HCV NS5A resistance-associated variants in a group of real-world Japanese patients chronically infected with HCV genotype 1b

Recent advances in interferon-free treatment could lead to the eradication of hepatitis C virus (HCV) from patients infected with HCV. One of the direct-acting anti-viral agents, HCV NS5A inhibitor, is available for these combination therapies. However, naturally occurring resistance-associated variants (RAVs) to HCV NS5A inhibitors in treatment-na < ve patients chronically infected with HCV genotype 1b are still unknown. We performed ultra-deep sequencing and analysed previously reported RAVs in a total 132 HCV genotype 1b-infected Japanese patients who had never used HCV NS5A inhibitors. We also performed direct-sequencing by Sanger method in consecutively selected 50 of the total 132 samples, and the differences between the results of the two methods were compared. In the comparison of the variant frequencies of ultra-deep sequencing with RAVs of direct-sequencing by Sanger method in 50 patients, we identified 32 RAVs by direct-sequencing with the Sanger method; minimum variant frequency was shown by ultra-deep sequencing to be 9 %. A total of 110 RAVs were identified only by ultra-deep sequencing. In the samples from all 132 patients, L31W (2.3 %), L31V (49.2 %), L31F (41.7 %), L31M (1.5 %), L31I (5.3 %), L31S (2.0 %), L31P (3.0 %) and L31R (0.8 %), and Y93N (2.3 %), Y93H (25 %), Y93C (0.8 %), Y93P (2.3 %) and Y93D (0.8 %) were identified. We demonstrated naturally-occurring RAVs of HCV NS5A inhibitors by ultra-deep sequencing and that several mutations including Y93H are common in HCV NS5A inhibitor-treatment-na < ve patients with chronic HCV genotype 1b. Careful attention should be paid to these RAVs, and further improvement of treatment options might be needed.