Immunological control of hepatitis C virus (HCV) is possible and is probably mediated by host T-cell responses, but the genetic diversity of the virus poses a major challenge to vaccine development. We considered monovalent and polyvalent candidates for an HCV vaccine, including natural, consensus and synthetic 'mosaic' sequence cocktails. Mosaic vaccine reagents were designed using a computational approach first applied to and demonstrated experimentally for human immunodeficiency virus type 1 (HIV-D). Mosaic proteins resemble natural proteins, but are assembled from fragments of natural sequences via a genetic algorithm and optimized to maximize the coverage of potential T-cell epitopes (all 9-mers) found in natural sequences and to minimize the inclusion of rare 9-mers to avoid vaccine-specific responses. Genotype 1-specific and global vaccine cocktails were evaluated. Among vaccine candidates considered, polyvalent mosaic sequences provided the best coverage of both known and potential epitopes and had the fewest rare epitopes. A global vaccine based on conserved proteins across genotypes may be feasible, as a five-antigen mosaic cocktail provided 90, 77 and 70 % coverage of the Core, NS3 and NS4 proteins, respectively; protein coverage diminished with increased protein variability, dropping to 38 % for NS2. For the genotype 1-specific vaccine, the H77 prototype vaccine sequence matched only 50 % of the potential epitopes in the population, whilst a polyprotein three-antigen mosaic cocktail increased potential epitope coverage to 83 %. More than 75 % coverage of all HCV proteins was achieved with a three-antigen mosaic cocktail, suggesting that genotype-specific vaccines could also include the more variable proteins.
INTRODUCTIONAn estimated 170 million people are infected with hepatitis C virus (HCV) worldwide (Armstrong et al., 2000;Lauer & Walker, 2001). Acute HCV infection leads to chronic infection in 70-80 % of infected individuals (Alter et al., 1999;Conry-Cantilena et al., 1996) and can result in liver cirrhosis, liver failure and hepatocellular carcinoma (Lauer & Walker, 2001). The current treatment with pegylated alpha interferon and the nucleoside analogue ribavirin has improved clinical outcomes (Davis et al., 1998;Fried et al., 2002; Manns et al., 2001;Zeuzem et al., 2000), but is expensive and requires sophisticated medical management, which is out of reach for the majority of infected people. Development of a prophylactic vaccine to prevent the spread of HCV infection remains paramount.Several findings indicate that immunological control of HCV is possible. In humans and chimpanzees, spontaneous eradication of HCV can occur during acute infection (Cooper et al., 1999; Gerlach et al., 1999Gerlach et al., , 2003Lechner et al., 2000; Thimme et al., 2001). Spontaneously cleared HCV infection reduced the likelihood of developing a chronic infection in continuously exposed drug users (Mehta et al., 2002). Reinfection after initial clearance had a shorter duration and a lower peak viraemia in the ch...