Prevalence of hepatitis C virus-resistant association substitutions to direct-acting antiviral agents in treatment-naïve hepatitis C genotype 1b-infected patients in western China

Abstract

Background

Direct-acting antivirals (DAAs) against hepatitis C virus (HCV) are potent and highly efficacious. However, resistance-associated substitutions (RASs) relevant to DAAs can impair treatment effectiveness even at baseline. Moreover, the prevalence of baseline RASs in HCV genotype 1b-infected patients in western China is still unclear.

Materials and methods

Direct sequencing of the HCV NS3, NS5A, and NS5B regions was performed in baseline serum samples of 70 DAAs treatment-naïve HCV 1b-infected patients in western China. The sequences were analyzed with MEGA version 5.05 software. Evolutionary patterns of RASs and amino-acid covariance patterns in the NS3, NS5A, and NS5B genes were analyzed by MEGA and Cytoscape (version 3.2.1), respectively.

Results

The presence of at least one RAS in the NS3 region (C16S, T54S, Q80R/L, A87T, R117H, S122G, V132I, V170I) was observed in 85.48% (53 of 62) of patients, RASs in the NS5A region (L28M, R30Q, Q54H, P58S/T, Q62H/R, Y93H) were observed in 42.42% (28 of 66) of patients, and RASs in the NS5B region (N142S, A300T, C316N, A338V, S365A, L392I, M414L, I424V, A442T, V499A, S556G) were observed in 100% (44 of 44) of patients. Evolutionary patterns of RASs and amino-acid covariance patterns for the NS3, NS5A, and NS5B genes are reported.

Conclusion

The prevalence of RASs relevant to DAAs detected in the NS3, NS5A, and NS5B regions of HCV 1b from DAA treatment-naïve patients is high. Therefore, more attention should be paid to RASs associated with DAAs in the upcoming DAA-treatment era in China.

Keywords:

• hepatitis C virus
• unstructured proteins
• resistance-associated substitutions
• direct-acting antiviral agents

Supplementary material

Figure S1 Chromatograms of Sanger sequencing.

Notes: Chromatograms of Sanger sequencing in part of NS3 segment with 80Q (A); with 80R (B). Amino acid site 80 occurring bases substitution leading to amino acid Q change to R which resistance to DAAs, thus, Q80R was described as a variant type.

Figure S2 The prevalence of clinically relevant resistance associated substitutions (without C316N) in various DAA classes.

Abbreviation: RASs, resistance-associated substitutions.

Figure S3 Phylogenetic trees for HCVGT1b NS3 and NS5B genes.

Notes: (A) Phylogenetic tree for HCV GT1b NS3 gene; (B) phylogenetic tree for HCV GT1b NS5B gene. Blue lines represent nonresistant lineages; black lines represent lineages carrying the resistance associated substitutions.

Table S1 Amplification and sequencing primers for HCV NS3,¹ NS5A,² and NS5B³ genes in genotype 1b patients

Table S2 Summary of HCV RASs to DAAs

Table S3 Baseline characteristics of patients with and without NS5A RASs

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Acknowledgments

This study was supported in part by grants from the National Natural Science Foundation of China (30930082, 81171561, 30972584, and 81772171) and the National Science and Technology Major Project of China (2008ZX10002-006, 2012ZX10002007001, 2017ZX10202203-007, and 2017ZX10202203-008).

Author contributions

PH and HR conceived the study, ZL and ZC conducted the experiments, ZL collected the data, and ZL, ZC, and HL analyzed the data. All authors contributed toward data analysis, drafting and revising the paper and agree to be accountable for all aspects of the work.

Disclosure

The authors report no conflicts of interest in this work.