Species and serotype diversity of human rhinoviruses from patients presenting with influenza like illness in Kenya in 2008

Abstract

Tract infections, the main cause of the common cold and recently have been associated with more serious respiratory infections. There are over 100 known serotypes of HRV, classified into 3 species (A, B and C). In Kenya, there is scanty information regarding the genotypic characteristics of HRV in circulation. Objective: To determine the species and serotype diversity of HRV that circulated in Kenya in 2008 among patients presenting with ILI.Methodology: 517 nasopharyngeal samples collected from patients >2months old who attended outpatient clinics included in the USAMRU-K respiratory diseases surveillance network were used. Real time RT-PCR was employed to detect HRV followed by targeted amplification of part of the 5’ non-coding region and the VP4/VP2 gene of all HRV-positive samples. Upon nucleotide sequencing, the sequences were then compared to prototype and homotypic rhinovirus reference strains to establish serotype identities and a phylogenetic tree was constructed. Results: HRV was detected in 131 (25%) samples. Of these 33 (25%) amplified successfully which upon nucleotide sequencing 29 (87%) yielded usable sequences. Phylogenetic analysis based on VP4/VP2 genomic region revealed separation of Kenyan strains into three clusters corresponding to HRV A, B and C species. Majority (n=17) belonged to HRVA species,(serotypes: 29 [n=2], -47, -1 [n=2], -56, -49[n=2], -30, -106, -20[n=2],-45, -58 [n=2], -45 and -78) three belonged to HRV B species: (-37, -84, and -91) whereas 9 belonged to HRV C species: (-2[n=3], -14, -7, -13[n=2], -31, and -36). Conclusion: This study demonstrates circulation of Human Rhinoviruses in Kenya and indicates high genetic diversity among these viruses. The findings suggest that HRV A and C strains played a key role in human respiratory infections in Kenya in 2008. Knowledge about circulating HRV strains is important as it may help guide development of therapeutic strategies against HRV infections