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Review

Hepatitis C virus: quasispecies dynamics, virus persistance and antiviral therapy

Pages 499-510 | Published online: 02 May 2007

Bibliography

  • SIMMONDS P: Genetic diversity and evolution of hepatitis C virus 15 years on. J. Gen. Virol. (2004) 85:3173-3188.
  • HOOFNAGLE JH: Course and outcome of hepatitis C. Hepatology (2002) 36:S21-S29.
  • PAWLOTSKY JM: The nature of IFN-α resistance in hepatitis C virus infection. Curr. Opin. Infect. Dis. (2003) 16:587-592.
  • SIMMONDS P, BUKH J, COMBET C et al.: Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes. Hematology (2005) 42:962-973.
  • YOU S, STUMP DD, BRANCH AD, RICE CM: A cis-acting replication element in the sequence encoding the NS5B RNA-dependent RNA polymerase is required for hepatitis C virus RNA replication. J. Virol. (2004) 78:1352-1366.
  • LEE H, SHIN H, WIMMER E, PAUL AV: Cis-acting RNA signals in the NS5B C-terminal coding sequence of the hepatitis C virus genome. J. Virol. (2004) 78:10865-10877.
  • PESTOVA TV, SHATSKY IN, FLETCHER SP, JACKSON RJ, HELLEN CU: A prokaryotic-like mode of cytoplasmic eukaryotic ribosome binging to the initiation codon during internal translation initiation of hepatitis C and classical swine fever virus RNAs. Genes. Dev. (1998) 12:6783.
  • PIZZI E, TRAMONTANO A, TOMEI L et al.: Molecular model of the specificity pocket of the hepatitis C virus protease: implications for substrate recognition. Proc. Natl. Acad. Sci USA (1994) 91:888-892.
  • FAILLA CM, PIZZI E, DE FRANCESCO R, TRAMONTANO A: Redesigning the substrate specificity of the hepatitis C virus NS3 protease. Fold Des. (1996) 1:3542.
  • KOLLYKHALOV AA, AGAPOV EV, RICE CM: Specificity of the hepatitis C NS3 serine protease: effects of substitutions at the 3/4A, 4A/4B, 4B/5A, and 5A/5B cleavage sites on polyprotein processing. J. Virol. (1994) 68:7525-7533.
  • KOMODA Y, HIJIKATA M, SATO S, ASABE S, KIMURA K, SHIMOTOHO K: Substrate requirements of hepatitis C virus serine proteinase for intermolecular polypeptide cleavage in Escherichia coli. J. Virol. (1994) 68:7351-7357.
  • SIMMONDS P, HOLMES EC, CHA TA et al.: Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region. J. Gen. Virol. (1993) 74:2391-2399.
  • LOLE KS, BOLLINGER RC, PARNJAPE RS et al.: Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J. Virol. (1999) 73:152-160.
  • CHAMBERS TJ, FAN X, DROLL DA et al.: Quasispecies heterogeneity within the E1/E2 region as a pretreatment variable during pegylated IFN therapy of chronic hepatitis C virus infection. J. Virol. (2005) 79:3071-3083.
  • CRISTINA J, LOPEZ F, MORATORIO G et al.: Hepatitis C virus F protein sequence reveals a lack of functional constraints and a variable pattern of amino acid substitution. J. Gen. Virol. (2005) 86:115-120.
  • FARCI P, SHIMODA A, COIANA A et al.: The outcome of acute hepatitis C predicted by the evolution of the viral quasispecies. Science (2000) 288:339-344.
  • DOMINGO E, MARTIN V, PERALES C, GRANDE-PEREZ A, GARCIA-ARRIAZA J, ARIAS A: The outcome of acute hepatitis C predicted by the evolution of the viral quasispecies. Curr. Top. Microbiol. Immunol. (2006) 299:51-82.
  • DOMINGO E, BARANOWSKI E, RUIZ-JARABO CM, MARTÍN-HERNANDEZ AM, SAIZ JC, ESCARAMIS C: Quasispecies structure and persistence of RNA viruses. Emerg. Infect. Dis. (1998) 4:521-527.
  • BIEBRICHER CK, EIGEN M: The error threshold. Virus Res. (2005) 107:117-127.
  • PUIG-BASAGOITI F, FORNS X, FURCIC I et al.: Dynamics of hepatitis C virus NS5A quasispecies during IFN and ribavirin therapy in responder and non-responder patients with genotype 1b chronic hepatitis C. J. Gen. Virol. (2005) 86:1067-1075.
  • KUIKEN C, YUSIM K, BOYKIN L, RICHARDON R: The HCV sequence database. Bioinformatics (2005) 21:379-384.
  • KUMAR S, TAMURA K, NEI M: MEGA3: integrated software for molecular evolultionary genetic analysis and sequence alignment. Brief Bioinformatics 5 (2004) 5(2):150-163.
  • PAWLOTSKY JM: Hepatitis C virus population dynamics during infection. Curr. Top. Microbiol. Immunol. (2006) 299:261-284.
  • CODY SH, NAINAN OV, GARFEIN RS et al.: Hepatitis C virus transmission from an anesthesiologist to a patient. Arch. Intern. Med. (2002) 162:345-350.
  • LIN HJ, SEEFF LB, BARBOSA L, HOLLINGER FB: Occurrence of identical hypervariable region 1 sequences of hepatitis C virus in transfusion recipients and their respective blood donors: divergence over time. Hepatology (2001) 34:424-429.
  • MANZIN A, SOLFOROSI L, DEBIAGGI M et al.: Dominant role of host selective pressure in driving hepatitis C virus evolution in perinatal infection. J. Virol. (2000) 74:4327-4334.
  • KOJIMA M, OSUGA T, TSUDA F, TANAKA T, OKAMOTO H: Influence of antibodies to the hypervariable region of E2/NS1 glycoprotein on the selective replication of hepatitiss C virus in chimpanzees. Virology (1994) 204:665-672.
  • HIJIKATA M, MIZUNO K, RIKIHISA T et al.: Selective transmission of hepatitis C virus in vivo and in vitro. Arch. Virol. (1995) 140:1623-1628.
  • TAN SL, KATZE MG: How hepatitis C virus counteracts the IFN response: the jury is still out on NS5A. Virology (2001) 284:112.
  • REYES GR: The nonstructural NS5A protein of hepatitis C virus: an expanding, multifunctional role in enhancing hepatitis C virus pathogenesis. J. Biomed. Sci. (2002) 9:187-197.
  • MACDONALD A, HARRIS M: Hepatitis C virus NS5A: tales of a promiscuous protein. J. Gen. Virol. (2004) 85:2485-1502.
  • SZABO G: Hepatitis C virus NS5A protein, a master regulator? Gastroenterology (2006) 130:995-998.
  • ENOMOTO N, SAKUMA I, ASAHINA Y et al.: Comparison of full-length sequences of IFN-sensitive and resistant hepatitis C virus 1b: sensitivity to IFN is conferred by amino acid substitution in the NS5A region. J. Clin. Invest. (1995) 96:224-230.
  • ENOMOTO N, SAKUMA I, ASAHINA Y et al.: Mutations in the non-structural protein 5A and response to IFN in patients with chronic hepatitis C virus 1b intection. N. Engl. J. Med. (1996) 334:77-81.
  • PUIG-BASAGOITI F, SAIZ JC, FORNS X et al.: Influence of the genetic heterogeneity of the ISDR and PePHD regions of hepatitis C virus on the response to IFN therapy in chronic hepatitis C. J. Med. Virol. (2001) 65:35-44.
  • GIMENEZ-BARCONS M, FRANCO S, SUAREZ Y et al.: High amino acid variability within the NS5A of hepatitis C virus (HCV) is associated with hepatocellular carcinoma in patients with HCV-1b-related cirrosis. Hepatology (2001) 34:158-167.
  • WITHERELL GW, BEINEKE P: Statistical analysis of combined substitutions in non-structural 5A region of hepatitis C virus and IFN response. J. Med. Virol. (2001) 63:8-16.
  • SCHINKEL J, SPOON WJ, KROES AC: Meta-analysis of mutations in the NS5A gene and hepatitis C virus resistance to IFN therapy: uniting discordant conclusions. Antivir Ther (2004) 9:275-286.
  • INCHAUSPE G, ZEBEDEE S, LEE DH, SUGITANI M, NASOFF M, PRINCE AM: Genomic structure of the human prototype strain H of hepatitis C virus: comparison with American and Japanese isolates. Proc. Natl. Acad. Sci. USA (1991) 88:10292-10296.
  • DUVERLIE G, KHORSI H, CASTELAIN S et al.: Sequence analysis of the NS5A protein of European hepatitis C virus 1b isolates and relation to IFN sensitivity. J. Gen. Virol. (1998) 79:1373-1381.
  • NOUSBAUM J, POLYAK SJ, RAY SC et al.: Prospective characterization of full-lenght hepatitis C virus NS5A quasispecies during induction and combination antiviral therapy. J. Virol. (2000) 74:9028-9038.
  • MURPHY MD, ROSEN HR, MAROUSEK GI, CHOU S: Analysis of sequence configurations of the ISDR, PKR-binding domain and V3 regions as predictors of response to induction IFN-α and ribavirin therapy in chronic hepatitis C infection. Dig. Dis. Sci. (2002) 47:1195-1205.
  • DAVIS GL, ESTEBAN-MUR R, RUSTGI V et al.: IFN-α2b alone or in combination with ribavirin for the treatment of relapse of chronic hepatitis C. N. Engl. J. Med. (1998) 339:1493-1499.
  • MC HUTCHINSON JG, GONDON SC, SCHIFF ER et al.: IFN-α2b alone or in combination with ribavirin as initial treatment for chronic hepatitis. N. Engl. J. Med. (1998) 339:1485-1492.
  • POYNARD T, MARCELLIN P, LEE SS et al.: Randomised trial of IFN-α2b plus ribavirin for 48 weeks or for 24 weeks versus IFN-α2b plus placebo for 48 weeks for treatment of chronic infection with hepatitis C virus. Lancet (1998) 352:1426-1432.
  • HU KQ, VIERLING JM, REDEKER AG: Viral, host and IFN-related factors modulating the effect of IFN therapy for hepatitis C virus infection. J. Viral Hepat. (2001) 8:1-18.
  • ZEUZEM S: Heterogenous virologic response rates to IFN-based therapy in patients with chronic hepatitis C: who responds less well? Ann. Intern. Med. (2004) 140:370-381.
  • FRIED MW, HADZIYANNIS SJ: Treatment of chronic hepatitis C infection with pegIFNs plus ribavirin. Semin. Liver Dis. (2004) 24:47-54.
  • TAYLOR DR, SHI ST, ROMANO PR, BARBER GN, LAI MM: Inhibition of the IFN-inducible protein kinase PKR by HCV E2 protein. Science (1999) 285:107-110.
  • GAUDY C, LAMBELE M, MOREAU A, VEILLON P, LUNEL F, GOUDEAU A: Mutations within the hepatitis C virus genotype 1b E2-PePHD domain do not correlate with treatment outcome. J. Clin. Microbiol. (2005) 43:750-754.
  • GUPTA R, SUBRAMANI M, KHAJA MN et al.: Analysis of mutations within the 5′ untranslated region, IFN sensitivity region, and PePHD region as a function of response to IFN therapy in hepatitis C virus-infected patients in India. J. Clin. Microbiol. (2006) 44:709-715.
  • CONTRERAS AM, HISASA Y, HE W, TERELLA A, SCHMIDT EV, CHUNG RT: Viral RNA mutations are region specific and increased by ribavirin in a full-length hepatitis C virus replication system. J. Virol. (2002) 76:8505-8517.
  • MAAG D, CASTRO C, HONG Z, CAMERON CE: Hepatitis C virus RNA-dependent RNA polymerase (NS5B) as a mediator of the antiviral activity of ribavirin. J. Biol. Chem. (2001) 276:46094-46098.
  • VIGNUZZI M, STONE JK, ANDINO R: Ribavirin and lethal mutagenesis of poliovirus: molecular mechanisms, resistance and biological implications. Virus Res. (2005) 107:173-181.
  • FANG SH, HWANG LH, CHEN DS, CHIANG BL: Ribavirin enhancement of hepatitis C virus core antigen-specific type 1 T helper cell response correlates with the increased IL-12 level. J. Hepatol. (2000) 33:791-8.
  • HONG Z, CAMERON CE: Pleiotropic mechanisms of ribavirin antiviral activities. Prog. Drug. Res. (2002) 59:41-69.
  • ZHANG Y, JAMALUDDIN M, WANG S et al.: Ribavirin treatment up-regulates antiviral gene expression via the IFN-stimulated response element in respiratory syncytial virus-infected epithelial cells. J. Virol. (2003) 77:5933-5947.
  • LEYSEEN P, BALZARINI J, DE CLERCQ E, NEYTS J: The predominant mechanism by wihch ribavirin exerts its antiviral activity in vitro against Flaviviruses and Paramyxoviruses is mediated by inhibition of IMP dehydrogenase. J. Virol. (2005) 79:1943-1947.
  • ZHOU S, LUI R, BAROUDY BM, MALCOLM BA, REYES GR: The effect of ribavirin and IMPDH inhibitors on hepatitis C virus subgenomic replicon RNA. Virology (2003) 310:333-342.
  • VO NV, YOUNG KC, LAI MM: Mutagenic and inhibitory effects of ribavirin on hepatitis C virus RNA polymerase. Biochemistry (2003) 42:10462-10471.
  • YOUNG KC, LINDSAY KL, LEE KJ et al.: Identification of a ribavirin-resistant NS5B mutation of hepatitis C virus during ribavirin monotherapy. Hepatology (2003) 38:869-878.
  • CHISARI FV: Unscrambling hepatitis C virus–host interactions. Nature (2005) 436:930-932.
  • HISCOTT J, NGUYEN TLA, ARGUELLO M, NAKHAEI, P, PAZ S: Manipulation of the nuclear factor-κB pathway and the innate immune response by viruses. Oncogene (2006) 25:6844-6867.
  • BREIMAN A, GRANDVAUX N, LIN R et al.: Inhibition of RIG-I-dependent signaling to the IFN pathway during hepatitis C virus expression and restoration of signaling by IKK epsilon. J. Virol. (2005) 79:3969-3978.
  • FOY E, LI K, SUMPTER R et al.: Control of antiviral defenses through hepatitis C virus disruption of retinoic acid-inducible gene-I signaling. Proc. Natl. Acad. Sci. USA (2005) 102:2986-2991.
  • GALE M, FOY EM: Evasion of intracellular host defense by hepatitis C virus. Nature (2005) 436:939-945.
  • TAN SL, HE Y, HUANG Y, GALE M, Jr.: Strategies for hepatitis C therapeutic intervention: now and next. Curr. Opin. Pharmacol. (2004) 4:465-112.
  • LOVE RA, PARGE HE, WICKERSHAM JA et al.: The crystal structure of hepatitis C virus NS3 proteinase reveals a trypsin-like fold and a structural zinc binding site. Cell (1996) 87:331-342.
  • LAMARRE D, ANDERSON PC, BAILEY M et al.: An NS3 protease inhibitor with antiviral effects in humans infected with hepatitis C virus. Nature (2003) 426:186-189.
  • REISER M, HINRICHSEN H, BENHAMOU B et al.: Antiviral efficacy of NS3-serine protease inhibitor BILN-2061 in patients with chronic genotype 2 and 3 hepatitis C. Hepatology (2005) 41:832-835.
  • THOMSON JA, PERNI RB: Hepatitis C virus NS3-4A protease inhibitors: countering viral subversion in vitro and showing promise in the clinic. Curr. Opin. Drug Discov. Devel. (2006) 9:606-617.
  • NI ZJ, WAGMAN AS: Progress and development of small molecule HCV antivirals. Curr. Opin. Drug Discov. Devel. (2004) 7:446- 459.
  • KOEV G, DEKHTYAR T, HAN L et al.: Antiviral interactions of an HCV polymerase inhibitor with an HCV protease inhibitor or IFN in vitro. Antiviral Res. (2007) 73:78-83.
  • CHEN SH, TAN SL: Discovery of small-molecule inhibitors of HCV NS3-4A protease as potential therapeutic agents against HCV infection. Curr. Med. Chem. (2005) 12:2317-2342.
  • ARASAPPAN A, NIOROGE FG, CHAN TY et al.: Hepatitis C virus NS3-4A serine protease inhibitors: SAR of P2 moiety with improved potency. Bioorg. Med. Chem. Lett. (2005) 15:4180-4184.
  • ONTORIA JM, DI MARCO S, CONTE I et al.: The design and enzyme-bound crystal structure of indoline based peptidomimetic inhibitors of hepatitis C virus NS3 protease. J. Med. Chem. (2004) 47:6443.
  • VENKATRAMAN S, BOGEN SL, ARASAPPAN A et al.: Discovery of (1R,5S)-N-[3-amino-1-(cyclobutylmethyl)-2,3-dioxopropyl]-3-[2(S)-[[[(1,1-dimethyl- ethyl)amino]carbonyl]amino]-3,3-dimethyl-1-oxobutyl]-6,6-dimethyl-3-azabicyclo- [3.1.0]hexan-2(S)-carboxamide (SCH 503034), a selective, potent, orally bioavailable hepatitis C virus NS3 protease inhibitor: a potential therapeutic agent for the treatment of hepatitis C infection. J. Med. Chem. (2006) 49:6074-7086.
  • POWERS JP, PIPER DE, LI Y et al.: SAR and mode of action of novel non-nucleoside inhibitors of hepatitis C NS5b RNA polymerase. J. Med. Chem. (2006) 49:1034-1046.
  • SHOUKRY N, GRAKOUI A, HOUGHTON M et al.: Memory CD8+ T cells are required for protection from persistent hepatitis C virus infection. J. Exp. Med. (2003) 197:1645-1655.
  • SODERHOLM J, AHLEN G, KAUL A et al.: Relation between viral fitness and immune escape within the hepatitis C virus protease. Gut (2006) 55:266-274.
  • SHIINA M, REHERMANN B: Hepatitis C vaccines: inducing and challenging memory T cells. Hepatology (2006) 43:1395-1398.
  • FOLGORI A, CAPONE S, RUGGERI L et al.: A T cell HCV vaccine eliciting effective immunity against heterologous virus challenge in chimpanzees. Nature Med. (2006) 12:190-197.
  • GUGLIETTA S, GARBUGLIA AR, PACCIANI V et al.: Positive selection of cytotoxic T lymphocyte escape variants during acute hepatitis C virus infection. Euro. J. Immunol. (2005) 35:2627-2637.
  • ZHU Q, QEI Y, MENDEL DB et al.: Novel robust hepatitis C virus mouse efficacy model. Antimicrob. Agents Chemother. (2006) 50:3260-3268.

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