Deep Sequencing and Phylogenetic Analysis of Variants Resistant to Interferon - Based 1 Protease Inhibitor Therapy in Chronic Hepatitis Induced by Genotype - 1 b Hepatitis

27 Because of recent advances in deep sequencing technology, detailed analysis of 28 hepatitis C virus (HCV) quasispecies and its dynamic change in response to direct 29 antiviral agents (DAAs) became possible although the role of quasispecies is not fully 30 understood. In this study, to clarify the evolution of viral quasispecies and the origin of 31 drug-resistant mutations induced by interferon-based protease inhibitor therapy, the 32 nonstructural-3 (NS3) region of genotype 1b HCV in 34 chronic hepatitis patients 33 treated with telaprevir (TVR)/pegylated-interferon (PEG-IFN)/ribavirin (RBV) was 34 subjected to a deep sequencing study coupled with phylogenetic analysis. Twenty-six 35 patients (76.5%) achieved a sustained viral response (SVR) while 8 patients did not 36 (non-SVR, 23.5%). When the complexity of the quasispecies was expressed as mutation 37 frequency or Shannon entropy, a significant decrease in the IFNL3 (rs8099917) TT 38 group and a marginal decrease in the SVR group were found soon (12 h) after the 39 introduction of treatment, whereas there was no decrease in the non-SVR group and no 40 significant decrease in mutation frequency in the IFNL3 TG/GG group. In the analysis 41 of viral quasispecies composition in non-SVR patients, major populations greatly 42 changed accompanied by the appearance of resistance and the compositions were 43 unlikely to return to the pretreatment composition even after the end of therapy. 44 Clinically TVR-resistant variants were observed in 5 non-SVR patients (5/8, 62.5%), all 45 of which were suspected to have acquired resistance by mutations through phylogenetic 46 analysis. In conclusion, results of the study have important implications for treatment 47 response and outcome in interferon-based protease inhibitor therapy. 48 49 IMPORTANCE 50 In the host, hepatitis C virus (HCV) consists of a variety of populations 51 on July 4, 2017 by gest http/jvi.asm .rg/ D ow nladed fom