183
Views
1
CrossRef citations to date
0
Altmetric
Original Research

Molecular Characterization of Hepatitis C Virus for Developed Antiviral Agents Resistance Mutations and New Insights into in-silico Prediction Studies

ORCID Icon, , ORCID Icon, & ORCID Icon
Pages 4235-4248 | Published online: 23 Nov 2020

References

  • El-Tahan RR, Ghoneim AM, Zaghloul H. 5′ UTR and NS5B-based genotyping of hepatitis C virus in patients from Damietta governorate, Egypt. J Adv Res. 2018;10:39–47. doi:10.1016/j.jare.2018.01.00430046475
  • Simmonds P, Bukh J, Combet C, et al. Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes. Hepatology. 2005;42:962–973. doi:10.1002/hep.2081916149085
  • Shier MK, El-Wetidy MS, Ali HH, Al-Qattan MM. Characterization of hepatitis C virus genotypes by direct sequencing of HCV 5ʹUTR region of isolates from Saudi Arabia. PLoS One. 2014;9:e103160. doi:10.1371/journal.pone.010316025099694
  • El-Shamy A. Impact of hepatitis C virus heterogeneity on interferon sensitivity: an overview. World J Gastroenterol. 2014;20(24):7555–7569. doi:10.3748/wjg.v20.i24.755524976696
  • Doss W, Shiha G, Hassany M, et al. Sofosbuvir plus ribavirin for treating Egyptian patients with hepatitis C genotype 4. J Hepatol. 2015;63(3):581–585. doi:10.1016/j.jhep.2015.04.02325937436
  • Kumar A, Rajput MK, Paliwal D, Yadav A, Chhabra R, Singh S. Genotyping & diagnostic methods for hepatitis C virus: A need of low-resource countries. Indian J Med Res. 2018;147(5):445–455. doi:10.4103/ijmr.IJMR_1850_1630082568
  • Olsson M, Søndergard C, Rostkowski M, Jensen J. PROPKA3: consistent Treatment of Internal and Surface Residues in Empirical pKa predictions. J Chem Theor Comput. 2011;7:525–537.
  • Jorgensen W, Maxwell D, Tirado-Rives J. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. Journal of the American Chemical Society. 1996;118(45):11225–11236. doi:10.1021/ja9621760
  • Šali A, Blundell T. Comparative Protein Modelling by Satisfaction of Spatial Restraints. Journal of Molecular Biology. 1993;10(3):779–815. doi:10.1006/jmbi.1993.1626
  • Ray SC, Arthur RR, Carella A, Bukh J, Thomas DL. Genetic epidemiology of hepatitis C virus throughout egypt. J Infect Dis. 2000;182(3):698–707. doi:10.1086/31578610950762
  • Shen M, Sali A. Statistical potential for assessment and prediction of protein structures. Protein Sci. 2006;15:2507–2524.17075131
  • El Hadad S, Al-Hamdan H, Linjawi S, Khudyakov YE. Partial sequencing analysis of the NS5B region confirmed the predominance of hepatitis C virus genotype 1 infection in Jeddah, Saudi Arabia. PLoS One. 2017;12(5):e0178225. doi:10.1371/journal.pone.017822528552946
  • Wu G, Robertson D, Brooks C, Vieth M. Detailed analysis of grid-based molecular docking: A case study of CDOCKER?A CHARMm-based MD docking algorithm.J Computational Chem. 2003;24(13):1549–1562. doi:10.1002/jcc.10306
  • Appleby T, Perry J, Murakami E, et al. Structural basis for RNA replication by the hepatitis C virus polymerase. Science. 2015;347(6223):771–775. doi:10.1126/science.125921025678663
  • Ali S, Leveque V, Le Pogam S, et al. Selected replicon variants with low-level in vitro resistance to the hepatitis C virus NS5B polymerase inhibitor PSI-6130 lack cross-resistance with R1479. Antimicrob Agents Chemother. 2008;52(12):4356–4369. doi:10.1128/AAC.00444-0818838588
  • Shi S, Lai M. HCV ‘5 and ‘3 UTR: when translation meets replication In: Tan S-L, editor. Hepatitis C Viruses: Genomes and Molecular Biology. horizon bioscience; 2006:49–87.
  • Fakhr AE, Pourkarim MR, Maes P, Atta AH, Marei A, Azab M. Hepatitis C Virus NS5B Sequence-Based Genotyping Analysis of Patients From the Sharkia Governorate, Egypt. Hepat Mon. 2013;13:e12706.24358038
  • Elkady A, Tanaka Y, Kurbanov F, Sugauchi F, Sugiyama M, Khan A. Genetic variability of hepatitis C virus in South Egypt and its possible clinical implication. J Med Virol. 2009;81(6):1015–1023. doi:10.1002/jmv.2149219382263
  • Genovese D, Dettori S, Argentini C, Villano U, Chionne P. Molecular epidemiology of hepatitis C virus genotype 4 isolates in Egypt and analysis of the variability of envelope proteins E1 and E2 in patients with chronic hepatitis. J Clin Microbiol. 2005;43(4):1902–1909. doi:10.1128/JCM.43.4.1902-1909.200515815016
  • Ranjith-Kumar CT, Kao CC. Biochemical Activities of the HCV NS5B RNA-Dependent RNA Polymerase. 2006.
  • Donaldson EF, Harrington PR, O’Rear JJ, Naeger LK. Clinical evidence and bioinformatics characterization of potential hepatitis C virus resistance pathways for sofosbuvir. Hepatology. 2015;61(1):56–65. doi:10.1002/hep.2737525123381
  • Ito J, Suda G, Yamamoto Y, et al. Prevalence and characteristics of naturally occurring sofosbuvir resistance-associated variants in patients with hepatitis C virus genotype 1b infection. Hepatol Res. 2016;46(13):1294–1303. doi:10.1111/hepr.1268526896756
  • Zeuzem S, Buggisch P, Agarwal K, et al. The protease inhibitor, GS-9256, and non-nucleoside polymerase inhibitor tegobuvir alone, with ribavirin, or pegylated interferon plus ribavirin in hepatitis C. Hepatology. 2012;55:749–758. doi:10.1002/hep.2474422006408
  • Migliaccio G, Tomassini JE, Carroll SS, et al. Characterization of resistance to non-obligate chain-terminating ribonucleoside analogs that inhibit hepatitis C virus replication in vitro. J Biol Chem. 2003;278:49164–49170. doi:10.1074/jbc.M30504120012966103
  • Dutartre H, Bussetta C, Boretto J, Canard B. General catalytic deficiency of hepatitis C virus RNA polymerase with an S282T mutation and mutually exclusive resistance towards 2ʹ-modified nucleotide analogues. Antimicrob Agents Chemother. 2006;50(12):4161–4169. doi:10.1128/AAC.00433-0617000745
  • Kulkarni AS, Damha MJ, Schinazi RF, et al. A Complex Network of Interactions between S282 and G283 of Hepatitis C Virus Nonstructural Protein 5B and the Template Strand Affects Susceptibility to Sofosbuvir and Ribavirin. Antimicrob Agents Chemother. 2016;60(4):2018–2027. doi:10.1128/AAC.02436-1526824949
  • Hamano K, Sakamoto N, Enomoto N, et al. Mutations in the NS5B region of the hepatitis C virus genome correlate with clinical outcomes of interferon-alpha plus ribavirin combination therapy. J Gastroenterol Hepatol. 2005;20(9):1401–1409. doi:10.1111/j.1440-1746.2005.04024.x16105128
  • Asahina Y, Izumi N, Enomoto N, et al. Mutagenic effects of ribavirin and response to interferon/ribavirin combination therapy in chronic hepatitis C. J Hepatol. 2005;43(4):623–629. doi:10.1016/j.jhep.2005.05.03216098627
  • Gededzha MP, Mphahlele MJ, Blackard JT, Selabe SG. Prevalence of NS5B Resistance Mutations in Hepatitis C Virus (HCV) Treatment Naive South Africans. Hepat Mon. 2017;17:e14248.
  • Yasmeen A, Siddiqui AA, Hamid S, Sultana T, Jafri W, Persson MA. Genetic variations in a well conserved 5ʹ-untranslated region of hepatitis C virus genome isolated in Pakistan. J Virol Methods. 2009;160:38–47. doi:10.1016/j.jviromet.2009.04.00719406160
  • Nelson DR, Gray AH, Kolberg JA, et al. Variations of hepatitis C virus NS5B sequence (nucleotides 8261-8566) do not correlate with response to interferon-alpha therapy. J Viral Hepat. 1995;2:285–292. doi:10.1111/j.1365-2893.1995.tb00043.x8732174
  • Zekri AR, El-Din HM, Bahnassy AA, et al. Genetic distance and heterogeneity between quasispecies is a critical predictor to IFN response in Egyptian patients with HCV genotype-4. Virol J. 2007;4(1):16. doi:10.1186/1743-422X-4-1617300723
  • Ji H, Kozak R, Biondi M, et al. Next generation sequencing of the hepatitis C virus NS5B gene reveals potential novel S282 drug resistance mutations. Virology. 2015;477:1–9.25600207
  • Uchida Y, Nakamura S, Kouyama JI, et al. Significance of NS5B Substitutions in Genotype 1b Hepatitis C Virus Evaluated by Bioinformatics Analysis. Sci Rep. 2018;8:8818. doi:10.1038/s41598-018-27291-729892096
  • Wing PAC, Jones M, Cheung M, et al. Amino Acid Substitutions in Genotype 3a Hepatitis C Virus Polymerase Protein Affect Responses to Sofosbuvir. Gastroenterology. 2019;157(3):692–704 e9. doi:10.1053/j.gastro.2019.05.00731078622
  • Ji H, Kozak R, Biondi M, et al. Next generation sequencing of the hepatitis C virus NS5B gene reveals potential novel S282 drug resistance mutations. Virology. 2015;477:1–9. doi:10.1016/j.virol.2014.12.03725600207
  • Howard J, Hoy V, O’Hagan D, Smith G. How good is fluorine as a hydrogen bond acceptor? Tetrahedron. 1996;52:12613–12622.