Identification of Resistance associated substitutions in NS3 and NS5A region of HCV among genotype 3 isolated from DAAs non-responders

Background and Aim: Hepatitis C virus (HCV) is one of the major causes of mortality and morbidity among humans. HCV prevalence rate in India at between 0.5% and 1.5%. Before 2011, a combination of pegylated-interferon (Peg-IFN) and Ribavirin (RIB) was the gold standard for HCV treatment. But, lower sustainable viral response (SVR) and adverse side effects to the patient lead to the introduction of Direct acting antivirals (DAAs). But globally treatment failure is reported. This study aims to conduct a detailed analysis of DAAs efficacy against HCV and to find resistance-associated substitutions (RAS) among DAAs non-responders. Methods: Over three years, 198 HCV sero-reactive patients were enrolled in this study. Blood samples were collected before and after the DAAs treatment and proceeded for viral RNA isolation. HCV RNA was quantified by using the qRT-PCR. HCV genotype was determined by nested RT-PCR of partial HCV core (405bp) gene amplification followed by Sanger sequencing and NCBI genotyping tool. GT-3 specific RAS was detected by amplifying whole NS3 and NS5A region followed by Next generation sequencing (NGS) and HCV Geno2pheno tool. Results: The efficiency of DAAs varied between ∼ 94% to 100%. Overall, non-responsive against DAAs was 5.55% (n=11). Most of the DAAs non-responsiveness was observed against SOF/DAC combination (n=7; 63.63%). DAAs non-responders were high among decompensated cirrhotic (90.9%) and HCV GT-3b infected patients (n=5, 45.45%). We performed RAS analysis of GT-3 specific NS3 and NS5B regions. A166S, Y56Y+Q168Q+I/V170I RAS were observed in NS3 region and Y93H, S/T62T and A30V+Y93H RAS were observed in NS5A region of HCV GT-3. Conclusion: HCV GT-3b infection with decompensated cirrhosis of liver patients was the major treatment failure against DAAs. More screening of RAS is needed which may be helpful to find new DAAs combinations in the future to reach our goal to eradicate HCV by 2030.