{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T05:49:35Z","timestamp":1785822575993,"version":"3.56.0"},"reference-count":67,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2022,2,25]],"date-time":"2022-02-25T00:00:00Z","timestamp":1645747200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003093","name":"Ministry of Higher Education Malaysia","doi-asserted-by":"crossref","award":["FRGS\/1\/2019\/WAB13\/UMP\/03\/1"],"award-info":[{"award-number":["FRGS\/1\/2019\/WAB13\/UMP\/03\/1"]}],"id":[{"id":"10.13039\/501100003093","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Sultan Ahmad Shah Medical Centre @ IIUM","award":["SRG21-040-0040"],"award-info":[{"award-number":["SRG21-040-0040"]}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>\n                    SARS-CoV-2 has spread throughout the world since its discovery in China, and Malaysia is no exception. WGS has been a crucial approach in studying the evolution and genetic diversity of SARS-CoV-2 in the ongoing pandemic. Despite considerable number of SARS-CoV-2 genome sequences have been submitted to GISAID and NCBI databases, there is still scarcity of data from Malaysia. This study aims to report new Malaysian lineages of the virus, responsible for the sustained spikes in COVID-19 cases during the third wave of the pandemic. Patients with nasopharyngeal and\/or oropharyngeal swabs confirmed COVID-19 positive by real-time RT-PCR with\n                    <jats:italic>C<\/jats:italic>\n                    <jats:sub>\n                      <jats:italic>T<\/jats:italic>\n                    <\/jats:sub>\n                    value &lt; 25 were chosen for WGS. The selected SARS-CoV-2 isolates were then sequenced, characterized and analyzed along with 986 sequences of the dominant lineages of D614G variants currently circulating throughout Malaysia. The prevalence of clade GH and G formed strong ground for the presence of two Malaysian lineages of AU.2 and B.1.524 that has caused sustained spikes of cases in the country. Statistical analysis on the association of gender and age group with Malaysian lineages revealed a significant association (\n                    <jats:italic>p<\/jats:italic>\n                    &lt;0.05). Phylogenetic analysis revealed dispersion of 41 lineages, of these, 22 lineages are still active. Mutational analysis showed presence of unique G1223C missense mutation in transmembrane domain of the spike protein. For better understanding of the SARS-CoV-2 evolution in Malaysia especially with reference to the reported lineages, large scale studies based on WGS are warranted.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0263678","type":"journal-article","created":{"date-parts":[[2022,2,25]],"date-time":"2022-02-25T14:00:50Z","timestamp":1645797650000},"page":"e0263678","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":12,"title":["Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia"],"prefix":"10.1371","volume":"17","author":[{"given":"Ummu Afeera","family":"Zainulabid","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aini Syahida","family":"Mat Yassim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mushtaq","family":"Hussain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ayesha","family":"Aslam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sharmeen Nellisa","family":"Soffian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohamad Shafiq","family":"Mohd Ibrahim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Norhidayah","family":"Kamarudin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohd Nazli","family":"Kamarulzaman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"How Soon","family":"Hin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2985-2496","authenticated-orcid":true,"given":"Hajar Fauzan","family":"Ahmad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,2,25]]},"reference":[{"issue":"3","key":"pone.0263678.ref001","doi-asserted-by":"crossref","first-page":"105924","DOI":"10.1016\/j.ijantimicag.2020.105924","article-title":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges","volume":"55","author":"CC Lai","year":"2020","journal-title":"Int J Antimicrob"},{"issue":"10224","key":"pone.0263678.ref002","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1016\/S0140-6736(20)30251-8","article-title":"Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding","volume":"395","author":"R Lu","year":"2020","journal-title":"Lancet"},{"key":"pone.0263678.ref003","doi-asserted-by":"crossref","DOI":"10.1038\/s41586-021-03767-x","article-title":"Mapping the human genetic architecture of COVID-19","author":"COVID-19 Host Genetics Initiative","year":"2021","journal-title":"Nature"},{"issue":"6","key":"pone.0263678.ref004","doi-asserted-by":"crossref","first-page":"715","DOI":"10.1038\/s41431-020-0636-6","article-title":"The COVID-19 host genetics initiative, a global initiative to elucidate the role of host genetic factors in susceptibility and severity of the SARS-CoV-2 virus pandemic","volume":"28","author":"COVID-19 Host Genetics Initiative","year":"2020","journal-title":"Eur J Hum Genet"},{"key":"pone.0263678.ref005","first-page":"371","article-title":"Virology, transmission, and pathogenesis of SARS-CoV-2","author":"M Cevik","year":"2020","journal-title":"BMJ"},{"key":"pone.0263678.ref006","unstructured":"WHO, WHO Coronavirus (COVID-19). 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