Recent sequence variation in probe binding site affected detection of respiratory syncytial virus group B by real-time RT-PCR.

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

SUBMITTER: Kamau E 

PROVIDER: S-EPMC5331890 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature