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pp 1-28 | Cite as

The Hepatitis C Virus Replicon System and Its Role in Drug Development

  • Ralf BartenschlagerEmail author
  • Volker Lohmann
Chapter
Part of the Topics in Medicinal Chemistry book series

Abstract

Infections with the hepatitis C virus (HCV) are an important medical problem as they can lead to chronic liver disease, including liver cirrhosis and hepatocellular carcinoma. The HCV genome was cloned molecularly in 1989, and around 25 years later, antiviral therapy has been established that eliminates the virus in more than 95% of infected individuals. To reach this goal, several hurdles had to be overcome, a major one having been the development of robust cell culture systems that were suitable for drug development, but also to study the individual steps of the HCV replication cycle. Here we summarize the step-by-step establishment of HCV cell culture systems with a focus on the replicon system that played a major role in the development of HCV-specific direct-acting antiviral drugs.

Keywords

Antiviral therapy Direct acting antiviral drugs Drug development HCV cell culture system NS5A inhibitor Replicon 

Abbreviations

cDNA

Complementary DNA

DAA

Direct-acting antiviral

EMCV

Encephalomyocarditis virus

HBV

Hepatitis B virus

HCV

Hepatitis C virus

HCVcc

Cell culture grown HCV

HDV

Hepatitis D virus

hVAP-A

Human vesicle-associated membrane protein-associated protein A

IFN

Interferon

IRES

Internal ribosomal entry site

MDA5

Melanoma differentiation antigen 5

MEF

Mouse embryonic fibroblasts

miR-122

microRNA-122

Npt

Neomycin phosphotransferase

NS

Nonstructural protein

NTR

Nontranslated region

PHHs

Primary human hepatocytes

PI4KA

Phosphatidylinositol-4-phosphate kinase IIIα

PI4P

Phosphatidylinositol-4-phosphate

RdRp

RNA-dependent RNA polymerase

REM

Replication-enhancing mutation

RIG-I

Retinoic acid inducible gene I

RT-PCR

Reverse transcription-polymerase chain reaction

TEM

Virus titer-enhancing mutation

Notes

Acknowledgments

We are deeply indebted to all past and present members of our research groups, who made valuable contributions to all of our work. Studies in the authors’ laboratories were supported by the Deutsche Forschungsgemeinschaft, the German Ministry for Research and Education (BMBF), and the European Union.

Compliance with Ethical Standards

Funding Work in the authors’ laboratory has been supported by the Deutsche Forschungsgemeinschaft, the Bundesministerium für Bildung und Forschung and the European Union.

Conflict of Interest

V.L. and R.B. are co-founders of ReBLikon GmbH, which holds commercial rights to hepatitis C virus replicon technology.

Ethical Approval

Work conducted in the authors’ laboratory did not involve studies with human participants or animals.

References

  1. 1.
    Choo QL, Kuo G, Weiner AJ, Overby LR, Bradley DW, Houghton M (1989) Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome. Science 244(4902):359–362Google Scholar
  2. 2.
    Lohmann V, Korner F, Koch J, Herian U, Theilmann L, Bartenschlager R (1999) Replication of subgenomic hepatitis C virus RNAs in a hepatoma cell line. Science 285(5424):110–113Google Scholar
  3. 3.
    Steinmann E, Pietschmann T (2013) Cell culture systems for hepatitis C virus. Curr Top Microbiol Immunol 369:17–48Google Scholar
  4. 4.
    Billerbeck E, de Jong Y, Dorner M, de la FC, Ploss A (2013) Animal models for hepatitis C. Curr Top Microbiol Immunol 369:49–86Google Scholar
  5. 5.
    Saeed M, Billerbeck E, Rice CM (2019) Molecular virology and animal models. Top Med Chem.  https://doi.org/10.1007/7355_2018_51Google Scholar
  6. 6.
    Egger D, Wolk B, Gosert R, Bianchi L, Blum HE, Moradpour D et al (2002) Expression of hepatitis C virus proteins induces distinct membrane alterations including a candidate viral replication complex. J Virol 76(12):5974–5984Google Scholar
  7. 7.
    Paul D, Madan V, Bartenschlager R (2014) Hepatitis C virus RNA replication and assembly: living on the fat of the land. Cell Host Microbe 16(5):569–579Google Scholar
  8. 8.
    Kuo G, Choo QL, Alter HJ, Gitnick GL, Redeker AG, Purcell RH et al (1989) An assay for circulating antibodies to a major etiologic virus of human non-A, non-B hepatitis. Science 244(4902):362–364Google Scholar
  9. 9.
    Seipp S, Mueller HM, Pfaff E, Stremmel W, Theilmann L, Goeser T (1997) Establishment of persistent hepatitis C virus infection and replication in vitro. J Gen Virol 78.(Pt 10:2467–2476Google Scholar
  10. 10.
    Tagawa M, Kato N, Yokosuka O, Ishikawa T, Ohto M, Omata M (1995) Infection of human hepatocyte cell lines with hepatitis C virus in vitro. J Gastroenterol Hepatol 10(5):523–527Google Scholar
  11. 11.
    Kato N, Nakazawa T, Mizutani T, Shimotohno K (1995) Susceptibility of human T-lymphotropic virus type I infected cell line MT-2 to hepatitis C virus infection. Biochem Biophys Res Commun 206(3):863–869Google Scholar
  12. 12.
    Shimizu YK, Iwamoto A, Hijikata M, Purcell RH, Yoshikura H (1992) Evidence for in vitro replication of hepatitis C virus genome in a human T-cell line. Proc Natl Acad Sci U S A 89(12):5477–5481Google Scholar
  13. 13.
    Nakajima N, Hijikata M, Yoshikura H, Shimizu YK (1996) Characterization of long-term cultures of hepatitis C virus. J Virol 70(5):3325–3329Google Scholar
  14. 14.
    Boyer JC, Haenni AL (1994) Infectious transcripts and cDNA clones of RNA viruses. Virology 198(2):415–426Google Scholar
  15. 15.
    Tanaka T, Kato N, Cho MJ, Shimotohno K (1995) A novel sequence found at the 3′ terminus of hepatitis C virus genome. Biochem Biophys Res Commun 215(2):744–749Google Scholar
  16. 16.
    Kolykhalov AA, Feinstone SM, Rice CM (1996) Identification of a highly conserved sequence element at the 3′ terminus of hepatitis C virus genome RNA. J Virol 70(6):3363–3371Google Scholar
  17. 17.
    Moormann RJ, van Gennip HG, Miedema GK, Hulst MM, van Rijn PA (1996) Infectious RNA transcribed from an engineered full-length cDNA template of the genome of a pestivirus. J Virol 70(2):763–770Google Scholar
  18. 18.
    Kolykhalov AA, Agapov EV, Blight KJ, Mihalik K, Feinstone SM, Rice CM (1997) Transmission of hepatitis C by intrahepatic inoculation with transcribed RNA. Science 277(5325):570–574Google Scholar
  19. 19.
    Yanagi M, Purcell RH, Emerson SU, Bukh J (1997) Transcripts from a single full-length cDNA clone of hepatitis C virus are infectious when directly transfected into the liver of a chimpanzee. Proc Natl Acad Sci U S A 94(16):8738–8743Google Scholar
  20. 20.
    Blight KJ, Kolykhalov AA, Rice CM (2000) Efficient initiation of HCV RNA replication in cell culture. Science 290:1972–1974Google Scholar
  21. 21.
    Bartenschlager R, Ahlborn LL, Mous J, Jacobsen H (1993) Nonstructural protein 3 of the hepatitis C virus encodes a serine-type proteinase required for cleavage at the NS3/4 and NS4/5 junctions. J Virol 67(7):3835–3844Google Scholar
  22. 22.
    Bartenschlager R (1999) The NS3/4A proteinase of the hepatitis C virus: unravelling structure and function of an unusual enzyme and a prime target for antiviral therapy. J Viral Hepat 10(11):1–2Google Scholar
  23. 23.
    Lohmann V, Korner F, Herian U, Bartenschlager R (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):8416–8428Google Scholar
  24. 24.
    Bartenschlager R, Schaller H (1992) Hepadnaviral assembly is initiated by polymerase binding to the encapsidation signal in the viral RNA genome. EMBO J 11(9):3413–3420Google Scholar
  25. 25.
    Kaplan G, Racaniello VR (1988) Construction and characterization of poliovirus subgenomic replicons. J Virol 62(5):1687–1696Google Scholar
  26. 26.
    Mittelholzer C, Moser C, Tratschin JD, Hofmann MA (1997) Generation of cytopathogenic subgenomic RNA of classical swine fever virus in persistently infected porcine cell lines. Virus Res 51(2):125–137Google Scholar
  27. 27.
    Castillo L, Diaz P, Inostroza J, Espinoza R, Millaqueo L, Calderara M et al (1993) Prevalence of hepatitis C virus antibodies in chronic hemodialysis and kidney transplantation patients. Rev Med Chil 121(9):1024–1028Google Scholar
  28. 28.
    Behrens SE, Grassmann CW, Thiel HJ, Meyers G, Tautz N (1998) Characterization of an autonomous subgenomic pestivirus RNA replicon. J Virol 72(3):2364–2372Google Scholar
  29. 29.
    Khromykh AA, Westaway EG (1997) Subgenomic replicons of the flavivirus Kunjin: construction and applications. J Virol 71(2):1497–1505Google Scholar
  30. 30.
    Guo JT, Bichko VV, Seeger C (2001) Effect of alpha interferon on the hepatitis C virus replicon. J Virol 75(18):8516–8523Google Scholar
  31. 31.
    Ikeda M, Yi M, Li K, Lemon SM (2002) Selectable subgenomic and genome-length dicistronic RNAs derived from an infectious molecular clone of the HCV-N strain of hepatitis C virus replicate efficiently in cultured Huh7 cells. J Virol 76(6):2997–3006Google Scholar
  32. 32.
    Lohmann V, Hoffmann S, Herian U, Penin F, Bartenschlager R (2003) Viral and cellular determinants of hepatitis C virus RNA replication in cell culture. J Virol 77(5):3007–3019Google Scholar
  33. 33.
    Kishine H, Sugiyama K, Hijikata M, Kato N, Takahashi H, Noshi T et al (2002) Subgenomic replicon derived from a cell line infected with the hepatitis C virus. Biochem Biophys Res Commun 293(3):993–999Google Scholar
  34. 34.
    Blight KJ, McKeating JA, Marcotrigiano J, Rice CM (2003) Efficient replication of hepatitis C virus genotype 1a RNAs in cell culture. J Virol 77(5):3181–3190Google Scholar
  35. 35.
    Grobler JA, Markel EJ, Fay JF, Graham DJ, Simcoe AL, Ludmerer SW et al (2003) Identification of a key determinant of hepatitis C virus cell culture adaptation in domain II of NS3 helicase. J Biol Chem 278(19):16741–16746Google Scholar
  36. 36.
    Gu B, Gates AT, Isken O, Behrens SE, Sarisky RT (2003) Replication studies using genotype 1a subgenomic hepatitis C virus replicons. J Virol 77(9):5352–5359Google Scholar
  37. 37.
    Kato T, Date T, Miyamoto M, Furusaka A, Tokushige K, Mizokami M et al (2003) Efficient replication of the genotype 2a hepatitis C virus subgenomic replicon. Gastroenterology 125(6):1808–1817Google Scholar
  38. 38.
    Krieger N, Lohmann V, Bartenschlager R (2001) Enhancement of hepatitis C virus RNA replication by cell culture-adaptive mutations. J Virol 75(10):4614–4624Google Scholar
  39. 39.
    Lohmann V, Körner F, Dobierzewska A, Bartenschlager R (2001) Mutations in hepatitis C virus RNAs conferring cell culture adaptation. J Virol 75:1437–1449Google Scholar
  40. 40.
    Yi M, Lemon SM (2002) Replication of subgenomic hepatitis A virus RNAs expressing firefly luciferase is enhanced by mutations associated with adaptation of virus to growth in cultured cells. J Virol 76(3):1171–1180Google Scholar
  41. 41.
    Harak C, Meyrath M, Romero-Brey I, Schenk C, Gondeau C, Schult P et al (2016) Tuning a cellular lipid kinase activity adapts hepatitis C virus to replication in cell culture. Nat Microbiol 2:16247Google Scholar
  42. 42.
    Reiss S, Rebhan I, Backes P, Romero-Brey I, Erfle H, Matula P et al (2011) Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment. Cell Host Microbe 9(1):32–45Google Scholar
  43. 43.
    Reiss S, Harak C, Romero-Brey I, Radujkovic D, Klein R, Ruggieri A et al (2013) The lipid kinase phosphatidylinositol-4 kinase III alpha regulates the phosphorylation status of hepatitis C virus NS5A. PLoS Pathog 9(5):e1003359Google Scholar
  44. 44.
    Wang H, Perry JW, Lauring AS, Neddermann P, De FR, Tai AW (2014) Oxysterol-binding protein is a phosphatidylinositol 4-kinase effector required for HCV replication membrane integrity and cholesterol trafficking. Gastroenterology 146(5):1373–1385Google Scholar
  45. 45.
    Stoeck IK, Lee JY, Tabata K, Romero-Brey I, Paul D, Schult P et al (2018) Hepatitis C virus replication depends on Endosomal cholesterol homeostasis. J Virol 92(1):e01196–e01117Google Scholar
  46. 46.
    Khan I, Katikaneni DS, Han Q, Sanchez-Felipe L, Hanada K, Ambrose RL et al (2014) Modulation of hepatitis C virus genome replication by glycosphingolipids and four-phosphate adaptor protein 2. J Virol 88(21):12276–12295Google Scholar
  47. 47.
    Bukh J, Pietschmann T, Lohmann V, Krieger N, Faulk K, Engle RE et al (2002) Mutations that permit efficient replication of hepatitis C virus RNA in Huh-7 cells prevent productive replication in chimpanzees. Proc Natl Acad Sci U S A 99(22):14416–14421Google Scholar
  48. 48.
    Pietschmann T, Zayas M, Meuleman P, Long G, Appel N, Koutsoudakis G et al (2009) Production of infectious genotype 1b virus particles in cell culture and impairment by replication enhancing mutations. PLoS Pathog 5(6):e1000475Google Scholar
  49. 49.
    Neddermann P, Quintavalle M, Di Pietro C, Clementi A, Cerretani M, Altamura S et al (2004) Reduction of hepatitis C virus NS5A hyperphosphorylation by selective inhibition of cellular kinases activates viral RNA replication in cell culture. J Virol 78(23):13306–13314Google Scholar
  50. 50.
    Evans MJ, Rice CM, Goff SP (2004) Phosphorylation of hepatitis C virus nonstructural protein 5A modulates its protein interactions and viral RNA replication. Proc Natl Acad Sci U S A 101(35):13038–13043Google Scholar
  51. 51.
    Blight KJ, McKeating JA, Rice CM (2002) Highly permissive cell lines for subgenomic and genomic hepatitis C virus RNA replication. J Virol 76(24):13001–13014Google Scholar
  52. 52.
    Murray EM, Grobler JA, Markel EJ, Pagnoni MF, Paonessa G, Simon AJ et al (2003) Persistent replication of hepatitis C virus replicons expressing the beta-lactamase reporter in subpopulations of highly permissive Huh7 cells. J Virol 77(5):2928–2935Google Scholar
  53. 53.
    Frese M, Pietschmann T, Moradpour D, Haller O, Bartenschlager R (2001) Interferon-alpha inhibits hepatitis C virus subgenomic RNA replication by an MxA-independent pathway. J Gen Virol 82.(Pt 4:723–733Google Scholar
  54. 54.
    Pietschmann T, Lohmann V, Rutter G, Kurpanek K, Bartenschlager R (2001) Characterization of cell lines carrying self-replicating hepatitis C virus RNAs. J Virol 75(3):1252–1264Google Scholar
  55. 55.
    Friebe P, Boudet J, Simorre JP, Bartenschlager R (2005) Kissing-loop interaction in the 3′ end of the hepatitis C virus genome essential for RNA replication. J Virol 79(1):380–392Google Scholar
  56. 56.
    Sumpter Jr R, Loo YM, Foy E, Li K, Yoneyama M, Fujita T et al (2005) Regulating intracellular antiviral defense and permissiveness to hepatitis C virus RNA replication through a cellular RNA helicase, RIG-I. J Virol 79(5):2689–2699Google Scholar
  57. 57.
    Hiet MS, Bauhofer O, Zayas M, Roth H, Tanaka Y, Schirmacher P et al (2015) Control of temporal activation of hepatitis C virus-induced interferon response by domain 2 of nonstructural protein 5A. J Hepatol 63(4):829–837Google Scholar
  58. 58.
    Cao X, Ding Q, Lu J, Tao W, Huang B, Zhao Y et al (2015) MDA5 plays a critical role in interferon response during hepatitis C virus infection. J Hepatol 62(4):771–778Google Scholar
  59. 59.
    Binder M, Kochs G, Bartenschlager R, Lohmann V (2007) Hepatitis C virus escape from the interferon regulatory factor 3 pathway by a passive and active evasion strategy. Hepatology 46(5):1365–1374Google Scholar
  60. 60.
    Keskinen P, Nyqvist M, Sareneva T, Pirhonen J, Melén K, Julkunen I (1999) Impaired antiviral response in human hepatoma cells. Virology 263:364–375Google Scholar
  61. 61.
    Saeed M, Andreo U, Chung HY, Espiritu C, Branch AD, Silva JM et al (2015) SEC14L2 enables pan-genotype HCV replication in cell culture. Nature 524(7566):471–475Google Scholar
  62. 62.
    Yamane D, McGivern DR, Wauthier E, Yi M, Madden VJ, Welsch C et al (2014) Regulation of the hepatitis C virus RNA replicase by endogenous lipid peroxidation. Nat Med 20(8):927–935Google Scholar
  63. 63.
    Pietschmann T, Lohmann V, Kaul A, Krieger N, Rinck G, Rutter G et al (2002) Persistent and transient replication of full-length hepatitis C virus genomes in cell culture. J Virol 76(8):4008–4021Google Scholar
  64. 64.
    Dreux M, Garaigorta U, Boyd B, Decembre E, Chung J, Whitten-Bauer C et al (2012) Short-range exosomal transfer of viral RNA from infected cells to plasmacytoid dendritic cells triggers innate immunity. Cell Host Microbe 12(4):558–570Google Scholar
  65. 65.
    Saeed M, Gondeau C, Hmwe S, Yokokawa H, Date T, Suzuki T et al (2013) Replication of hepatitis C virus genotype 3a in cultured cells. Gastroenterology 144(1):56–58Google Scholar
  66. 66.
    Saeed M, Scheel TK, Gottwein JM, Marukian S, Dustin LB, Bukh J et al (2012) Efficient replication of genotype 3a and 4a hepatitis C virus replicons in human hepatoma cells. Antimicrob Agents Chemother 56(10):5365–5373Google Scholar
  67. 67.
    Peng B, Yu M, Xu S, Lee YJ, Tian Y, Yang H et al (2013) Development of robust hepatitis C virus genotype 4 subgenomic replicons. Gastroenterology 144(1):59–61Google Scholar
  68. 68.
    Wose Kinge CN, Espiritu C, Prabdial-Sing N, Sithebe NP, Saeed M, Rice CM (2014) Hepatitis C virus genotype 5a subgenomic replicons for evaluation of direct-acting antiviral agents. Antimicrob Agents Chemother 58(9):5386–5394Google Scholar
  69. 69.
    Yu M, Peng B, Chan K, Gong R, Yang H, Delaney W et al (2014) Robust and persistent replication of the genotype 6a hepatitis C virus replicon in cell culture. Antimicrob Agents Chemother 58(5):2638–2646Google Scholar
  70. 70.
    Zhu Q, Guo JT, Seeger C (2003) Replication of hepatitis C virus subgenomes in nonhepatic epithelial and mouse hepatoma cells. J Virol 77(17):9204–9210Google Scholar
  71. 71.
    Date T, Kato T, Miyamoto M, Zhao Z, Yasui K, Mizokami M et al (2004) Genotype 2a hepatitis C virus subgenomic replicon can replicate in HepG2 and IMY-N9 cells. J Biol Chem 279(21):22371–22376Google Scholar
  72. 72.
    Kato T, Date T, Miyamoto M, Zhao Z, Mizokami M, Wakita T (2005) Nonhepatic cell lines HeLa and 293 support efficient replication of the hepatitis C virus genotype 2a subgenomic replicon. J Virol 79(1):592–596Google Scholar
  73. 73.
    Chang KS, Cai Z, Zhang C, Sen GC, Williams BR, Luo G (2006) Replication of hepatitis C virus (HCV) RNA in mouse embryonic fibroblasts: protein kinase R (PKR)-dependent and PKR-independent mechanisms for controlling HCV RNA replication and mediating interferon activities. J Virol 80(15):7364–7374Google Scholar
  74. 74.
    Narbus CM, Israelow B, Sourisseau M, Michta ML, Hopcraft SE, Zeiner GM et al (2011) HepG2 cells expressing microRNA miR-122 support the entire hepatitis C virus life cycle. J Virol 85(22):12087–12092Google Scholar
  75. 75.
    Thibault PA, Huys A, Dhillon P, Wilson JA (2013) MicroRNA-122-dependent and -independent replication of hepatitis C virus in Hep3B human hepatoma cells. Virology 436(1):179–190Google Scholar
  76. 76.
    Jopling CL, Yi M, Lancaster AM, Lemon SM, Sarnow P (2005) Modulation of hepatitis C virus RNA abundance by a liver-specific MicroRNA. Science 309(5740):1577–1581Google Scholar
  77. 77.
    Yi M, Bodola F, Lemon SM (2002) Subgenomic hepatitis C virus replicons inducing expression of a secreted enzymatic reporter protein. Virology 304(2):197–210Google Scholar
  78. 78.
    Vrolijk JM, Kaul A, Hansen BE, Lohmann V, Haagmans BL, Schalm SW et al (2003) A replicon-based bioassay for the measurement of interferons in patients with chronic hepatitis C. J Virol Methods 110(2):201–209Google Scholar
  79. 79.
    Moradpour D, Evans MJ, Gosert R, Yuan Z, Blum HE, Goff SP et al (2004) Insertion of green fluorescent protein into nonstructural protein 5A allows direct visualization of functional hepatitis C virus replication complexes. J Virol 78(14):7400–7409Google Scholar
  80. 80.
    Wolk B, Buchele B, Moradpour D, Rice CM (2008) A dynamic view of hepatitis C virus replication complexes. J Virol 82(21):10519–10531Google Scholar
  81. 81.
    Wakita T, Pietschmann T, Kato T, Date T, Miyamoto M, Zhao Z et al (2005) Production of infectious hepatitis C virus in tissue culture from a cloned viral genome. Nat Med 11(7):791–796Google Scholar
  82. 82.
    Lindenbach BD, Evans MJ, Syder AJ, Wolk B, Tellinghuisen TL, Liu CC et al (2005) Complete replication of hepatitis C virus in cell culture. Science 309(5734):623–626Google Scholar
  83. 83.
    Zhong J, Gastaminza P, Cheng G, Kapadia S, Kato T, Burton DR et al (2005) Robust hepatitis C virus infection in vitro. Proc Natl Acad Sci U S A 102(26):9294–9299Google Scholar
  84. 84.
    Bartenschlager R, Pietschmann T (2005) Efficient hepatitis C virus cell culture system: what a difference the host cell makes. Proc Natl Acad Sci U S A 102(28):9739–9740Google Scholar
  85. 85.
    Zhong J, Gastaminza P, Chung J, Stamataki Z, Isogawa M, Cheng G et al (2006) Persistent hepatitis C virus infection in vitro: coevolution of virus and host. J Virol 80(22):11082–11093Google Scholar
  86. 86.
    Russell RS, Meunier JC, Takikawa S, Faulk K, Engle RE, Bukh J et al (2008) Advantages of a single-cycle production assay to study cell culture-adaptive mutations of hepatitis C virus. Proc Natl Acad Sci U S A 105(11):4370–4375Google Scholar
  87. 87.
    Kaul A, Woerz I, Meuleman P, Leroux-Roels G, Bartenschlager R (2007) Cell culture adaptation of hepatitis C virus and in vivo viability of an adapted variant. J Virol 81(23):13168–13179Google Scholar
  88. 88.
    Delgrange D, Pillez A, Castelain S, Cocquerel L, Rouille Y, Dubuisson J et al (2007) Robust production of infectious viral particles in Huh-7 cells by introducing mutations in hepatitis C virus structural proteins. J Gen Virol 88.(Pt 9:2495–2503Google Scholar
  89. 89.
    Yi M, Ma Y, Yates J, Lemon SM (2007) Compensatory mutations in E1, p7, NS2, and NS3 enhance yields of cell culture-infectious intergenotypic chimeric hepatitis C virus. J Virol 81(2):629–638Google Scholar
  90. 90.
    Scheel TK, Gottwein JM, Carlsen TH, Li YP, Jensen TB, Spengler U et al (2011) Efficient culture adaptation of hepatitis C virus recombinants with genotype-specific core-NS2 by using previously identified mutations. J Virol 85(6):2891–2906Google Scholar
  91. 91.
    Gottwein JM, Scheel TK, Jensen TB, Lademann JB, Prentoe JC, Knudsen ML et al (2009) Development and characterization of hepatitis C virus genotype 1-7 cell culture systems: role of CD81 and scavenger receptor class B type I and effect of antiviral drugs. Hepatology 49(2):364–377Google Scholar
  92. 92.
    Pietschmann T, Kaul A, Koutsoudakis G, Shavinskaya A, Kallis S, Steinmann E et al (2006) Construction and characterization of infectious intra- and intergenotypic hepatitis c virus chimeras. Proc Natl Acad Sci U S A 103(19):7408–7413Google Scholar
  93. 93.
    Gottwein JM, Scheel TK, Hoegh AM, Lademann JB, Eugen-Olsen J, Lisby G et al (2007) Robust hepatitis C genotype 3a cell culture releasing adapted intergenotypic 3a/2a (S52/JFH1) viruses. Gastroenterology 133(5):1614–1626Google Scholar
  94. 94.
    Jensen TB, Gottwein JM, Scheel TK, Hoegh AM, Eugen-Olsen J, Bukh J (2008) Highly efficient JFH1-based cell-culture system for hepatitis C virus genotype 5a: failure of homologous neutralizing-antibody treatment to control infection. J Infect Dis 198(12):1756–1765Google Scholar
  95. 95.
    Koutsoudakis G, Kaul A, Steinmann E, Kallis S, Lohmann V, Pietschmann T et al (2006) Characterization of the early steps of hepatitis C virus infection by using luciferase reporter viruses. J Virol 80(11):5308–5320Google Scholar
  96. 96.
    Tscherne DM, Jones CT, Evans MJ, Lindenbach BD, McKeating JA, Rice CM (2006) Time- and temperature-dependent activation of hepatitis C virus for low-pH-triggered entry. J Virol 80(4):1734–1741Google Scholar
  97. 97.
    Jones CT, Murray CL, Eastman DK, Tassello J, Rice CM (2007) Hepatitis C virus p7 and NS2 proteins are essential for production of infectious virus. J Virol 81(16):8374–8383Google Scholar
  98. 98.
    Gottwein JM, Jensen TB, Mathiesen CK, Meuleman P, Serre SB, Lademann JB et al (2011) Development and application of hepatitis C reporter viruses with genotype 1 to 7 core-nonstructural protein 2 (NS2) expressing fluorescent proteins or luciferase in modified JFH1 NS5A. J Virol 85(17):8913–8928Google Scholar
  99. 99.
    Schaller T, Appel N, Koutsoudakis G, Kallis S, Lohmann V, Pietschmann T et al (2007) Analysis of hepatitis C virus superinfection exclusion by using novel fluorochrome gene-tagged viral genomes. J Virol 81(9):4591–4603Google Scholar
  100. 100.
    Schoggins JW, Wilson SJ, Panis M, Murphy MY, Jones CT, Bieniasz P et al (2011) A diverse range of gene products are effectors of the type I interferon antiviral response. Nature 472(7344):481–485Google Scholar
  101. 101.
    Yi M, Ma Y, Yates J, Lemon SM (2009) Trans-complementation of an NS2 defect in a late step in hepatitis C virus (HCV) particle assembly and maturation. PLoS Pathog 5(5):e1000403Google Scholar
  102. 102.
    Merz A, Long G, Hiet MS, Brugger B, Chlanda P, Andre P et al (2011) Biochemical and morphological properties of hepatitis C virus particles and determination of their lipidome. J Biol Chem 286(4):3018–3032Google Scholar
  103. 103.
    Catanese MT, Uryu K, Kopp M, Edwards TJ, Andrus L, Rice WJ et al (2013) Ultrastructural analysis of hepatitis C virus particles. Proc Natl Acad Sci U S A 110(23):9505–9510Google Scholar
  104. 104.
    Paul D, Hoppe S, Saher G, Krijnse-Locker J, Bartenschlager R (2013) Morphological and biochemical characterization of the membranous hepatitis C virus replication compartment. J Virol 87(19):10612–10627Google Scholar
  105. 105.
    Yi M, Villanueva RA, Thomas DL, Wakita T, Lemon SM (2006) Production of infectious genotype 1a hepatitis C virus (Hutchinson strain) in cultured human hepatoma cells. Proc Natl Acad Sci U S A 103(7):2310–2315Google Scholar
  106. 106.
    Yi M, Lemon SM (2004) Adaptive mutations producing efficient replication of genotype 1a hepatitis C virus RNA in normal Huh7 cells. J Virol 78(15):7904–7915Google Scholar
  107. 107.
    Li YP, Ramirez S, Jensen SB, Purcell RH, Gottwein JM, Bukh J (2012) Highly efficient full-length hepatitis C virus genotype 1 (strain TN) infectious culture system. Proc Natl Acad Sci U S A 109(48):19757–19762Google Scholar
  108. 108.
    Li YP, Ramirez S, Gottwein JM, Scheel TK, Mikkelsen L, Purcell RH et al (2012) Robust full-length hepatitis C virus genotype 2a and 2b infectious cultures using mutations identified by a systematic approach applicable to patient strains. Proc Natl Acad Sci U S A 109(18):E1101–E1110Google Scholar
  109. 109.
    Date T, Kato T, Kato J, Takahashi H, Morikawa K, Akazawa D et al (2012) Novel cell culture-adapted genotype 2a hepatitis C virus infectious clone. J Virol 86(19):10805–10820Google Scholar
  110. 110.
    Ramirez S, Li YP, Jensen SB, Pedersen J, Gottwein JM, Bukh J (2014) Highly efficient infectious cell culture of three HCV genotype 2b strains and sensitivity to lead protease, NS5A, and polymerase inhibitors. Hepatology 59(2):395–407Google Scholar
  111. 111.
    Kim S, Date T, Yokokawa H, Kono T, Aizaki H, Maurel P et al (2014) Development of hepatitis C virus genotype 3a cell culture system. Hepatology 60(6):1838–1850Google Scholar
  112. 112.
    Ramirez S, Mikkelsen LS, Gottwein JM, Bukh J (2016) Robust HCV genotype 3a infectious cell culture system permits identification of escape variants with resistance to sofosbuvir. Gastroenterology 151(5):973–985Google Scholar
  113. 113.
    Scheel TK, Gottwein JM, Mikkelsen LS, Jensen TB, Bukh J (2011) Recombinant HCV variants with NS5A from genotypes 1-7 have different sensitivities to an NS5A inhibitor but not interferon-alpha. Gastroenterology 140(3):1032–1042Google Scholar
  114. 114.
    Gottwein JM, Scheel TK, Jensen TB, Ghanem L, Bukh J (2011) Differential efficacy of protease inhibitors against HCV genotypes 2a, 3a, 5a, and 6a NS3/4A protease recombinant viruses. Gastroenterology 141(3):1067–1079Google Scholar
  115. 115.
    Li YP, Ramirez S, Humes D, Jensen SB, Gottwein JM, Bukh J (2014) Differential sensitivity of 5'UTR-NS5A recombinants of hepatitis C virus genotypes 1-6 to protease and NS5A inhibitors. Gastroenterology 146(3):812–821Google Scholar
  116. 116.
    Koutsoudakis G, Herrmann E, Kallis S, Bartenschlager R, Pietschmann T (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):588–598Google Scholar
  117. 117.
    Scholtes C, Ramiere C, Rainteau D, Perrin-Cocon L, Wolf C, Humbert L et al (2012) High plasma level of nucleocapsid-free envelope glycoprotein-positive lipoproteins in hepatitis C patients. Hepatology 56(1):39–48Google Scholar
  118. 118.
    Andre P, Komurian-Pradel F, Deforges S, Perret M, Berland JL, Sodoyer M et al (2002) Characterization of low- and very-low-density hepatitis C virus RNA-containing particles. J Virol 76(14):6919–6928Google Scholar
  119. 119.
    Bartenschlager R, Penin F, Lohmann V, Andre P (2011) Assembly of infectious hepatitis C virus particles. Trends Microbiol 19(2):95–103Google Scholar
  120. 120.
    Windisch MP, Frese M, Kaul A, Trippler M, Lohmann V, Bartenschlager R (2005) Dissecting the interferon-induced inhibition of hepatitis C virus replication by using a novel host cell line. J Virol 79(21):13778–13793Google Scholar
  121. 121.
    Zhu H, Dong H, Eksioglu E, Hemming A, Cao M, Crawford JM et al (2007) Hepatitis C virus triggers apoptosis of a newly developed hepatoma cell line through antiviral defense system. Gastroenterology 133(5):1649–1659Google Scholar
  122. 122.
    Ali S, Pellerin C, Lamarre D, Kukolj G (2004) Hepatitis C virus subgenomic replicons in the human embryonic kidney 293 cell line. J Virol 78(1):491–501Google Scholar
  123. 123.
    Fletcher NF, Yang JP, Farquhar MJ, Hu K, Davis C, He Q et al (2010) Hepatitis C virus infection of neuroepithelioma cell lines. Gastroenterology 139(4):1365–1374Google Scholar
  124. 124.
    Long G, Hiet MS, Windisch MP, Lee JY, Lohmann V, Bartenschlager R (2011) Mouse hepatic cells support assembly of infectious hepatitis C virus particles. Gastroenterology 141(3):1057–1066Google Scholar
  125. 125.
    Frentzen A, Kusuma A, Guerlevik E, Hueging K, Knocke S, Ginkel C et al (2014) Cell entry, efficient RNA replication, and production of infectious hepatitis C virus progeny in mouse liver-derived cells. Hepatology 59(1):78–88Google Scholar
  126. 126.
    Uprichard SL, Chung J, Chisari FV, Wakita T (2006) Replication of a hepatitis C virus replicon clone in mouse cells. Virol J 3:89Google Scholar
  127. 127.
    Vogt A, Scull MA, Friling T, Horwitz JA, Donovan BM, Dorner M et al (2013) Recapitulation of the hepatitis C virus life-cycle in engineered murine cell lines. Virology 444(1–2):1–11Google Scholar
  128. 128.
    Bengrine A, Brochot E, Louchet M, Herpe YE, Duverlie G (2016) Modeling of HBV and HCV hepatitis with hepatocyte-like cells. Front Biosci (Schol Ed) 8:97–105Google Scholar
  129. 129.
    Grakoui A, McCourt DW, Wychowski C, Feinstone SM, Rice CM (1993) Characterization of the hepatitis C virus-encoded serine proteinase: determination of proteinase-dependent polyprotein cleavage sites. J Virol 67(5):2832–2843Google Scholar
  130. 130.
    Tomei L, Failla C, Santolini E, De FR, La MN (1993) NS3 is a serine protease required for processing of hepatitis C virus polyprotein. J Virol 67(7):4017–4026Google Scholar
  131. 131.
    Hijikata M, Mizushima H, Tanji Y, Komoda Y, Hirowatari Y, Akagi T et al (1993) Proteolytic processing and membrane association of putative nonstructural proteins of hepatitis C virus. Proc Natl Acad Sci U S A 90(22):10773–10777Google Scholar
  132. 132.
    Behrens SE, Tomei L, De FR (1996) Identification and properties of the RNA-dependent RNA polymerase of hepatitis C virus. EMBO J 15(1):12–22Google Scholar
  133. 133.
    Pawlotsky JM (2003) The nature of interferon-alpha resistance in hepatitis C virus infection. Curr Opin Infect Dis 16(6):587–592Google Scholar
  134. 134.
    Gao M, Nettles RE, Belema M, Snyder LB, Nguyen VN, Fridell RA et al (2010) Chemical genetics strategy identifies an HCV NS5A inhibitor with a potent clinical effect. Nature 465(7294):96–100Google Scholar
  135. 135.
    Delang L, Neyts J, Vliegen I, Abrignani S, Neddermann P, De FR (2013) Hepatitis C virus-specific directly acting antiviral drugs. Curr Top Microbiol Immunol 369:289–320Google Scholar
  136. 136.
    Sarrazin C, Hezode C, Zeuzem S, Pawlotsky JM (2012) Antiviral strategies in hepatitis C virus infection. J Hepatol 56(Suppl 1):S88–S100Google Scholar
  137. 137.
    Kalaghatgi P, Sikorski AM, Knops E, Rupp D, Sierra S, Heger E et al (2016) Geno2pheno[HCV] – a web-based interpretation system to support hepatitis C treatment decisions in the era of direct-acting antiviral agents. PLoS One 11(5):e0155869Google Scholar
  138. 138.
    Watashi K, Hijikata M, Hosaka M, Yamaji M, Shimotohno K (2003) Cyclosporin A suppresses replication of hepatitis C virus genome in cultured hepatocytes. Hepatology 38(5):1282–1288Google Scholar
  139. 139.
    Yang F, Robotham JM, Nelson HB, Irsigler A, Kenworthy R, Tang H (2008) Cyclophilin A is an essential cofactor for hepatitis C virus infection and the principal mediator of cyclosporine resistance in vitro. J Virol 82(11):5269–5278Google Scholar
  140. 140.
    Kaul A, Stauffer S, Berger C, Pertel T, Schmitt J, Kallis S et al (2009) Essential role of cyclophilin A for hepatitis C virus replication and virus production and possible link to polyprotein cleavage kinetics. PLoS Pathog 5(8):e1000546Google Scholar
  141. 141.
    Lanford RE, Hildebrandt-Eriksen ES, Petri A, Persson R, Lindow M, Munk ME et al (2010) Therapeutic silencing of microRNA-122 in primates with chronic hepatitis C virus infection. Science 327(5962):198–201Google Scholar
  142. 142.
    van der Ree MH, van der Meer AJ, de BJ, Maan R, van VA, Welzel TM et al (2014) Long-term safety and efficacy of microRNA-targeted therapy in chronic hepatitis C patients. Antivir Res 111:53–59Google Scholar
  143. 143.
    Kaufmann SHE, Dorhoi A, Hotchkiss RS, Bartenschlager R (2018) Host-directed therapies for bacterial and viral infections. Nat Rev Drug Discov 17(1):35–56Google Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Infectious Diseases, Molecular VirologyHeidelberg UniversityHeidelbergGermany
  2. 2.Division of Virus-Associated CarcinogenesisGerman Cancer Research Center (DKFZ)HeidelbergGermany

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