ArticleJournal of clinical virology : the official publication of the Pan American Society for Clinical Virology2017
Recent sequence variation in probe binding site affected detection of respiratory syncytial virus group B by real-time RT-PCR.
Article in Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 55 citations in OpenAlex.
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- Comment on "Results From the Third and Fourth WHO External Quality Assessments for the Molecular Detection of Respiratory Syncytial Virus".Influenza and other respiratory viruses · 2026Article
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- Improved performance of nucleic acid-based assays for genetically diverse norovirus surveillance.Applied and environmental microbiology · 2023Article
- Results from the second WHO external quality assessment for the molecular detection of respiratory syncytial virus, 2019-2020.Influenza and other respiratory viruses · 2023Article
- Rhinovirus dynamics across different social structures.Npj viruses · 2023Article
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- Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from Kenya.Scientific reports · 2022Article
- Surveillance of respiratory viruses at health facilities from across Kenya, 2014.Wellcome open research · 2022Article
- Rare Variants in RPPH1 Real-Time Quantitative PCR Control Assay Binding Sites Result in Incorrect Copy Number Calls.The Journal of molecular diagnostics : JMD · 2022Article
- Multiple detection and spread of novel strains of the SARS-CoV-2 B.1.177 (B.1.177.75) lineage that test negative by a commercially available nucleocapsid gene real-time RT-PCR.Emerging microbes & infections · 2021Article
- Molecular Characterization of Associated Pathogens in Febrile Patients during Inter-Epidemic Periods of Urban Arboviral Diseases in Tapachula Southern Mexico.Pathogens (Basel, Switzerland) · 2021Article
- Recommendations for respiratory syncytial virus surveillance at the national level.The European respiratory journal · 2021Article
Corrections and comments
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Authors and funding
9 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundDirect immuno-fluorescence test (IFAT) and multiplex real-time RT-PCR have been central to RSV diagnosis in Kilifi, Kenya. Recently, these two methods showed discrepancies with an increasing number of PCR undetectable RSV-B viruses.
objectivesEstablish if mismatches in the primer and probe binding sites could have reduced real-time RT-PCR sensitivity. STUDY
designNucleoprotein (N) and glycoprotein (G) genes were sequenced for real-time RT-PCR positive and negative samples. Primer and probe binding regions in N gene were checked for mismatches and phylogenetic analyses done to determine molecular epidemiology of these viruses. New primers and probe were designed and tested on the previously real-time RT-PCR negative samples.
resultsN gene sequences revealed 3 different mismatches in the probe target site of PCR negative, IFAT positive viruses. The primers target sites had no mismatches. Phylogenetic analysis of N and G genes showed that real-time RT-PCR positive and negative samples fell into distinct clades. Newly designed primers-probe pair improved detection and recovered previous PCR undetectable viruses.
conclusionsAn emerging RSV-B variant is undetectable by a quite widely used real-time RT-PCR assay due to polymorphisms that influence probe hybridization affecting PCR accuracy.
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