UNDERSTANDING THE SOURCES OF INTRODUCTIONS AND GENETIC DIVERSITY OF ROTAVIRUS A STRAINS THROUGH WHOLE GENOME ANALYSIS OF ROTAVIRUS G8P[4] AND G9P[8] STRAINS DETECTED IN KILIFI KENYA, 2010 - 2019

Abstract

Background: Rotavirus Group A (RVA) is the primary cause of severe dehydrating diarrhoea in young children. Notwithstanding the introduction of the RVA vaccination in several countries, RVA continues to be a major cause of childhood hospitalization due to a variety of factors including imperfect protection from available vaccines and antigenic variability in circulating RVA strains. Several RVA genotypes occur in nature that can infect humans, some common others uncommon depending on geographic region and time period e.g. as exemplified by the genotypes G9P[8] and G8P[4] which have been observed to fluctuate in prevalence patterns in recent coastal Kenya studies. The sources of introductions, genetic relatedness and full genotype constellation of G9P[8] and G8P[4] strains detected before and after vaccine introduction in Kilifi, remains unknown. The current study aimed to understand the sources and genetic diversity within G8P[4] and G9P[8] strains detected in Kilifi before and after rotavirus vaccine introduction in Kenya in July 2014 through whole genome sequence analysis. This study provides improved understanding on the genomic epidemiology of RVA. Materials and Methods: Available nucleotide sequences from RVA positive samples of two genotypes, namely, G8P[4] (n=47) and G9P[8] (n=13) collected at Kilifi County Hospital (KCH) between 2010 and 2019 were utilized for this study. Contemporaneous global sequence data were retrieved from public databases for comparative phylogenetic analysis. Genotypic and phylogenetic relationships of these strains were investigated using Virus Pathogen Database Resource and Iqtree tools. Local-global comparative phylogenetic analyses were undertaken to explore genetic relatedness and origins of Kilifi strains and their placement in the global context. Bayesian phylogenetic inference was exploited to establish the nucleotide substitution rate and divergence time of the two outer capsid proteins (VP4 and VP7) of the examined G8P[4] and G9P[8] strains. vi Results: The analyzed strains showed a conserved genomic constellation over the entire surveillance period (2010-2019), i.e., typical DS-1-like and Wa-like constellations for G8P[4] and G9P[8] strains, respectively. The study strains exhibited high sequence similarities for both nucleotide and amino acid sequences (mean nucleotide and amino acid sequence identities of more than 99.90%) indicating limited genetic diversity among strains of these two genotypes which were detected during the study period. Whereas the Kilifi G9P[8] strains occurred in multiple clusters on the global tree, the Kilifi G8P[4] isolates formed a monophyletic cluster in majority of the segments across the RVA genome. Across all segment phylogenies, the post-vaccine G8P[4] strains clustered closely to the local pre-vaccine strains suggesting local persistence of G8P[4] strains. G9 strains exhibited a faster rate of evolution compared to genes of strains P[8], G8 and P[4] investigated. For both G8P[4] and G9P[8], clustering did not occur by the vaccination status or the year the strains were identified. Conclusion: Closely related G9P[8] and G8P[4] strains circulated in Kilifi over a nine year period (both pre- and post-vaccine era). Local endemicity from the pre-vaccine era and limited introduction event(s) from elsewhere might be among the factors sustaining continued detection of the G8P[4] and G9P[8] strains in Kilifi, Coastal Kenya