Hepatitis C virus (HCV) research and drug discovery have been facilitated by the introduction of cell lines with self-replicating subgenomic HCV replicons. Early attempts to carry out robust, high-throughput screens (HTS) using HCV replicons have met with limited success. Specifically, selectable replicons have required laborious reverse transcription-PCR quantitation, and reporter replicons have generated low signal-to-noise ratios. In this study, we constructed a dicistronic single reporter (DSR)-selectable HCV replicon that contained a humanized Renilla luciferase (hRLuc) gene separated from the selectable Neo r marker by a short peptide cleavage site. The mutations E1202G, T1280I, and S2197P were introduced to enhance replicative capability. Approximately 170 million people globally test positive for hepatitis C virus (HCV) (9, 11). Infection by HCV results in a high degree of chronic hepatitis. In addition to inducing liver damage, a significant proportion of these infections also result in hepatocellular carcinoma. Although current treatments for hepatitis caused by HCV include interferon in combination with ribavirin (18), approximately 50 to 60% of individuals still are not able to resolve infection (15). Therefore, there is an unmet medical need to develop more effective therapies to treat HCV infection. Until 1999, all cell-based screening efforts for HCV drug discovery relied on surrogate viral systems, such as bovine viral diarrhea virus, and the potential development of assays where activities of specific viral targets could be monitored. In 1999, a significant breakthrough in studying HCV RNA replication occurred when the Bartenschlager laboratory developed the HCV replicon system, a tissue culture system that faithfully mimicked all of the RNA replication events of the HCV life cycle (21). This initiated a phase of intensified research into the mechanisms of HCV RNA translation, replication, and protein processing. It also ushered in a new era for HCV drug discovery, since it was now possible to test the effects of inhibitors of traditional targets, such as NS3 protease, helicase, and NS5B polymerase, in an authentic, in vitro HCV RNA replication system (1).The original replicon system (21) was constructed by replacement of genes from the HCV genome that are not essential for HCV RNA replication, e.g., the structural genes, p7 and NS2, with a genetic cassette carrying an antibiotic resistance gene and the internal ribosomal entry site (IRES) from encephalomyocarditis virus (EMCV). This resulted in the formation of a dicistronic, selectable, subgenomic HCV replicon (2-4, 21) whose replication requires RNA elements in both nontranslated regions as well as the nonstructural proteins, including NS3 protease, helicase, and polymerase. Therefore, the HCV replicon system can be used for identifying inhibitors against all of these components (1).Cell-based screening efforts in a high-throughput format to identify novel inhibitors and viral or host targets have recently been described (6,23,34). The first ...