{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,20]],"date-time":"2026-01-20T02:12:06Z","timestamp":1768875126782,"version":"3.49.0"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2021,2,13]],"date-time":"2021-02-13T00:00:00Z","timestamp":1613174400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Tou-Yan Innovation Team Program of the Heilongjiang Province","award":["2019\u201315"],"award-info":[{"award-number":["2019\u201315"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61871160"],"award-info":[{"award-number":["61871160"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Heilongjiang Province Postdoctoral Fund","award":["LBH-TZ20"],"award-info":[{"award-number":["LBH-TZ20"]}]},{"name":"Young Innovative Talents in Colleges and Universities of Heilongjiang Province","award":["2018\u201369"],"award-info":[{"award-number":["2018\u201369"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,3,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Since the first report of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019, the COVID-19 pandemic has spread rapidly worldwide. Due to the limited virus strains, few key mutations that would be very important with the evolutionary trends of virus genome were observed in early studies. Here, we downloaded 1809 sequence data of SARS-CoV-2 strains from GISAID before April 2020 to identify mutations and functional alterations caused by these mutations. Totally, we identified 1017 nonsynonymous and 512 synonymous mutations with alignment to reference genome NC_045512, none of which were observed in the receptor-binding domain (RBD) of the spike protein. On average, each of the strains could have about 1.75 new mutations each month. The current mutations may have few impacts on antibodies. Although it shows the purifying selection in whole-genome, ORF3a, ORF8 and ORF10 were under positive selection. Only 36 mutations occurred in 1% and more virus strains were further analyzed to reveal linkage disequilibrium (LD) variants and dominant mutations. As a result, we observed five dominant mutations involving three nonsynonymous mutations C28144T, C14408T and A23403G and two synonymous mutations T8782C, and C3037T. These five mutations occurred in almost all strains in April 2020. Besides, we also observed two potential dominant nonsynonymous mutations C1059T and G25563T, which occurred in most of the strains in April 2020. Further functional analysis shows that these mutations decreased protein stability largely, which could lead to a significant reduction of virus virulence. In addition, the A23403G mutation increases the spike-ACE2 interaction and finally leads to the enhancement of its infectivity. All of these proved that the evolution of SARS-CoV-2 is toward the enhancement of infectivity and reduction of virulence.<\/jats:p>","DOI":"10.1093\/bib\/bbab042","type":"journal-article","created":{"date-parts":[[2021,1,29]],"date-time":"2021-01-29T20:12:34Z","timestamp":1611951154000},"page":"1442-1450","source":"Crossref","is-referenced-by-count":36,"title":["Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6665-6710","authenticated-orcid":false,"given":"Liang","family":"Cheng","sequence":"first","affiliation":[{"name":"NHC and CAMS Key Laboratory of Molecular Probe and Targeted Theranostics, Harbin Medical University, Harbin, Heilongjiang 150028, China"},{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China"}]},{"given":"Xudong","family":"Han","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China"}]},{"given":"Zijun","family":"Zhu","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China"}]},{"given":"Changlu","family":"Qi","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China"}]},{"given":"Ping","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China"}]},{"given":"Xue","family":"Zhang","sequence":"additional","affiliation":[{"name":"NHC and CAMS Key Laboratory of Molecular Probe and Targeted Theranostics, Harbin Medical University, Harbin, Heilongjiang 150028, China"},{"name":"McKusick-Zhang Center for Genetic Medicine, Peking Union Medical College, Beijing 100005, China"}]}],"member":"286","published-online":{"date-parts":[[2021,2,13]]},"reference":[{"key":"2021032314373627000_ref1","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1002\/jmv.25678","article-title":"Outbreak of pneumonia of unknown etiology in Wuhan, China: the mystery and the miracle","volume":"92","author":"Lu","year":"2020","journal-title":"J Med Virol"},{"key":"2021032314373627000_ref2","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1080\/22221751.2020.1723441","article-title":"An emerging coronavirus causing pneumonia outbreak in Wuhan, China: calling for developing therapeutic and prophylactic strategies","volume":"9","author":"Jiang","year":"2020","journal-title":"Emerg Microbes Infect"},{"key":"2021032314373627000_ref3","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1016\/j.tim.2016.03.003","article-title":"Epidemiology, genetic 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nCoV-2019","author":"Wong","year":"2020","journal-title":"bioRxiv"},{"key":"2021032314373627000_ref7","doi-asserted-by":"crossref","first-page":"1012","DOI":"10.1093\/nsr\/nwaa036","article-title":"On the origin and continuing evolution of SARS-CoV-2","volume":"7","author":"Tang","year":"2020","journal-title":"Natl Sci Rev"},{"key":"2021032314373627000_ref8","doi-asserted-by":"crossref","first-page":"9241","DOI":"10.1073\/pnas.2004999117","article-title":"Phylogenetic network analysis of SARS-CoV-2 genomes","volume":"117","author":"Forster","year":"2020","journal-title":"Proc Natl Acad Sci USA"},{"key":"2021032314373627000_ref9","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"key":"2021032314373627000_ref10","first-page":"418","article-title":"Simple methods for 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