{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,20]],"date-time":"2026-02-20T15:49:32Z","timestamp":1771602572286,"version":"3.50.1"},"reference-count":51,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2023,3,28]],"date-time":"2023-03-28T00:00:00Z","timestamp":1679961600000},"content-version":"vor","delay-in-days":86,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31970548"],"award-info":[{"award-number":["31970548"]}],"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","award":["91631110"],"award-info":[{"award-number":["91631110"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"the National Key Research and Development Projects of the Ministry of Science and Technology of China","award":["2021YFC2301300"],"award-info":[{"award-number":["2021YFC2301300"]}]},{"name":"the Natural Science Foundation of Hubei Province","award":["2021CFA012"],"award-info":[{"award-number":["2021CFA012"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,11,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Analyses of viral inter- and intra-host mutations could better guide the prevention and control of infectious diseases. For a long time, studies on viral evolution have focused on viral inter-host variations. Next-generation sequencing has accelerated the investigations of viral intra-host diversity. However, the theoretical basis and dynamic characteristics of viral intra-host mutations remain unknown. Here, using serial passages of the SA14-14-2 vaccine strain of Japanese encephalitis virus (JEV) as the in vitro model, the distribution characteristics of 1,788 detected intra-host single-nucleotide variations (iSNVs) and their mutated frequencies from 477 deep-sequenced samples were analyzed. Our results revealed that in adaptive (baby hamster kidney (BHK)) cells, JEV is under a nearly neutral selection pressure, and both non-synonymous and synonymous mutations represent an S-shaped growth trend over time. A higher positive selection pressure was observed in the nonadaptive (C6\/36) cells, and logarithmic growth in non-synonymous iSNVs and linear growth in synonymous iSNVs were observed over time. Moreover, the mutation rates of the NS4B protein and the untranslated region (UTR) of the JEV are significantly different between BHK and C6\/36 cells, suggesting that viral selection pressure is regulated by different cellular environments. In addition, no significant difference was detected in the distribution of mutated frequencies of iSNVs between BHK and C6\/36 cells.<\/jats:p>","DOI":"10.1093\/ve\/veac103","type":"journal-article","created":{"date-parts":[[2023,3,29]],"date-time":"2023-03-29T01:14:35Z","timestamp":1680052475000},"source":"Crossref","is-referenced-by-count":8,"title":["Viral intra-host evolutionary dynamics revealed via serial passage of Japanese encephalitis virus <i>in vitro<\/i>"],"prefix":"10.1093","volume":"9","author":[{"given":"Bangyao","family":"Sun","sequence":"first","affiliation":[{"name":"School of Medical Laboratory, Weifang Medical University , Baotong West Street, Weifang 261053, China"},{"name":"CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences , Xiaohongshan 44#, Wuhan 430000, China"},{"name":"Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences , Xiaohongshan 44#, Wuhan 430000, China"},{"name":"University of Chinese Academy of Sciences , Yuquan Road 19#, Beijing 100049, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ming","family":"Ni","sequence":"additional","affiliation":[{"name":"Beijing Institute of Radiation Medicine , Taiping Road 27#, Beijing 100850, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haizhou","family":"Liu","sequence":"additional","affiliation":[{"name":"Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences , Xiaohongshan 44#, Wuhan 430000, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3693-2726","authenticated-orcid":false,"given":"Di","family":"Liu","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences , Xiaohongshan 44#, Wuhan 430000, China"},{"name":"Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences , Xiaohongshan 44#, Wuhan 430000, China"},{"name":"University of Chinese Academy of Sciences , Yuquan Road 19#, Beijing 100049, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,3,28]]},"reference":[{"key":"2023120101374228700_R1","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1038\/nature12861","article-title":"Mutational and Fitness Landscapes of an RNA Virus Revealed through Population Sequencing","volume":"505","author":"Acevedo","year":"2014","journal-title":"Nature"},{"key":"2023120101374228700_R2","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1016\/j.virol.2015.03.022","article-title":"Viral 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Section F, Structural Biology Communications"},{"key":"2023120101374228700_R50","doi-asserted-by":"crossref","DOI":"10.1093\/ve\/veab078","article-title":"Intra-Host Evolution during SARS-CoV-2 Prolonged Infection","volume":"7","author":"Voloch","year":"2021","journal-title":"Virus Evolution"},{"key":"2023120101374228700_R51","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2164-14-674","article-title":"V-Phaser 2: Variant Inference for Viral Populations","volume":"14","author":"Yang","year":"2013","journal-title":"BMC Genomics"}],"container-title":["Virus Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/ve\/advance-article-pdf\/doi\/10.1093\/ve\/veac103\/49678660\/veac103.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ve\/article-pdf\/9\/1\/veac103\/53959186\/veac103.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ve\/article-pdf\/9\/1\/veac103\/53959186\/veac103.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,1]],"date-time":"2023-12-01T01:41:32Z","timestamp":1701394892000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ve\/article\/doi\/10.1093\/ve\/veac103\/7091593"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,1,1]]},"references-count":51,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2023,11,29]]}},"URL":"https:\/\/doi.org\/10.1093\/ve\/veac103","relation":{},"ISSN":["2057-1577"],"issn-type":[{"value":"2057-1577","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,1,1]]},"published":{"date-parts":[[2023,1,1]]},"article-number":"veac103"}}