Modeling Viral Evolutionary Dynamics after Telaprevir-Based Treatment

PLoS Computational Biology

Volumn 10, Issue 8, 2014, Pages

  Haseltine, Eric L ^a   De Meyer, Sandra ^b   Dierynck, Inge ^b   Bartels, Doug J ^a   Ghys, Anne ^b   Davis, Andrew ^a   Zhang, Eileen Z ^a   Tigges, Ann M ^a   Spanks, Joan ^a   Picchio, Gaston ^c   Kieffer, Tara L ^a   Sullivan, James C ^a  

^a VERTEX PHARMACEUTICALS   (United States)

^b JANSSEN RESEARCH FOUNDATION   (Belgium)

^c JANSSEN RESEARCH AND DEVELOPMENT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMIDES; ANTIVIRAL AGENTS; DRUG THERAPY; POPULATION STATISTICS; VIRUSES;

CLINICAL STUDY; EVOLUTIONARY DYNAMICS; HEPATITIS C VIRUS; IN-PHASE; INTERFERON ALFA; PEGYLATED; POST TREATMENT; RIBAVIRIN; SEQUENCE ANALYSIS; SEQUENCE DATA;

DYNAMICS;

TELAPREVIR; ANTIVIRUS AGENT; OLIGOPEPTIDE;

ACCURACY; ARTICLE; CLONAL EVOLUTION; COMPUTER PREDICTION; CONTROLLED STUDY; DRUG EFFICACY; DRUG TREATMENT FAILURE; GENOTYPE; HEPATITIS C; HEPATITIS C VIRUS; HUMAN; INTERMETHOD COMPARISON; MAJOR CLINICAL STUDY; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; NONHUMAN; OUTCOME ASSESSMENT; PHASE 3 CLINICAL TRIAL (TOPIC); QUANTITATIVE ANALYSIS; SENSITIVITY ANALYSIS; SEQUENCE ANALYSIS; VIRUS RESISTANCE; ANTIVIRAL RESISTANCE; BIOLOGICAL MODEL; BIOLOGY; CLASSIFICATION; DRUG COMBINATION; DRUG EFFECTS; GENETICS; HEPACIVIRUS; VIROLOGY; VIRUS LOAD;

ANTIVIRAL AGENTS; COMPUTATIONAL BIOLOGY; DRUG RESISTANCE, VIRAL; DRUG THERAPY, COMBINATION; HEPACIVIRUS; HEPATITIS C; HUMANS; MODELS, BIOLOGICAL; OLIGOPEPTIDES; VIRAL LOAD;

EID: 84928703225     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003772     Document Type: Article

References (26)

1. World Health Organization (2012) Hepatitis C: Surveillance and Control. Available: http://www.who.int/csr/disease/hepatitis/whocdscsrlyo2003/en/index4.html. Accessed 18 December 2012.
2. El-Serag HB, (2011) Hepatocellular Carcinoma. New England Journal of Medicine 365: 1118–1127.
3. Davis G, (2003) Projecting future complications of chronic hepatitis C in the United States. Liver Transplantation 9: 331–338.
4. Kwong AD, Kauffman RS, Hurter P, Mueller P, (2011) Discovery and development of telaprevir: an NS3-4A protease inhibitor for treating genotype 1 chronic hepatitis C virus. Nature Biotechnology 29: 993–1003.
5. Lin K, Perni RB, Kwong AD, Lin C, (2006) VX-950, a Novel Hepatitis C Virus (HCV) NS3-4A Protease Inhibitor, Exhibits Potent Antiviral Activities in HCV Replicon Cells. Antimicrob Agents Chemother 50: 1813–1822.
6. Perni RB, Almquist SJ, Byrn RA, Chandorkar G, Chaturvedi PR, et al. (2006) Preclinical Profile of VX-950, a Potent, Selective, and Orally Bioavailable Inhibitor of Hepatitis C Virus NS3-4A Serine Protease. Antimicrob Agents Chemother 50: 899–909.
7. Jacobson IM, McHutchison JG, Dusheiko G, Di Bisceglie AM, Reddy KR, et al. (2011) Telaprevir for Previously Untreated Chronic Hepatitis C Virus Infection. New England Journal of Medicine 364: 2405–2416.
8. Zeuzem S, Andreone P, Pol S, Lawitz E, Diago M, et al. (2011) Telaprevir for Retreatment of HCV Infection. New England Journal of Medicine 364: 2417–2428.
9. Jiang M, Mani N, Lin C, Ardzinski A, Nelson M, et al. (2013) In Vitro Phenotypic Characterization of Hepatitis C Virus NS3 Protease Variants Observed in Clinical Studies of Telaprevir. Antimicrob Agents Chemother AAC.01578–13.
10. Sarrazin C, Kieffer TL, Bartels D, Hanzelka B, Müh U, et al. (2007) Dynamic Hepatitis C Virus Genotypic and Phenotypic Changes in Patients Treated With the Protease Inhibitor Telaprevir. Gastroenterology 132: 1767–1777.
11. Hézode C, Forestier N, Dusheiko G, Ferenci P, Pol S, et al. (2009) Telaprevir and Peginterferon with or without Ribavirin for Chronic HCV Infection. New England Journal of Medicine 360: 1839–1850.
12. Kieffer TL, De Meyer S, Bartels DJ, Sullivan JC, Zhang EZ, et al. (2012) Hepatitis C Viral Evolution in Genotype 1 Treatment-Naïve and Treatment-Experienced Patients Receiving Telaprevir-Based Therapy in Clinical Trials. PLoS ONE 7: e34372.
13. INCIVEK (telaprevir) [US Prescribing Information] (2013)
14. Sullivan JC, De Meyer S, Bartels DL, Dierynck I, Zhang EZ, et al. (2013) Evolution of Treatment-Emergent Resistant Variants in Telaprevir Phase 3 Clinical Trials. Clinical Infectious Diseases 57: 221–229.
15. Leitner T, Halapi E, Scarlatti G, Rossi P, Albert J, et al. (1993) Analysis of heterogeneous viral populations by direct DNA sequencing. BioTechniques 15: 120–127.
16. Barnard RJO, Howe JA, Ogert RA, Zeuzem S, Poordad F, et al. (2013) Analysis of boceprevir resistance associated amino acid variants (RAVs) in two phase 3 boceprevir clinical studies. Virology 444: 329–336.
17. Hernandez D, Zhou N, Ueland J, Monikowski A, McPhee F, (2013) Natural prevalence of NS5A polymorphisms in subjects infected with hepatitis C virus genotype 3 and their effects on the antiviral activity of NS5A inhibitors. Journal of Clinical Virology 57: 13–18.
18. Bartels DJ, Sullivan JC, Zhang EZ, Tigges AM, Dorrian JL, et al. (2013) Hepatitis C Virus Variants with Decreased Sensitivity to Direct-Acting Antivirals (DAAs) Were Rarely Observed in DAA-Naive Patients prior to Treatment. J Virol 87: 1544–1553.
19. Dierynck I, De Meyer S, Thys K, Ghys A, Sullivan J, et al. (2012) Deep Sequencing of the HCV NS3/4A Region Confirms Low Prevalence of Telaprevir-resistant Variants Both at Baseline and End of Study. Presented at the 63rd Annual Meeting of the American Association for the Study of Liver Diseases. Boston, MA.
20. Adiwijaya BS, Herrmann E, Hare B, Kieffer T, Lin C, et al. (2010) A Multi-Variant, Viral Dynamic Model of Genotype 1 HCV to Assess the in vivo Evolution of Protease-Inhibitor Resistant Variants. PLoS Comput Biol 6: e1000745.
21. Adiwijaya BS, Kieffer TL, Henshaw J, Eisenhauer K, Kimko H, et al. (2012) A Viral Dynamic Model for Treatment Regimens with Direct-acting Antivirals for Chronic Hepatitis C Infection. PLoS Comput Biol 8: e1002339.
22. Rong L, Dahari H, Ribeiro RM, Perelson AS, (2010) Rapid Emergence of Protease Inhibitor Resistance in Hepatitis C Virus. Sci Transl Med 2: 30ra32–30ra32.
23. Ganusov VV, Neher RA, Perelson AS, (2013) Mathematical modeling of escape of HIV from cytotoxic T lymphocyte responses. J Stat Mech 2013: P01010.
24. Sherman KE, Flamm SL, Afdhal NH, Nelson DR, Sulkowski MS, et al. (2011) Response-Guided Telaprevir Combination Treatment for Hepatitis C Virus Infection. New England Journal of Medicine 365: 1014–1024.
25. Kwong AD-Y, Frantz JD, Bartels DJ, Lin C, Shames B, et al. (2010) Methods for amplifying hepatitis C virus nucleic acids. Patent WO/20120/090857. Vertex Pharmaceuticals, Inc. (assignee), Boston, MA.
26. Mayne DQ, Rawlings JB, Rao CV, Scokaert POM, (2000) Constrained model predictive control: Stability and optimality. Automatica 36: 789–814.