2026-10-14T07:47:43Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33802615 2026-09-15T15:23:12Z portal_1197 item_type_3 month_year_09_2026

Data for Recent sequence variation in probe binding site affected detection of respiratory syncytial virus group B by real-time RT-PCR D. James Nokes (9117189) Evelyn Kamau (645564) Respiratory syncytial virus Polymerase chain reaction Migrated from ePrints 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.<br><br>Data record consists of a single data file in PDF format. This dataset comprises of Nucleotide sequences used to match primers and probes, and for phylogenetic inferences. In our analysis, we observed inconsistencies between two routine RSV diagnostic methods applied in our labs, one method utilizes immunofluorescence microscopy and other molecular probes, and set out to determine. Sequence data cleaning and contig assembly was done using Sequencher program v.5.1; sequence alignment done using MAFFT v.1.8; phylogenetic inferences done in MEGA v1.6; custom BLAST of the primers and probes done using geneious v8.1.8 All sequence data reported is freely available in Genbank with accession numbers from KX775772 - KX775940. 2017-05-14T00:00:00Z Dataset Dataset 10.82444/warw.33802615.v1 https://figshare.com/articles/dataset/Data_for_Recent_sequence_variation_in_probe_binding_site_affected_detection_of_respiratory_syncytial_virus_group_B_by_real-time_RT-PCR/33802615 CC BY 4.0