{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,26]],"date-time":"2026-06-26T09:47:53Z","timestamp":1782467273002,"version":"3.54.5"},"reference-count":49,"publisher":"Wiley","issue":"6","license":[{"start":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T00:00:00Z","timestamp":1781740800000},"content-version":"vor","delay-in-days":17,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T00:00:00Z","timestamp":1780272000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Journal of Medical Virology"],"published-print":{"date-parts":[[2026,6]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Mutations in SARS\u2010CoV\u20102 primer\/probe targets can compromise RT\u2010PCR sensitivity, leading to false negatives and undetected viral transmission. This study evaluated mutational landscapes of 20 primer\/probe sets targeting\n                    <jats:italic>E<\/jats:italic>\n                    ,\n                    <jats:italic>N<\/jats:italic>\n                    ,\n                    <jats:italic>Orf1b\u2010nsp14<\/jats:italic>\n                    ,\n                    <jats:italic>RdRp<\/jats:italic>\n                    , and\n                    <jats:italic>S<\/jats:italic>\n                    genes using 1,35,852 high\u2010quality genomes across ten countries, five major variants, and three time periods (pre\u2010vaccination, post\u2010vaccination, and recent). Mutations were classified as high\u2010risk or moderate\u2010risk based on their positional susceptibility and mismatch burden. Mutation rate, impact risk, and population frequency within primer\/probe targets was calculated along with their geographical\u2010, variant\u2010, and time\u2010dependent variations. Most\n                    <jats:italic>E<\/jats:italic>\n                    ,\n                    <jats:italic>N<\/jats:italic>\n                    ,\n                    <jats:italic>RdRp<\/jats:italic>\n                    , and\n                    <jats:italic>S<\/jats:italic>\n                    primer\/probe targets showed higher and geographically variable mutation rates that increased with time. Variant\u2010wise analysis revealed that mutational accumulation in targets was significantly lower in early variants, that increased sharply with Delta and was most pronounced in Omicron (with its sub\u2010variants). High\u2010risk high\u2010frequency mutations were identified in targets of\n                    <jats:italic>N<\/jats:italic>\n                    \u2010CCDC\u2010forward primer,\n                    <jats:italic>N<\/jats:italic>\n                    \u2010NIH\u2010reverse primer,\n                    <jats:italic>RdRp<\/jats:italic>\n                    \u2010Charit\u00e9\u2010forward primer,\n                    <jats:italic>S<\/jats:italic>\n                    \u2010Young\u2010forward primer, and\n                    <jats:italic>S<\/jats:italic>\n                    \u2010Sigma (S1\/S2)\u2010probes. Moderate\u2010risk high\u2010frequency mutations were observed in\n                    <jats:italic>E<\/jats:italic>\n                    \u2010Charit\u00e9\u2010forward primer,\n                    <jats:italic>N<\/jats:italic>\n                    \u2010UCDC (N1)\u2010probe, and\n                    <jats:italic>S<\/jats:italic>\n                    \u2010Chan\u2010probe. Mutation frequencies differed across countries due to circulating variants and also across time periods, with some mutations approaching fixation (\u2265\u200995%) in the population.\n                    <jats:italic>Orf1b\u2010nsp14<\/jats:italic>\n                    and selected\n                    <jats:italic>N<\/jats:italic>\n                    \u2010gene targets like N\u2010Chan, N\u2010NIID, N\u2010UCDC (N2) sets remained mutation\u2010resilient, indicating their diagnostic reliability. A global and regional surveillance\u2010driven, threshold\u2010based strategy which involves periodic mutation monitoring every 6\u201312 months, consideration of primer\/probe redesign when target mutations reach \u2265\u200910% frequency, and incorporating mutation\u2010resilient targets into multiplex assays is recommended to enhance SARS CoV\u20102 RT\u2010PCR diagnostic accuracy.\n                  <\/jats:p>","DOI":"10.1002\/jmv.71023","type":"journal-article","created":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T12:00:37Z","timestamp":1781784037000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["SARS\u2010CoV\u20102 Evolution and Its Implications for RT\u2010PCR Diagnostic Performance"],"prefix":"10.1002","volume":"98","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6349-806X","authenticated-orcid":false,"given":"Shubhangi","family":"Gupta","sequence":"first","affiliation":[{"name":"Department of Biological Sciences and Engineering, Computational and Structural Biology Laboratory Netaji Subhas University of Technology Dwarka New Delhi India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-6179-8032","authenticated-orcid":false,"given":"Abhishek","family":"Chaudhary","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences and Engineering, Computational and Structural Biology Laboratory Netaji Subhas University of Technology Dwarka New Delhi India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8818-4240","authenticated-orcid":false,"given":"Sonika","family":"Bhatnagar","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences and Engineering, Computational and Structural Biology Laboratory Netaji Subhas University of Technology Dwarka New Delhi India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,6,18]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/S2666-5247(21)00214-7"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41563-020-00906-z"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.3390\/diagnostics10110905"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.4155\/bio-2021-0078"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.3390\/diagnostics11010115"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1080\/14737159.2020.1757437"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.talanta.2020.121726"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.7150\/thno.47649"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jiph.2020.06.005"},{"key":"e_1_2_10_11_1","doi-asserted-by":"publisher","DOI":"10.1128\/cmr.00228-20"},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms10081559"},{"key":"e_1_2_10_13_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcv.2020.104412"},{"key":"e_1_2_10_14_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cca.2021.12.004"},{"key":"e_1_2_10_15_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00216-020-02889-x"},{"key":"e_1_2_10_16_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-00852-z"},{"key":"e_1_2_10_17_1","doi-asserted-by":"publisher","DOI":"10.1021\/acsinfecdis.0c00464"},{"key":"e_1_2_10_18_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-88532-w"},{"key":"e_1_2_10_19_1","article-title":"Evaluation of the Effects of SARS\u2010CoV\u20102 Genetic Mutations on Diagnostic RT\u2010PCR Assays","author":"Nakabayashi T.","year":"2021","journal-title":"bioRxiv"},{"key":"e_1_2_10_20_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-21953-3"},{"key":"e_1_2_10_21_1","doi-asserted-by":"publisher","DOI":"10.2353\/jmoldx.2010.090035"},{"issue":"10","key":"e_1_2_10_22_1","first-page":"1561","article-title":"Improvement of Pcr Amplification Bias for Community Structure Analysis of Soil Bacteria by Denaturing Gradient Gel Electrophoresis","volume":"16","author":"Ahn J. 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