BMS-790052 is the most potent hepatitis C virus (HCV) inhibitor reported to date, with 50% effective concentrations (EC 50 s) of <50 pM against genotype 1 replicons. This exceptional potency translated to rapid viral load declines in a phase I clinical study. By targeting NS5A, BMS-790052 is distinct from most HCV inhibitors in clinical evaluation. As an initial step toward correlating in vitro and in vivo resistances, multiple cell lines and selective pressures were used to identify BMS-790052-resistant variants in genotype 1 replicons. Similarities and differences were observed between genotypes 1a and 1b. For genotype 1b, L31F/V, P32L, and Y93H/N were identified as primary resistance mutations. L23F, R30Q, and P58S acted as secondary resistance substitutions, enhancing the resistance of primary mutations but themselves not conferring resistance. For genotype 1a, more sites of resistance were identified, and substitutions at these sites (M28T, Q30E/H/R, L31M/V, P32L, and Y93C/H/N) conferred higher levels of resistance. For both subtypes, combining two resistance mutations markedly decreased inhibitor susceptibility. Selection studies with a 1b/1a hybrid replicon highlighted the importance of the NS5A N-terminal region in determining genotype-specific inhibitor responses. As single mutations, Q30E and Y93N in genotype 1a conferred the highest levels of resistance. For genotype 1b, BMS-790052 retained subnanomolar potency against all variants with single amino acid substitutions, suggesting that multiple mutations will likely be required for significant in vivo resistance in this genetic background. Importantly, BMS-790052-resistant variants remained fully sensitive to alpha interferon and small-molecule inhibitors of HCV protease and polymerase.Hepatitis C virus (HCV) is a major cause of chronic liver disease, affecting up to 180 million people worldwide (24, 32). HCV is an enveloped, positive-strand RNA virus and is the sole member of the Hepacivirus genus of the Flaviviridae family (17). HCV is classified into six major genotypes, each with multiple subtypes, based on sequence diversity (17, 33). The current standard of care for HCV infection includes therapy with a combination of pegylated alpha interferon (pegIFN-␣) and ribavirin. This treatment is often associated with limiting side effects, and effectiveness is highly genotype dependent (3,30,38). For genotypes 1a and 1b, accounting for ϳ60% of global infections, long-term efficacy or a sustained virological response is achieved in only ϳ50% of chronically infected individuals (3, 24). An increasing number of small-molecule inhibitors targeting specific viral proteins are entering into clinical evaluation (1,25,27,30,38). Collectively, these inhibitors are often referred to as direct-acting antiviral agents (DAA). The most advanced of these inhibitors target enzymatic activities of the HCV nonstructural proteins NS3 (serine protease) and NS5B (RNA-dependent RNA polymerase) (1, 27). We recently described a potent inhibitor of HCV RNA replication, BMS-79005...