Characterization of nucleotide sequences from European hepatitis C virus isolates

We characterized the 5' end and parts of the structural genes of European isolates of hepatitis C virus (HCV) and compared them with recently published RNA sequences of American and Japanese HCV isolates. The cDNA, obtained by reverse transcription of viral RNA extracted from different sera, was amplified by nested PCR, cloned and sequenced. Within 239 nucleotides (nt) of the 5' end, we found only three single-nt exchanges compared to two sequences of Japanese origin and one exchange to the prototype HCV sequence (ptHCV) (homology greater than 99%). The sequence of the core region (534 nt) in two European isolates showed a homology of about 97-98% on the nt level, as compared to ptHCV and one Japanese isolate, and 90% to other Japanese isolates. The amino acid (aa) homology was between 98-99% among all published sequences. A greater discrepancy was found in the European isolates within the 434 nt sequenced from the N-terminus of the putative envelope region, where the nt homology to ptHCV and one Japanese isolate was 90-93% (aa homology 93-95%), and to other Japanese isolates was 72-73% (aa homology 77-78%), indicating that the European isolates may be more closely related to the ptHCV and one Japanese isolate than to the other Japanese isolates. Amplified genes encoding structural proteins (core, envelope) were expressed in Escherichia coli. Sera from chronically infected patients reacted strongly with the recombinant core protein, but no specific immunoreactivity occurred with the putative envelope protein.