mikemwanga/MSC-Project

Whole genome analysis of RVA G1P[8] strain before and after vaccine introduction in Kenya # MSC-Project Whole genome analysis of RVA G1P[8] strain before and after vaccine introduction in Kenya ## Abstract Group A rotaviruses (RVA) are a leading cause of severe acute gastroenteritis in young children worldwide. RVA clinical isolates show extensive genetic variability especially within the two outer capsid proteins named, VP7 (G) and VP4 (P) that are key targets of human immune responses. These two proteins form the basis for its binary (GP) RVA classification system. Kenya introduced the monovalent Rotarix® vaccine (derived from a live attenuated G1P[8] rotavirus strain) in July 2014. This vaccine is expected to provide homotypic and heterotypic protection against circulating RVA strains. However, RVA vaccines including Rotarix® have shown lower efficacy in developing countries compared to developed countries for reasons that remain unclear to date. Continual RVA surveillance in Kilifi (coastal Kenya), since 2010, has shown a high prevalence of G1P[8] strains in both pre- and post-vaccination periods. Analysis of whole genome sequence data has potential to provide insight on the reasons underlying the vaccine underperformance and local persistence of G1P[8] strains despite ongoing nation-wide Rotarix® vaccination. Genomic mutations, frequent genetic reassortment, and increased vaccine mediated-immunity might lead to antigenic evolution and development of vaccine escape strains. Further, close monitoring of G1P[8] is needed to provide insight into the origin of continued RVA cases as incidence declines. During this proposed project, I will undertake a whole-genomic analysis of G1P[8] strains collected in Kilifi Kenya before and after the Rotarix® vaccination programme took effect to determine the patterns of genome-wide variation of G1P[8] strains and temporal patterns of RVA phylogeny. This will advance the understanding of the impact of vaccination on RVA genetic diversity and transmission, particularly G1P[8] genotype. ## Problem Statement RVA has …