SPATIAL-TEMPORAL DISTRIBUTION AND SEQUENCE DIVERSITY OF GROUP A HUMAN
RESPIRATORY SYNCYTIAL VIRUSES IN KENYA PRECEDING THE EMERGENCE OF ON1
GENOTYPE
Abstract
Background: Human respiratory syncytial virus (HRSV) is a major cause of
severe viral acute respiratory illness and contributes significantly to
severe pneumonia cases in Africa. Little is known about its
spatial-temporal distribution as defined by its genetic diversity.
Methods: A retrospective study conducted utilizing archived
nasopharyngeal specimens from patients attending outpatient clinics in
hospitals located in five demographically and climatically distinct
regions of Kenya; Coast, Western, Highlands, Eastern and Nairobi. The
viral total RNA was extracted and tested using multiplex real time
RT-PCR (reverse transcriptase polymerase chain reaction). A segment of
the G-gene was amplified using one-step RT-PCR and sequenced by Sanger
di-deoxy method. Bayesian analysis of phylogeny was utilized and
subsequently median joining methods for haplotype network
reconstruction. Results: Three genotypes of HRSVA were detected; GA5
(14.0%), GA2 (33.1%) and NA1 (52.9%). HRSVA prevalence varied by
location from 33% to 13.2% in the Highlands and the Eastern regions
respectively. The mean nucleotide diversity (Pi(π)) varied by genotype:
highest of 0.018 for GA5 and lowest of 0.005 for NA1. A total of 58
haplotypes were identified (GA5 10; GA2 20; NA1 28). These haplotypes
were introduced into the population locally by single haplotypes and
additional subsidiary seeds amongst the GA2 and the NA1 haplotypes.
Conclusions: HRSVA was found across all the regions throughout the study
period and comprised three genotypes; GA5, GA2 and NA1 genotypes. The
genotypes were disproportionately distributed across the regions with
GA5 gradually increasing towards the Western zones and decreasing
towards the Eastern zones of the country.