The current commercially licensed enzyme-linked immunosorbent assays (ELISAs) for hepatitis C virus (HCV) mainly use recombinant proteins containing linear epitopes. There is evidence, however, that conformational epitopes of HCV are more immunoreactive. Thus, we have designed an HCV antibody assay that employs a conformational protein, NS3NS4a PI (with functional protease and helicase activities), and a linear fusion protein, multiple-epitope fusion antigen 7.1 (MEFA 7.1) or MEFA 7.2. We have shown that NS3NS4a PI detects early-seroconversion conformation-sensitive antibodies better than c33c antigen. The correct conformation of NS3NS4a PI also cross-reacts with different genotype samples better than the c33c antigen. MEFA 7.1 and MEFA 7.2 incorporate all the major immunodominant and genotype-specific epitopes of HCV core, E1, E2 hypervariable region 1 (HVR1), E2 HVR1-plus-HVR2 consensus, NS3, NS4, and NS5. Since MEFA 7.1 is degraded by the active NS3NS4a PI protease, we designed a second MEFA 7.2 construct in which the six protease cleavage sites found in MEFA 7.1 were eliminated by amino acid mutation. We demonstrate here that MEFA 7.2 remains intact in the presence of NS3NS4a PI and preserves the epitopes present in MEFA 7.1. Compared to currently licensed assays, an ELISA incorporating a combination of the two antigens NS3NS4a PI and MEFA 7.1 or 7.2 demonstrates better serotype sensitivity and detects seroconversion earlier in many commercially available panels. We believe that an assay using NS3NS4a PI and MEFA 7.1 or 7.2 may have the potential to replace current HCV immunoassays for better sensitivity.Hepatitis C virus (HCV) is the major etiologic agent for blood transfusion-associated and community-acquired non-A, non-B viral hepatitis (1,9,19). HCV currently affects approximately 3% of the world's population, and 70% of those individuals develop chronic HCV infection, which often progresses to liver cirrhosis and hepatocellular carcinomas (3,19,23). The incidence of posttransfusion HCV has steadily declined since the implementation of routine screening for HCV antibodies and HCV nucleic acid amplification testing among blood donors (21). Despite the proven utility of these assays for blood screening and for the diagnosis of HCV infection in symptomatic patients, important challenges to the improvement of immunoassay performance remain. Such challenges include detecting antibody earlier, improving the detection of HCV samples from immunosuppressed patients, and increasing assay sensitivity to detect antibodies to the different HCV genotype-specific epitopes.HCV is an enveloped virus with a single-stranded positivesense RNA genome of approximately 9.5 kb that encodes about 3,010 amino acids (10, 24). The HCV polyprotein is processed by host and viral proteases into several mature proteins: core protein (C), envelope glycoproteins (E1 and E2), and six nonstructural proteins (NS2, NS3, NS4a, NS4b, NS5a, NS5b) (14,17). NS3 is a 630-amino-acid protein with three enzymatic activities: the N-terminal 180 amino ...