A near full-length open reading frame next generation sequencing assay for genotyping and identification of resistance-associated variants in hepatitis C virus.

•A near full-length HCV amplicon was generated using a single set of primers.•HCV genotype 1a, 1b, 2b, 3a, 3b, 3h, 4a, 4d, 4o, 4r samples were sequenced.•Samples with HCV RNA down to 4 Log IU/mL were sequenced.•Method generated variation was estimated below 1%.•The method identified dual infections and the presence of subgenomic replicons.