Hepatitis C virus adaption to host immune responses during early infection: relevance to infection and treatment outcome

In 1989, Choo and colleagues identified the hepatitis C virus (HCV) as the causative agent for non-A non-B hepatitis or hepatitis C. There is still no vaccine available to prevent HCV infection and the virus has continued to spread within the human population and today is a major global health problem. An estimated 170 million people worldwide are chronically infected with HCV with about three million people newly infected each year. In Australia, Hepatitis C is the most common blood-borne infection and is the leading cause of liver transplantation.

Among the individuals exposed to HCV, only 20-45% will spontaneously clear the virus while the majority will develop viral persistence. Until recently, standard of care for chronic HCV infection involved the combination of pegylated interferon-alpha and ribavirin (pegIFN-α/RBV). However, only 40-80% of chronic HCV-infected subjects treated with this combination clear the virus. As such, the limited efficacy of this treatment against the common genotype 1 strain and associated adverse side-effects has led to the development of numerous direct-acting antivirals (DAAs). DAAs represent new hope for the therapeutic management of individuals infected with the virus but these new treatment options (including regimens containing multiple DAAs with or without IFN currently in pre-clinical trials) do not prevent re-infection, which is common in high-risk HCV exposure populations. Furthermore, the expense of the new and future treatment regimens of DAAs make it unlikely these drugs will be readily available in developing countries with high prevalence rates. Accordingly, there is still a need for a preventative HCV vaccine. Importantly, unlike HIV, natural immunity exists in humans and numerous studies have shown that a broad and durable cellular immune response is the hallmark of an effective response against HCV and should provide leads in the development of an effective universal HCV vaccine. Impairing the ability of researchers to develop such a vaccine is the inherent ability of HCV to rapidly evolve under selective pressures. HCV has a high mutation rate and the virus uses this characteristic as a strategy to escape the host’s immune response and treatment that aim at controlling the infection. The acute phase of the infection is an important phase where de novo mutations are observed within host T-cell targets (epitopes) as part of the adaptive immune pressure as well as sequence polymorphisms can be found characteristic of an NK cell immunity for the innate immune response. These variations can be maintained during the course of the infection suggesting a limited fitness cost associated with these variants or the presence of compensatory mutations. In this thesis, samples from subjects with recently acquired HCV infection were analysed using both low and high-resolution sequencing technologies to examine, firstly, how the host’s immune response affects viral diversity during the natural history of the infection and under IFN-based treatment; and secondly, how it influences infection outcome. The results presented in this thesis suggest that HCV adaptation to host immune pressure (as indicated by viral adaptations to human leucocyte antigen (HLA)-restricted T-cell and NK cell immune responses) is likely to be relevant to infection and treatment outcomes. Such adaptation is dependent on the plasticity of the virus and its capacity to develop compensatory mutations to offset the fitness cost associated with its “strategic” variations. The use of high-resolution next generation sequencing technologies showed viral variants present at levels below the detectable threshold for sanger-based bulk or population sequencing (ie <20%). Additionally, a protective role for telomeric KIR genes against viral persistence was observed with B-haplotype-defining KIR genes more prevalent in spontaneous resolvers. This provides a new approach for studying the complexity of the viral population within a host and identifying minor variants, which could potentially become dominant over the course of the infection. Furthermore, using high-resolution sequencing shows mutations likely to affect the efficacy of the new DAA drugs in circulating viruses within high-risk exposure populations but these strains typically occur at low frequencies. Finally, a better understanding of HCV adaptation to the host’s immune response is important in predicting infection outcomes, in the design of a universal vaccine and new therapies.