ArticleDiagnostics (Basel, Switzerland)2022
Unusual N Gene Dropout and Ct Value Shift in Commercial Multiplex PCR Assays Caused by Mutated SARS-CoV-2 Strain.
Article in Diagnostics (Basel, Switzerland), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 17 citations in OpenAlex.
- Using machine learning models to predict the impact of template mismatches on polymerase chain reaction assay performance.Scientific reports · 2025Article
- Review
- Testing for SARS-CoV-2: lessons learned and current use cases.Clinical microbiology reviews · 2024Review
- Partial N-gene target failure in the Seegene Allplex SARS-CoV-2 Master Assay as a proxy of SARS-CoV-2 BA.2.86.Microbiology spectrum · 2024Article
- Explaining the impact of mutations on quantification of SARS-CoV-2 in wastewater.Scientific reports · 2024Article
- Underestimation of SARS-CoV-2 in wastewater due to single or double mutations in the N1 qPCR probe binding region.Water research X · 2024Article
- First sequenced cases of Omicron BA.2 sublineage in Ecuador.Virus research · 2023Article
- Cycle Threshold (Ct) Values of SARS-CoV-2 Detected with the GeneXpertCurrent issues in molecular biology · 2023Article
- Rapid Shift from SARS-CoV-2 Delta to Omicron Sub-Variants within a Dynamic Southern U.S. Borderplex.Viruses · 2023Article
- Remdesivir Influence on SARS-CoV-2 RNA Viral Load Kinetics in Nasopharyngeal Swab Specimens of COVID-19 Hospitalized Patients: A Real-Life Experience.Microorganisms · 2023Article
- Long-term validation of a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 from March 2020 to October 2021 in Central Africa, Gabon.PLoS neglected tropical diseases · 2022Article
- Comparative Analysis of COVID-19 Gene Target Dropout/Failure Results using Thermofisher TaqPath COVID-19 Combo Kit and Nextstrain CoVariants Genomic Databases.Journal of healthcare, science and the humanitiesArticle
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Several SARS-CoV-2 variants have emerged and early detection for monitoring their prevalence is crucial. Many identification strategies have been implemented in cases where sequencing data for confirmation is pending or not available. The presence of B.1.1.318 among prevalent variants was indicated by an unusual amplification pattern in various RT-qPCR commercial assays. Positive samples for SARS-CoV-2, as determined using the Allplex SARS-CoV-2 Assay, the Viasure SARS-CoV-2 Real Time Detection Kit and the GeneFinder COVID-19 Plus RealAmp Kit, presented a delay or failure in the amplification of the N gene, which was further investigated. Whole-genome sequencing was used for variant characterization. The differences between the mean Ct values for amplification of the N gene vs. other genes were calculated for each detection system and found to be at least 14 cycles. Sequencing by WGS revealed that all the N gene dropout samples contained the B.1.1.318 variant. All the isolates harbored three non-synonymous mutations in the N gene, which resulted in four amino acid changes (R203K, G204R, A208G, Met234I). Although caution should be taken when the identification of SARS-CoV-2 variants is based on viral gene amplification failure, such patterns could serve as a basis for rapid and cost-effective screening, functioning as indicators of community circulation of specific variants, requiring subsequent verification via sequencing.
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