Systematic Investigation on the Relationship of HCV Genetic Heterogeneity and In Vitro Resistance to Direct Acting Antivirals and Attempts to Develop a HCV Genotype 3 Cell Culture System

Abstract

This doctoral work has investigated whether mutation supply in HCV is sufficiently large to allow the selection of it s variants during dual or triple DAA treatment associated with augmented virus fitness or impairment. Randomly-mutagenized HCV full-genome libraries were engineered to create a highly diverse population of replication-competent variants in cell culture. These variants exhibited escape when treated with NS5A/NS5B inhibitors (daclatasvir/sofosbuvir), and relapse on treatment with a combination of NS3/NS5A/NS5B inhibitors (simeprevir or paritaprevir/daclatasvir/sofosbuvir). Drug escape variants (beneficial variants) were studied for the relationship between fold-resistance and fitness, variants influence on host factors phosphatidylinositol 4-phosphate accumulation and Cyclophilin dependency, and cross-resistance. Further, the role of RNA replication and/or infectious virus production in escape of drug pressure was investigated. This comprehensive doctoral study demonstrates a possible role for HCV fitness of overcoming drug-mediated selection pressure. Attempts were made to establish the HCV GT3 replication system, which showed signs of viral replication. newline