Assays for RNA synthesis and replication by the hepatitis C virus

Abstract

At least six major genotypes of Hepatitis C virus (HCV) cause liver diseases worldwide. The efficacy rates with current standard of care are about 50% against genotype 1, the most prevalent strain in the United States, Europe and Japan. Therefore more effective pan-genotypic therapies are needed. HCV RNA replication provides a number of validated targets for virus-specific and potentially pan-genotypic inhibitors. In vitro assays capturing the different steps of RNA synthesis are needed not only to identify new inhibitors, but also to examine their mechanisms of action. This review attempts to provide a comprehensive summary of the biochemical, cell-based and animal model systems to assess HCV polymerase activity and HCV RNA replication that should be useful for both basic research and applied studies.

Keywords

assay / RNA synthesis and replication / hepatitis C virus

References

[1] AmakoY, Tsukiyama-KoharaK, KatsumeA, HirataY, SekiguchiS, TobitaY, HayashiY, HishimaT, FunataN, YonekawaH, KoharaM (2010). Pathogenesis of hepatitis C virus infection in Tupaia belangeri.J Virol, 84(1): 303-311

[2] AntonysamyS S, AubolB, BlaneyJ, BrownerM F, GiannettiA M, HarrisS F, HébertN, HendleJ, HopkinsS, JeffersonE, KissingerC, LevequeV, MarcianoD, McGeeE, NájeraI, NolanB, TomimotoM, TorresE, WrightT (2008). Fragment-based discovery of hepatitis C virus NS5b RNA polymerase inhibitors.Bioorg Med Chem Lett, 18(9): 2990-2995

[3] AriumiY, KurokiM, MakiM, IkedaM, DansakoH, WakitaT, KatoN (2011). The ESCRT system is required for hepatitis C virus production.PLoS ONE, 6(1): e14517

[4] BaconB R, GordonS C, LawitzE, MarcellinP, VierlingJ M, ZeuzemS, PoordadF,GoodmanZ D, SingsH L ,BoparaiN, BurroughsM, BrassC A, AlbrechtJ K ,EstebanR ,and the HCV RESPOND-2 Investigators (2011). Boceprevir for previously treated chronic HCV genotype 1 infection.N Engl J Med, 364(13): 1207-1217

[5] BartenschlagerR, SparacioS (2007). Hepatitis C virus molecular clones and their replication capacity in vivo and in cell culture.Virus Res, 127(2): 195-207

[6] BehrensS E, TomeiL, De FrancescoR (1996). Identification and properties of the RNA-dependent RNA polymerase of hepatitis C virus.EMBO J, 15(1): 12-22

[7] BensadounP, RodriguezC, SoulierA, HiggsM, ChevaliezS, PawlotskyJ M (2011). Genetic background of hepatocyte cell lines: are in vitro hepatitis C virus research data reliable?Hepatology, 54(2): 748

[8] BiswalB K, CherneyM M, WangM, ChanL, YannopoulosC G, BilimoriaD, NicolasO, BedardJ, JamesM N (2004). Crystal structures of the RNA-dependent RNA polymerase genotype 2a of hepatitis C virus reveal two conformations and suggest mechanisms of inhibition by non-nucleoside inhibitors.J Biol Chem, 280(18): 18202-18210

[9] BlightK J, McKeatingJ A, MarcotrigianoJ, RiceC M (2003). Efficient replication of hepatitis C virus genotype 1a RNAs in cell culture.J Virol, 77(5): 3181-3190

[10] BoonstraA, van der LaanL J, VanwolleghemT, JanssenH L (2009). Experimental models for hepatitis C viral infection.Hepatology, 50(5): 1646-1655

[11] BrassV, GouttenoireJ, WahlA, PalZ, BlumH E, PeninF, MoradpourD (2010). Hepatitis C virus RNA replication requires a conserved structural motif within the transmembrane domain of the NS5B RNA-dependent RNA polymerase.J Virol, 84(21): 11580-11584

[12] BressanelliS, TomeiL, RousselA, IncittiI, VitaleR L, MathieuM, De FrancescoR, ReyF A (1999). Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus.Proc Natl Acad Sci USA, 96(23): 13034-13039

[13] BuckM (2008). Direct infection and replication of naturally occurring hepatitis C virus genotypes 1, 2, 3 and 4 in normal human hepatocyte cultures..PLoS ONE, 3(7): e2660

[14] BukhJ (2004). A critical role for the chimpanzee model in the study of hepatitis C.Hepatology, 39(6): 1469-1475

[15] BurtonJ R Jr, EversonG T (2009). HCV NS5B polymerase inhibitors.Clin Liver Dis, 13(3): 453-465

[16] CarrollS S, TomassiniJ E, BossermanM, GettyK, StahlhutM W, EldrupA B, BhatB, HallD, SimcoeA L, LaFeminaR, RutkowskiC A, WolanskiB, YangZ, MigliaccioG, De FrancescoR, KuoL C, MacCossM, OlsenD B (2003). Inhibition of hepatitis C virus RNA replication by 2′-modified nucleoside analogs.J Biol Chem, 278(14): 11979-11984

[17] ChatterjiU, BobardtM, SelvarajahS, YangF, TangH, SakamotoN, VuagniauxG, ParkinsonT, GallayP (2009). The isomerase active site of cyclophilin A is critical for hepatitis C virus replication.J Biol Chem, 284(25): 16998-17005

[18] ChinnaswamyS, CaiH, KaoC (2010a). An update on small molecule inhibitors of the HCV NS5B polymerase: effects on RNA synthesis in vitro and in cultured cells, and potential resistance in viral quasispecies.Virus Adaptation and Treatment, 2: 73-89

[19] ChinnaswamyS, MuraliA, CaiH, YiG, PalaninathanS, KaoC C (2010b). Conformations of the monomeric Hepatitis C Virus RNA-dependent RNA Polymerase.Virus Treatments and Adaptation, 2: 21-39

[20] ChinnaswamyS, MuraliA, LiP, FujisakiK, KaoC C (2010c). Regulation of de novo-initiated RNA synthesis in hepatitis C virus RNA-dependent RNA polymerase by intermolecular interactions.J Virol, 84(12): 5923-5935

[21] ChinnaswamyS, YarbroughI, PalaninathanS, KumarC T, VijayaraghavanV, DemelerB, LemonS M, SacchettiniJ C, KaoC C (2008). A locking mechanism regulates RNA synthesis and host protein interaction by the hepatitis C virus polymerase.J Biol Chem, 283(29): 20535-20546

[22] ChooQ L, KuoG, WeinerA J, OverbyL R, BradleyD W, HoughtonM (1989). Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome.Science, 244(4902): 359-362

[23] Clemente-CasaresP, López-JiménezA J, Bellón-EcheverríaI, EncinarJ A, Martínez-AlfaroE, Pérez-FloresR, MasA (2011). De novo polymerase activity and oligomerization of hepatitis C virus RNA-dependent RNA-polymerases from genotypes 1 to 5.PLoS ONE, 6(4): e18515

[24] DevalJ, PowdrillM H, D’AbramoC M, CellaiL, GötteM (2007). Pyrophosphorolytic excision of nonobligate chain terminators by hepatitis C virus NS5B polymerase.Antimicrob Agents Chemother, 51(8): 2920-2928

[25] Di MarcoS, VolpariC, TomeiL, AltamuraS, HarperS, NarjesF, KochU, RowleyM, De FrancescoR, MigliaccioG, CarfíA (2005). Interdomain communication in hepatitis C virus polymerase abolished by small molecule inhibitors bound to a novel allosteric site.J Biol Chem, 280(33): 29765-29770

[26] DingC B, HangJ P, ZhaoY, PengZ G, SongD Q, JiangJ D (2011). Zebrafish as a potential model organism for drug test against hepatitis C virus. PLoS One, epub ahead of print: 6(8): e22921

[27] DivineyS, TuplinA, StruthersM, ArmstrongV, ElliottR M, SimmondsP, EvansD J (2008). A hepatitis C virus cis-acting replication element forms a long-range RNA-RNA interaction with upstream RNA sequences in NS5B.J Virol, 82(18): 9008-9022

[28] DornerM, HorwitzJ A, RobbinsJ B, BarryW T, FengQ, MuK, JonesC T, SchogginsJ W, CataneseM T, BurtonD R, LawM, RiceC M, PlossA (2011). A genetically humanized mouse model for hepatitis C virus infection.Nature, 474(7350): 208-211

[29] DouglasD N, KawaharaT, SisB, BondD, FischerK P, TyrrellD L, LewisJ T, KnetemanN M (2010). Therapeutic efficacy of human hepatocyte transplantation in a SCID/uPA mouse model with inducible liver disease.PLoS ONE, 5(2): e9209

[30] DutartreH, BussettaC, BorettoJ, CanardB (2006). General catalytic deficiency of hepatitis C virus RNA polymerase with an S282T mutation and mutually exclusive resistance towards 2′-modified nucleotide analogues.Antimicrob Agents Chemother, 50(12): 4161-4169

[31] EggerD, WölkB, GosertR, BianchiL, BlumH E, MoradpourD, BienzK (2002). Expression of hepatitis C virus proteins induces distinct membrane alterations including a candidate viral replication complex.J Virol, 76(12): 5974-5984

[32] EI-SeragH B (2004). Hepatocellular carcinoma: recent trends in the United States.Gastroenterology, 127(5 Suppl 1): S27-S34

[33] FreseM, SchwärzleV, BarthK, KriegerN, LohmannV, MihmS, HallerO, BartenschlagerR (2002). Interferon-gamma inhibits replication of subgenomic and genomic hepatitis C virus RNAs.Hepatology, 35(3): 694-703

[34] GaleM Jr, FoyE M (2005). Evasion of intracellular host defence by hepatitis C virus.Nature, 436(7053): 939-945

[35] GaleM Jr, SenG C (2009). Viral evasion of the interferon system.J Interferon Cytokine Res, 29(9): 475-476

[36] GeD, FellayJ, ThompsonA J, SimonJ S, ShiannaK V, UrbanT J, HeinzenE L, QiuP, BertelsenA H, MuirA J, SulkowskiM, McHutchisonJ G, GoldsteinD B (2009). Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance.Nature, 461(7262): 399-401

[37] MoH, HebnerC, HarrisJBaeA,WongK, DelaneyW, OldachD, MillerMD (2011). Characterization of viral resistance mutations in genotype 1 HCV patients receiving combination therapy with a protease inhibitor and a polymerase inhibitor with or without Ribavirin Gilead. EASL 46th Annual Meeting. Apr 3rd2011

[38] GrakouiA, HansonH L, RiceC M (2001). Bad time for Bonzo? Experimental models of hepatitis C virus infection, replication, and pathogenesis.Hepatology, 33(3): 489-495

[39] HangJ Q, YangY, HarrisS F, LevequeV, WhittingtonH J, RajyaguruS, Ao-IeongG, McCownM F, WongA, GiannettiA M, Le PogamS, TalamásF, CammackN, NájeraI, KlumppK (2009). Slow binding inhibition and mechanism of resistance of non-nucleoside polymerase inhibitors of hepatitis C virus.J Biol Chem, 284(23): 15517-15529

[40] HardyR W, MarcotrigianoJ, BlightK J, MajorsJ E, RiceC M (2003). Hepatitis C virus RNA synthesis in a cell-free system isolated from replicon-containing hepatoma cells.J Virol, 77(3): 2029-2037

[41] HarrusD, Ahmed-El-SayedN, SimisterP C, MillerS, TriconnetM, HagedornC H, MahiasK, ReyF A, Astier-GinT, BressanelliS (2010). Further insights into the roles of GTP and the C terminus of the hepatitis C virus polymerase in the initiation of RNA synthesis.J Biol Chem, 285(43): 32906-32918

[42] HeckJ A, LamA M, NarayananN, FrickD N (2008). Effects of mutagenic and chain-terminating nucleotide analogs on enzymes isolated from hepatitis C virus strains of various genotypes.Antimicrob Agents Chemother, 52(6): 1901-1911

[43] HorscroftN, LaiV C, CheneyW, YaoN, WuJ Z, HongZ, ZhongW (2005). Replicon cell culture system as a valuable tool in antiviral drug discovery against hepatitis C virus.Antivir Chem Chemother, 16(1): 1-12

[44] HsuM, ZhangJ, FlintM, LogvinoffC, Cheng-MayerC, RiceC M, McKeatingJ A (2003). Hepatitis C virus glycoproteins mediate pH-dependent cell entry of pseudotyped retroviral particles.Proc Natl Acad Sci USA, 100(12): 7271-7276

[45] HsuN Y, IlnytskaO, BelovG, SantianaM, ChenY H, TakvorianP M, PauC, van der SchaarH, Kaushik-BasuN, BallaT, CameronC E, EhrenfeldE, van KuppeveldF J, Altan-BonnetN (2010). Viral reorganization of the secretory pathway generates distinct organelles for RNA replication.Cell, 141(5): 799-811

[46] HuangH, SunF, OwenD M, LiW, ChenY, GaleM Jr, YeJ (2007). Hepatitis C virus production by human hepatocytes dependent on assembly and secretion of very low-density lipoproteins.Proc Natl Acad Sci USA, 104(14): 5848-5853

[47] IlanE, AraziJ, NussbaumO, ZaubermanA, ErenR, LubinI, NevilleL, Ben-MosheO, KischitzkyA, LitchiA, MargalitI, GopherJ, MounirS, CaiW, DaudiN, EidA, JurimO, CzerniakA, GalunE, DaganS (2002). The hepatitis C virus (HCV)-Trimera mouse: a model for evaluation of agents against HCV.J Infect Dis, 185(2): 153-161

[48] JoplingC L, YiM, LancasterA M, LemonS M, SarnowP (2005). Modulation of hepatitis C virus RNA abundance by a liver-specific MicroRNA.Science, 309(5740): 1577-1581

[49] KaoC C, YangX, KlineA, WangQ M, BarketD, HeinzB A (2000). Template requirements for RNA synthesis by a recombinant hepatitis C virus RNA-dependent RNA polymerase.J Virol, 74(23): 11121-11128

[50] KatoN, MoriK, AbeK, DansakoH, KurokiM, AriumiY, WakitaT, IkedaM (2009). Efficient replication systems for hepatitis C virus using a new human hepatoma cell line.Virus Res, 146(1-2): 41-50

[51] KhromykhA A, WestawayE G (1997). Subgenomic replicons of the flavivirus Kunjin: construction and applications.J Virol, 71(2): 1497-1505

[52] KlumppK, LévêqueV, Le PogamS, MaH, JiangW R, KangH, GranycomeC, SingerM, LaxtonC, HangJ Q, SarmaK, SmithD B, HeindlD, HobbsC J, MerrettJ H, SymonsJ, CammackN, MartinJ A, DevosR, NájeraI (2006). The novel nucleoside analog R1479 (4′-azidocytidine) is a potent inhibitor of NS5B-dependent RNA synthesis and hepatitis C virus replication in cell culture.J Biol Chem, 281(7): 3793-3799

[53] KoutsoudakisG, HerrmannE, KallisS, BartenschlagerR, PietschmannT (2007). The level of CD81 cell surface expression is a key determinant for productive entry of hepatitis C virus into host cells.J Virol, 81(2): 588-598

[54] KriegerN, LohmannV, BartenschlagerR (2001). Enhancement of hepatitis C virus RNA replication by cell culture-adaptive mutations.J Virol, 75(10): 4614-4624

[55] LeeJ C, TsengC K, ChenK J, HuangK J, LinC K, LinY T (2010). A cell-based reporter assay for inhibitor screening of hepatitis C virus RNA-dependent RNA polymerase.Anal Biochem, 403(1-2): 52-62

[56] LesburgC A, CableM B, FerrariE, HongZ, MannarinoA F, WeberP C (1999). Crystal structure of the RNA-dependent RNA polymerase from hepatitis C virus reveals a fully encircled active site.Nat Struct Biol, 6(10): 937-943

[57] LindenbachB D, EvansM J, SyderA J, WölkB, TellinghuisenT L, LiuC C, MaruyamaT, HynesR O, BurtonD R, McKeatingJ A, RiceC M (2005). Complete replication of hepatitis C virus in cell culture.Science, 309(5734): 623-626

[58] LindenbachB D, MeulemanP, PlossA, VanwolleghemT, SyderA J, McKeatingJ A, LanfordR E, FeinstoneS M, MajorM E, Leroux-RoelsG, RiceC M (2006). Cell culture-grown hepatitis C virus is infectious in vivo and can be recultured in vitro.Proc Natl Acad Sci USA, 103(10): 3805-3809

[59] LohmannV, KörnerF, DobierzewskaA, BartenschlagerR (2001). Mutations in hepatitis C virus RNAs conferring cell culture adaptation.J Virol, 75(3): 1437-1449

[60] LohmannV, KörnerF, HerianU, BartenschlagerR (1997). Biochemical properties of hepatitis C virus NS5B RNA-dependent RNA polymerase and identification of amino acid sequence motifs essential for enzymatic activity.J Virol, 71(11): 8416-8428

[61] LohmannV, KörnerF, KochJ, HerianU, TheilmannL, BartenschlagerR (1999). Replication of subgenomic hepatitis C virus RNAs in a hepatoma cell line.Science, 285(5424): 110-113

[62] LoveR A, PargeH E, YuX, HickeyM J, DiehlW, GaoJ, WriggersH, EkkerA, WangL, ThomsonJ A, DragovichP S, FuhrmanS A (2003). Crystallographic identification of a noncompetitive inhibitor binding site on the hepatitis C virus NS5B RNA polymerase enzyme.J Virol, 77(13): 7575-7581

[63] LuC, XuH, Ranjith-KumarC T, BrooksM T, HouT Y, HuF, HerrA B, StrongR K, KaoC C, LiP (2010). The structural basis of 5′ triphosphate double-stranded RNA recognition by RIG-I C-terminal domain.Structure, 18(8): 1032-1043

[64] LuoG, HamatakeR K, MathisD M, RacelaJ, RigatK L, LemmJ, ColonnoR J (2000). De novo initiation of RNA synthesis by the RNA-dependent RNA polymerase (NS5B) of hepatitis C virus.J Virol, 74(2): 851-863

[65] MaH, LevequeV, De WitteA, LiW, HendricksT, ClausenS M, CammackN, KlumppK (2005). Inhibition of native hepatitis C virus replicase by nucleotide and non-nucleoside inhibitors.Virology, 332(1): 8-15

[66] McLauchlanJ (2009). Hepatitis C virus: viral proteins on the move.Biochem Soc Trans, 37(5): 986-990

[67] MeanwellN A, KadowJ F, ScolaP M (2009). Chapter 20, Progress towards the discovery and development of specifically targeted inhibitors of hepatitis C virus. Ann Reports in Med Chem,44:397-440

[68] MercerD F, SchillerD E, ElliottJ F, DouglasD N, HaoC, RinfretA, AddisonW R, FischerK P, ChurchillT A, LakeyJ R, TyrrellD L, KnetemanN M (2001). Hepatitis C virus replication in mice with chimeric human livers.Nat Med, 7(8): 927-933

[69] MicallefJ M, KaldorJ M, DoreG J (2006). Spontaneous viral clearance following acute hepatitis C infection: a systematic review of longitudinal studies.J Viral Hepat, 13(1): 34-41

[70] MoradpourD, EvansM J, GosertR, YuanZ, BlumH E, GoffS P, LindenbachB D, RiceC M (2004). Insertion of green fluorescent protein into nonstructural protein 5A allows direct visualization of functional hepatitis C virus replication complexes.J Virol, 78(14): 7400-7409

[71] MoradpourD, PeninF, RiceC M (2007). Replication of hepatitis C virus.Nat Rev Microbiol, 5(6): 453-463

[72] MoriishiK, MatsuuraY (2007). Host factors involved in the replication of hepatitis C virus.Rev Med Virol, 17(5): 343-354

[73] MunakataT, LiangY, KimS, McGivernD R, HuibregtseJ, NomotoA, LemonS M (2007). Hepatitis C virus induces E6AP-dependent degradation of the retinoblastoma protein.PLoS Pathog, 3(9): 1335-1347

[74] MurakamiE, NiuC, BaoH, Micolochick SteuerH M, WhitakerT, NachmanT, SofiaM A, WangP, OttoM J, FurmanP A (2008). The mechanism of action of beta-D-2′-deoxy-2′-fluoro-2′-C-methylcytidine involves a second metabolic pathway leading to beta-D-2′-deoxy-2′-fluoro-2′-C-methyluridine 5′-triphosphate, a potent inhibitor of the hepatitis C virus RNA-dependent RNA polymerase.Antimicrob Agents Chemother, 52(2): 458-464

[75] NyanguileO, DevogelaereB, VijgenL, Van den BroeckW, PauwelsF, CummingsM D, De BondtH L, VosA M, BerkeJ M, LenzO, VandercruyssenG, VermeirenK, MostmansW, DehertoghP, DelouvroyF, VendevilleS, VanDyckK, DockxK, CleirenE, RaboissonP, SimmenK A, FanningG C (2010). 1a/1b subtype profiling of nonnucleoside polymerase inhibitors of hepatitis C virus.J Virol, 84(6): 2923-2934

[76] O’FarrellD, TrowbridgeR, RowlandsD, JägerJ (2003). Substrate complexes of hepatitis C virus RNA polymerase (HC-J4): structural evidence for nucleotide import and de-novo initiation.J Mol Biol, 326(4): 1025-1035

[77] OhJ W, ItoT, LaiM M (1999). A recombinant hepatitis C virus RNA-dependent RNA polymerase capable of copying the full-length viral RNA.J Virol, 73(9): 7694-7702

[78] OlsenD B, EldrupA B, BartholomewL, BhatB, BossermanM R, CeccacciA, ColwellL F, FayJ F, FloresO A, GettyK L, GroblerJ A, LaFeminaR L, MarkelE J, MigliaccioG, PrhavcM, StahlhutM W, TomassiniJ E, MacCossM, HazudaD J, CarrollS S (2004). A 7-deaza-adenosine analog is a potent and selective inhibitor of hepatitis C virus replication with excellent pharmacokinetic properties.Antimicrob Agents Chemother, 48(10): 3944-3953

[79] PangP S, PlanetP J, GlennJ S (2009). The evolution of the major hepatitis C genotypes correlates with clinical response to interferon therapy.PLoS ONE, 4(8): e6579

[80] PauwelsF, MostmansW, QuirynenL M, Mm van derHelmL, BouttonC W, RueffA, CleirenE, RaboissonP, SurlerauxD, NyanguileO, SimmonK A (2007). Binding-site identification and genotypic profiling of hepatitis C virus polymerase inhibitors. J Virol. 81:6909-6919Pichlmair A, Schulz O, Tan CP, Näslund TI, Liljeström P, Weber F, Reis e Sousa C (2006). RIG-I-mediated antiviral responses to single-stranded RNA bearing 5′-phosphates.Science, 314(5801): 997-1001

[81] PichlmairASchulzO, TanCP, NäslundTL, LiljeströmP, WeberF, C R (2006). RIG-I-Mediated Antiviral Responses to Single-Stranded RNA Bearing 5'-Phosphates. Science, 314(5801): 997-1001

[82] PietschmannT, KaulA, KoutsoudakisG, ShavinskayaA, KallisS, SteinmannE, AbidK, NegroF, DreuxM, CossetF L, BartenschlagerR (2006). Construction and characterization of infectious intragenotypic and intergenotypic hepatitis C virus chimeras.Proc Natl Acad Sci USA, 103(19): 7408-7413

[83] PietschmannT, LohmannV, RutterG, KurpanekK, BartenschlagerR (2001). Characterization of cell lines carrying self-replicating hepatitis C virus RNAs.J Virol, 75(3): 1252-1264

[84] PrinceA M, BrotmanB, LeeD H, RenL, MooreB S, ScheffelJ W (1999). Significance of the anti-E2 response in self-limited and chronic hepatitis C virus infections in chimpanzees and in humans.J Infect Dis, 180(4): 987-991

[85] Ranjith-KumarC T, GutshallL, KimM J, SariskyR T, KaoC C (2002). Requirements for de novo initiation of RNA synthesis by recombinant flaviviral RNA-dependent RNA polymerases.J Virol, 76(24): 12526-12536

[86] Ranjith-KumarC T, WenY, BaxterN, BhardwajK, Cheng KaoC (2011). A cell-based assay for RNA synthesis by the HCV polymerase reveals new insights on mechanism of polymerase inhibitors and modulation by NS5A.PLoS ONE, 6(7): e22575

[87] RhimJ A, SandgrenE P, DegenJ L, PalmiterR D, BrinsterR L (1994). Replacement of diseased mouse liver by hepatic cell transplantation.Science, 263(5150): 1149-1152

[88] SaitoT, OwenD M, JiangF, MarcotrigianoJ, GaleM Jr (2008). Innate immunity induced by composition-dependent RIG-I recognition of hepatitis C virus RNA.Nature, 454(7203): 523-527

[89] SarrazinC, KiefferT L, BartelsD, HanzelkaB, MühU, WelkerM, WincheringerD, ZhouY, ChuH M, LinC, WeeginkC, ReesinkH, ZeuzemS, KwongA D (2007). Dynamic hepatitis C virus genotypic and phenotypic changes in patients treated with the protease inhibitor telaprevir.Gastroenterology, 132(5): 1767-1777

[90] ShiS T, HerlihyK J, GrahamJ P, FuhrmanS A, DoanC, PargeH, HickeyM, GaoJ, YuX, ChauF, GonzalezJ, LiH, LewisC, PatickA K, DuggalR (2008). In vitro resistance study of AG-021541, a novel nonnucleoside inhibitor of the hepatitis C virus RNA-dependent RNA polymerase.Antimicrob Agents Chemother, 52(2): 675-683

[91] ShimakamiT, HondaM, KusakawaT, MurataT, ShimotohnoK, KanekoS, MurakamiS (2006). Effect of hepatitis C virus (HCV) NS5B-nucleolin interaction on HCV replication with HCV subgenomic replicon.J Virol, 80(7): 3332-3340

[92] ShimakamiT, LanfordR E, LemonS M (2009). Hepatitis C: recent successes and continuing challenges in the development of improved treatment modalities.Curr Opin Pharmacol, 9(5): 537-544

[93] SimmondsP, BukhJ, CombetC, DeléageG, EnomotoN, FeinstoneS, HalfonP, InchauspéG, KuikenC, MaertensG, MizokamiM, MurphyD G, OkamotoH, PawlotskyJ M, PeninF, SablonE, Shin-IT, StuyverL J, ThielH J, ViazovS, WeinerA J, WidellA (2005). Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes.Hepatology, 42(4): 962-973

[94] SteitzT A (1999). DNA polymerases: structural diversity and common mechanisms.J Biol Chem, 274(25): 17395-17398

[95] SumpterR Jr, LooY M, FoyE, LiK, YoneyamaM, FujitaT, LemonS M, GaleM Jr (2005). Regulating intracellular antiviral defense and permissiveness to hepatitis C virus RNA replication through a cellular RNA helicase, RIG-I.J Virol, 79(5): 2689-2699

[96] SunX L, JohnsonR B, HockmanM A, WangQ M (2000). De novo RNA synthesis catalyzed by HCV RNA-dependent RNA polymerase.Biochem Biophys Res Commun, 268(3): 798-803

[97] TatenoC, YoshizaneY, SaitoN, KataokaM, UtohR, YamasakiC, TachibanaA, SoenoY, AsahinaK, HinoH, AsaharaT, YokoiT, FurukawaT, YoshizatoK (2004). Near completely humanized liver in mice shows human-type metabolic responses to drugs.Am J Pathol, 165(3): 901-912

[98] TheofilopoulosA N, BaccalaR, BeutlerB, KonoD H (2005). Type I interferons (alpha/beta) in immunity and autoimmunity.Annu Rev Immunol, 23(1): 307-335

[99] ThomasD L, ThioC L, MartinM P, QiY, GeD, O’HuiginC, KiddJ, KiddK, KhakooS I, AlexanderG, GoedertJ J, KirkG D, DonfieldS M, RosenH R, ToblerL H, BuschM P, McHutchisonJ G, GoldsteinD B, CarringtonM (2009). Genetic variation in IL28B and spontaneous clearance of hepatitis C virus.Nature, 461(7265): 798-801

[100] TomassiniJ E, BootsE, GanL, GrahamP, MunshiV, WolanskiB, FayJ F, GettyK, LaFeminaR (2003). An in vitro Flaviviridae replicase system capable of authentic RNA replication.Virology, 313(1): 274-285

[101] TomeiL, AltamuraS, BartholomewL, BiroccioA, CeccacciA, PaciniL, NarjesF, GennariN, BisbocciM, IncittiI, OrsattiL, HarperS, StansfieldI, RowleyM, De FrancescoR, MigliaccioG (2003). Mechanism of action and antiviral activity of benzimidazole-based allosteric inhibitors of the hepatitis C virus RNA-dependent RNA polymerase.J Virol, 77(24): 13225-13231

[102] TomeiL, VitaleR L, IncittiI, SerafiniS, AltamuraS, VitelliA, De FrancescoR (2000). Biochemical characterization of a hepatitis C virus RNA-dependent RNA polymerase mutant lacking the C-terminal hydrophobic sequence.J Gen Virol, 81(Pt 3): 759-767

[103] TriyatniM, BergerE A, SaunierB (2011). A new model to produce infectious hepatitis C virus without the replication requirement.PLoS Pathog, 7(4): e1001333

[104] van DijkA A, MakeyevE V, BamfordD H (2004). Initiation of viral RNA-dependent RNA polymerization.J Gen Virol, 85(5): 1077-1093

[105] VrolijkJ M, KaulA, HansenB E, LohmannV, HaagmansB L, SchalmS W, BartenschlagerR (2003). A replicon-based bioassay for the measurement of interferons in patients with chronic hepatitis C.J Virol Methods, 110(2): 201-209

[106] WakitaT, PietschmannT, KatoT, DateT, MiyamotoM, ZhaoZ, MurthyK, HabermannA, KräusslichH G, MizokamiM, BartenschlagerR, LiangT J (2005). Production of infectious hepatitis C virus in tissue culture from a cloned viral genome.Nat Med, 11(7): 791-796

[107] WakitaT, TayaC, KatsumeA, KatoJ, YonekawaH, KanegaeY, SaitoI, HayashiY, KoikeM, KoharaM (1998). Efficient conditional transgene expression in hepatitis C virus cDNA transgenic mice mediated by the Cre/loxP system.J Biol Chem, 273(15): 9001-9006

[108] WangQ M, HockmanM A, StaschkeK, JohnsonR B, CaseK A, LuJ, ParsonsS, ZhangF, RathnachalamR, KirkegaardK, ColacinoJ M (2002). Oligomerization and cooperative RNA synthesis activity of hepatitis C virus RNA-dependent RNA polymerase.J Virol, 76(8): 3865-3872

[109] WangQ M, JohnsonR B, ChenD, LévêqueV J, RenJ, HockmanM A, AbeK, HachisuT, KondoY, IsakaY, SatoA, FujiwaraT (2004). Expression and purification of untagged full-length HCV NS5B RNA-dependent RNA polymerase.Protein Expr Purif, 35(2): 304-312

[110] WasleyA, AlterM J (2000). Epidemiology of hepatitis C: geographic differences and temporal trends.Semin Liver Dis, 20(1): 1-16

[111] WengL, HirataY, AraiM, KoharaM, WakitaT, WatashiK, ShimotohnoK, HeY, ZhongJ, ToyodaT (2010). Sphingomyelin activates hepatitis C virus RNA polymerase in a genotype-specific manner.J Virol, 84(22): 11761-11770

[112] YiM, BodolaF, LemonS M (2002). Subgenomic hepatitis C virus replicons inducing expression of a secreted enzymatic reporter protein.Virology, 304(2): 197-210

[113] YiM, VillanuevaR A, ThomasD L, WakitaT, LemonS M (2006). Production of infectious genotype 1a hepatitis C virus (Hutchinson strain) in cultured human hepatoma cells.Proc Natl Acad Sci USA, 103(7): 2310-2315

[114] ZeuzemS, AndreoneP, PolS, LawitzE, DiagoM, RobertsS, FocacciaR, YounossiZ, FosterG R, HorbanA, FerenciP, NevensF, MüllhauptB, PockrosP, TergR, ShouvalD, van HoekB, WeilandO, Van HeeswijkR, De MeyerS, LuoD, BoogaertsG, PoloR, PicchioG, BeumontM, and the REALIZE Study Team (2011). Telaprevir for retreatment of HCV infection.N Engl J Med, 364(25): 2417-2428

[115] ZhongJ, GastaminzaP, ChengG, KapadiaS, KatoT, BurtonD R, WielandS F, UprichardS L, WakitaT, ChisariF V (2005). Robust hepatitis C virus infection in vitro.Proc Natl Acad Sci USA, 102(26): 9294-9299

[116] ZhongW, UssA S, FerrariE, LauJ Y, HongZ (2000). De novo initiation of RNA synthesis by hepatitis C virus nonstructural protein 5B polymerase.J Virol, 74(4): 2017-2022

[117] ZonL I, PetersonR T (2005). In vivo drug discovery in the zebrafish.Nat Rev Drug Discov, 4(1): 35-44

RIGHTS & PERMISSIONS

Higher Education Press and Springer-Verlag Berlin Heidelberg