ArticleJournal of medical virology2026
SARS-CoV-2 Evolution and Its Implications for RT-PCR Diagnostic Performance.
Article in Journal of medical virology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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3 authors.
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Abstract
Mutations in SARS-CoV-2 primer/probe targets can compromise RT-PCR sensitivity, leading to false negatives and undetected viral transmission. This study evaluated mutational landscapes of 20 primer/probe sets targeting E, N, Orf1b-nsp14, RdRp, and S genes using 1,35,852 high-quality genomes across ten countries, five major variants, and three time periods (pre-vaccination, post-vaccination, and recent). Mutations were classified as high-risk or moderate-risk 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-, variant-, and time-dependent variations. Most E, N, RdRp, and S primer/probe targets showed higher and geographically variable mutation rates that increased with time. Variant-wise 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-variants). High-risk high-frequency mutations were identified in targets of N-CCDC-forward primer, N-NIH-reverse primer, RdRp-Charité-forward primer, S-Young-forward primer, and S-Sigma (S1/S2)-probes. Moderate-risk high-frequency mutations were observed in E-Charité-forward primer, N-UCDC (N1)-probe, and S-Chan-probe. Mutation frequencies differed across countries due to circulating variants and also across time periods, with some mutations approaching fixation (≥ 95%) in the population. Orf1b-nsp14 and selected N-gene targets like N-Chan, N-NIID, N-UCDC (N2) sets remained mutation-resilient, indicating their diagnostic reliability. A global and regional surveillance-driven, threshold-based strategy which involves periodic mutation monitoring every 6-12 months, consideration of primer/probe redesign when target mutations reach ≥ 10% frequency, and incorporating mutation-resilient targets into multiplex assays is recommended to enhance SARS CoV-2 RT-PCR diagnostic accuracy.
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