ArticleScientific reports2019
In silico re-assessment of a diagnostic RT-qPCR assay for universal detection of Influenza A viruses.
Article in Scientific reports, 2019. 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.
- Diagnostic sensitivity and specificity of metagenomic sequencing and qPCR for detection of viruses associated with bovine respiratory disease estimated using Bayesian latent class models.Frontiers in veterinary science · 2026Article
- Rapid and specific on-site H5Nx avian influenza diagnosis via RPA and PAM-independent CRISPR-Cas12a assay combined with anti-NP antibody-based viral RNA purification.Frontiers in veterinary science · 2025Article
- Redesign and Validation of a Real-Time RT-PCR to Improve Surveillance for Avian Influenza Viruses of the H9 Subtype.Viruses · 2022Article
- Novel Quantitative PCR forAnimals : an open access journal from MDPI · 2022Article
- Development of Real-Time Molecular Assays for the Detection of Wesselsbron Virus in Africa.Microorganisms · 2022Article
- Meta-Analysis of qPCR for Bovine Respiratory Disease Based on MIQE Guidelines.Frontiers in molecular biosciences · 2022Article
- A Colorimetric Test to Differentiate Patients Infected with Influenza from COVID-19.Small structures · 2021Article
- Virus Detection: A Review of the Current and Emerging Molecular and Immunological Methods.Frontiers in molecular biosciences · 2021Review
- Article
- Evaluation of the Sequence Variability within the PCR Primer/Probe Target Regions of the SARS-CoV-2 Genome.Bio-protocol · 2020Article
- Development of ssDNA Aptamers for Diagnosis and Inhibition of the Highly Pathogenic Avian Influenza Virus Subtype H5N1.Biomolecules · 2020Article
- Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome.Royal Society open science · 2020Article
- Influenza: National Trends Using the National Inpatient Sample Database from 1993 to 2015.Cureus · 2020Article
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Authors and funding
5 authors.
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Abstract
The ongoing evolution of microbial pathogens represents a significant issue in diagnostic PCR/qPCR. Many assays are burdened with false negativity due to mispriming and/or probe-binding failures. Therefore, PCR/qPCR assays used in the laboratory should be periodically re-assessed in silico on public sequences to evaluate the ability to detect actually circulating strains and to infer potentially escaping variants. In the work presented we re-assessed a RT-qPCR assay for the universal detection of influenza A (IA) viruses currently recommended by the European Union Reference Laboratory for Avian Influenza. To this end, the primers and probe sequences were challenged against more than 99,000 M-segment sequences in five data pools. To streamline this process, we developed a simple algorithm called the SequenceTracer designed for alignment stratification, compression, and personal sequence subset selection and also demonstrated its utility. The re-assessment confirmed the high inclusivity of the assay for the detection of avian, swine and human pandemic H1N1 IA viruses. On the other hand, the analysis identified human H3N2 strains with a critical probe-interfering mutation circulating since 2010, albeit with a significantly fluctuating proportion. Minor variations located in the forward and reverse primers identified in the avian and swine data were also considered.
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