HCV Genotype 6: A Model for HCV Genetics and Molecular Epidemiology Studies

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DESCRIPTION (provided by applicant): Among six genotypes, the genotype 6 represents the oldest, most diverse and genetically most complex viruses. This genotype currently has 22 subtypes, including 6r-6v we designated. We have sequenced the first complete genomes of 16 subtypes and 2 equivalents. We have also discovered 16 variants that may represent 14 new subtypes and 36 variants that show great genetic differences. The overall goal of this application is to define the genetic variation and virology properties of HCV by conducting detailed analyses on a full panel of genotype 6 complete sequences that will be determined from these variants. Based on the sequences, we will assemble full length HCV genomes and use for developing new HCV cell culture models. The rationale is that clarifying these HCV sequences will enable many bioinformatics analyses that have applications linking to basic research to patient care. The Specific Aims are to: (1) determine the complete genomes of 71 genotype 6 variants showing substantial genetic variations; (2) determine the epidemic dynamics of HCV that is represented by the oldest genotype 6 variants; and (3) develop HCV genotype 6 cell culture models using unique HCV genomes that are defined in (1). It is hypothesized that HCV genotype 6 represents a "living viral fossil" that will best reflect the past history of the virus and that, being the most complex among all HCV genotypes, the genotype 6 variants may have higher divergent properties that may make them more suitable for cell cultures. To accomplish these aims, we will employ an improved DNA walking strategy that can sequence a complete HCV genome from only 100 ¿l of serum. We will use the BEAST software that combines various coalescent methods. Novel strategies will be recruited to obtain the full length HCV genomes from the most infectious virus particles. In wild type or in chimeras with the JFH1 isolate, these genomes will be used to develop new HCV cell culture models that will have many applications. The successful completion of these studies will contribute the missing and fundamental knowledge to the epidemic dynamics of HCV, bioinformatic definition of its genetic variations, and the novel approaches in developing new HCV cell culture models. These models with the sequence will be vital for basic HCV research and for patient care and public health. PUBLIC HEALTH RELEVANCE: successful completion of these studies will contribute new viral sequences and cell culture models to understand the HCV genetic variation, epidemiology behavior, and virology mechanisms. This information and the derived models are vital for better strategies of HCV diagnosis and treatment, and the improved designs of antivirals and vaccines.