Analysis of the putative E1 envelope and NS4a epitope regions of HCV type 3

Using a Line Probe Assay, type 3 HCV genotype-infected sera were selected from Brazilian blood donors. The partial nucleotide sequences of the core/E1 and NS4a epitope-containing regions and the NS5b typing region were determined. The E1 region had a nucleic acid homology of only 61 to 65% with the type 1 prototype genomes, and 56 to 58% homology with the type 2 prototype HCV genomes. Similar homologies were also found for the NS4a epitope region and for NS5. Furthermore, the deduced amino acid sequence of type 3 NS4a was used to generate synthetic peptides which were strongly reactive with human HCV-infected sera which were previously determined as anti-NS4 negative, indicating that a type-specific antibody response to the NS4a protein may exist.