Cloning and phylogenetic analysis of the core, E2, and NS3/NS4 regions of the hepatitis C virus type 5a.

By means of the Line Probe Assay, a hepatitis C virus type 5a infected serum from a Belgian patient was selected. The complete core region (573 bp), the carboxyterminal part of E1 and the aminoterminal part of E2/NS1 (661 bp), and an epitope containing region in NS3-NS4 (1452 bp) were cloned and sequenced. The deduced amino acid sequence revealed type-specific variations in regions of core and NS4 which were previously recognized as evoking a type-specific antibody response. In addition, the aminoterminal region of E2 showed high variability when compared with sequences of type 1, 2, and 3. Phylogenetic analysis showed separate branching of this isolate. The analysis in the core region was not conclusive for some of the strains included and should therefore be carried out in combination with the NS5B region.