Abstract
The hepatitis C virus (HCV) NS5B protein is an RNA-dependent RNA polymerase that is required for viral genome replication and constitutes the most important target region for drugs being developed as direct-acting antivirals (DAAs) against HCV genotype 1. However, the extreme genetic variability leading to drug resistance mutations and genetic barriers has dramatically compromised the effectiveness of DAA therapy. The purpose of this study was to analyze the genetic variability of NS5B polymerase in HCV patients from different provinces of China to identify the impact of these resistance sites on genetic barriers. We analyzed 3489 NS5B sequences of HCV strains circulating in different regions of China, obtained from the GenBank database, 153 of which were from three cities in Sichuan Province (Yibin, Zigong and Zhangzhou). Sequence alignment was conducted using MEGA 6.0, the genetic information was translated into amino acids, and the percentage of polymorphic amino acid sites was calculated. The Vijver method was used to evaluate the occurrence of genetic barriers in HCV NS5B sequences. Blood samples were collected from 153 HCV patients from Sichuan for NS5B sequence analysis using real-time PCR and the Sanger method. Of the 17 antiviral drug resistance sites summarized from the published literature, nine were found in Chinese NS5B sequences, and C316Y was identified as the dominant mutation. Analysis of genetic barriers revealed that the probability of mutation to a drug-resistance-associated amino acid, in response to selective pressure from antiviral drugs was 100% at site 96 and 99.7% at site 282. Our study is the first to analyze the drug resistance sites and to evaluate genetic barriers in NS5B sequences that could affect the responsiveness of Chinese HCV patients to DAA therapy. The results provide a valuable basis for drug development and introduction of foreign-origin antiviral drugs in China that targeting the HCV NS5B region.
Similar content being viewed by others
References
Messina JP, Humphreys I, Flaxman A, Brown A, Cooke GS, Pybus OG, Barnes E (2015) Global distribution and prevalence of hepatitis C virus genotypes. Hepatology 61(1):77–87
Calvaruso V, Petta S, Craxì A (2018) Is global elimination of HCV realistic? Liver Int 38:40–46
Zaltron S, Spinetti A, Biasi L et al (2012) Chronic HCV infections: epidemiological and clinical relevance. BMC Infect Dis 12(suppl2):S2
Vaccination for hepatitis C virus: closing in on an evasive target. Expert Rev Vaccines 10(5):659–672
Geller R, Estada Ú, Peris JB, Andreu I, Bou JV, Garijo R, Sanjuán R (2016) Highly heterogeneous mutation rates in the hepatitis C virus genome. Nat Microbiol 1(7):1–7
Lu L, Nakano T, He Y et al (2005) Hepatits C virus genotype distribution in China: predominance of closely related subtype 1b isolates and existence of new genotype 6 variants. J Med Virol 75:538–549
Nie B, Zhang G, Guo Y et al (2015) Phylogenetic analysis of HCV subgenotypes in patients from Sichuan province in China based on the NS5B region. Int J Mol Med 36(4):1028–1034
Cai Q, Zhao Z, Liu Y et al (2013) Comparison of three different HCV genotyping methods: core, NS5B sequence analysis and line probe assay. Int J Mol Med 31:347–352
Choi JW, Lee JS, Paik WH et al (2016) Acute pancreatitis associated with pegylated interferon-alpha-2a therapy in chronic hepatitis C. Clin Mol Hepatol 22:168–171
Zeuzem S, Berg T, Moeller B et al (2009) Expert opinion on the treatment of patients with chronic hepatits C. J Viral Hepat 16:75–90
Paparin JL, Amador A, Badaroux E, Bot S, Caillet C, Convard T et al (2017) Discovery of benzophosphadiazine drug candidate IDX375: A novel hepatitis C allosteric NS5B RdRp inhibitor. Bioorgan Med Chem Lett 27(11):2634–2640
Soriano V, Vispo E, Poveda E et al (2011) Directly acting antivirals against hepatits C virus. J Antimicrob Chemother 66:1673–1686
Poveda E, Wyles DL, Mena A et al (2014) Update on hepatits C virus resistance to direct-acting antiviral agents. Antiviral Res 108:181–191
Bruno R, Cima S, Maiocchi L et al (2011) Forthcoming challenges in the management of direct-acting antiviral agents (DAAs) for hepatitis C. Dig Liver Dis 43:337–344
Kliemann DA, Tovo CV, Da Veiga ABG, Machado AL, West J (2016) Genetic barrier to direct acting antivirals in HCV sequences deposited in the European databank. PloS One 11(8):e0159924
Alves R, Queiroz AT, Pessoa MG et al (2013) The presence of resistance mutations to protease and polymerase inhibitors in hepatits C virus sequences from the Los Alamos databank. J Viral Hepat 20:414–421
Van de Vijver DA, Wensing AM, Angarano G et al (2006) The calculated genetic barrier for antiretroviral drug resistance substitutions is largely similar for different HIV-1 subtypes. J Acquir Immune Defic Syndr 41:352–360
Pawlotsky JM, Chevaiez S, McHutchison JG (2007) The hepatitis C virus life cycle as a target for new antiviral therapies. Gastroenterology 132:1979–1998
Pawlotsky JM (2011) Treatment failure and resistance with direct-acting antiviral drugs against hepatits C virus. Hepatology 53:1742–1751
Kiser JJ, Burton JR, Everson GT (2013) Drug-drug interactions during antiviral therapy for chronic hepatits C. Nat Rev Gastroenterol Hepatol 10:596–606
Cooper C, Lawitz EJ, Ghali P et al (2009) Evaluation of VCH-759 monotherapy in hepatits C infection. J Hepatol 51:39–46
Sarrazin C, Zeuzem S (2010) Resistance to direct antiviral agents in patients with hepatitis C virus infection. Gastroenterology 138(2):447–462
Barreca ML, Iraci N, Manfroni G et al (2011) Allosteric inhibition of the hepatitis C virus NS5B polymerase: in silico strategies for drug discovery and development. Future Med Chem 3:1027–1055
Pirakitikulr N, Kohlway A, Lindenbach BD et al (2016) The coding region of the HCV genome contains a network of regulatory RNA structures. Mol Cell 62:111–120
McPhee F, Hernandez D, Yu F et al (2013) Resistance analysis of hepatitis C virus genotype 1 prior treatment null responders receiving daclatasivr and asunaprevir. Hepatology 58:902–911
Troke PJ, Lewis M, Simpson P et al (2012) Characterization of resistance to the non-nucleoside NS5B inhibitor filibuvir in hepatitis C virus infected patients. Antimicrob Agents Chemother 56:1331–1341
Jiao P, Xue W, Shen Y et al (2014) Understanding the drug resistance mechanism of hepatitis C virus NS5B to PF-00868554 due to mutations of the 423 site: a computational study. Mol Biosyst 10:767–777
Hsu CS (2013) Sofosbuvir for previously untreated chronic hepatits C infection. N Engl J Med 369:678
Keating GM (2014) Sofosbuvir: a review of its use in patients with chronic hepatits C. Drugs 74:1127–1146
Lam AM, Espiritu C, Bansal S, Steuer HMM, Niu C, Zennou V et al (2012) Genotype and subtype profiling of PSI-7977 as a nucleotide inhibitor of hepatitis C virus. Antimicrob Agents Chemother 56(6):3359–3368
Tong X, Le Pogam S, Li L, Haines K, Piso K, Baronas V, Yan JM, So SS, Klumpp K, Najera I (2014) In vivo emer-gence of a novel mutant L159F/L320F in the NS5B polymerase confers low-level resistance to the HCV polymerase inhibi-tors mericitabine and sofosbuvir. J Infect Dis 209:668–675
Acknowledgements
The present study was supported by the Science and Technology Bureau of Yibin City (no. 2015 SF 027).
Author information
Authors and Affiliations
Contributions
Conception and design of the research, Bin Nie, and Kaijiong Zhang; acquisition and analysis of data, Kaijiong Zhang and Jinbo Liu; obtaining funding, Sunguang Yun; drafting the manuscript, Bin Nie; revision of manuscript, Bin Nie and Sunguang Yun. All authors reviewed the manuscript before submission and approved the final manuscript.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare no competing interest pertaining to the publication of this paper.
Ethical statement
All procedures in the present study, which involves human participants, were in strict accordance with the ethical standards of the 1964 Helsinki declaration and its later amendments. Written consent was obtained from all of the subjects.
Additional information
Handling Editor: Zhongjie Shi.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Nie, B., Guo, Y., Zhang, K. et al. Analysis of drug-resistance-associated mutations and genetic barriers in hepatitis C virus NS5B sequences in China. Arch Virol 165, 2013–2020 (2020). https://doi.org/10.1007/s00705-020-04713-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00705-020-04713-4