Genetic Diversity of Rotavirus Associated with Gastroenteritis

Abstract

Diarrheal infections have been the cause of disease burden and child mortality around the globe and the foremost viral agent involved in such an illness is Rotavirus. Although different groups of rotaviruses have been identified, Group A rotavirus (RVA) is the primary cause of gastrointestinal infections in children and the focus of our study. The present research work includes hospital based study on rotavirus isolates, the epidemiological aspects and the genetic diversity found in the circulating strains of the samples collected from local hospitals of Rawalpindi and Islamabad, Pakistan. Before the start of this research project in 2008, no incessant data was available on the strain prevalence of rotavirus from Rawalpindi. Epidemiological data from patients presented with gastroenteritis was collected to further investigate the seasonal pattern, age distribution and the related symptoms of the virus in addition to diarrhea (Chapter III). Partial sequencing of the VP7 and VP4 gene was done to analyze the strains at phylogenetic level. Genotyping by direct sequencing of the VP6 and NSP4 genes of the Pakistani RVA strains was done (Chapter IV). These genes have not been investigated before from Pakistani strains. For both genes Wa and DS-1 like genotypes were found for the studied strains. Genetic linkage was also observed in both genes for most of the isolates except two RVA strains which showed discordant genetic linkage. Phylogenetic analysis of VP6 and NSP4 genes in addition to Wa and DS-1 like genotype clustering also represented reassortment with animal gene segments of bovine and partially porcine origins. The E2 genotype of NSP4 gene had unknown origin for majority of the strains except one which had bovine origin. The NSP4 gene was also investigated by comparative protein modeling (Chapter IV). The recent emergence of full genome sequencing necessitated to explore Pakistani RVA strains on full genome basis which will act as pioneer strains of rotavirus in future research on this virus. Eight Pakistani RVA strains with various G/P combinations were selected for the investigation. Sequencing showed that the strains had typical Wa (I1-R1- M1-C1-A1-N1-T1-E1-H1) and DS-1 like (I2-R2-C2-M2-A2-N2-T2-E2-H2) backbone mostly referred to as ‘genotype 1’ and ‘genotype 2’. Furthermore, the phylogenetic analysis of the 11 gene segments of these strains showed inter and intragenogroup reassortment and transmission of animal gene segments (Chapter V). Complete genome sequencing of the unusual strain G6P[1], isolated for the first time from Pakistan, showed that out of the 11 gene segments 10 of them cluster with bovine strains and only NSP5 gene cluster with human strains having Wa like genotype (Chapter VI). This led us to speculate that the origin of this strain is the result of a direct interspecies transmission event between a bovine and human strain, with a single reassorment episode. The findings of this thesis have great implementation for the yet to be introduced rotavirus vaccine program in Pakistan since the country is still going through its pre- vaccine era. The introduction of the licensed vaccines, Rotarix and Rotateq, have shown heterotypic protection against RVA strains in most countries, however, its effectiveness is yet to be seen in our population. The data presented here show huge diversification in the strain prevalence and also introduction of animal gene segments might have an effect on the vaccine efficacy.