Persons with hepatitis C virus (HCV) genotype 1a (GT1a) infections harboring a baseline Q80K polymorphism in nonstructural protein 3 (NS3) have a reduced virologic response to simeprevir in combination with pegylated interferon-alfa and ribavirin. We aimed to develop, validate, and freely disseminate an NS3 clinical sequencing assay to detect the Q80K polymorphism and potentially other HCV NS3 drug resistance mutations. HCV RNA was extracted from frozen plasma using a NucliSENS easyMAG automated nucleic acid extractor, amplified by nested reverse transcription-PCR, and sequenced using Sanger and/or next-generation (MiSeq) methods. Sanger chromatograms were analyzed using in-house software (RECall), and nucleotide mixtures were called automatically. MiSeq reads were iteratively mapped to the H77 reference genome, and consensus NS3 sequences were generated with nucleotides present at >20% called as mixtures. The accuracy, precision, and sensitivity for detecting the Q80K polymorphism were assessed in 70 samples previously sequenced by an external laboratory. A comparison of the sequences generated by the Sanger and MiSeq methods with those determined by an external lab revealed >98.5% nucleotide sequence concordance and zero discordant calls of the Q80K polymorphism. The results were both highly repeatable and reproducible (>99.7% nucleotide concordance and 100% Q80K concordance). The limits of detection (>2 and ϳ5 log 10 IU/ml for the Sanger and MiSeq assays, respectively) are sufficiently low to allow genotyping in nearly all chronically infected treatment-naive persons. No systematic bias in the under-or overamplification of minority variants was observed. Coinfection with other viruses (e.g., HIV and hepatitis B virus [HBV]) did not affect the assay results. The two independent HCV NS3 sequencing assays with the automated analysis procedures described here are useful tools to screen for the Q80K polymorphism and other HCV protease inhibitor drug resistance mutations.
Until recently, the standard of care for treating hepatitis C virus (HCV) infection has been combination antiviral therapy with pegylated interferon-alfa and ribavirin (Peg-IFN/RBV). In 2011, the nonstructural protein 3 (NS3) protease inhibitors (PI) telaprevir and boceprevir, in combination with Peg-IFN/RBV, were the first direct-acting antiviral (DAA) agents approved for treatment of chronic HCV genotype 1 infection (1-3). The success of HCV therapy with DAA, however, is complicated by the incredible genetic diversity of the virus and its capacity to mutate in response to drug selection pressure (4, 5). Treatment failure is often accompanied by the emergence of resistance mutations in the genes targeted by these drugs (6, 7). Furthermore, certain drug resistance mutations exist as naturally occurring polymorphisms in a small proportion of treatment-naive patients and can compromise PI treatment in these individuals (8)(9)(10)(11).In combination with Peg-IFN/RBV, the second-generation PI simeprevir was approved in Canada in 2013 for the treatment...
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