A perspective on modelling hepatitis C virus infection

Journal of Viral Hepatitis

Volumn 17, Issue 12, 2010, Pages 825-833

  Guedj, J ^a   Rong, L ^b   Dahari, H ^c   Perelson, A S ^a  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

^b OAKLAND UNIVERSITY   (United States)

^c UNIVERSITY OF ILLINOIS   (United States)

Author keywords

direct acting antiviral agents; drug resistance; HCV; IFN; modelling; viral kinetics

Indexed keywords

CILUPREVIR; PEGINTERFERON; PEGINTERFERON ALPHA2A; PEGINTERFERON ALPHA2B; RIBAVIRIN; TELAPREVIR; TMC 435350; VIRUS RNA;

ANTIVIRAL RESISTANCE; ANTIVIRAL THERAPY; DRUG RESPONSE; GENETIC VARIABILITY; GENOTYPE; HEPATITIS C; HUMAN; MATHEMATICAL MODEL; NONHUMAN; PATIENT COMPLIANCE; PRIORITY JOURNAL; REVIEW; RNA REPLICATION; VIRUS GENOME; VIRUS MUTANT; VIRUS MUTATION; WILD TYPE;

ANTIVIRAL AGENTS; DRUG RESISTANCE, VIRAL; HEPACIVIRUS; HEPATITIS C; HUMANS; INTERFERON ALFA-2A; INTERFERON ALFA-2B; KINETICS; MODELS, BIOLOGICAL; POLYETHYLENE GLYCOLS; RIBAVIRIN; RNA, VIRAL;

EID: 78649251945     PISSN: 13520504     EISSN: 13652893     Source Type: Journal    
DOI: 10.1111/j.1365-2893.2010.01348.x     Document Type: Review

References (70)

1. World Health Organization. Hepatitis C. Fact sheet No. 164. Revised October 2000.
2. Alter HJ,. HCV natural history: the retrospective and prospective in perspective. J Hepatol 2005; 43 (4): 550 - 552.
3. Awad T, Thorlund K, Hauser G, Mabrouk M, Gluud C,. Peginterferon alpha-2a is associated with higher sustained virological response than peginterferon alfa-2b in chronic hepatitis C: a systematic review of randomized trials. Hepatology 2010; 51 (4): 1176 - 1184.
4. Perelson AS, Herrmann E, Micol F, Zeuzem S,. New kinetic models for the hepatitis C virus. Hepatology 2005; 42 (4): 749 - 754.
5. Mihm U, Herrmann E, Sarrazin C, Zeuzem S,. Review article: predicting response in hepatitis C virus therapy. Aliment Pharmacol Ther 2006; 23 (8): 1043 - 1054.
6. Neumann AU, Lam NP, Dahari H, et al. Hepatitis C viral dynamics in vivo and the antiviral efficacy of interferon-alpha therapy. Science 1998; 282: 103 - 107.
7. Neumann AU, Lam NP, Dahari H, et al. Differences in viral dynamics between genotypes 1 and 2 of hepatitis C virus. J Infect Dis 2000; 182 (1): 28 - 35.
8. Layden-Almer JE, Ribeiro RM, Wiley T, Perelson AS, Layden TJ,. Viral dynamics and response differences in HCV-infected African American and white patients treated with IFN and ribavirin. Hepatology 2003; 37 (6): 1343 - 1350.
9. Sherman K, Shire N, Rouster S, et al. Viral kinetics in hepatitis C or hepatitis C/human immunodeficiency virus-infected patients. Gastroenterology 2005; 128 (2): 313 - 327.
10. Dahari D, Layden-Almer JE, Perelson AS, Layden TJ,. Hepatitis C viral kinetics in special populations. Curr Hepat Rep 2008; 7: 97 - 105.
11. Neumann A, Layden T, Reddy K, Levi-Drummer R, Poulakos J,. The 2nd phase slope of HCV decline is highly predictive of sustained virologic response following consensus IFN treatment for chronic hepatitis C and is determined by genotype but not dose. Hepatology 2000; 32: 356A.
12. Callaway DC, Perelson AS,. HIV-1 infection and low steady state viral loads. Bull Math Biol 2002; 64: 29 - 64.
13. Dahari H, Lo A, Ribeiro RM, Perelson AS,. Modeling hepatitis C virus dynamics: liver regeneration and critical drug efficacy. J Theor Biol 2007; 247 (2): 371 - 381.
14. Reluga TC, Dahari H, Perelson AS,. Analysis of hepatitis C virus infection models with hepatocyte homeostasis. SIAM J App Math 2009; 69 (4): 999 - 1023.
15. Powers KA, Dixit NM, Ribeiro RM, Golia P, Talal AH, Perelson AS,. Modeling viral and drug kinetics: hepatitis C virus treatment with pegylated interferon alfa-2b. Semin Liver Dis 2003; 23 (Suppl 1): 13 - 18.
16. Formann E, Jessner W, Bennett L, Ferenci P,. Twice-weekly administration of peginterferon-alpha-2b improves viral kinetics in patients with chronic hepatitis C genotype 1. J Viral Hepat 2003; 10 (4): 271 - 276.
17. Buti M, Sanchez-Avila F, Lurie Y, et al. Viral kinetics in genotype 1 chronic hepatitis C patients during therapy with 2 different doses of peginterferon alfa-2b plus ribavirin. Hepatology 2002; 35 (4): 930 - 936.
18. Shudo E, Ribeiro RM, Perelson AS,. Modelling hepatitis C virus kinetics during treatment with pegylated interferon alpha-2b: errors in the estimation of viral kinetic parameters. J Viral Hepat 2008; 15 (5): 357 - 362. (Pubitemid 351473629)
19. Holford NHG, Sheiner LB,. Kinetics of pharmacologie response. Pharmacol Ther 1982; 16 (2): 143 - 166.
20. Dixit NM, Perelson AS,. Complex patterns of viral load decay under antiretroviral therapy: influence of pharmacokinetics and intracellular delay. J Theor Biol 2004; 226 (1): 95 - 109.
21. Talal AH, Ribeiro RM, Powers KA, et al. Pharmacodynamics of PEG-IFN alpha differentiate HIV/HCV coinfected sustained virological responders from nonresponders. Hepatology 2006; 43 (5): 943 - 953.
22. Dahari D, Affonso de Araujo ES, Haagmans BL, et al. Pharmacodynamics of PEG-IFN alpha-2a in HIV/HCV co-infected patients: implications for treatment outcomes. J Hepatol (in press). doi
23. Bruno R, Sacchi P, Ciappina V, et al. Viral dynamics and pharmacokinetics of peginterferon alpha-2a and peginterferon alpha-2b in naive patients with chronic hepatitis C: a randomized, controlled study. Antivir Ther 2004; 2: 1359 - 1365.
24. Silva M, Poo J, Wagner F, et al. A randomised trial to compare the pharmacokinetic, pharmacodynamic, and antiviral effects of peginterferon alfa-2b and peginterferon alfa-2a in patients with chronic hepatitis C (COMPARE). J Hepatol 2006; 45 (2): 204 - 213.
25. Shudo E, Ribeiro RM, Talal AH, Perelson AS,. A hepatitis C viral kinetic model that allows for time-varying drug effectiveness. Antivir Ther 2008; 13 (7): 919 - 926.
26. Glue P, Fang JW, Rouzier-Panis R, et al. Pegylated interferon-alpha2b: pharmacokinetics, pharmacodynamics safety, and preliminary efficacy data. Clin Pharmacol Ther 2000; 68 (5): 556 - 567.
27. Harris JM, Martin NE, Modi M,. Pegylation: a novel process for modifying pharmacokinetics. Clin Pharmacol Ther 2001; 40 (7): 539 - 551.
28. Zeuzem S, Welsch C, Herrmann E,. Pharmacokinetics of peginterferons. Semin Liver Dis 2003; 23: 23 - 28.
29. Herrmann E,. Effect of ribavirin on hepatitis C viral kinetics in patients treated with pegylated interferon. Hepatology 2003; 37 (6): 1351 - 1358.
30. Sentjens RE, Weegink CJ, Beld MG, Cooreman MC, Reesink HW,. Viral kinetics of hepatitis C virus RNA in patients with chronic hepatitis C treated with 18 MU of interferon alpha daily. Eur J Gastroenterol Hepatol 2002; 14 (8): 833 - 840.
31. Bekkering F, Brouwer J, Hansen B, Schalm S,. Hepatitis C viral kinetics in difficult to treat patients receiving high dose interferon and ribavirin. J Hepatol 2001; 34 (3): 435 - 440.
32. Dahari D, Layden-Almer JE, Kallwitz E, et al. A mathematical model of hepatitis C virus dynamics in patients with high baseline viral loads or advanced liver disease. Gastroenterology 2009; 136 (4): 1402 - 1409.
33. Dahari H, Shudo E, Cotler SJ, Layden TJ, Perelson AS,. Modelling hepatitis C virus kinetics: the relationship between the infected cell loss rate and the final slope of viral decay. Antivir Ther 2009; 14 (3): 459 - 464.
34. Layden J, Layden T, Reddy K, Levy-Drummer R, Poulakos J, Neumann A,. First phase viral kinetic parameters as predictors of treatment response and their influence on the second phase viral decline. J Viral Hepat 2002; 9 (5): 340 - 345.
35. Neumann AU, Bain VE, Yoshida EM, Patel K, Pulkstenis E, Subramanian GM,. Early prediction of sustained virological response at day 3 of treatment with albinterferon-α-2b in patients with genotype 2/3 chronic hepatitis C. Liver Int 2009; 29 (9): 1350 - 1355.
36. Marcos A, Fisher R, Ham J, et al. Liver regeneration and function in donor and recipient after right lobe adult to adult living donor liver transplantation. Transplantation 2000; 69 (7): 1375 - 1379. (Pubitemid 30238727)
37. Borden EC, Sen GC, Uze G, et al. Interferons at age 50: past, current and future impact on biomedicine. Nat Rev Drug Discov 2007; 6 (12): 975 - 990.
38. Pawlotsky JM, Chevaliez S, McHutchison JG,. The hepatitis C virus life cycle as a target for new antiviral therapies. Gastroenterology 2007; 132 (5): 1979 - 1998.
39. Lin C, Gates CA, Rao BG, et al. In vitro studies of cross-resistance mutations against two hepatitis C virus serine protease inhibitors, VX-950 and BILN 2061. J Biol Chem 2005; 280 (44): 36784 - 36791.
40. Sarrazin C, Kieffer TL, Bartels D, et al. Dynamic hepatitis C virus genotypic and phenotypic changes in patients treated with the protease inhibitor telaprevir. Gastroenterology 2007; 132 (5): 1767 - 1777.
41. Kieffer TL, Sarrazin C, Miller JS, et al. Telaprevir and pegylated interferon-alpha-2a inhibit wild-type and resistant genotype 1 hepatitis C virus replication in patients. Hepatology 2007; 46 (3): 631 - 639.
42. Rong L, Dahari D, Ribeiro RM, Perelson AS,. Rapid emergence of protease inhibitor resistance in hepatitis C virus. Sci Transl Med 2010; 2 (30): 30ra32.
43. Domingo E,. Biological significance of viral quasispecies. Viral Hepatitis Rev 1996; 2: 247 - 261.
44. Cuevas JM, Gonzalez-Candelas F, Moya A, Sanjuan R,. Effect of ribavirin on the mutation rate and spectrum of hepatitis C virus in vivo. J Virol 2009; 83 (11): 5760 - 5764.
45. Duffy S, Shackelton LA, Holmes EC,. Rates of evolutionary change in viruses: patterns and determinants. Nat Rev Genet 2008; 9 (4): 267 - 276.
46. Zhang YY, Summers J,. Low dynamics state of viral competition in a chronic avian hepadnavirus infection. J Virol 2000; 74 (11): 5257 - 5265.
47. Adiwijaya BS, Herrmann E, Hare B, et al. A multi-variant, viral dynamic model of genotype 1 HCV to assess the in vivo evolution of protease-inhibitor resistant variants. PLoS Comput Biol 2010; 6 (4): 1 - 13.
48. Forestier N, Reesink HW, Weegink CJ, et al. Antiviral activity of telaprevir (VX-950) and peginterferon alfa-2a in patients with hepatitis C. Hepatology 2007; 46 (3): 640 - 648.
49. Hezode C, Forestier N, Dusheiko G, et al. Telaprevir and peginterferon with or without ribavirin for chronic HCV infection. N Engl J Med 2009; 360 (18): 1839 - 1850.
50. McHutchison JG, Everson GT, Gordon SC, et al. Telaprevir with peginterferon and ribavirin for chronic HCV genotype 1 infection. N Engl J Med 2009; 360 (18): 1827 - 1838.
51. Liu-Young G, Kozal MJ,. Hepatitis C protease and polymerase inhibitors in development. AIDS Patient Care STDS. 2008; 22 (16): 449 - 457.
52. Herrmann E, Zeuzem S, Sarrazin C, et al. Viral kinetics in patients with chronic hepatitis C treated with the serine protease inhibitor BILN 2061. Antivir Ther 2006; 11 (3): 371 - 376.
53. Adiwijaya B, Hare B, Caron P, et al. Rapid decrease of wild-type hepatitis C virus on telaprevir treatment. Antivir Ther 2009; 14 (4): 591 - 595.
54. Reesink HWFG, Farha KA, Weegink C, et al. Rapid HCV-RNA decline with once daily TMC435: a phase I study in healthy volunteers and hepatitis C patients. Gastroenterology 2010; 138 (3): 913 - 921.
55. Foy E, Li K, Wang C, et al. Regulation of interferon regulatory factor-3 by the hepatitis C virus serine protease. Sci Signal 2003; 300 (5622): 1145 - 1148.
56. Feld JJ, Hoofnagle JH,. Mechanism of action of interferon and ribavirin in treatment of hepatitis C. Nature 2005; 436 (7053): 967 - 972.
57. Lindenbach BD, Rice CM,. Unravelling hepatitis C virus replication from genome to function. Nature 2005; 436 (7053): 933 - 938.
58. Guidotti L, Rochford R, Chung J, Shapiro M, Purcell R, Chisari F,. Viral clearance without destruction of infected cells during acute HBV infection. Science 1999; 284: 825 - 829.
59. Lewin SR, Ribeiro RM, Walters T, et al. Analysis of hepatitis B viral load decline under potent therapy: complex decay profiles observed. Hepatology 2001; 34 (5): 1012 - 1020.
60. Dahari H, Major M, Zhang X, et al. Mathematical modeling of primary hepatitis C infection: noncytolytic clearance and early blockage of virion production. Gastroenterology 2005; 128 (4): 1056 - 1066.
61. Dahari H, Ribeiro RM, Rice CM, Perelson AS,. Mathematical Modeling of Subgenomic Hepatitis C Virus Replication in Huh-7 Cells? J Virol 2007; 81 (2): 750 - 760.
62. Dahari H, Sainz Jr B, Perelson AS, Uprichard S,. Modeling subgenomic hepatitis C virus RNA kinetics during treatment with alpha interferon. J Virol 2009; 83 (13): 6383 - 6390.
63. Thiébaut R, Guedj J, Jacqmin-Gadda H, et al. Estimation of dynamical model parameters taking into account undetectable marker values. BMC Med Res Methodol 2006; 6 (1): 1 - 10.
64. Guedj J, Thiébaut R, Commenges D,. Maximum likelihood estimation in dynamical models of HIV. Biometrics 2007; 63 (4): 1198 - 1206.
65. Wu H, Ding A, De Gruttola V,. Estimation of HIV dynamic parameters. Stat Med 1998; 17 (21): 2463 - 2485.
66. Pinheiro J, Bates D,. Mixed-Effects Models in S and S-PLUS. Springer, Verlag, 2000.
67. Han C, Chaloner K,. Bayesian experimental design for nonlinear mixed-effects models with application to HIV dynamic. Biometrics 2004; 60: 25 - 33.
68. Guedj J, Thiébaut R, Commenges D,. Practical Identifiability of HIV dynamics models. Bull Math Biol 2007; 69 (8): 2493 - 2513.
69. Ge D, Fellay J, Thompson AJ, et al. Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance. Nature 2009; 461 (7262): 399 - 401.
70. Bekkering FC, Neumann AU, Brouwer JT, Levi-Drummer RS, Schalm SW,. Changes in anti-viral effectiveness of interferon after dose reduction in chronic hepatitis C patients: a case control study. BMC Gastroenterol 2001; 1: 14.