The Virology Core will be responsible for the generating full-length viral genome sequences from the majority of study subjects in this U19 through a highly organized, and high-throughput 454 sequencing approach. As these data can be generated rapidly, these data will also serve to identify subjects and epitopes for downstream analysis for the proposed specific studies on outlined in Projects 1-4. To rule out any confounding effects on our study design of possible virus-specific interferon resistance associated with prior interferon therapy failure, the Virology Core will also determine whether there is any evidence of genotypic resistance to interferon in subjects previously having failed interferon therapy. Specifically, the Virology Core will: Aim 1: Characterize full genome viral sequences from all HCV+ study subjects to identify epitope-specific sequence data for downstream phenotype and functional assays. Aim 2: Determine whether subjects who failed to achieve prior sustained virologic response (SVR) under interferon and ribavirin therapy exhibit any IFN genotypic resistance markers

Knowledge of each subject's viral sequence will be important to ensure that the proper reagents (peptides, tetramers) are used for each assay, and to enable where needed autologous peptide screening to known T cell epitopes, but even more importantly to also ensure that viral escape has not altered the immune response or phenotype of responding cells to be included in analyses. It will also be important to demonstrate that prior interferon treatment failure is not due to development of interferon resistance.