Amino acid (aa) substitution at position 93 of the HCV NS5A region predicts the effectiveness of combination therapy with the protease inhibitor and NS5A inhibitor. The qualitative analysis assay and the comparative quantitative analysis assay based on the PCR-Invader technology, were developed to detect drug-resistance substitution at aa93 with high levels of sensitivity. In the mixtures of plasmids containing wild-type and drug-resistance substitution, both assays were able to be distinguished up to a mixed population containing 1%drug-resistance substitution. Clinical samples at the baseline of HCV therapy were examined by the PCR-Invader assays and direct sequencing. The PCR-Invader assays found drug-resistance substitutions that were detected by direct sequencing. Furthermore, they illustrated the presence of drug-resistance substitution that direct sequencing couldn't discover. The PCR-Invader assays were useful in detecting drug-resistance substitution at aa93 of the HCV NS5A region.
