Unifying the Epidemiological and Evolutionary Dynamics of Pathogens

Science

Volumn 303, Issue 5656, 2004, Pages 327-332

  Grenfell, Bryan T ^a   Pybus, Oliver G ^b   Gog, Julia R ^a   Wood, James L N ^c   Daly, Janet M ^c   Mumford, Jenny A ^c   Holmes, Edward C ^b  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c ANIMAL HEALTH TRUST   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIOSYNTHESIS; DISEASES; GENES; IMMUNOLOGY; RNA; VIRUSES;

INFECTIOUS DISEASES; PATHOGENS;

EPIDEMIOLOGY;

DISEASE; DISEASE TRANSMISSION; EPIDEMIOLOGY; EVOLUTION; GENETIC VARIATION; PATHOGEN;

BACTERIAL TRANSMISSION; DISEASE TRANSMISSION; EVOLUTION; GENETIC VARIABILITY; IMMUNITY; INFECTION; MOLECULAR DYNAMICS; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; REVIEW; RNA VIRUS;

ADAPTATION, PHYSIOLOGICAL; ANIMALS; ANTIGENIC VARIATION; DISEASE OUTBREAKS; EVOLUTION; GENETICS, POPULATION; HUMANS; IMMUNITY; MUTATION; PHYLOGENY; POPULATION DYNAMICS; RNA VIRUS INFECTIONS; RNA VIRUSES; SELECTION (GENETICS); TIME FACTORS; VACCINATION;

BACTERIA (MICROORGANISMS); RNA VIRUSES; VERTEBRATA;

EID: 0346373759     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.1090727     Document Type: Review

References (47)

1. R. M. Anderson, R. M. May, Infectious Diseases of Humans: Dynamics and Control (Oxford Univ. Press, 1991).
2. B. T. Grenfell, A. P. Dobson, Eds., Ecology of Infectious Diseases in Natural Populations (Cambridge Univ. Press, Cambridge, 1995).
3. V. Andreasen, J. Lin, S. A. Levin, J. Math. Biol. 35, 82S (1997).
4. S. Gupta et al., Nature Med. 2, 437 (1996).
5. N. M. Ferguson, A. P. Galvani, R. M. Bush, Nature 422, 428 (2003).
6. J. R. Gog, B. T. Grenfell, Proc. Natl. Acad. Sci. U.S.A. 99, 17209 (2002).
7. B. T. Grenfell, O. N. Bjørnstad, J. Kappey, Nature 414, 716 (2001).
8. B. T. Grenfell, O. N. Bjørnstad, B. F. Finkenstädt, Ecol. Monogr. 72, 185 (2002).
9. R. M. Bush, C. A. Bender, K. Subbarao, N. J. Cox, W. M. Fitch, Science 286, 1921 (1999).
10. J. M. Daly et al., J. Gen. Virol. 77, 661 (1996).
11. K. G. Nicholson, R. G. Webster, A. J. Hay, Eds., Textbook of Influenza (Blackwell, Oxford, 1998).
12. D. T. Haydon, A. D. Bastos, N. J. Knowles, A. R. Samuel, Genetics 157, 7 (2001).
13. M. A. Nowak, R. M. May, Proc. R. Soc. Lond. B. Biol. Sci. 255, 81 (1994).
14. P. Rohani, C. J. Green, N. B. Mantilla-Beniers, B. T. Grenfell, Nature 422, 885 (2003).
15. E. C. Holmes, S. S. Twiddy, Infect. Genet. Evol. 3, 19 (2003).
16. S. Gupta, N. Ferguson, R. Anderson, Science 280, 912 (1998).
17. N. Ferguson, R. Anderson, S. Gupta, Proc. Natl. Acad. Sci. U.S.A. 96, 790 (1999).
18. L. Heyndrickx et al., J. Virol. 74, 363 (2000).
19. P. Simmonds, Hepatology 21, 570 (1995).
20. C. B. Moore et al., Science 296, 1439 (2002).
21. P. Farci et al., Science 288, 339 (2000).
22. S. C. Ray et al., J. Virol. 73, 2938 (1999).
23. Y. Yamaguchi-Kabata, T. Gojobori, J. Virol. 74, 4335 (2000).
24. A. S. Perelson, A. U. Neumann, M. Markowitz, J. M. Leonard, D. D. Ho, Science 271, 1582 (1996).
25. E. C. Holmes, L. Q. Zhang, P. Simmonds, C. A. Ludlam, A. J. L. Brown, Proc. Natl. Acad. Sci. U.S.A. 89, 4835 (1992).
26. R. Shankarappa et al., J. Virol. 73, 10489 (1999).
27. M. A. Nowak, R. M. May, Virus Dynamics: The Mathematical Foundations of Virology and Immunology (Oxford Univ. Press, Oxford, 2000).
28. J. A. Mumford, T. M. Chambers, in (11), pp. 146-162.
29. a is large. This simple model ignores many factors, such as varying population size, clonal interference, and epistatic interactions.
30. G. Rossi et al., Blood 90, 1309 (1997).
31. S. M. Wolinsky et al., Science 272, 537 (1996).
32. M. A. Rey-Cuille et al., J. Virol. 72, 3872 (1998).
33. S. Williamson, Mol. Biol. Evol. 20, 1318 (2003).
34. x N(t)I(t) Figure 2B was constructed using this equation. EIP(x) represents the average amount of viral adaptation transmitted to a susceptible contacted at time x after initial infection. N(t) and I(t) in Fig. 2B were obtained with a standard susceptible-infected-recovered-type model, with a time delay between viral appearance and the onset of the immune response. This initial model is simplistic; future refinements will require more realistic relationships between viral load, infectivity, the immune response, and the distribution of selection coefficients.
35. J. A. Mumford, D. Hannant, D. M. Jessett, Equine Vet. J. 22, 93 (1990).
36. J. R. Gog, G. F. Rimmelzwaan, A. D. M. E. Osterhaus, B. T. Grenfell, Proc. Natl. Acad. Sci. U.S.A. 100, 11143 (2003).
37. R. Miralles, P. J. Gerrish, A. Moya, S. F. Elena, Science 285, 1745 (1999).
38. O. G. Pybus, A. Rambaut, P. H. Harvey, Genetics 155, 1429 (2000).
39. O. G. Pybus et al., Science 292, 2323 (2001).
40. 1 will be small. Nφ is the shape of the black adaptation rate curve in Fig. 2A.
41. A. P. Galvani, Trends Ecol. Evol. 18, 132 (2003).
42. D. J. Smith, S. Forrest, R. R. Hightower, A. S. Perelson, J. Theor. Biol. 189, 141 (1997).
43. M. Kimura, Genetics 47, 713 (1962).
44. INSERM, Situation Epidémiologique, available at http://rhone.b3e.jussieu.fr/senti/php/navigation/accueil/.
45. Public Health Laboratory Service, AIDS and STD Centre, www.hpa.org.uk (cited 25 August 2003).
46. D. L. Swofford, PAUP* [Phylogenetic Analysis Using Parsimony (*and Other Methods)], Version 4, Sinauer Associates, Sunderland, MA (2002).
47. Supported by The Wellcome Trust (B.G. and O.G.P.); the UK Biology and Biotechnology Research Council (B.G. and J.D.); Queens' College, Cambridge (J.R.G.); and the UK Horserace Betting Levy Board (J.L.N.W., J.D., and J.A.M.).