FIG. 1.

Proposed model of secondary RNA structures of JFH1 within the 5′ NTR and the 5′ end of the capsid-coding sequence. The major structural domains are indicated by SL (stem-loop) followed by roman numerals. The authentic initiator AUG codon is highlighted in SLIV. The presence of SLV and SLVI has been suggested by Smith and Simmonds (51) and adapted to JFH1 based on the structure also presented by Vassilaki and collaborators (54). Mutated residues are indicated with arrows that point out the two nucleotides of each codon that were replaced with GC to obtain an alanine. The position of each basic residue and the different amino acid mutants that were initially modified are indicated. Basic residues that are conserved with more than 99% of the listed sequences in the European HCV database (http://euhcvdb.ibcp.fr) are indicated by asterisks. The other residues are conserved in 95 to 99% of these sequences.