Global Epidemiology of HCV Subtypes and Resistance-associated Substitutions Evaluated by Sequencing-Based Subtype Analyses

摘要

Background & Aims Hepatitis C virus (HCV) is highly variable with 7 genotypes and 67 subtypes characterized to date. HCV genotype (GT) and subtype, and presence of resistance associated substitutions (RASs) represent the key viral determinants for the selection of direct-acting antiviral (DAA) treatment regimens. However, currently available HCV genotyping assays have limitations in differentiating between HCV subtypes and RAS prevalence in different subtypes is largely undefined. Methods In this study, we compared HCV GT and subtypes with INNO-LiPA 2.0 vs. amplicon sequencing among 8,945 patients from phase II/III clinical trials of DAAs. We also investigated global HCV molecular epidemiology in 12,615 patients. Subtype RAS prevalence was determined by population or deep sequencing, and phylogenetic analyses investigating subtype diversity were performed. Results Though there was high concordance between INNO-LiPA and sequencing for GT determination, INNO-LiPA was insufficient for subtype determination for GT2, 3, 4, and 6. Sequencing provided subtype refinement for 42%, 10%, 81%, and 78% of GT2, 3, 4, and 6 patients, respectively. GT discordance (GT2-GT1) was observed in 28 of 950 (3%) GT2 patients, consistent with inter-genotype recombinants. Sequencing-based analyses demonstrated variations in regional subtype prevalence, notably within GT2, 4 and 6. RAS prevalence varied by subtype, with the clinically relevant NS3 RAS Q80K found in GT1a, 5a and 6a and the NS5A RAS Y93H in GT1b, 3a, 4b, 4r and 7. Conclusions Together, these analyses provide an understanding of subtyping accuracy and RAS distribution that are crucial for the implementation of global HCV treatment strategies. Lay Summary The sequencing analyses performed on 12,615 patients with HCV infection investigated three main questions: (1) the concordance between NS5B amplicon sequencing and INNO-LiPA for HCV genotype (GT) determination; (2) the prevalence of HCV subtypes for each genotype around the world; and (3) the prevalence of resistance-associated substitutions (RASs) in different subtypes. Overall, there was high INNO-LiPA and sequencing concordance for GT determination, but subtype determination for GT2, 3, 4, and 6 needed sequencing refinements. Sequencing-based analyses demonstrated variations in regional subtype prevalence for some genotypes, notably within GT2, 4 and 6, and RAS prevalence varied by subtype, with the clinically relevant NS3 RAS Q80K found in GT1a, 5a and 6a and the NS5A RAS Y93H in GT1b, 3a, 4b, 4r and 7.