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Data for Recent sequence variation in probe binding site affected detection of respiratory syncytial virus group B by real-time RT-PCR
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Nokes, D. James and Kamau, Evelyn (2017) Data for Recent sequence variation in probe binding site affected detection of respiratory syncytial virus group B by real-time RT-PCR. [Dataset]
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Official URL: https://doi.org/10.7910/DVN/B2PT24
Abstract
Background
Direct 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.
Objectives
Establish if mismatches in the primer and probe binding sites could have reduced real-time RT-PCR sensitivity.
Study design
Nucleoprotein (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.
Results
N 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.
Conclusions
An 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.
Item Type: | Dataset | ||||||
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Subjects: | Q Science > QR Microbiology > QR355 Virology | ||||||
Divisions: | Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School | ||||||
Type of Data: | Experimental data | ||||||
Library of Congress Subject Headings (LCSH): | Respiratory syncytial virus, Polymerase chain reaction | ||||||
Publisher: | University of Warwick, Warwick Medical School | ||||||
Official Date: | 14 May 2017 | ||||||
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Status: | Not Peer Reviewed | ||||||
Publication Status: | Published | ||||||
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Access rights to Published version: | Open Access (Creative Commons) | ||||||
Copyright Holders: | University of Warwick | ||||||
Description: | Data record consists of a single data file in PDF format. |
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