Treatment of patients infected with hepatitis C virus (HCV) with direct acting antivirals can lead to the emergence of drug-resistant variants that may pose a long-term threat to viral eradication. HCV replicons have been used to select resistance mutations; however, genotype 2a JFH-1-based viruses provide the opportunity to perform resistance selection in a bona fide infection system. In this study, we used a tissue culture-adapted J6/JFH-1 virus to select resistance to the NS3 protease inhibitors BILN-2061 and VX-950. Lunet-CD81 cells were infected with J6/JFH-1 virus and maintained in the presence of inhibitors until high-titer viral supernatant was produced. Viral supernatants were passaged over naive cells at escalating drug concentrations, and the resulting viruses were then characterized. Three NS3 resistance mutations were identified in BILN-2061-resistant viruses: A156G, D168A, and D168V. Interestingly, D168A, D168V, and A156T/V, but not A156G, were selected in parallel using a genotype 2a replicon. For VX-950, the T54A and A156S NS3 resistance mutations were identified in the virus selections, whereas only A156T/V emerged in genotype 2a replicon selections. Of note, VX-950 resistance mutations selected using the 2a virus (T54A and A156S) were also observed during VX-950 clinical studies in genotype 2 patients. We also performed viral fitness evaluations and determined that the mutations selected in the viral system did not confer marked reductions in virus production kinetics or peak titers. Overall, the HCV infection system is an efficient tool for drug resistance selections and has advantages for the rapid identification and characterization of clinically relevant resistance mutations.Chronic hepatitis C virus (HCV) infection represents a significant and immediate worldwide health burden (2, 40). Accordingly, tremendous resources have been directed toward discovering and developing novel therapies to treat HCV infection. Currently, a number of direct-acting antiviral agents (DAAs) are under clinical development (7,35,37). Various DAAs have been designed to target distinct HCV viral proteins (3, 4, 6), including NS3 protease, NS5A, and the NS5B RNA-dependent RNA polymerase. During short-term monotherapy studies in HCV-infected patients, many of these DAAs have elicited pronounced antiviral effects (e.g., Ն3 log HCV viral load reductions in as few as 3 days of treatment). However, even in these short-term studies the selection of viral resistance was apparent and thus poses a significant challenge to the long-term efficacy of these novel agents (6,11,32,35).The HCV replicon has been a useful in vitro tool for identifying and characterizing resistance mutations for multiple classes of DAAs (11,32,35). For example, the NS3 mutations R155K, A156T/V, and D168A/V were selected in replicons using the first clinically active NS3 protease inhibitor, BILN-2061 (a prototype noncovalent NS3 inhibitor) (16,19). Unfortunately, the resistance profile of BILN-2061 in the clinic has not been reported, making it imposs...