Functional Profiles of Hepatitis C Virus Genome at Single Nucleotide Resolution

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DESCRIPTION: HCV has emerged as a major human health concern with an estimate of 170 million people who are persistently infected worldwide. HCV infections cause liver diseases including chronic hepatitis, cirrhosis, and hepatocellular carcinoma, especially in HIV- infected persons. Viral hepatitis progresses faster and more devastating among AIDS patients, which has become the leading cause of non AIDS-related deaths. Studies aiming to evaluate the effect of HCV elimination on the incidence of HCC indicate that successful eradication of HCV can reduce the risk for failure of liver function and HCC development. However, neither prophylactic nor therapeutic vaccine is available for HCV infection. Before the recent approval of the two protease inhibitors, the standard treatment has been combination therapy with interferon (IFN-?) and ribavirin which only offers limited response rate. Therefore, there is a need for understanding the mechanisms by which HCV develops resistance to the antiviral function of IFN. It's known that type I interferon (IFN) response can defend mammalian host from virus infection. However, viruses have evolved to utilize different strategies to evade from multiple layers of immune response. As a result, HCV persist in the host despite induction of IFN response and thereby approximately 50% of HCV patients are resistant to IFN-? treatment. To study the mechanisms by which HCV antagonizes the IFN response, the proposed study will systematically map HCV sequences, which is critical for anti-IFN function at single amino acid resolution with a high-throughput, quantitative, genome-scale profiling platform. The concept behind this approach is to randomly mutagenize every base pair on the virus genome, select for the mutant library in the presence or absence of IFN-?, and perform massively parallel sequencing to determine which mutations are diminished in the selection, which is presumably due to their loss of anti-IFN function. The research specific aims are the following: (1) Establish a single nucleotide mutant HCV library with high complexity; (2) Screen the library with treatment of IFN-? to identify the viral sequences critical for counteracting the IFN response; (3) Characterize individual mutants and verify the interaction between HCV with IFN response. The study is expected to map the viral sequences in the entire HCV genome responsible for its resistance to IFN therapy in a systemic and unbiased manner. Identification of these sequences will provide knowledge in understanding the reasons why HCV can evade the IFN response and establish resistance to the treatment. Additionally, this study will provide a depth of knowledge for vaccine development. Selection of the mutant library in the absence of IFN treatment will also reveal the sequence stretches with high genetic barrier to mutate, which will serve as novel targets for vaccine development. Therefore, it will offer novel antiviral treatment strategies to overcome viral resistance.