ArticleScientific reports2022
Identification of mutations in SARS-CoV-2 PCR primer regions.
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 20 citations in OpenAlex.
- SARS-CoV-2 Evolution and Its Implications for RT-PCR Diagnostic Performance.Journal of medical virology · 2026Article
- RAZOR: a database of PCR primers targeting human respiratory viruses.NAR genomics and bioinformatics · 2026Article
- One Assay, Nine Targets: Advancing Viral Surveillance with Multiplex RT-ddPCR.Analytical chemistry · 2025Article
- [Preclinical Development Process and Prospects of Real-time Fluorescence Quantitative Polymerase Chain Reaction Detection Kits].Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition · 2025Review
- Reality check: testing theFrontiers in cellular and infection microbiology · 2025Article
- ViralPrimer: a web server to monitor viral nucleic acid amplification tests' primer efficiency during pandemics, with emphasis on SARS-CoV-2 and Mpox.Bioinformatics (Oxford, England) · 2024Article
- Efficient SARS-CoV-2 variant detection and monitoring with Spike Screen next-generation sequencing.Briefings in bioinformatics · 2024Article
- Development and Evaluation of an In-House Real-Time RT-PCR Targeting nsp10 Gene for SARS-CoV-2 Detection.International journal of molecular sciences · 2024Article
- Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses.Microbial genomics · 2024Article
- Development of a robust TaqMan probe-based one-step multiplex RT-qPCR for simultaneous detection of SARS-CoV-2 and Influenza A/B viruses.BMC microbiology · 2023Article
- The Mutational Landscape of SARS-CoV-2.International journal of molecular sciences · 2023Article
- A full genome tiling array enhanced the inspection and quarantine of SARS-CoV-2.Virology journal · 2023Article
- The clinical characteristics of pediatric patients infected by SARS-CoV-2 Omicron variant and whole viral genome sequencing analysis.PloS one · 2023Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 3 countries.
Funding
Abstract
Due to the constantly increasing number of mutations in the SARS-CoV-2 genome, concerns have emerged over the possibility of decreased diagnostic accuracy of reverse transcription-polymerase chain reaction (RT-PCR), the gold standard diagnostic test for SARS-CoV-2. We propose an analysis pipeline to discover genomic variations overlapping the target regions of commonly used PCR primer sets. We provide the list of these mutations in a publicly available format based on a dataset of more than 1.2 million SARS-CoV-2 samples. Our approach distinguishes among mutations possibly having a damaging impact on PCR efficiency and ones anticipated to be neutral in this sense. Samples are categorized as "prone to misclassification" vs. "likely to be correctly detected" by a given PCR primer set based on the estimated effect of mutations present. Samples susceptible to misclassification are generally present at a daily rate of 2% or lower, although particular primer sets seem to have compromised performance when detecting Omicron samples. As different variant strains may temporarily gain dominance in the worldwide SARS-CoV-2 viral population, the efficiency of a particular PCR primer set may change over time, therefore constant monitoring of variations in primer target regions is highly recommended.
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Registered trials
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