FIG 1.

Substitutions identified in the NS3Ps of HCV genotype 1 to 6 escape viruses during treatment with telaprevir or boceprevir. Huh7.5 cells were infected with viruses with the NS3P/NS4A of genotype (isolate) 1a (TN), 2a (JFH1 or J6), 3a (S52 or 452), 4a (ED43), 5a (SA13), or 6a (HK6a) (see Fig. S1 in the supplemental material), treated with telaprevir or boceprevir, and followed as described in Materials and Methods and in Fig. S2 in the supplemental material. At the time of viral escape, the NS3Ps of viruses recovered at two different time points were amplified using reverse transcription-PCR and were directly sequenced. NS3P positions at which a substitution for at least one of the viruses treated with telaprevir or boceprevir was identified are shown. Rel. NS3P aa no., NS3 protease amino acid number relative to that in the genotype 1a reference strain H77 (GenBank accession no. AF009606); the H77 amino acid residues are indicated. For each of the viruses studied, a dot indicates that the amino acid residue at the respective position is identical to that in strain H77, and a single letter neither shaded nor circled indicates the amino acid identity at a nonidentical residue. Substitutions occurring at one or more time points under PI treatment are indicated by colored filled rectangles for telaprevir and by colored circle outlines for boceprevir. The color of the rectangle or the circle outline indicates the highest multiple of the EC₅₀ of the PI at which the substitution was identified. The letter to the left of each arrow represents the original amino acid, while the letter(s) to the right indicates the substitution(s) identified in escape variants. Different substitutions identified at the same position are separated by a slash. The substitutions estimated to be present in at least 50% of viral genomes are indicated by capital letters, while substitutions estimated to be present in a minor percentage are indicated by lowercase letters. Substitutions that were also identified in nontreated cultures are not shown. The genotype 6a (isolate HK6a) recombinant contains the cell culture-adaptive substitution V14L (boxed in red). For further details, see Tables S2 to S17 in the supplemental material.