The nature and consequences of the hepatitis C virus E1E2 envelope gene variability

The majority of Hepatitis C Virus (HCV) infections result in chronic infection, which can ultimately, cause hepatocellular carcinoma and liver failure. Within the infected host, the virus exists as a population of heterogeneous viral variants called a quasispecies. The envelope region of HCV genome is the most heterogeneous among the whole genome. The envelope proteins mediate viral entry and are also the target of the host immune response. Studying envelope gene evolution can provide important molecular insights into. entry and antibody escape, which ultimately can inform vaccine and therapy developments. Despite this, the influence of host antibody response in driving envelope gene evolution and its role in immune evasion is unclear. To address this shortfall we studied the evolution of HCV envelope genes, over a period of 7-15 years, in treatment naive chronically infected patients. The pattern of HCV evolution was patient specific and clustering of quasispecies was not dependant on the sampling time, which is in stark contrast with other related viruses. The hyper variable region I (HVR-l) was under strong selective pressure. The residues from HVR-l and downstream region, in and around receptor and antibodies binding sites were positively selected during viral evolution. The isolated envelope genes from only two patients (40%) were functional in the retroviral pseudo-particle assay (HCVpp). The functional envelope genes isolated from sequential samples showed variations in infectivity, which could be attributed to substitutions at multiple residues acquired during the course of evolution. Construction of El E2 chimeras derived from infectious and non-infectious clones showed that the region downstream of HVR-l was an important determinant of in vitro infectivity. The patients' isolated HCVpp functional envelope genes were efficiently neutralised by autologous IgGs, and there was no obvious evidence of antibody escape. One of the EIE2 chimeras showed differential sensitivity to well-defined CD81 binding-site-specific neutralising mono clonal antibody, demonstrating the existence of complex mechanisms underpinning antibody resistance. Finally, studies of quasi species transmission in a xenomouse model showed the occurrence of a transmission bottleneck. In multiple transmission experiments a minor variant within the inoculum consistently became established within the recipient mouse host. The established variant harboured amino acid substitutions at amino acid residues 198, 448 and 474 of the virus polyprotein, including loss of a predicted glycosylation site (N448D). It was not possible to define the phenotypic effects of the substitutions as the EIE2 clones were non-infectious in the HCVpp assays. Defining viral determinants involved in successful transmission will help the design of vaccines.EThOS - Electronic Theses Online ServiceGBUnited Kingdo