Pipeline for specific subtype amplification and drug resistance detection in hepatitis C virus

We have established a robust pipeline for the amplification and next-generation sequencing of samples derived from HCV-infected patients. This procedure is based on the design of subtype-specific oligonucleotide primers that amplify HCV genomic regions in a subtype-specific manner, as validated with patient's viral samples. Cut-off values for reliable quantification of mutations associated with drug resistance have been established that may guide treatment planning. The method can also be adapted to sequence new HCV subtypes, as they arise in the course of HCV diversification.