Canalization of the evolutionary trajectory of the human influenza virus

BMC Biology

Volumn 10, Issue , 2012, Pages

  Bedford, Trevor ^a,b   Rambaut, Andrew ^b,c   Pascual, Mercedes ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HUMAN INFLUENZA VIRUS; ORTHOMYXOVIRIDAE;

VIRUS ANTIGEN;

ANTIGENIC VARIATION; ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; EVOLUTION; GENETICS; HUMAN; IMMUNOLOGY; INFLUENZA; INFLUENZA VIRUS A H3N2; MOLECULAR EVOLUTION; MUTATION; PHENOTYPE; VIROLOGY;

ANTIGENIC VARIATION; ANTIGENS, VIRAL; BIOLOGICAL EVOLUTION; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; HUMANS; INFLUENZA A VIRUS, H3N2 SUBTYPE; INFLUENZA, HUMAN; MODELS, BIOLOGICAL; MODELS, GENETIC; MUTATION; PHENOTYPE;

EID: 84861232312     PISSN: None     EISSN: 17417007     Source Type: Journal    
DOI: 10.1186/1741-7007-10-38     Document Type: Article

References (42)

1. WHO Influenza Fact Sheet. WHO., http://www.who.int/mediacentre/factsheets/fs211/en/
2. Nelson MI, Holmes EC. The evolution of epidemic influenza. Nat Rev Genet 2007, 8(3):196-205. 10.1038/nrg2053, 17262054.
3. Fitch WM, Bush RM, Bender CA, Cox NJ. Long term trends in the evolution of H(3) HA1 human influenza type A. Proc Natl Acad Sci USA 1997, 94(15):7712-7718. 10.1073/pnas.94.15.7712, 33681, 9223253.
4. Ferguson NM, Galvani AP, Bush RM. Ecological and immunological determinants of influenza evolution. Nature 2003, 422(6930):428-433. 10.1038/nature01509, 12660783.
5. Tria F, Lässig M, Peliti L, Franz S. A minimal stochastic model for influenza evolution. J Stat Mech 2005, doi:10.1088/1742-5468/2005/07/P07008.
6. Koelle K, Cobey S, Grenfell B, Pascual M. Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans. Science 2006, 314(5807):1898-1903. 10.1126/science.1132745, 17185596.
7. Recker M, Pybus O, Nee S, Gupta S. The generation of influenza outbreaks by a network of host immune responses against a limited set of antigenic types. Proc Natl Acad Sci USA 2007, 104(18):7711-7716. 10.1073/pnas.0702154104, 1855915, 17460037.
8. Hirst G. Studies of antigenic differences among strains of influenza A by means of red cell agglutination. J Exp Med 1943, 78(5):407-423. 10.1084/jem.78.5.407, 2135416, 19871338.
9. Smith DJ, Lapedes AS, de Jong JC, Bestebroer TM, Rimmelzwaan GF, Osterhaus ADME, Fouch-ier RAM. Mapping the antigenic and genetic evolution of influenza virus. Science 2004, 305(5682):371-376. 10.1126/science.1097211, 15218094.
10. Monto A, Sullivan K. Acute respiratory illness in the community. Frequency of illness and the agents involved. Epidemiol Infect 1993, 110(01):145-160. 10.1017/S0950268800050779, 2271959, 8432318.
11. Koelle K, Kamradt M, Pascual M. Understanding the dynamics of rapidly evolving pathogens through modeling the tempo of antigenic change: influenza as a case study. Epidemics 2009, 1(2):129-137. 10.1016/j.epidem.2009.05.003, 21352760.
12. Bedford T, Cobey S, Pascual M. Strength and temp of selection revealed in viral gene genealogies. BMC Evol Biol 2011, 11:220. 10.1186/1471-2148-11-220, 3199772, 21787390.
13. Bush R, Fitch W, Bender C, Cox N. Positive selection on the H3 hemagglutinin gene of human influenza virus A. Mol Biol Evol 1999, 16(11):1457-1465. 10.1093/oxfordjournals.molbev.a026057, 10555276.
14. Wolf YI, Viboud C, Holmes EC, Koonin EV, Lipman DJ. Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus. Biol Direct 2006, 1:34. 10.1186/1745-6150-1-34, 1647279, 17067369.
15. Park S, Krug J. Clonal interference in large populations. Proc Natl Acad Sci USA 2007, 104(46):18135-18140. 10.1073/pnas.0705778104, 2084309, 17984061.
16. Russell CA, Jones TC, Barr IG, Cox NJ, Garten RJ, Gregory V, Gust ID, Hampson AW, Hay AJ, Hurt AC, de Jong JC, Kelso A, Klimov AI, Kageyama T, Komadina N, Lapedes AS, Lin YP, Mosterin A, Obuchi M, Odagiri T, Osterhaus ADME, Rimmelzwaan GF, Shaw MW, Skepner E, Stohr K, Tashiro M, Fouchier RAM, Smith DJ. The global circulation of seasonal influenza A (H3N2) viruses. Science 2008, 320(5874):340-346. 10.1126/science.1154137, 18420927.
17. Bedford T, Cobey S, Beerli P, Pascual M. Global migration dynamics underlie evolution and persistence in human influenza A (H3N2). PLoS Pathog 2010, 6:e1000918. 10.1371/journal.ppat.1000918, 2877742, 20523898.
18. Adams B, McHardy A. The impact of seasonal and year-round transmission regimes on the evolution of influenza A virus. Proc R Soc B 2011, 278(1716):2249-2256. 10.1098/rspb.2010.2191, 21177678.
19. Koelle K, Ratmann O, Rasmussen D, Pasour V, Mattingly J. A dimensionless number for under-standing the evolutionary dynamics of antigenically variable RNA viruses. Proc R Soc Lond B Biol Sci 2011, doi: 10.1098/rspb.2011.0435.
20. Finkelman B, Viboud C, Koelle K, Ferrari M, Bharti N, Grenfell B. Global patterns in seasonal activity of influenza A/H3N2, A/H1N1, and B from 1997 to 2005: viral coexistence and latitudinal gradients. PLoS One 2007, 2(12):e1296. 10.1371/journal.pone.0001296, 2117904, 18074020.
21. Bhatt S, Holmes E, Pybus O. The genomic rate of molecular adaptation of the human influenza A virus. Mol Biol Evol 2011, doi: 10.1093/molbev/msr044.
22. Goldstein E, Cobey S, Takahashi S, Miller J, Lipsitch M. Predicting the epidemic sizes of influenza A/H1N1, A/H3N2, and B: a statistical method. PLoS Med 2011, 8(7):e1001051. 10.1371/journal.pmed.1001051, 3130020, 21750666.
23. Voeten J, Bestebroer T, Nieuwkoop N, Fouchier R, Osterhaus A, Rimmelzwaan G. Antigenic drift in the influenza A virus (H3N2) nucleoprotein and escape from recognition by cytotoxic T lymphocytes. J Virol 2000, 74(15):6800-6807. 10.1128/JVI.74.15.6800-6807.2000, 112197, 10888619.
24. O'Brien J, Minin V, Suchard M. Learning to count: robust estimates for labeled distances between molecular sequences. Mol Biol Evol 2009, 26(4):801-814. 10.1093/molbev/msp003, 2734148, 19131426.
25. Yang Z. Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A. Journal of Molecular Evolution 2000, 51(5):423-432.
26. Gould S. Wonderful Life 1989, New York: Norton.
27. Barr IG, McCauley J, Cox N, Daniels R, Engelhardt OG, Fukuda K, Grohmann G, Hay A, Kelso A, Klimov A, Odagiri T, Smith D, Russell C, Tashiro M, Webby R, Wood J, Ye Z, Zhang W, . Writing Committee of the World Health Organization Consultation on Northern Hemisphere Influenza Vaccine Composition for 2009-2010 Epidemiological, antigenic and genetic characteristics of seasonal influenza A (H1N1), A (H3N2) and B influenza viruses: basis for the WHO recommendation on the composition of influenza vaccines for use in the 2009-2010 Northern Hemisphere season. Vaccine 2010, 28(5):1156-1167. 10.1016/j.vaccine.2009.11.043, 20004635, Writing Committee of the World Health Organization Consultation on Northern Hemisphere Influenza Vaccine Composition for 2009-2010.
28. Weinreich D, Delaney N, DePristo M, Hartl D. Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 2006, 312(5770):111-114. 10.1126/science.1123539, 16601193.
29. Lin J, Andreasen V, Levin S. Dynamics of influenza A drift: the linear three-strain model. Math Biosci 1999, 162(1-2):33-51. 10.1016/S0025-5564(99)00042-5, 10616279.
30. Gog J, Grenfell B. Dynamics and selection of many-strain pathogens. Proc Natl Acad Sci USA 2002, 99(26):17209-17214. 10.1073/pnas.252512799, 139294, 12481034.
31. Kryazhimskiy S, Dieckmann U, Levin S, Dushoff J. On state-space reduction in multi-strain pathogen models, with an application to antigenic drift in influenza A. PLoS Comp Biol 2007, 3(8):e159.
32. Koelle K, Khatri P, Kamradt M, Kepler T. A two-tiered model for simulating the ecological and evolutionary dynamics of rapidly evolving viruses, with an application to influenza. J R Soc Interface 2010, 7(50):1257-1274. 10.1098/rsif.2010.0007, 2894885, 20335193.
33. Volz E, Kosakovsky Pond S, Ward M, Leigh Brown A, Frost S. Phylodynamics of infectious disease epidemics. Genetics 2009, 183(4):1421-1430. 10.1534/genetics.109.106021, 2787429, 19797047.
34. O'Dea E, Wilke C. Contact heterogeneity and phylodynamics: how contact networks shape parasite evolutionary trees. Interdiscip Perspect Infect Dis 2011, 2011:238743. 2995904, 21151699.
35. Chowell G, Miller M, Viboud C. Seasonal influenza in the United States, France, and Australia: transmission and prospects for control. Epidemiol Infect 2008, 136(06):852-864. 2680121,2680121, 17634159.
36. Viboud C, Bjørnstad O, Smith D, Simonsen L, Miller M, Grenfell B. Synchrony, waves, and spatial hierarchies in the spread of influenza. Science 2006, 312(5772):447-451. 10.1126/science.1125237, 16574822.
37. 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. Am J Epidemiol 2008, 167(7):775-785. 10.1093/aje/kwm375, 18230677.
38. Park A, Daly J, Lewis N, Smith D, Wood J, Grenfell B. Quantifying the impact of immune escape on transmission dynamics of influenza. Science 2009, 326(5953):726-728. 10.1126/science.1175980, 19900931.
39. Gupta V, Earl D, Deem M. Quantifying influenza vaccine efficacy and antigenic distance. Vaccine 2006, 24(18):3881-3888. 10.1016/j.vaccine.2006.01.010, 16460844.
40. Truscott J, Fraser C, Cauchemez S, Meeyai A, Hinsley W, Donnelly C, Ghani A, Ferguson N. Essential epidemiological mechanisms underpinning the transmission dynamics of seasonal influenza. J R Soc Interface 2011, doi: 10.1098/rsif.2011.0309.
41. Rambaut A, Pybus OG, Nelson MI, Viboud C, Taubenberger JK, Holmes EC. The genomic and epidemiological dynamics of human influenza A virus. Nature 2008, 453(7195):615-619. 10.1038/nature06945, 2441973, 18418375.
42. Kucharski A, Gog JR. Influenza emergence in the face of evolutionary constraints. Proc R Soc B 2012, 279(1729):645-652. 10.1098/rspb.2011.1168, 3248728, 21775331.