{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,21]],"date-time":"2026-03-21T09:14:51Z","timestamp":1774084491224,"version":"3.50.1"},"reference-count":29,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2024,10,17]],"date-time":"2024-10-17T00:00:00Z","timestamp":1729123200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000061","name":"Fogarty International Center","doi-asserted-by":"publisher","award":["TW005572"],"award-info":[{"award-number":["TW005572"]}],"id":[{"id":"10.13039\/100000061","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008551","name":"Fondation M\u00e9rieux","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008551","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:sec id=\"sec001\">\n<jats:title>Background<\/jats:title>\n<jats:p>The widespread increase in multiple variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) since 2020 is causing significant health concerns worldwide. While whole-genome sequencing (WGS) has played a leading role in surveillance programs, many local laboratories lack the expertise and resources. Thus, we aimed to investigate the circulating SARS-CoV-2 variants and evaluate the performance of multiplexed real-time reverse transcription-PCR (RT-PCR) for screening and monitoring the emergence of new SARS-CoV-2 variants in Bangladesh.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec002\">\n<jats:title>Methods<\/jats:title>\n<jats:p>A total of 600 confirmed SARS-CoV-2-positive cases were enrolled either prospectively or retrospectively from two divisions of Bangladesh. The samples were screened by variant RT-PCR targeting five mutations of the spike gene (N501Y, P681R, L452R, E484K, E484Q). A subsample of the study population was also selected for third-generation sequencing (TGS) and the results were compared to the variant RT-PCR screening. An in-depth comparison was made between the two methods in terms of congruence and cost-benefit.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec003\">\n<jats:title>Result<\/jats:title>\n<jats:p>Seven variants were detected among samples, with similar distributions of the variants across both divisions. Variant RT-PCR for the targeted mutations lead to a 98.5% call rate; only nine samples failed to be determined. No association was found regarding the demographic features, clinical criteria, or routine RT-PCR Ct values across the variants. The clade diversity of the sequenced subpopulation (<jats:italic>n<\/jats:italic> = 99) exhibited similar distributions across the two study sites and other epidemiologic variables. Variant RT-PCR successfully distinguished variants of concern (VOCs) and variants of interest (VOIs); however, 8% discrepancy was observed for the closest lineages. Moreover, the variant RT-PCR represented an ideal balance of cost, time, and accuracy that outweigh their limitations.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec004\">\n<jats:title>Conclusion<\/jats:title>\n<jats:p>Based on the strong agreement of variant RT-PCR with TGS, such rapid, easily accessible approaches of rapid strain typing are essential in the context of pandemic responses to guide both treatment decisions and public health measures.<\/jats:p>\n<\/jats:sec>","DOI":"10.1371\/journal.pone.0311993","type":"journal-article","created":{"date-parts":[[2024,10,17]],"date-time":"2024-10-17T17:36:46Z","timestamp":1729186606000},"page":"e0311993","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":1,"title":["SARS-CoV-2 variant survey: Comparison of RT-PCR screening with TGS and variant distribution across two divisions of Bangladesh"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7628-137X","authenticated-orcid":true,"given":"Zannat","family":"Kawser","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-2432-5588","authenticated-orcid":true,"given":"Saikt","family":"Rahman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emilie","family":"Westeel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohammad Tanbir","family":"Habib","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohabbat","family":"Hossain","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Md. Rakibul Hassan","family":"Bulbul","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-8608-8753","authenticated-orcid":true,"given":"Sharmin Aktar","family":"Mukta","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Md. Zahirul","family":"Islam","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Md. Zakir","family":"Hossain","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mokibul Hassan","family":"Afrad","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manjur Hossain","family":"Khan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tahmina","family":"Shirin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3405-2146","authenticated-orcid":true,"given":"Md. Shakeel","family":"Ahmed","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6337-3715","authenticated-orcid":true,"given":"Jean-Luc","family":"Berland","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1023-0796","authenticated-orcid":true,"given":"Florence","family":"Komurian-Pradel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Firdausi","family":"Qadri","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2024,10,17]]},"reference":[{"issue":"10","key":"pone.0311993.ref001","doi-asserted-by":"crossref","first-page":"1195","DOI":"10.3390\/vaccines9101195","article-title":"Emerging SARS CoV-2 Variants: A Review of Its Mutations, Its Implications and Vaccine Efficacy.","volume":"9","author":"S Ramesh","year":"2021","journal-title":"Vaccines (Basel)"},{"key":"pone.0311993.ref002","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/j.virol.2021.10.005","article-title":"Dynamics of SARS-CoV-2 variants of concern (VOC) in Bangladesh during the first half of 2021.","volume":"565","author":"SZ Afrin","year":"2022","journal-title":"Virology"},{"issue":"1","key":"pone.0311993.ref003","doi-asserted-by":"crossref","first-page":"22","DOI":"10.14745\/ccdr.v48i01a04","article-title":"Epidemiological analysis of the emergence and disappearance of the SARS-CoV-2 Kappa variant within a region of British Columbia, Canada.","volume":"48","author":"C Ghafari","year":"2022","journal-title":"Can Commun Dis Rep"},{"issue":"2\u20133","key":"pone.0311993.ref004","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1007\/s00430-022-00729-6","article-title":"Molecular variants of SARS-CoV-2: antigenic properties and current vaccine efficacy","volume":"211","author":"A Rayati Damavandi","year":"2022","journal-title":"Med Microbiol Immunol"},{"issue":"8","key":"pone.0311993.ref005","doi-asserted-by":"crossref","first-page":"197","DOI":"10.3390\/tropicalmed7080197","article-title":"Transmission Dynamics and Genomic Epidemiology of Emerging Variants of SARS-CoV-2 in Bangladesh.","volume":"7","author":"MA Sayeed","year":"2022","journal-title":"Trop Med Infect Dis"},{"issue":"8","key":"pone.0311993.ref006","doi-asserted-by":"crossref","first-page":"e0092621","DOI":"10.1128\/JCM.00926-21","article-title":"Mutation-Specific SARS-CoV-2 PCR Screen: Rapid and Accurate Detection of Variants of Concern and the Identification of a Newly Emerging Variant with Spike L452R Mutation","volume":"59","author":"H Wang","year":"2021","journal-title":"J Clin Microbiol"},{"key":"pone.0311993.ref007","first-page":"104905","article-title":"RT-PCR based SARS-CoV-2 variant screening assays require careful quality control.","volume":"141","author":"JV Camp","journal-title":"J Clin Virol. 2021 Aug"},{"issue":"7","key":"pone.0311993.ref008","doi-asserted-by":"crossref","first-page":"1542","DOI":"10.3390\/microorganisms9071542","article-title":"SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India.","volume":"9","author":"S Cherian","year":"2021","journal-title":"Microorganisms"},{"key":"pone.0311993.ref009","doi-asserted-by":"crossref","first-page":"114462","DOI":"10.1016\/j.jviromet.2022.114462","article-title":"SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021.","volume":"301","author":"JYL Fu","year":"2022","journal-title":"J Virol Methods"},{"issue":"1","key":"pone.0311993.ref010","doi-asserted-by":"crossref","first-page":"11094","DOI":"10.1038\/s41598-023-37866-8","article-title":"Rapid screening of SARS-CoV-2 variants, a key tool for pandemic surveillance.","volume":"13","author":"I Mu\u00f1oz-Gallego","year":"2023","journal-title":"Sci Rep."},{"issue":"7896","key":"pone.0311993.ref011","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1038\/s41586-021-04245-0","article-title":"The N501Y spike substitution enhances SARS-CoV-2 infection and transmission","volume":"602","author":"Y Liu","year":"2022","journal-title":"Nature"},{"issue":"11","key":"pone.0311993.ref012","doi-asserted-by":"crossref","first-page":"1803","DOI":"10.3390\/genes12111803","article-title":"Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India.","volume":"12","author":"J Singh","year":"2021","journal-title":"Genes (Basel)."},{"key":"pone.0311993.ref013","doi-asserted-by":"crossref","first-page":"751778","DOI":"10.3389\/fimmu.2021.751778","article-title":"The Global Epidemic of the SARS-CoV-2 Delta Variant, Key Spike Mutations and Immune Escape.","volume":"12","author":"D Tian","year":"2021","journal-title":"Front Immunol."},{"key":"pone.0311993.ref014","article-title":"Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant.","volume":"5","author":"Y Liu","year":"2021","journal-title":"bioRxiv [Preprint]"},{"key":"pone.0311993.ref015","article-title":"Spread of SARS-CoV-2 Delta variant infections bearing the S:E484Q and S:T95I mutations in July and August 2021 in France.","volume":"2021","author":"L Verdurme","journal-title":"medRxiv [Preprint]."},{"key":"pone.0311993.ref016","doi-asserted-by":"crossref","first-page":"e00950","DOI":"10.1128\/mra.00950-22","article-title":"Genome Sequences of 23 SARS-CoV-2 Omicron-Lineage Strains from Bangladesh.","volume":"12","author":"M Hossain","year":"2023","journal-title":"Microbiol Resour Announc."},{"key":"pone.0311993.ref017","doi-asserted-by":"crossref","first-page":"894613","DOI":"10.3389\/fcimb.2022.894613","article-title":"Rapid and Accurate Identification of SARS-CoV-2 Variants Using Real Time PCR Assays.","volume":"12","author":"GA Borillo","year":"2022","journal-title":"Front Cell Infect Microbiol"},{"issue":"4","key":"pone.0311993.ref018","doi-asserted-by":"crossref","first-page":"677","DOI":"10.3390\/microorganisms9040677","article-title":"SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing.","volume":"9","author":"AR Goncalves Cabecinhas","year":"2021","journal-title":"Microorganisms"},{"issue":"5","key":"pone.0311993.ref019","doi-asserted-by":"crossref","first-page":"e3001236","DOI":"10.1371\/journal.pbio.3001236","article-title":"Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2","volume":"19","author":"CBF Vogels","year":"2021","journal-title":"PLoS 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values and COVID-19 new daily cases: a multicenter cross-sectional study.","volume":"29","author":"A Abdulrahman","year":"2021","journal-title":"Infez Med."},{"issue":"4","key":"pone.0311993.ref024","doi-asserted-by":"crossref","first-page":"845","DOI":"10.4269\/ajtmh.22-0068","article-title":"An Assessment of a Rapid SARS-CoV-2 Antigen Test in Bangladesh","volume":"107","author":"Z Kawser","year":"2022","journal-title":"Am J Trop Med Hyg"},{"issue":"7","key":"pone.0311993.ref025","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1038\/s41579-021-00573-0","article-title":"SARS-CoV-2 variants, spike mutations and immune escape","volume":"19","author":"WT Harvey","year":"2021","journal-title":"Nat Rev Microbiol"},{"issue":"1","key":"pone.0311993.ref026","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1038\/s41421-021-00347-1","article-title":"Cross-neutralization of SARS-CoV-2 Kappa and Delta variants by inactivated vaccine-elicited serum and monoclonal antibodies","volume":"7","author":"L Cheng","year":"2021","journal-title":"Cell Discov"},{"issue":"1","key":"pone.0311993.ref027","doi-asserted-by":"crossref","first-page":"193","DOI":"10.3390\/vaccines11010193","article-title":"S Trimer Derived from SARS-CoV-2 B.1.351 and B.1.618 Induced Effective Immune Response against Multiple SARS-CoV-2 Variants.","volume":"11","author":"H Wang","year":"2023","journal-title":"Vaccines (Basel)."},{"issue":"12","key":"pone.0311993.ref028","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1038\/s41576-021-00408-x","article-title":"The biological and clinical significance of emerging SARS-CoV-2 variants","volume":"22","author":"K Tao","year":"2021","journal-title":"Nat Rev Genet"},{"issue":"12","key":"pone.0311993.ref029","doi-asserted-by":"crossref","first-page":"3180","DOI":"10.3201\/eid2712.211792","article-title":"Breakthrough Infections of E484K-Harboring SARS-CoV-2 Delta Variant, Lombardy, Italy","volume":"27","author":"A Baj","year":"2021","journal-title":"Emerg Infect Dis"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0311993","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,17]],"date-time":"2024-10-17T17:36:56Z","timestamp":1729186616000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0311993"}},"subtitle":[],"editor":[{"given":"Haitham Mohamed","family":"Amer","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2024,10,17]]},"references-count":29,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2024,10,17]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0311993","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,10,17]]}}}