{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T15:16:29Z","timestamp":1789139789296,"version":"build-2803163510"},"reference-count":82,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2022,8,8]],"date-time":"2022-08-08T00:00:00Z","timestamp":1659916800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"MOST","award":["109-2311-B-002-023-MY3"],"award-info":[{"award-number":["109-2311-B-002-023-MY3"]}]},{"name":"MOST","award":["109-2327-B-002-009"],"award-info":[{"award-number":["109-2327-B-002-009"]}]},{"name":"MOST","award":["109-2634-F-002-043"],"award-info":[{"award-number":["109-2634-F-002-043"]}]},{"name":"MOST","award":["110-2621-B-001-003"],"award-info":[{"award-number":["110-2621-B-001-003"]}]},{"name":"MOST","award":["111-2321-B-002-017"],"award-info":[{"award-number":["111-2321-B-002-017"]}]},{"name":"MOST","award":["111-2634-F-002-017"],"award-info":[{"award-number":["111-2634-F-002-017"]}]},{"name":"National Taiwan University, College of Medicine","award":["NSC-131-5"],"award-info":[{"award-number":["NSC-131-5"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>One of the unique features of SARS-CoV-2 is its apparent neutral evolution during the early pandemic (before February 2020). This contrasts with the preceding SARS-CoV epidemics, where viruses evolved adaptively. SARS-CoV-2 may exhibit a unique or adaptive feature which deviates from other coronaviruses. Alternatively, the virus may have been cryptically circulating in humans for a sufficient time to have acquired adaptive changes before the onset of the current pandemic. To test the scenarios above, we analyzed the SARS-CoV-2 sequences from minks (Neovision vision) and parental humans. In the early phase of the mink epidemic (April to May 2020), nonsynonymous to synonymous mutation ratio per site in the spike protein is 2.93, indicating a selection process favoring adaptive amino acid changes. Mutations in the spike protein were concentrated within its receptor-binding domain and receptor-binding motif. An excess of high-frequency derived variants produced by genetic hitchhiking was found during the middle (June to July 2020) and late phase I (August to September 2020) of the mink epidemic. In contrast, the site frequency spectra of early SARS-CoV-2 in humans only show an excess of low-frequency mutations, consistent with the recent outbreak of the virus. Strong positive selection in the mink SARS-CoV-2 implies that the virus may not be preadapted to a wide range of hosts and illustrates how a virus evolves to establish a continuous infection in a new host. Therefore, the lack of positive selection signal during the early pandemic in humans deserves further investigation.<\/jats:p>","DOI":"10.1093\/molbev\/msac156","type":"journal-article","created":{"date-parts":[[2022,8,8]],"date-time":"2022-08-08T04:38:42Z","timestamp":1659933522000},"source":"Crossref","is-referenced-by-count":3,"title":["Contrasting Patterns in the Early Stage of SARS-CoV-2 Evolution between Humans and Minks"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4283-3118","authenticated-orcid":false,"given":"Jui-Hung","family":"Tai","sequence":"first","affiliation":[{"name":"Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University , Taipei , Taiwan"},{"name":"Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica , Taipei , Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hsiao-Yu","family":"Sun","sequence":"additional","affiliation":[{"name":"Taipei Municipal Zhongshan Girls High School , Taipei , Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi-Cheng","family":"Tseng","sequence":"additional","affiliation":[{"name":"Institute of Ecology and Evolutionary Biology, National Taiwan University , Taipei , Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6955-5571","authenticated-orcid":false,"given":"Guanghao","family":"Li","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sui-Yuan","family":"Chang","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University , Taipei , Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiou-Hwei","family":"Yeh","sequence":"additional","affiliation":[{"name":"Department of Microbiology, College of Medicine, National Taiwan University , Taipei , Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8316-3785","authenticated-orcid":false,"given":"Pei-Jer","family":"Chen","sequence":"additional","affiliation":[{"name":"Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University , Taipei , Taiwan"},{"name":"Department of Microbiology, College of Medicine, National Taiwan University , Taipei , Taiwan"},{"name":"Hepatitis Research Center, National Taiwan University College of Medicine and National Taiwan University Hospital , Taipei , Taiwan"},{"name":"Department of Internal Medicine, National Taiwan University College of Medicine and National Taiwan University Hospital , Taipei , Taiwan"},{"name":"Department of Medical Research, National Taiwan University College of Medicine and National Taiwan University Hospital , Taipei , Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2499-7071","authenticated-orcid":false,"given":"Shu-Miaw","family":"Chaw","sequence":"additional","affiliation":[{"name":"Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica , Taipei , Taiwan"},{"name":"Biodiversity Research Center, Academia Sinica , Taipei , Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1708-8734","authenticated-orcid":false,"given":"Hurng-Yi","family":"Wang","sequence":"additional","affiliation":[{"name":"Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University , Taipei , Taiwan"},{"name":"Institute of Ecology and Evolutionary Biology, National Taiwan University , Taipei , 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