Anticipating the emergence of infectious diseases

Journal of the Royal Society Interface

Volumn 14, Issue 132, 2017, Pages

  Brett, Tobias S ^a   Drake, John M ^a   Rohani, Pejman ^a  

^a UNIVERSITY OF GEORGIA   (United States)

Author keywords

Complex systems; Early warning signals; Epidemiology; Modelling of infectious disease

Indexed keywords

DYNAMICAL SYSTEMS; EPIDEMIOLOGY; LARGE SCALE SYSTEMS; MODEL STRUCTURES; RANDOM PROCESSES; STOCHASTIC MODELS; STOCHASTIC SYSTEMS;

CRITICAL SLOWING DOWN; EARLY WARNING; INFECTIOUS DISEASE;

DISEASES;

ARTICLE; BIRTH; DEATH; EPIDEMIC; HUMAN; INFECTION; INFECTION SENSITIVITY; MARKOV CHAIN; PREDICTION; RELIABILITY; STATISTICAL MODEL; THEORETICAL MODEL; TIME; BIOLOGICAL MODEL; COMMUNICABLE DISEASE; POPULATION DYNAMICS; REPRODUCIBILITY;

COMMUNICABLE DISEASES; COMMUNICABLE DISEASES, EMERGING; DISEASE OUTBREAKS; HUMANS; LIKELIHOOD FUNCTIONS; MODELS, BIOLOGICAL; POPULATION DYNAMICS; REPRODUCIBILITY OF RESULTS; STOCHASTIC PROCESSES;

EID: 85026767663     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2017.0115     Document Type: Article

References (42)

1. Lenton TM, Held H, Kriegler E, Hall JW, Lucht W, Rahmstorf S, Schellnhuber HJ. 2008 Tipping elements in the Earth's climate system. Proc. Natl Acad. Sci. USA 105, 1786-1793. (doi:10.1073/pnas.0705414105)
2. Scheffer M, Carpenter SR. 2003 Catastrophic regime shifts in ecosystems: linking theory to observation. Trends Ecol. Evol. 18, 648-656. (doi:10.1016/j.tree.2003.09.002)
3. Drake JM, Griffen BD. 2010 Early warning signals of extinction in deteriorating environments. Nature 467, 456-459. (doi:10.1038/nature09389)
4. Scheffer M et al. 2009 Early-warning signals for critical transitions. Nature 461, 53-59. (doi:10.1038/nature08227)
5. Carpenter SR et al. 2011 Early warnings of regime shifts: a whole-ecosystem experiment. Science 332, 1079-1082. (doi:10.1126/science.1203672)
6. Dai L, Vorselen D, Korolev KS, Gore J. 2012 Generic indicators for loss of resilience before a tipping point leading to population collapse. Science 336, 1175-1177. (doi:10.1126/science.1219805)
7. Kéfi S, Rietkerk M, Alados CL, Pueyo Y, Papanastasis VP, ElAich A, De Ruiter PC. 2007 Spatial vegetation patterns and imminent desertification in Mediterranean arid ecosystems. Nature 449, 213-217. (doi:10.1038/nature06111)
8. Dakos V, Scheffer M, van Nes EH, Brovkin V, Petoukhov V, Held H. 2008 Slowing down as an early warning signal for abrupt climate change. Proc. Natl Acad. Sci. USA 105, 14 308-14 312. (doi:10.1073/pnas.0802430105)
9. Lam TT-Y et al. 2013 The genesis and source of the H7N9 influenza viruses causing human infections in China. Nature 502, 241-244. (doi:10.1038/nature12515)
10. Menachery VD et al. 2015 A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence. Nat. Med. 21, 1508-1513. (doi:10.1038/nm.3985)
11. Rohani P, Drake JM. 2011 The decline and resurgence of pertussis in the US. Epidemics 3, 183-188. (doi:10.1016/j.epidem.2011.10.001)
12. Altizer S, Ostfeld RS, Johnson PT, Kutz S, Harvell CD. 2013 Climate change and infectious diseases: from evidence to a predictive framework. Science 341, 514-519. (doi:10.1126/science.1239401)
13. O'Regan SM, Drake JM. 2013 Theory of early warning signals of disease emergence and leading indicators of elimination. Theor. Ecol. 6, 333-357. (doi:10.1007/s12080-013-0185-5)
14. Rimoin AW et al. 2010 Major increase in human monkeypox incidence 30 years after smallpox vaccination campaigns cease in the Democratic Republic of Congo. Proc. Natl Acad. Sci. USA 107, 16 262-16 267. (doi:10.1073/pnas.1005769107)
15. Jansen VA, Stollenwerk N, Jensen HJ, Ramsay M, Edmunds W, Rhodes C. 2003 Measles outbreaks in a population with declining vaccine uptake. Science 301, 804-804. (doi:10.1126/science.1086726)
16. Grenfell BT, Pybus OG, Gog JR, Wood JL, Daly JM, Mumford JA, Holmes EC. 2004 Unifying the epidemiological and evolutionary dynamics of pathogens. Science 303, 327-332. (doi:10.1126/science.1090727)
17. Mooi FR, van der Maas NAT, De Melker HE. 2013 Pertussis resurgence: waning immunity and pathogen adaptation-two sides of the same coin. Epidemiol. Infect. 142, 685-694. (doi:10.1017/S0950268813000071)
18. Bart MJ et al. 2014 Global population structure and evolution of Bordetella pertussis and their relationship with vaccination. mBio 5, e01074. (doi:10.1128/mBio.01074-14)
19. Riolo MA, King AA, Rohani P. 2013 Can vaccine legacy explain the British pertussis resurgence? Vaccine 31, 5903-5908. (doi:10.1016/j.vaccine.2013.09.020)
20. Keeling MJ, Rohani P. 2008 Modeling infectious diseases in humans and animals. Princeton, NJ: Princeton University Press.
21. Lloyd-Smith JO, Schreiber SJ, Kopp PE, Getz W. 2005 Superspreading and the effect of individual variation on disease emergence. Nature 438, 355-359. (doi:10.1038/nature04153)
22. Anderson RM, May RM. 1991 Infectious diseases of humans: dynamics and control. Oxford, UK: Oxford University Press.
23. Bailey NTJ. 1990 The elements of stochastic processes with applications to the natural sciences, vol. 25. New York, NY: John Wiley & Sons
24. Boettiger C, Hastings A. 2012 Quantifying limits to detection of early warning for critical transitions. J. R. Soc. Interface 9, 2527-2539. (doi:10.1098/rsif.2012.0125)
25. Gibson MA, Bruck J. 2000 Efficient exact stochastic simulation of chemical systems with many species and many channels. J. Phys. Chem. A 104, 1876-1889. (doi:10.1021/jp993732q)
26. Anderson DF. 2007 A modified next reaction method for simulating chemical systems with time dependent propensities and delays. J. Chem. Phys. 127, 214107. (doi:10.1063/1.2799998)
27. O'Regan SM, Lillie JW, Drake JM. 2016 Leading indicators of mosquito-borne disease elimination. Theor. Ecol. 9, 269-286. (doi:10.1007/s12080-015-0285-5)
28. van Kampen NG. 1981 Stochastic processes in physics and chemistry. Amsterdam, The Netherlands: North Holland.
29. Black AJ, McKane AJ. 2012 Stochastic formulation of ecological models and their applications. Trends Ecol. Evol. 27, 337-345. (doi:10.1016/j.tree.2012.01.014)
30. Harris TE. 1963 The theory of branching processes. New York, NY: Dover Publications.
31. Singh S, Myers CR. 2014 Outbreak statistics and scaling laws for externally driven epidemics. Phys. Rev. E 89, 042108. (doi:10.1103/PhysRevE.89.042108)
32. Heesterbeek J, Dietz K. 1996 The concept of R0 in epidemic theory. Stat. Neerl. 50, 89-110. (doi:10.1111/j.1467-9574.1996.tb01482.x)
33. Cover TM, Thomas JA. 1991 Elements of information theory. New York, NY: Wiley-Interscience.
34. Kaspar F, Schuster H. 1987 Easily calculable measure for the complexity of spatiotemporal patterns. Phys. Rev. A 36, 842-848. (doi:10.1103/PhysRevA.36.842)
35. Rohani P, Miramontes O. 1995 Host-parasitoid metapopulations: the consequences of parasitoid aggregation on spatial dynamics and searching efficiency. Proc. R. Soc. Lond. B 260, 335-342. (doi:10.1098/rspb.1995.0101)
36. Ashcroft P, Galla T. 2013 Pattern formation in individual-based systems with time-varying parameters. Phys. Rev. E 88, 062104. (doi:10.1103/PhysRevE.88.062104)
37. Dibble CJ, O'Dea EB, Park AW, Drake JM. 2016 Waiting time to infectious disease emergence. J. R. Soc. Interface 13, 20160540. (doi:10.1098/rsif.2016.0540)
38. Blumberg S, Lloyd-Smith JO. 2013 Inference of R0 and transmission heterogeneity from the size distribution of stuttering chains. PLoS Comput. Biol. 9, e1002993. (doi:10.1371/journal.pcbi.1002993)
39. Cross PC, Johnson PL, Lloyd-Smith JO, Getz WM. 2007 Utility of R0 as a predictor of disease invasion in structured populations. J. R. Soc. Interface 4, 315-324. (doi:10.1098/rsif.2006.0185)
40. Cowling BJ, Park M, Fang VJ, Wu P, Leung GM, Wu JT. 2015 Preliminary epidemiologic assessment of MERS-CoV outbreak in South Korea, May-June 2015. Euro Surveill. 20, 7-13.
41. He D, Ionides EL, King AA. 2009 Plug-and-play inference for disease dynamics: measles in large and small populations as a case study. J. R. Soc. Interface 7, 271-283. (doi:10.1098/rsif.2009.0151)
42. Brett TS, Drake JM, Rohani P. 2017 Data from: Anticipating the emergence of infectious diseases. Dryad Digital Repository. (doi:10.5061/dryad.7kt3h)