Influenza A gradual and epochal evolution: Insights from simple models

PLoS ONE

Volumn 4, Issue 10, 2009, Pages

  Ballesteros, Sébastien ^a   Vergu, Elisabeta ^b   Cazelles, Bernard ^a,c  

^a ECOLE NORMALE SUPÉRIEURE   (France)

^b UR341 National Agronomical Research Institute (INRA)   (France)

^c Sorbonne Universités   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIGENICITY; ARTICLE; CLUSTER ANALYSIS; CONCEPTUAL FRAMEWORK; CONTROLLED STUDY; GENETIC DRIFT; HISTORY BASED MODEL WITH REDUCED INFECTIVITY; HISTORY BASED MODEL WITH REDUCED SUSCEPTABILITY; IMMUNITY; INFLUENZA VIRUS A; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MOLECULAR EVOLUTION; STATUS BASED MODEL WITH REDUCED INFECTIVITY; STATUS BASED MODEL WITH REDUCED SUSCEPTABILITY; STOCHASTIC MODEL; VIRUS INFECTION; BIOLOGICAL MODEL; GENETICS; HUMAN; IMMUNE SYSTEM; IMMUNOLOGY; INFLUENZA; MULTIGENE FAMILY; MUTATION; STATISTICS; THEORETICAL MODEL; VIROLOGY;

ANTIGEN;

ANTIGENS; EVOLUTION, MOLECULAR; GENETIC DRIFT; HUMANS; IMMUNE SYSTEM; INFLUENZA A VIRUS; INFLUENZA, HUMAN; MODELS, IMMUNOLOGICAL; MODELS, THEORETICAL; MULTIGENE FAMILY; MUTATION; STOCHASTIC PROCESSES;

EID: 70449397091     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0007426     Document Type: Article

References (65)

1. Nelson MI, Holmes EC (2007) The evolution of epidemic influenza. Nat Rev Genet 8: 196-205.
2. WHO (2003) Fact sheet number 211. influenza. WHO Fact sheets.
3. Pease CM (1987) An evolutionary epidemiological mechanism, with applications to type a influenza. Theor Popul Biol 31: 422-452.
4. Andreasen V, Lin J, Levin SA (1997) The dynamics of cocirculating influenza strains conferring partial cross-immunity. Journal of Mathematical Biology 35: 825-842.
5. Gog JR, Grenfell BT (2002) Dynamics and selection of many-strain pathogens. Proc Natl Acad Sci U S A 99: 17209-17214.
6. Smith DJ, Lapedes AS, de Jong JC, Bestebroer TM, Rimmelzwaan GF, et al. (2004) Mapping the antigenic and genetic evolution of influenza virus. Science 305: 371-376.
7. Ferguson NM, Galvani AP, Bush RM (2003) Ecological and immunological determinants of influenza evolution. Nature 422: 428-433.
8. Girvan M, Callaway DS, Newman MEJ, Strogatz SH (2002) Simple model of epidemics with pathogen mutation. Phys Rev E Stat Nonlin Soft Matter Phys 65: 031915.
9. Grenfell BT, Pybus OG, Gog JR, Wood JLN, Daly JM, et al. (2004) Unifying the epidemiological and evolutionary dynamics of pathogens. Science 303: 327-332.
10. Andreasen V, Sasaki A (2006) Shaping the phylogenetic tree of influenza by cross-immunity. Theor Popul Biol 70: 164-173.
11. Minayev P, Ferguson N (2009) Improving the realism of deterministic multistrain models: implications for modelling influenza A. J R Soc Interface 6: 509-518.
12. Webster RG, Bean WJ, Gorman OT, Chambers TM, Kawaoka Y (1992) Evolution and ecology of influenza A viruses. Microbiol Rev 56: 152-179.
13. Tria F, M Lässig LP, Franz S (2005) A minimal stochastic model for influenza evolution. Journal of Statistical Mechanics: Theory and Experiment 2005: P07008.
14. Koelle K, Cobey S, Grenfell B, Pascual M (2006) Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans. Science 314: 1898-1903.
15. Blackburne BP, Hay AJ, Goldstein RA (2008) Changing selective pressure during antigenic changes in human influenza H3. PLoS Pathog 4: e1000058.
16. Wolf YI, Viboud C, Holmes EC, Koonin EV, Lipman DJ (2006) Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus. Biol Direct 1: 34.
17. Dawes JHP, Gog JR (2002) The onset of oscillatory dynamics in models of multiple disease strains. J Math Biol 45: 471-510.
18. Dieckmann U, Metz J, Sabelis M, Sigmund K (2002) Adaptive Dynamics of Infectious Diseases: In Pursuit of Virulence Management. Cambridge University Press.
19. Du X, Wang Z, Wu A, Song L, Cao Y, et al. (2008) Networks of genomic co-occurrence capture characteristics of human influenza A (H3N2) evolution. Genome Res 18: 178-187.
20. Gog JR, Swinton J (2002) A status-based approach to multiple strain dynamics. J Math Biol 44: 169-184.
21. Kryazhimskiy S, Dieckmann U, Levin SA, Dushoff J (2007) On state-space reduction in multi-strain pathogen models, with an application to antigenic drift in influenza A. PLoS Comput Biol 3: e159.
22. Gog JR (2008) The impact of evolutionary constraints on influenza dynamics. Vaccine 26 Suppl 3: C15-C24.
23. Kamo M, Sasaki A (2002) The effect of cross-immunity and seasonal forcing in a multi-strain epidemic model. pyhysica D 165: 228-241.
24. Gupta S, Ferguson N, Anderson R (1998) Chaos, persistence, and evolution of strain structure in antigenically diverse infectious agents. Science 280: 912-915.
25. Minayev P, Ferguson N (2009) Incorporating demographic stochasticity into multi-strain epidemic models: application to influenza A. J R Soc Interface.
26. Gillespie DT (1977) Exact stochastic simulation of coupled chemical reactions. The Journal of Physical Chemistry 81: 2340-2361.
27. Galassi M, Davies J, Theiler J, Gough B, Jungman G, et al. (2003) Gnu Scientific Library: Reference Manual. Network Theory Ltd.
28. Gökaydin D, Oliveira-Martins JB, Gordo I, Gomes MGM (2007) The reinfection threshold regulates pathogen diversity: the case of influenza. J R Soc Interface 4: 137-142.
29. Cauchemez S, Carrat F, Viboud C, Valleron AJ, Boëlle PY (2004) A bayesian mcmc approach to study transmission of influenza: application to household longitudinal data. Stat Med 23: 3469-3487.
30. Lavenu A, Valleron AJ, Carrat F (2004) Exploring cross-protection between influenza strains by an epidemiological model. Virus Res 103: 101-105.
31. Ferguson NM, Cummings DAT, Cauchemez S, Fraser C, Riley S, et al. (2005) Strategies for containing an emerging influenza pandemic in southeast asia. Nature 437: 209-214.
32. Bartlett MS (1957) Measles periodicity and community size. Journal of the Royal Statistical Society Series A (General) 120: 48-70.
33. Bartlett MS (1960) The critical community size for measles in the united states. Journal of the Royal Statistical Society Series A (General) 123: 37-44.
34. Bartlett MS (1964) The relevance of stochastic models for large-scale epidemiological phenomena. Applied Statistics 13: 2-8.
35. Keeling MJ, Grenfell BT (1997) Disease extinction and community size: modeling the persistence of measles. Science 275: 65-67.
36. Nåsell I (2005) A new look at the critical community size for childhood infections. Theor Popul Biol 67: 203-216.
37. Lloyd-Smith JO, Cross PC, Briggs CJ, Daugherty M, Getz WM, et al. (2005) Should we expect population thresholds for wildlife disease? Trends in Ecology & Evolution 20: 511-519.
38. Conlan AJK, Grenfell BT (2007) Seasonality and the persistence and invasion of measles. Proc Biol Sci 274: 1133-1141.
39. Diekmann O, Heesterbeek J (2000) Mathematical Epidemiology of Infectious Diseases: model building, analysis and interpretation. John Wiley and Sons, Chichester.
40. Keeling M (2000) Evolutionary trade-offs at two time-scales: competition versus persistence. Proc Biol Sci 267: 385-391.
41. Olinky R, Huppert A, Stone L (2008) Seasonal dynamics and thresholds governing recurrent epidemics. Journal of Mathematical Biology 56: 827-839.
42. Bjornstad ON, Finkenstadt BF, Grenfell BT (2002) Dynamics of measles epidemics: Estimating scaling of transmission rates using a time series sir model. Ecological Monographs 72: 169-184.
43. Keeling MJ, Grenfell BT (2002) Understanding the persistence of measles: reconciling theory, simulation and observation. Proc Biol Sci 269: 335-343.
44. Cobey S, Koelle K (2008) Capturing escape in infectious disease dynamics. Trends Ecol Evol 23: 572-577.
45. Rambaut A, Pybus OG, Nelson MI, Viboud C, Taubenberger JK, et al. (2008) The genomic and epidemiological dynamics of human influenza A virus. Nature 453: 615-619.
46. Frank SA (2002) Immunology and evolution of infectious disease. Princeton University Press.
47. Francis T (1953) Influenza: the new acquayantance. Ann Intern Med 39: 203-221.
48. de St Groth F, Webster RG (1966) Disquisitions of original antigenic sin. i. evidence in man. J Exp Med 124: 331-345.
49. Janeway C, Travers P, Walport M, Capra J (1999) Immunobiology. The immune system in health and disease. 4th Edition. Current Biology Ltd./ Garland Publishing Inc. Churchill Livingstone.
50. Gomes MGM, White LJ, Medley GF (2004) Infection, reinfection, and vaccination under suboptimal immune protection: epidemiological perspectives. J Theor Biol 228: 539-549.
51. Gomes MGM, White LJ, Medley GF (2005) The reinfection threshold. J Theor Biol 236: 111-113.
52. Finkenstädt BF, Morton A, Rand DA (2005) Modelling antigenic drift in weekly flu incidence. Stat Med 24: 3447-3461.
53. Shih ACC, Hsiao TC, Ho MS, Li WH (2007) Simultaneous amino acid substitutions at antigenic sites drive influenza A hemagglutinin evolution. Proc Natl Acad Sci U S A 104: 6283-6288.
54. Suzuki Y (2008) Positive selection operates continuously on hemagglutinin during evolution of H3N2 human influenza A virus. Gene 427: 111-116.
55. Wagner R, Matrosovich M, Klenk HD (2002) Functional balance between haemagglutinin and neuraminidase in influenza virus infections. Rev Med Virol 12: 159-166.
56. Earn DJ, Rohani P, Bolker BM, Grenfell BT (2000) A simple model for complex dynamical transitions in epidemics. Science 287: 667-670.
57. Mathews JD, McCaw CT, McVernon J, McBryde ES, McCaw JM (2007) A biological model for influenza transmission: Pandemic planning implications of asymptomatic infection and immunity. PLoS ONE 2: e1220.
58. Recker M, Pybus OG, Nee S, Gupta S (2007) The generation of influenza outbreaks by a network of host immune responses against a limited set of antigenic types. Proc Natl Acad Sci U S A 104: 7711-7716.
59. Francis J Thomas (1960) On the doctrine of original antigenic sin. Proceedings of the American Philosophical Society 104: 572-578.
60. Alonso WJ, Viboud C, Simonsen L, Hirano EW, Daufenbach LZ, et al. (2007) Seasonality of influenza in brazil: a traveling wave from the amazon to the subtropics. Am J Epidemiol 165: 1434-1442.
61. Nelson MI, Simonsen L, Viboud C, Miller MA, Holmes EC (2007) Phylogenetic analysis reveals the global migration of seasonal influenza A viruses. PLoS Pathog 3: 1220-1228.
62. Holmes EC, Ghedin E, Miller N, Taylor J, Bao Y, et al. (2005) Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol 3: e300.
63. Nelson MI, Simonsen L, Viboud C, Miller MA, Taylor J, et al. (2006) Stochastic processes are key determinants of short-term evolution in influenza A virus. PLoS Pathog 2: e125.
64. Viboud C, Alonso WJ, Simonsen L (2006) Influenza in tropical regions. PLoS Med 3: e89.
65. Russell CA, Jones TC, Barr IG, Cox NJ, Garten RJ, et al. (2008) The global circulation of seasonal influenza A (H3N2) viruses. Science 320: 340-346.