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.