Natural epitope variants of the hepatitis C virus impair cytotoxic T lymphocyte activity

Figure 1 Summary of sequence changes detected over time within the hepatitis C virus (HCV) non-structural 3 (NS3) fragment of a single patient. HCV RNA extracted from patient sera at months 12, 28 and 63 was amplified by reverse transcription polymerase chain reaction (RT-PCR). A panel of molecular clones spanning the NS3 fragment was aligned with the wild-type consensus sequence which is shown on top (underlined). From a total of 51 nucleotide substitutions found, 39 were nonsynonymous, causing amino acid alterations (capital letters). The amplified NS3 fragment encompasses epitopes NS3 1073-1081, 1131-1139 and 1169-1177. Dashed lines indicate identity to the consensus sequences, whereas positions of synonymous mutations not causing amino acid alterations are marked with the greek delta sign (Δ).