Understanding the dynamics of rapidly evolving pathogens through modeling the tempo of antigenic change: Influenza as a case study

Epidemics

Volumn 1, Issue 2, 2009, Pages 129-137

  Koelle, Katia ^a,b,c   Kamradt, Meredith ^a   Pascual, Mercedes ^c,d  

^a DUKE UNIVERSITY   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

^c UNIVERSITY OF MICHIGAN   (United States)

^d HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

Multi strain model; Rapid evolution; RNA virus

Indexed keywords

ARTICLE; DYNAMICS; EVOLUTION; INFLUENZA; MODEL; PRIORITY JOURNAL; SIMULATION;

ANTIGENIC VARIATION; ANTIGENS, VIRAL; BIOLOGICAL EVOLUTION; CLUSTER ANALYSIS; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; HUMANS; INFLUENZA A VIRUS, H3N2 SUBTYPE; INFLUENZA, HUMAN; MODELS, BIOLOGICAL; STOCHASTIC PROCESSES;

EID: 67649432813     PISSN: 17554365     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.epidem.2009.05.003     Document Type: Article

References (33)

1. Andreasen V., Lin J., and Levin S. The dynamics of cocirculating influenza strains conferring partial cross-immunity. J. Math. Biol. 35 (1997) 825-842
2. Boni M.F., Gog J.R., Andreasen V., and Feldman M. Epidemic dynamics and antigenic evolution in a single season of influenza A. Proc. R. Soc. Lond. B 273 (2006) 1307-1316
3. Cazelles B., Chavez M., McMichael A.J., and Hales S. Nonstationary influence of El Niño on the synchronous dengue epidemics in Thailand. PLoS Medicine 2 (2005) e106
4. Cobey S., and Koelle K. Capturing escape in infectious disease dynamics. Trends Ecol. Evol. 23 (2008) 572-577
5. Cox N.J., and Bender C.A. The molecular epidemiology of influenza viruses. Semin. Virol. 6 (1995) 359-370
6. Cox N.J., and Subbarao K. Global epidemiology of influenza: past and present. Annu. Rev. Med. 51 (2000) 407-421
7. Dawes J.H.P., and Gog J.R. The onset of oscillatory dynamics in models of multiple disease strains. J. Math. Biol. 45 (2002) 471-510
8. Ferguson N.M., Galvani A.P., and Bush R.M. Ecological and immunological determinants of influenza evolution. Nature 422 (2003) 428-433
9. Finkelman B.S., Viboud C., Koelle K., Ferrari M.J., Bharti N., and Grenfell B.T. Global patterns in seasonal activity of influenza A/H3N2, A/H1N1, and B from 1997 to 2005: viral coexistence and latitudinal gradients. PLoS One 12 e1296 (2007) 1-10
10. Finkenstädt B., and Grenfell B. Time series modelling of childhood diseases: a dynamical systems approach. J. R. Stat. Soc., Ser. C, Appl. Stat. 49 (2000) 187-205
11. Girvan M., Callaway D.S., Newman M.E.J., and Strogatz S.H. Simple model of epidemics with pathogen mutation. Phys. Rev. E 65 (2002) 1-9
12. Gog J.R., and Grenfell B.T. Dynamics and selection of many-strain pathogens. Proc. Natl. Acad. Sci. 99 (2002) 17209-17214
13. Gökaydin D., Oliveira-Martins J.B., Gordo I., and Gomes G.M. The reinfection threshold regulates pathogen diversity: the case of influenza. J. R. Soc. Interface 4 (2007) 137-142
14. Greene S.K., Ionides E.L., and Wilson M.L. Patterns of influenza-associated mortality among US elderly by geographic region and virus subtype, 1968-1998. Am. J. Epidemiol. 163 (2006) 316-326
15. Greene S.K., Koopman J.S., and Wilson M.L. Modeling the influence of climate variability on influenza A epidemic patterns. In: Kawaoka Y. (Ed). Proceedings of the International Conference on Options for the Control of Influenza V (2004) 795-798
16. Grenfell B.T., Pybus O.G., Gog J.R., Wood J.L.N., Daly J.M., Mumford J.A., and Holmes E.C. Unifying the epidemiological and evolutionary dynamics of pathogens. Science 303 (2004) 327-332
17. Kepler T.B., and Perelson A.S. Modeling and optimization of populations subject to time-dependent mutation. PNAS 92 (1995) 8219-8223
18. Koelle K., Cobey S., Grenfell B.T., and Pascual M. Epochal evolution shapes the phylodynamics of influenza A (H3N2) in humans. Science 314 (2006) 1898-1903
19. Kryazhimskiy S., Dieckmann U., Levin S.A., and Dushoff J. On state-space reduction in multi-strain pathogen models, with an application to antigenic drift in influenza A. PLoS Computational Biology 3 (2007) e159
20. Lindesmith L.C., Donaldson E.F., LoBue A.D., Cannon J.L., Zheng D., Vinje J., and Baric R.S. Mechanisms of GII.4 norovirus persistence in human populations. PLoS Med. 5 (2008) 269-290
21. Pease C.M. An evolutionary epidemiological mechanism, with applications to type A influenza. Theor. Popul. Biol. 31 (1987) 422-452
22. Plotkin J.B., Dushoff J., and Levin S.A. Hemagglutinin sequence clusters and the antigenic evolution of influenza A virus. PNAS 99 (2002) 6263-6268
23. Rambaut A., Pybus O.G., Nelson M.I., Viboud C., Taubenberger J.K., and Holmes E.C. The genomic and epidemiological dynamics of human influenza A virus. Nature 453 (2008) 615-620
24. Rohani P., Keeling M.J., and Grenfell B.T. The interplay between determinism and stochasticity in childhood diseases. Am. Nat. 159 (2002) 469-481
25. Russell C.A., Jones T.C., Barr I.G., Cox N.J., Garten R.J., Gregory V., Gust I.D., Hampson A.W., Hay A.J., Hurt A.C., de Jong J.C., Kelso A., Klimov A.I., Kageyama T., Komadina N., Lapedes A.S., Lin Y.P., Mosterin A., Obuchi M., Odagiri T., Osterhaus A.D.M.E., Rimmelzwaan G.F., Shaw M.W., Skepner E., Stohr K., Tashiro M., Fouchier R.A.M., and Smith D.J. The global circulation of seasonal influenza A (H3N2) viruses. Science 320 (2008) 340-346
26. Schuster P., Fontana W., Stadler P.F., and Hofacker I.L. From sequences to shapes and back: a case study in RNA secondary structures. Proc. R. Soc. Lond. B 255 (1994) 279-284
27. Shioda T., Oka S., Ida S., Nokihara K., Toriyoshi H., Mori S., Takebe Y., Kimura S., Shimada K., and Nagai Y. A naturally occurring single basic amino acid substitution in the V3 region of the human immunodeficiency virus type 1 env protein alters the cellular host range and antigenic structure of the virus. J. Virol. 68 (1994) 7689-7696
28. Siebenga J.J., Vennema H., Renckens B., de Bruin E., van der Veer B., Siezen R.J., and Koopmans M. Epochal evolution of GGII.4 norovirus capsid proteins from 1995 to 2006. J. Virol. 81 (2007) 9932-9941
29. Smith D.J., Lapedes A.S., de Jong J.C., Bestebroer T.M., Rimmelzwaan G.F., Osterhaus A.D.M., and Fouchier R.A.M. Mapping the antigenic and genetic evolution of influenza virus. Science 305 (2004) 371-376
30. Tria F., Lässig M., Peliti L., and Franz S. A minimal stochastic model for influenza evolution. J. Stat. Mech. P07008 (2005) 1-11
31. van Nimwegen E. Influenza escapes immunity along neutral networks. Science 314 (2006) 1884-1886
32. Viboud C., Pakdaman K., Boelle P., Wilson M.L., Myers M.F., Valleron A., and Flahault A. Association of influenza epidemics with global climate variability. Eur. J. Epidemiol. 19 (2004) 1055-1059
33. Wolfs T.F.W., Zwart G., Bakker M., Valk M., Kuiken C.L., and Goudsmit J. Naturally occurring mutations within HIV-1 V3 genomic RNA lead to antigenic variation dependent on a single amino acid substitution. Virology 185 (1991) 195-205