Design considerations in building in silico equivalents of common experimental influenza virus assays

Autoimmunity

Volumn 44, Issue 4, 2011, Pages 282-293

  Holder, Benjamin P ^a   Liao, Laura E ^a   Simon, Philippe ^b   Boivin, Guy ^b   Beauchemin, Catherine A A ^a,c  

^a RYERSON UNIVERSITY   (Canada)

^b LAVAL UNIVERSITY   (Canada)

^c NONE   (Canada)

Author keywords

agent based models; in vitro methods; Influenza; mathematical modeling; viral plaque

Indexed keywords

OSELTAMIVIR;

ANTIVIRAL RESISTANCE; ARTICLE; CELL DEATH; COMPUTER MODEL; EXPERIMENTATION; HUMAN; IN VITRO STUDY; INFLUENZA; INFLUENZA VIRUS A H1N1; MATHEMATICAL MODEL; NONHUMAN; PROCESS DESIGN; TARGET CELL; THEORETICAL MODEL; VIROGENESIS; VIRUS CELL INTERACTION; VIRUS PLAQUE;

ANIMALS; ANTIVIRAL AGENTS; COMPUTER SIMULATION; HUMANS; MODELS, BIOLOGICAL; ORTHOMYXOVIRIDAE; ORTHOMYXOVIRIDAE INFECTIONS; PLAQUE ASSAY;

EID: 79952551697     PISSN: 08916934     EISSN: 1607842X     Source Type: Journal    
DOI: 10.3109/08916934.2011.523267     Document Type: Article

References (35)

1. Carrat F, Vergu E, Ferguson NM, Lemaitre M, Cauchemez S, Leach S, Valleron AJ. Time lines of infection and disease in human influenza: A review of volunteer challenge studies. AmJ Epidemiol 2008;167:775-785. (Pubitemid 351451744)
2. Baz M, Abed Y, Simon P, Hamelin M, Boivin G. Effect of the neuraminidase mutation H274Y conferring resistance to oseltamivir on the replicative capacity and virulence of old and recent human influenza A(H1N1) viruses. J Infect Dis 2010;201:740-745.
3. Yen HL, Herlocher LM, Hoffmann E, Matrosovich MN, Monto AS, Webster RG, Govorkova EA. Neuraminidase inhibitor-resistant influenza viruses may differ substantially in fitness and transmissibility. Antimicrob Agents Chemother 2005;49:4075-4084. (Pubitemid 41400949)
4. Matrosovich MN, Matrosovich T, Carr J, Roberts NA, Klenk HD. Overexpression of the a-2,6-Sialyltransferase in MDCK cells increases influenza virus sensitivity to neuraminidase inhibitors. J Virol 2003;77:8418-8425. (Pubitemid 36871470)
5. Hatakeyama S, Sakai-Tagawa Y, Kiso M, Goto H, Kawakami C, Mitamura K, Sugaya N, Suzuki Y, Kawaoka Y. Enhanced expression of an a-2,6-linked sialic acid on MDCK cells improves isolation of human influenza viruses and evaluation of their sensitivity to a neuraminidase inhibitor. J Clin Microbiol 2005;43:4139-4146. (Pubitemid 41129710)
6. Tisdale M. Monitoring of viral susceptibility: New challenges with the development of influenza NA inhibitors. Rev Med Virol 2000;10:45-55. (Pubitemid 30103133)
7. Beauchemin C, McSharry J, Drusano G, Nguyen J, Went G, Ribeiro R, Perelson A. Modeling amantadine treatment of influenza A virus in vitro. J Theor Biol 2008;254:439-451.
8. Dahari H, Ribeiro R, Rice C, Perelson A. Mathematical modeling of subgenomic hepatitis C virus replication in Huh-7 cells. J Virol 2007;81:750-760. (Pubitemid 46067901)
9. Möhler L, Flockerzi D, Sann H, Reichl U. Mathematical model of influenza A virus production in large-scale microcarrier culture. Biotechnol Bioeng 2005;90:46-58. (Pubitemid 40547038)
10. Baccam P, Beauchemin C, Macken C, Hayden F, Perelson A. Kinetics of influenza A virus infection in humans. J Virol 2006; 80:7590-7599. (Pubitemid 44092580)
11. Kermack W, McKendrick A. Contributions to the mathematical theory of epidemics, Part I. Proc R Soc Lond Ser A 1927; 115:700-721.
12. Anderson R, May R. Population biology of infectious diseases: Part I. Nature 1979;280:361-367.
13. Anderson R, May R. Population biology of infectious diseases: Part II. Nature 1979;280:455-461. (Pubitemid 9234555)
14. Nowak M, May R, Anderson R. The evolutionary dynamics of HIV-1 quasispecies and the development of immunodeficiencydisease. AIDS 1990;4:1095-1103.
15. + T cells. Math Biosci 1993;114:81-125.
16. Nowak M, Bonhoeffer S, Hill A, Bohme R, Thomas H, McDade H. Viral dynamics in hepatitis B infection. Proc Natl Acad Sci USA 1996;93:4398-4404.
17. Hethcote H, Tudor D. Integral equation models for endemic infectious diseases. J Math Biol 1980;9:37-47. (Pubitemid 10116366)
18. Handel A, Longini I, Antia R. Neuraminidase inhibitor resistance in influenza: Assessing the danger of its generation and spread. PLoS Comput Biol 2007;3:2456-2464.
19. Handel A, Longini I, Antia R. Towards a quantitative understanding of the within-host dynamics of influenza A infections. J R Soc Interface 2010;7:35-47.
20. Dulbecco R, Vogt M. Plaque formation and isolation of pure lines with poliomyelitis viruses. J Exp Med 1954;99:167-182.
21. Hahon N, Booth J, Eckert H. Cell attachment and penetration by influenza virus. Infect Immun 1973;7:341-351.
22. Smith A, Adler F, Perelson A. An accurate two-phase approximate solution to an acute viral infection model. J Math Biol 2010;60:711-726.
23. Hale B, Knebel A, Botting C, Galloway C, Precious B, Jackson D, Elliott R, Randall R. CDK/ERK-mediated phosphorylation of the human influenza A virus NS1 protein at threonine-215. Virology 2009;383:6-11.
24. Beauchemin C, Forrest S, Koster F. Modeling influenza viral dynamics in tissue. Lect Notes Comput Sci 2006;4163:23.
25. Holder BP, Simon P, Liao LE, Abed Y, Bouhy X, Beauchemin CAA, Boivin G. Assessing fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model 2010, Submitted.
26. Lloyd AL. Dependence of viral parameter estimates on the assumed viral life cycle: Limitations of studies of viral load data. Proc R Soc Lond B Biol Sci 2001;268:847-854. (Pubitemid 32391654)
27. Mittler JE, Sulzer B, Neumann AU, Perelson AS. Influence of delayed viral production on viral dynamics in HIV-1 infected patients. Math Biosci 1998;152:143-163. (Pubitemid 28450733)
28. Grossman Z, Feinberg M, Kuznetsov V, Dimitrov D, Paul W. HIV infection: How effective is drug combination treatment? Immunol Today 1998;19:528-532. (Pubitemid 28518033)
29. Banks H, Bortz DM, Holte SE. Incorporation of variability into the modeling of viral delays in HIV infection dynamics. Math Biosci 2003;183:63-91. (Pubitemid 36343663)
30. Wearing HJ, Rohani P, Keeling MJ. Appropriate models for the management of infectious diseases. PLoS Med 2005;2: 621-627.
31. Feng Z, Xu D, Zhao H. Epidemiological models with non-exponentially distributed disease stages and applications to disease control. Bull Math Biol 2007;69:1511-1536. (Pubitemid 46955665)
32. Beauchemin C. Probing the effects of the well-mixed assumption on viral infection dynamics. J Theor Biol 2006; 242:464-477. (Pubitemid 44232822)
33. Monto A, McKimm-Breschkin J, Macken C, Hampson A, Hay A, Klimov A, Tashiro M, Webster R, Aymard M, Hayden F, Zambon M. Detection of influenza viruses resistant to neuraminidase inhibitors in global surveillance during the first 3 years of their use. Antimicrob Agents Chemother 2006; 50:2395-2402. (Pubitemid 43993177)
34. Matrosovich M, Matrosovich T, Garten W, Klenk H. New low-viscosity overlay medium for viral plaque assays. Virol J 2006;3:63.
35. Beauchemin CA. MASyV: A Multi-Agent System Visualization package. Free open-source GNU GPL software available online on SourceForge.net 2007.