Evolution of Resistance-Associated Variants of All-Oral Direct-Acting Antiviral Therapy of Hepatitis C in a Clinical Setting

Abstract

Because of the high variability of Hepatitis C virus (HCV), it might be important to characterize in vivo the evolution of resistance-associated mutations (RAVs) to direct-acting antivirals (DAAs) in different genotypes. NS3-, NS5A- and NS5B-HCV substitutions were studied by next generation sequencing (NGS) on 74 HCVinfected patients who started a DAA regimen. RAVs with frequencies of 1% and 15% were analyzed. Globally, 43, 15, 12 and 4 patients were infected with subtype 1a, 1b, genotype 4 and subtype 3a, respectively. The majority of patients (64.8%) had cirrhosis, 70.3% were HIV-coinfected and 14.9% were DAA-experienced. Overall baseline prevalence of RAVs was 74.3%, 52.2%, 45.9% and 36.8% to any NS3, NS5B and NS5A inhibitors available at that time, respectively, and dropped to 39.2%, 26.1%, 22.8% and 16.2%, respectively, when only mutations associated with the ongoing regimen were considered. The highest proportion of mutations was detected in subtype 1a (81.4%, p=.026), particularly in NS3 region (76.9%, p<.001). Among the 7 failing patients, 57.1% had a baseline sequence showing substitutions as majority species. At the time of viral relapse two patients accumulated further RAVs that were missing even as minority variants at baseline Although almost half of the patients showed natural substitutions at baseline, these substitutions did not induce resistance to DAAs. A limited role of NGS with a low cut-off was suggested by our study, as the detection of minor species seems not to predict the selection for resistant variants at the time of failure. The impact of pre-treatment RAVs on the achievement of sustained virologic response with DAA is limited.