{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T16:11:39Z","timestamp":1787242299317,"version":"build-2736575974"},"reference-count":22,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2024,1,12]],"date-time":"2024-01-12T00:00:00Z","timestamp":1705017600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100020884","name":"QIAGEN","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100020884","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100023950","name":"QIAGEN","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100023950","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100023950","name":"QIAGEN","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100023950","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100023950","name":"QIAGEN","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100023950","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100023950","name":"QIAGEN","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100023950","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100023950","name":"QIAGEN","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100023950","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100023950","name":"QIAGEN","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100023950","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100023950","name":"QIAGEN","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100023950","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100023950","name":"QIAGEN","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100023950","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100023950","name":"QIAGEN","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100023950","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100023950","name":"QIAGEN","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100023950","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100023950","name":"QIAGEN","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100023950","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100023950","name":"QIAGEN","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100023950","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>Objective<\/jats:title>\n                    <jats:p>The speed at which Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is mutating has made it necessary to frequently assess how these genomic changes impact the performance of diagnostic real-time polymerase chain reaction (RT-PCR) assays. Herein, we describe a generic three-step workflow to assess the effect of genomic mutations on inclusivity and sensitivity of RT-PCR assays.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec002\">\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      Sequences collected from the Global Initiative on Sharing All Influenza Data (GISAID) were mapped to a SARS-CoV-2 reference genome to evaluate the position and prevalence of mismatches in the oligonucleotide-binding sites of the QIAstat-Dx, an RT-PCR panel designed to detect SARS-CoV-2. The frequency of mutations and their impact on melting temperature were assessed, and sequences flagged by risk-based criteria were examined\n                      <jats:italic>in vitro<\/jats:italic>\n                      .\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec003\">\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Out of 8,900,393 SARS-CoV-2 genome sequences analyzed, only 173 (0.0019%) genomes contained potentially critical mutations for the QIAstat-Dx; follow-up\n                      <jats:italic>in-vitro<\/jats:italic>\n                      testing confirmed no impact on the assays\u2019 performance.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec004\">\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>The current study demonstrates that SARS-CoV-2 genetic variants do not affect the performance of the QIAstat-Dx device. It is recommended that manufacturers incorporate this workflow into obligatory post-marketing surveillance activities, as this approach could potentially enhance genetic monitoring of their product.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1371\/journal.pone.0294271","type":"journal-article","created":{"date-parts":[[2024,1,12]],"date-time":"2024-01-12T13:32:35Z","timestamp":1705066355000},"page":"e0294271","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":1,"title":["Monitoring SARS-CoV-2 genetic variability: A post-market surveillance workflow for combined bioinformatic and laboratory evaluation of commercial RT-PCR assay performance"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4709-5556","authenticated-orcid":true,"given":"Barbara","family":"Kosi\u0144ska-Selbi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Justyna","family":"Kowalczyk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2550-5606","authenticated-orcid":true,"given":"Jagoda","family":"Piersci\u0144ska","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jaros\u0142aw","family":"We\u0142eszczuk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luis","family":"Pe\u00f1arrubia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin","family":"Turner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9075-3417","authenticated-orcid":true,"given":"Josep","family":"Pareja","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roberto","family":"Porco","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rubi","family":"Diaz-Hernandez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mart\u00ed","family":"Juanola-Falgarona","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melisa","family":"Rey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Davide","family":"Manissero","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7853-0111","authenticated-orcid":true,"given":"Anna","family":"Blacha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2024,1,12]]},"reference":[{"issue":"3","key":"pone.0294271.ref001","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1038\/nrmicro.2015.13","article-title":"Within-host evolution of bacterial pathogens","volume":"14","author":"X Didelot","year":"2016","journal-title":"Nat Rev Microbiol"},{"issue":"1821","key":"pone.0294271.ref002","first-page":"20150488","article-title":"Genomic perspectives on the evolution and spread of bacterial pathogens","volume":"282","author":"SD Bentley","year":"2015","journal-title":"Proc Biol Sci"},{"issue":"2","key":"pone.0294271.ref003","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1080\/14737159.2022.2037425","article-title":"True or false: what are the factors that influence COVID-19 diagnosis by RT-qPCR?","volume":"22","author":"L Benevides Lima","year":"2022","journal-title":"Expert Rev Mol Diagn"},{"key":"pone.0294271.ref004","first-page":"59","article-title":"SARS-CoV-2 E Gene Variant Alters Analytical Sensitivity","author":"S Tahan","year":"2021","journal-title":"Journal of Clinical Microbiology"},{"key":"pone.0294271.ref005","first-page":"225","volume":"97","author":"L Pe\u00f1arrubia","year":"2020","journal-title":"Multiple assays in a real-time RT-PCR SARS-CoV-2 panel can mitigate the risk of loss of sensitivity by new genomic variants during the COVID-19 outbreak."},{"key":"pone.0294271.ref006","first-page":"1","author":"B. Akra","year":"2022","journal-title":"The Post-Market Gambit\u2014After EU MDR and IVDR: A Systematic Compliance Framework for Driving MedTech Innovation: Huma.AI"},{"key":"pone.0294271.ref007","author":"FDA","year":"2023","journal-title":"Policy for Evaluating Impact of Viral Mutations on COVID-19 Tests | FDA"},{"issue":"2","key":"pone.0294271.ref008","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/j.cll.2022.02.005","article-title":"An Overview of SARS-CoV-2 Molecular Diagnostics in Europe.","volume":"42","author":"E Davies","year":"2022","journal-title":"Clin Lab Med."},{"key":"pone.0294271.ref009","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1016\/j.ijid.2021.01.049","article-title":"In response to: Multiple assays in a real-time RT-PCR severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) panel can mitigate the risk of loss of sensitivity by new genomic variants during the COVID-19 outbreak.","volume":"105","author":"L Pe\u00f1arrubia","year":"2021","journal-title":"International Journal of Infectious Diseases"},{"key":"pone.0294271.ref010","article-title":"Respiratory SARS-CoV- 2 Panel Instructions for Use (Handbook)","author":"GmbH Qiagen\u00ae","year":"2020","journal-title":"Qiagen\u00ae GmbH, Qiagen\u00ae;"},{"issue":"49","key":"pone.0294271.ref011","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.46234\/ccdcw2021.255","article-title":"GISAID\u2019s Role in Pandemic Response.","volume":"3","author":"S Khare","year":"2021","journal-title":"China CDC Wkly."},{"key":"pone.0294271.ref012","first-page":"1","author":"CDC","year":"2022","journal-title":"SARS-CoV-2 Variant Classifications and Definitions COVID-19"},{"key":"pone.0294271.ref013","first-page":"2022","author":"ECDC","year":"2022","journal-title":"SARS-CoV-2 variants of concern as of"},{"key":"pone.0294271.ref014","first-page":"1","author":"UKHSA","year":"2022","journal-title":"Investigation of SARS-CoV-2 variants: technical briefings"},{"key":"pone.0294271.ref015","author":"WHO","year":"2022","journal-title":"Tracking SARS-CoV-2 variants"},{"key":"pone.0294271.ref016","author":"WHO","year":"2022","journal-title":"Previously circulating VOIs"},{"key":"pone.0294271.ref017","first-page":"1","author":"PANGO","year":"2022","journal-title":"Pango Lineages: Latest epidemiological lineages of SARS-CoV-2"},{"key":"pone.0294271.ref018","author":"WHO","year":"2015","journal-title":"Post-Market Surveillance of In Vitro Diagnostics"},{"issue":"8","key":"pone.0294271.ref019","doi-asserted-by":"crossref","first-page":"1559","DOI":"10.3390\/microorganisms10081559","article-title":"SARS-CoV-2 Mutations and Variants May Muddle the Sensitivity of COVID-19 Diagnostic Assays.","volume":"10","author":"M Alkhatib","year":"2022","journal-title":"Microorganisms"},{"key":"pone.0294271.ref020","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1016\/j.ijid.2020.10.086","article-title":"Analysis of the potential impact of genomic variants in global SARS-CoV-2 genomes on molecular diagnostic assays","volume":"102","author":"A Jain","year":"2021","journal-title":"Int J Infect Dis"},{"issue":"6","key":"pone.0294271.ref021","doi-asserted-by":"crossref","first-page":"e0135522","DOI":"10.1128\/spectrum.01355-22","article-title":"Design and Implementation of Improved SARS-CoV-2 Diagnostic Assays To Mitigate the Impact of Genomic Mutations on Target Failure: the Xpert Xpress SARS-CoV-2 Experience","volume":"10","author":"B Burns","year":"2022","journal-title":"MIcrobiology Spectrum"},{"issue":"10","key":"pone.0294271.ref022","doi-asserted-by":"crossref","first-page":"e01598","DOI":"10.1128\/JCM.01598-20","article-title":"A Recurrent Mutation at Position 26340 of SARS-CoV-2 Is Associated with Failure of the E Gene Quantitative Reverse Transcription-PCR Utilized in a Commercial Dual-Target Diagnostic Assay","volume":"58","author":"M Artesi","year":"2020","journal-title":"Journal of Clinical Microbiology"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0294271","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,12]],"date-time":"2024-01-12T13:32:50Z","timestamp":1705066370000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0294271"}},"subtitle":[],"editor":[{"given":"Vittorio","family":"Sambri","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2024,1,12]]},"references-count":22,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,1,12]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0294271","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,1,12]]}}}