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Global epidemiology of HCV subtypes and resistance-associated substitutions evaluated by sequencing-based subtype analyses

Published:March 23, 2017DOI:https://doi.org/10.1016/j.jhep.2017.03.014

      Background & Aims

      HCV genotype, subtype, and presence of resistance-associated substitutions (RASs) are key determinants for the selection of direct-acting antiviral (DAA) treatment regimens. However, current HCV genotyping assays have limitations in differentiating between HCV subtypes, and RAS prevalence is largely undefined. The aim of this study was to investigate HCV epidemiology in 12,615 patient samples from 28 different countries across five geographic regions.

      Methods

      We compared HCV genotype and subtypes using INNO-LiPA 2.0 vs. amplicon sequencing among 8,945 patients from phase II/III clinical trials of DAAs. Global HCV molecular epidemiology in 12,615 patients was investigated. Subtype RAS prevalence was determined by population or deep sequencing, and phylogenetic analyses investigating subtype diversity were performed.

      Results

      Although there was high concordance between INNO-LiPA and sequencing for genotype determination, INNO-LiPA was insufficient for subtype determination for genotype 2, 3, 4, and 6. Sequencing provided subtype refinement for 42%, 10%, 81%, and 78% of genotype 2, 3, 4, and six patients, respectively. Genotype discordance (genotype 2–genotype 1) was observed in 28 of 950 (3%) genotype 2 patients, consistent with inter-genotype recombinants. Sequencing-based analyses demonstrated variations in regional subtype prevalence, notably within genotype 2, 4 and 6. RAS prevalence varied by subtype, with the clinically relevant NS3 RAS Q80K found in genotype 1a, 5a and 6a and the NS5A RAS Y93H in genotype 1b, 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

      Hepatitis C virus (HCV) is highly variable, with seven genotypes and 67 subtypes characterized to date. The aim of this study was to i) compare two different methods of discriminating between genotypes; ii) investigate the prevalence of HCV subtypes for each genotype around the world; iii) find the prevalence of resistance-associated substitutions (RASs) in different subtypes. We found that both methods showed high concordance in genotype discrimination, but specific subtypes were not always identified accurately. Sequencing-based analyses demonstrated variations in regional subtype prevalence for some genotypes, notably within GT2, 4 and 6. RAS prevalence also varied by subtype. These variations could determine how successful different drugs are for treating HCV.

      Graphical abstract

      Keywords

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      References

        • Shepard C.W.
        • Finelli L.
        • Alter M.J.
        Global epidemiology of hepatitis C virus infection.
        Lancet Infect Dis. 2005; 5: 558-567
        • Lauer G.M.
        • Walker B.D.
        Hepatitis C virus infection.
        N Engl J Med. 2001; 345: 41-52
        • Smith D.B.
        • Bukh J.
        • Kuiken C.
        • Muerhoff A.S.
        • Rice C.M.
        • Stapleton J.T.
        • et al.
        Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: updated criteria and genotype assignment web resource.
        Hepatology. 2014; 59: 318-327
        • Timm J.
        • Roggendorf M.
        Sequence diversity of hepatitis C virus: implications for immune control and therapy.
        World J Gastroenterol. 2007; 13: 4808-4817
        • Asselah T.
        • Boyer N.
        • Saadoun D.
        • Martinot-Peignoux M.
        • Marcellin P.
        Direct-acting antivirals for the treatment of hepatitis C virus infection: optimizing current IFN-free treatment and future perspectives.
        Liver Int. 2016; 36: 47-57
        • Sulkowski M.S.
        • Gardiner D.F.
        • Rodriguez-Torres M.
        • Reddy K.R.
        • Hassanein T.
        • Jacobson I.
        • et al.
        Daclatasvir plus sofosbuvir for previously treated or untreated chronic HCV infection.
        N Engl J Med. 2014; 370: 211-221
        • Lawitz E.
        • Mangia A.
        • Wyles D.
        • Rodriguez-Torres M.
        • Hassanein T.
        • Gordon S.C.
        • et al.
        Sofosbuvir for previously untreated chronic hepatitis C infection.
        N Engl J Med. 2013; 368: 1878-1887
        • Feld J.J.
        • Jacobson I.M.
        • Hezode C.
        • Asselah T.
        • Ruane P.J.
        • Gruener N.
        • et al.
        Sofosbuvir and velpatasvir for HCV genotype 1, 2, 4, 5, and 6 infection.
        N Engl J Med. 2015; 373: 2599-2607
        • Foster G.R.
        • Afdhal N.
        • Roberts S.K.
        • Brau N.
        • Gane E.J.
        • Pianko S.
        • et al.
        Sofosbuvir and velpatasvir for HCV genotype 2 and 3 infection.
        N Engl J Med. 2015; 373: 2608-2617
        • Gower E.
        • Estes C.
        • Blach S.
        • Razavi-Shearer K.
        • Razavi H.
        Global epidemiology and genotype distribution of the hepatitis C virus infection.
        J Hepatol. 2014; 61: S45-S57
        • Messina J.P.
        • Humphreys I.
        • Flaxman A.
        • Brown A.
        • Cooke G.S.
        • Pybus O.G.
        • et al.
        Global distribution and prevalence of hepatitis C virus genotypes.
        Hepatology. 2015; 61: 77-87
        • Rehman I.U.
        • Idrees M.
        • Ali M.
        • Ali L.
        • Butt S.
        • Hussain A.
        • et al.
        Hepatitis C virus genotype 3a with phylogenetically distinct origin is circulating in Pakistan.
        Genet Vaccines Ther. 2011; 9: 2
        • McNaughton A.L.
        • Cameron I.D.
        • Wignall-Fleming E.B.
        • Biek R.
        • McLauchlan J.
        • Gunson R.N.
        • et al.
        Spatiotemporal reconstruction of the introduction of hepatitis C virus into Scotland and its subsequent regional transmission.
        J Virol. 2015; 89: 11223-11232
        • Akkarathamrongsin S.
        • Hacharoen P.
        • Tangkijvanich P.
        • Theamboonlers A.
        • Tanaka Y.
        • Mizokami M.
        • et al.
        Molecular epidemiology and genetic history of hepatitis C virus subtype 3a infection in Thailand.
        Intervirology. 2013; 56: 284-294
        • Karchava M.
        • Waldenstrom J.
        • Parker M.
        • Hallack R.
        • Sharvadze L.
        • Gatserelia L.
        • et al.
        High incidence of the hepatitis C virus recombinant 2k/1b in Georgia: Recommendations for testing and treatment.
        Hepatol Res. 2015; 45: 1292-1298
        • Raghwani J.
        • Thomas X.V.
        • Koekkoek S.M.
        • Schinkel J.
        • Molenkamp R.
        • van de Laar T.J.
        • et al.
        Origin and evolution of the unique hepatitis C virus circulating recombinant form 2k/1b.
        J Virol. 2012; 86: 2212-2220
        • Kalinina O.
        • Norder H.
        • Mukomolov S.
        • Magnius L.O.
        A natural intergenotypic recombinant of hepatitis C virus identified in St Petersburg.
        J Virol. 2002; 76: 4034-4043
        • Wyles D.L.
        Antiviral resistance and the future landscape of hepatitis C virus infection therapy.
        J Infect Dis. 2013; 207: S33-S39
        • Paolucci S.
        • Fiorina L.
        • Mariani B.
        • Gulminetti R.
        • Novati S.
        • Barbarini G.
        • et al.
        Naturally occurring resistance mutations to inhibitors of HCV NS5A region and NS5B polymerase in DAA treatment-naive patients.
        Virol J. 2013; 10: 355
        • Sarrazin C.
        • Lathouwers E.
        • Peeters M.
        • Daems B.
        • Buelens A.
        • Witek J.
        • et al.
        Prevalence of the hepatitis C virus NS3 polymorphism Q80K in genotype 1 patients in the European region.
        Antiviral Res. 2015; 116: 10-16
        • Stuyver L.
        • Rossau R.
        • Wyseur A.
        • Duhamel M.
        • Vanderborght B.
        • Van Heuverswyn H.
        • et al.
        Typing of hepatitis C virus isolates and characterization of new subtypes using a line probe assay.
        J Gen Virol. 1993; 74: 1093-1102
        • Stuyver L.
        • Wyseur A.
        • van Arnhem W.
        • Lunel F.
        • Laurent-Puig P.
        • Pawlotsky J.M.
        • et al.
        Hepatitis C virus genotyping by means of 5'-UR/core line probe assays and molecular analysis of untypeable samples.
        Virus Res. 1995; 38: 137-157
        • Altschul S.F.
        • Madden T.L.
        • Schaffer A.A.
        • Zhang J.
        • Zhang Z.
        • Miller W.
        • et al.
        Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
        Nucleic Acids Res. 1997; 25: 3389-3402
        • Hedskog C.
        • Chodavarapu K.
        • Ku K.S.
        • Xu S.
        • Martin R.
        • Miller M.D.
        • et al.
        Genotype- and subtype-independent full-genome sequencing assay for hepatitis C virus.
        J Clin Microbiol. 2015; 53: 2049-2059
        • Thompson J.D.
        • Higgins D.G.
        • Gibson T.J.
        CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
        Nucleic Acids Res. 1994; 22: 4673-4680
        • Zwickl D.J.
        Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion.
        (Ph.D. dissertation) The University of Texas at Austin, 2006
        • Anisimova M.
        • Gascuel O.
        Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative.
        Syst Biol. 2006; 55: 539-552
        • Guindon S.
        • Dufayard J.F.
        • Lefort V.
        • Anisimova M.
        • Hordijk W.
        • Gascuel O.
        New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.
        Syst Biol. 2010; 59: 307-321
        • Hedskog C.
        • Doehle B.
        • Chodavarapu K.
        • Gontcharova V.
        • Crespo Garcia J.
        • De Knegt R.
        • et al.
        Characterization of hepatitis C virus intergenotypic recombinant strains and associated virological response to sofosbuvir/ribavirin.
        Hepatology. 2015; 61: 471-480
        • Schreiber J.
        • McNally J.
        • Chodavarapu K.
        • Svarovskaia E.
        • Moreno C.
        Treatment of a patient with genotype 7 HCV infection with sofosbuvir and velpatasvir.
        Hepatology. 2016; 64: 983-985
        • Frank C.
        • Mohamed M.K.
        • Strickland G.T.
        • Lavanchy D.
        • Arthur R.R.
        • Magder L.S.
        • et al.
        The role of parenteral antischistosomal therapy in the spread of hepatitis C virus in Egypt.
        Lancet. 2000; 355: 887-891
        • Lin M.V.
        • Chung R.
        Recent FDA approval of sofosbuvir and simeprevir. Implications for current HCV treatment.
        Clin Liver Dis. 2014; 3: 65-68
        • Kumada H.
        • Suzuki Y.
        • Ikeda K.
        • Toyota J.
        • Karino Y.
        • Chayama K.
        • et al.
        Daclatasvir plus asunaprevir for chronic HCV genotype 1b infection.
        Hepatology. 2014; 59: 2083-2091
        • Nakamoto S.
        • Kanda T.
        • Wu S.
        • Shirasawa H.
        • Yokosuka O.
        Hepatitis C virus NS5A inhibitors and drug resistance mutations.
        World J Gastroenterol. 2014; 20: 2902-2912
        • Lam A.M.
        • Espiritu C.
        • Bansal S.
        • Micolochick Steuer H.M.
        • Niu C.
        • Zennou V.
        • et al.
        Genotype and subtype profiling of PSI-7977 as a nucleotide inhibitor of hepatitis C virus.
        Antimicrob Agents Chemother. 2012; 56: 3359-3368
        • Bouchardeau F.
        • Cantaloube J.F.
        • Chevaliez S.
        • Portal C.
        • Razer A.
        • Lefrere J.J.
        • et al.
        Improvement of hepatitis C virus (HCV) genotype determination with the new version of the INNO-LiPA HCV assay.
        J Clin Microbiol. 2007; 45: 1140-1145
        • De Keukeleire S.
        • Descheemaeker P.
        • Reynders M.
        Diagnosis of hepatitis C virus genotype 2k/1b needs NS5B sequencing.
        Int J Infect Dis. 2015; 41: 1-2
        • Noppornpanth S.
        • Sablon E.
        • De Nys K.
        • Truong X.L.
        • Brouwer J.
        • Van Brussel M.
        • et al.
        Genotyping hepatitis C viruses from Southeast Asia by a novel line probe assay that simultaneously detects core and 5' untranslated regions.
        J Clin Microbiol. 2006; 44: 3969-3974
        • Svarovskaia E.S.
        • Gane E.
        • Dvory-Sobol H.
        • Martin R.
        • Doehle B.
        • Hedskog C.
        • et al.
        L159F and V321A sofosbuvir-associated hepatitis C virus NS5B substitutions.
        J Infect Dis. 2016; 213: 1240-1247
        • Abergel A.
        • Metivier S.
        • Samuel D.
        • Jiang D.
        • Kersey K.
        • Pang P.S.
        • et al.
        Ledipasvir plus sofosbuvir for 12 weeks in patients with hepatitis C genotype 4 infection.
        Hepatology. 2016; 64: 1049-1056
        • Zeuzem S.
        • Mizokami M.
        • Pianko S.
        • Mangia A.
        • Han K.H.
        • Martin R.
        • et al.
        NS5A resistance-associated substitutions in patients with genotype 1 hepatitis C virus: prevalence and effect on treatment outcome.
        J Hepatol. 2017; 66: 910-918