Molecular analysis of Human Respiratory Syncytial Virus Group B strains
isolated in Kenya concurrent with the emergence of Pandemic Influenza
A/H1N1
Abstract
We conducted a retrospective study to explore molecular insights into
human respiratory syncytial virus (HRSV) group B strains among patients
attending outpatient clinics at government medical facilities both
before and during the influenza A/H1N1/2009 pandemic outbreak. We
screened 2300 nasopharyngeal swabs using multiplex real time reverse
transcriptase polymerase chain reaction. We amplified a segment of the
first and second hypervariable regions, as well as the conserved portion
of the third domain of the G-gene using HRSV-B specific primers,
sequenced by Sanger di-deoxy chain termination method and thereafter
analyzed the sequences. We characterized the circulating strains into 3
known genotypes: SAB4 (1.4%), BA7(1.4%) and multiple lineages of BA9
(97.2%). The majority of BA9 viruses were uniquely Kenyan with only 4%
aligning with BA9 lineages found elsewhere. The mean evolutionary rate
of the HRSV-B was estimated to be 3.08 × 10 -3
substitutions per site per year. Our findings indicate that the
circulating HRSV-B viruses in Kenya underwent more rapid evolution
during the overlapping period of 2007 to 2012. Additionally, our
findings reveal the existence of unique lineages as well as new variants
that have not been reported elsewhere to date.