{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T14:36:45Z","timestamp":1792593405191,"version":"4.5.0"},"reference-count":60,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2022,8,1]],"date-time":"2022-08-01T00:00:00Z","timestamp":1659312000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Taif University Researchers Supporting Program, Taif University, Saudi Arabia","award":["TURSP-2020\/128"],"award-info":[{"award-number":["TURSP-2020\/128"]}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>In spite of the availability of vaccine, the health burden associated with the COVID-19 pandemic continues to increase. An estimated 5 million people have died with SARS-CoV-2 infection. Analysis of evolution and genomic diversity can provide sufficient information to reduce the health burden of the pandemic. This study focused to conduct worldwide genomic surveillance. About 7.6 million genomic data were analyzed during 2019 to 2022. Multiple sequence alignment was conducted by using maximum likelihood method. Clade GK (52%) was the most predominant followed by GRY (12%), GRA (11%), GR (8%), GH (7%), G (6%), GV (3%), and O (1%), respectively. VOC Delta (66%) was the most prevalent variant followed by VOC Alpha (18%), VOC Omicron (13%), VOC Gamma (2%) and VOC Beta (1%), respectively. The frequency of point mutations including E484K, N501Y, N439K, and L452R at spike protein has increased 10%-92%. Evolutionary rate of the variants was 23.7 substitution per site per year. Substitution mutations E484K and N501Y had significant correlation with cases (<jats:italic>r<\/jats:italic> = .45, <jats:italic>r<\/jats:italic> = .23), fatalities (<jats:italic>r<\/jats:italic> = .15, <jats:italic>r<\/jats:italic> = .44) and growth rate R<jats:sub>0<\/jats:sub> (<jats:italic>r<\/jats:italic> = .28, <jats:italic>r<\/jats:italic> = .54). This study will help to understand the genomic diversity, evolution and the impact of the variants on the outcome of the COVID-19 pandemic.<\/jats:p>","DOI":"10.1371\/journal.pone.0271074","type":"journal-article","created":{"date-parts":[[2022,8,1]],"date-time":"2022-08-01T18:04:11Z","timestamp":1659377051000},"page":"e0271074","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":23,"title":["Genomic surveillance, evolution and global transmission of SARS-CoV-2 during 2019\u20132022"],"prefix":"10.1371","volume":"17","author":[{"given":"Nadim","family":"Sharif","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6688-0106","authenticated-orcid":true,"given":"Khalid J.","family":"Alzahrani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shamsun Nahar","family":"Ahmed","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Afsana","family":"Khan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hamsa Jameel","family":"Banjer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fuad M.","family":"Alzahrani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anowar Khasru","family":"Parvez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2440-5673","authenticated-orcid":true,"given":"Shuvra Kanti","family":"Dey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,8,1]]},"reference":[{"issue":"7798","key":"pone.0271074.ref001","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1038\/s41586-020-2008-3","article-title":"A new coronavirus associated with human respiratory disease in China","volume":"579","author":"F Wu","year":"2020","journal-title":"Nature"},{"issue":"3","key":"pone.0271074.ref002","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1007\/s11481-020-09944-5","article-title":"The natural history, pathobiology, and clinical manifestations of SARS-CoV-2 infections","volume":"15","author":"J Machhi","year":"2020","journal-title":"Journal of Neuroimmune Pharmacology"},{"issue":"1","key":"pone.0271074.ref003","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1080\/01652176.2020.1727993","article-title":"Emerging novel coronavirus (2019-nCoV)\u2014current scenario, evolutionary perspective based on genome analysis and recent developments","volume":"40","author":"YS Malik","year":"2020","journal-title":"Veterinary quarterly"},{"issue":"2","key":"pone.0271074.ref004","doi-asserted-by":"crossref","first-page":"138","DOI":"10.7883\/yoken.JJID.2014.266","article-title":"Detection of the human coronavirus 229E, HKU1, NL63, and OC43 between 2010 and 2013 in Yamagata, Japan","volume":"68","author":"Y Matoba","year":"2015","journal-title":"Japanese journal of infectious diseases"},{"issue":"3","key":"pone.0271074.ref005","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1038\/s41579-018-0118-9","article-title":"Origin and evolution of pathogenic coronaviruses","volume":"17","author":"J Cui","year":"2019","journal-title":"Nature Reviews Microbiology"},{"key":"pone.0271074.ref006","article-title":"Mutations, recombination and insertion in the evolution of 2019-nCoV","author":"A Wu","year":"2020","journal-title":"BioRxiv"},{"issue":"2","key":"pone.0271074.ref007","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1016\/j.cell.2020.03.035","article-title":"A genomic perspective on the origin and emergence of SARS-CoV-2","volume":"181","author":"YZ Zhang","year":"2020","journal-title":"Cell"},{"key":"pone.0271074.ref008","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1016\/j.ijid.2020.03.004","article-title":"The SARS-CoV-2 outbreak: what we know","volume":"94","author":"D Wu","year":"2020","journal-title":"International Journal of Infectious Diseases"},{"key":"pone.0271074.ref009","unstructured":"Worldometer. 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