The present invention relates to molecular approaches to the production of nucleic acid sequences, which comprises the genome of infectious hepatitis C virus. In particular, the invention provides nucleic acid sequences which comprise the genomes of infectious hepatitis C viruses of either genotype 3a (strain S52) or genotype 4a (strain ED43). The invention therefore relates to the use of the nucleic acid sequences and polypeptides encoded by all or part of the sequences in the development of vaccines and diagnostic assays for HCV and in the development of screening assays for the identification of antiviral agents for HCV. The invention therefore also relates to the use of viral particles derived from laboratory animals infected with S52 and ED43 viruses.

The present invention relates to molecular approaches to the production of nucleic acid sequences, which comprises the genome of infectious hepatitis C virus. In particular, the invention provides nucleic acid sequences which comprise the genomes of infectious hepatitis C viruses of either genotype 3a (strain S52) or genotype 4a (strain ED43). The invention therefore relates to the use of the nucleic acid sequences and polypeptides encoded by all or part of the sequences in the development of vaccines and diagnostic assays for HCV and in the development of screening assays for the identification of antiviral agents for HCV. The invention therefore also relates to the use of viral particles derived from laboratory animals infected with S52 and ED43 viruses.

Synthetic representative HCV subtypes, including a 1a and 1b genome, dubbed Bole1a and Bole1b, are provided using an inventive method of Bayesian phylogenetic tree analysis, ancestral sequence reconstruction and covariance analysis. Bole1a branches centrally among 390 full-genome sequences used in its design, a carefully curated 143 sequence full-genome dataset, and separate genomic regions including an independent set of 214 E1E2 sequences from a Baltimore cohort. Bole1a is phylogenetically representative of widely circulating strains. Full genome non-synonymous diversity comparison and 9-mer peptide coverage analysis showed that Bole1a is able to provide more coverage (94% and 78% respectively) than any other sequence in the dataset including H77, a traditional reference sequence. Bole1a also provides unsurpassed epitope coverage when compared to all known T cell epitopes.