.2020.06.001","type":"journal-article","created":{"date-parts":[[2020,7,12]],"date-time":"2020-07-12T03:45:19Z","timestamp":1594525519000},"page":"640-647","update-policy":"http:\/\/dx.doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":39,"title":["Population Genetics of SARS-CoV-2: Disentangling Effects of Sampling Bias and Infection Clusters"],"prefix":"10.1093","volume":"18","author":[{"ORCID":"http:\/\/orcid.org\/0000-0002-7892-5965","authenticated-orcid":false,"given":"Qi","family":"Liu","sequence":"first","affiliation":[{"name":"Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101 , China"},{"name":"China National Center for Bioinformation , Beijing 100101 , China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049 , China"}]},{"ORCID":"http:\/\/orcid.org\/0000-0001-7262-1322","authenticated-orcid":false,"given":"Shilei","family":"Zhao","sequence":"additional","affiliation":[{"name":"Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101 , China"},{"name":"China National Center for Bioinformation , Beijing 100101 , China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049 , China"}]},{"ORCID":"http:\/\/orcid.org\/0000-0003-0237-4092","authenticated-orcid":false,"given":"Cheng-Min","family":"Shi","sequence":"additional","affiliation":[{"name":"Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101 , China"},{"name":"China National Center for Bioinformation , Beijing 100101 , China"}]},{"ORCID":"http:\/\/orcid.org\/0000-0003-2409-8770","authenticated-orcid":false,"given":"Shuhui","family":"Song","sequence":"additional","affiliation":[{"name":"Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101 , China"},{"name":"China National Center for Bioinformation , Beijing 100101 , China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049 , China"}]},{"ORCID":"http:\/\/orcid.org\/0000-0002-1610-2234","authenticated-orcid":false,"given":"Sihui","family":"Zhu","sequence":"additional","affiliation":[{"name":"Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101 , China"},{"name":"China National Center for Bioinformation , Beijing 100101 , China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049 , China"}]},{"ORCID":"http:\/\/orcid.org\/0000-0002-0276-355X","authenticated-orcid":false,"given":"Yankai","family":"Su","sequence":"additional","affiliation":[{"name":"Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101 , China"},{"name":"China National Center for Bioinformation , Beijing 100101 , China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049 , China"}]},{"ORCID":"http:\/\/orcid.org\/0000-0002-4396-8287","authenticated-orcid":false,"given":"Wenming","family":"Zhao","sequence":"additional","affiliation":[{"name":"Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101 , China"},{"name":"China National Center for Bioinformation , Beijing 100101 , China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049 , China"}]},{"ORCID":"http:\/\/orcid.org\/0000-0003-1041-1172","authenticated-orcid":false,"given":"Mingkun","family":"Li","sequence":"additional","affiliation":[{"name":"Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101 , China"},{"name":"China National Center for Bioinformation , Beijing 100101 , China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049 , China"},{"name":"Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences , Kunming 650223 , China"}]},{"ORCID":"http:\/\/orcid.org\/0000-0002-9922-9723","authenticated-orcid":false,"given":"Yiming","family":"Bao","sequence":"additional","affiliation":[{"name":"Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101 , China"},{"name":"China National Center for Bioinformation , Beijing 100101 , China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049 , China"}]},{"ORCID":"http:\/\/orcid.org\/0000-0002-6895-8472","authenticated-orcid":false,"given":"Yongbiao","family":"Xue","sequence":"additional","affiliation":[{"name":"Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101 , China"},{"name":"China National Center for Bioinformation , Beijing 100101 , China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049 , China"}]},{"ORCID":"http:\/\/orcid.org\/0000-0002-9829-6561","authenticated-orcid":false,"given":"Hua","family":"Chen","sequence":"additional","affiliation":[{"name":"Beijing Institute of 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Published by Elsevier B.V. and Science Press on behalf of Beijing Institute of Genomics, Chinese Academy of Sciences and Genetics Society of China.","name":"copyright","label":"Copyright"}]}}
