Epidemic predictions in an imperfect world: Modelling disease spread with partial data

Proceedings of the Royal Society B: Biological Sciences

Volumn 282, Issue 1808, 2015, Pages

  Dawson, Peter M ^a   Werkman, Marleen ^b,c   Brooks Pollock, Ellen ^d   Tildesley, Michael J ^b,e  

^a UNIVERSITY OF WARWICK   (United Kingdom)

^b UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^c WAGENINGEN UNIVERSITY   (Netherlands)

^d UNIVERSITY OF BRISTOL   (United Kingdom)

^e NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Epidemics; Livestock networks; Partial datav

Indexed keywords

DISEASE SPREAD; DISEASE TRANSMISSION; EPIDEMIOLOGY; EUROPEAN UNION; GOVERNANCE APPROACH; INFECTIOUS DISEASE; LIVESTOCK; POLICY MAKING; SPATIAL ANALYSIS; CATTLE; DATABASE; EPIDEMIC; MOVEMENT; NETWORK ANALYSIS; PREDICTION; TRADE FLOW;

UNITED KINGDOM; UNITED STATES;

BOS;

ANIMAL; BOVINE; CATTLE DISEASES; DEVELOPING COUNTRY; EPIDEMIC; THEORETICAL MODEL; TRANSMISSION; UNITED KINGDOM; UNITED STATES; VETERINARY;

ANIMALS; CATTLE; CATTLE DISEASES; DEVELOPING COUNTRIES; EPIDEMICS; MODELS, THEORETICAL; UNITED KINGDOM; UNITED STATES;

EID: 84929303262     PISSN: 09628452     EISSN: 14712954     Source Type: Journal    
DOI: 10.1098/rspb.2015.0205     Document Type: Article

References (49)

1. Ferguson NM, Donnelly CA, Anderson RM. 2001 The foot-and-mouth epidemic in Great Britain: pattern of spread and impact of interventions. Science (New York, NY) 292, 1155–1160. (doi:10.1126/science.1061020)
2. Fraser C et al. 2009 Pandemic potential of a strain of influenza A (H1N1): early findings. Science (New York, NY) 324, 1557–1561. (doi:10.1126/science.1176062)
3. Keeling MJ. 2001 Dynamics of the 2001 UK foot and mouth epidemic: stochastic dispersal in a heterogeneous landscape. Science (New York, NY) 294, 813–817. (doi:10.1126/science.1065973)
4. Lipsitch M. 2003 Transmission dynamics and control of severe acute respiratory syndrome. Science 300, 1966–1970. (doi:10.1126/science.1086616)
5. Morris RS, Wilesmith JW, Stern MW, Sanson RL, Stevenson MA. 2001 Predictive spatial modelling of alternative control strategies for the foot-and-mouth disease epidemic in Great Britain, 2001. Vet. Rec. 149, 137–144. (doi:10.1136/vr.149.5.137)
6. Keeling MJ, Woolhouse MEJ, May RM, Davies G, Grenfell BT. 2003 Modelling vaccination strategies against foot-and-mouth disease. Nature 421, 136–142. (doi:10.1038/nature01343)
7. Tildesley MJ, Savill NJ, Shaw DJ, Deardon R, Brooks SP, Woolhouse MEJ, Grenfell BT, Keeling MJ. 2006 Optimal reactive vaccination strategies for a footand- mouth outbreak in the UK. Nature 440, 83–86. (doi:10.1038/nature04324)
8. Tildesley MJ, Deardon R, Savill NJ, Bessell PR, Brooks SP, Woolhouse MEJ, Grenfell BT, Keeling MJ. 2008 Accuracy of models for the 2001 foot-andmouth epidemic. Proc. R. Soc. B 275, 1459–1468. (doi:10.1098/rspb.2008.0006)
9. Tildesley MJ, Bessell PR, Keeling MJ, Woolhouse MEJ. 2009 The role of pre-emptive culling in the control of foot-and-mouth disease. Proc. R. Soc. B 276, 3239–3248. (doi:10.1098/rspb.2009.0427)
10. Gibbens JC, Sharpe CE, Wilesmith JW, Mansley LM, Michalopoulou E, Ryan JB, Hudson M. 2001 Descriptive epidemiology of the 2001 foot-andmouth disease epidemic in Great Britain: the first five months. Vet. Rec. 149, 729–743.
11. Gilbert M, Aktas S, Mohammed H, Roeder P, Sumption K, Tufan M, Slingenbergh J. 2005 Patterns of spread and persistence of foot-and-mouth disease types A, O and Asia-1 in Turkey: a metapopulation approach. Epidemiol. Infect. 133, 537–545. (doi:10.1017/S0950268804003516)
12. Brooks-Pollock E, Keeling MJ. 2009 Herd size and bovine tuberculosis persistence in cattle farms in Great Britain. Prev. Vet. Med. 92, 360–365. (doi:10.1016/j.prevetmed.2009.08.022)
13. Brooks-Pollock E, Roberts GO, Keeling MJ. 2014 A dynamic model of bovine tuberculosis spread and control in Great Britain. Nature 511, 228–231. (doi:10.1038/nature13529)
14. Reid SA. 2002 Trypanosoma evansi control and containment in Australasia. Trends Parasitol. 18, 219–224. (doi:10.1016/S1471-4922(02)02250-X)
15. Févre EM, Picozzi K, Fyfe J, Waiswa C, Odiit M, Coleman PG, Welburn SC. 2005 A burgeoning epidemic of sleeping sickness in Uganda. Lancet 366, 745–747. (doi:10.1016/S0140-6736(05)67179-6)
16. Chevalier V et al. 2004 Epidemiological processes involved in the emergence of vector-borne diseases: West Nile fever, Rift Valley fever, Japanese encephalitis and Crimean-Congo haemorrhagic fever. Rev. Sci. Tech. 23, 535–555.
17. Green DM, Kiss IZ, Kao RR. 2006 Modelling the initial spread of foot-and-mouth disease through animal movements. Proc. R. Soc. B 273, 2729–2735. (doi:10.1098/rspb.2006.3648)
18. Ortiz-Pelaez A, Pfeiffer DU, Soares-Magalhães RJ, Guitian FJ. 2006 Use of social network analysis to characterize the pattern of animal movements in the initial phases of the 2001 foot and mouth disease (FMD) epidemic in the UK. Prev. Vet. Med. 76, 40–55. (doi:10.1016/j.prevetmed.2006.04.007)
19. Green DM, Kiss IZ, Mitchell AP, Kao RR. 2008 Estimates for local and movement-based transmission of bovine tuberculosis in British cattle. Proc. R. Soc. B 275, 1001–1005. (doi:10.1098/rspb.2007.1601)
20. Zhang X-S, Chase-Topping ME, McKendrick IJ, Savill NJ, Woolhouse MEJ. 2010 Spread of E. coli O157 infection among Scottish cattle farms: stochastic models and model selection. Epidemics 2, 11–20. (doi:10.1016/j.epidem.2010.02.001)
21. Buhnerkempe MG, Grear DA, Portacci K, Miller RS, Lombard JE, Webb CT. 2014 A national-scale picture of U.S. cattle movements obtained from Interstate Certificate of Veterinary Inspection data. Prev. Vet. Med. 112, 318–319. (doi:10.1016/j.prevetmed.2013.08.002)
22. Nickbakhsh S, Matthews L, Bessell PR, Reid SWJ, Kao RR. 2011 Generating social network data using partially described networks: an example informing avian influenza control in the British poultry industry. BMC Vet. Res. 7, 66. (doi:10.1186/1746-6148-7-66)
23. Wesolowski A, Buckee CO, Pindolia DK, Eagle N, Smith DL, Garcia AJ, Tatem AJ. 2013 The use of census migration data to approximate human movement patterns across temporal scales. PLoS ONE 8, e52971. (doi:10.1371/journal.pone.0052971)
24. Pindolia D, Garcia AJ, Huang Z, Smith DL, Alegana VA, Noor AM, Snow RW, Tatem AJ. 2013 The demographics of human and malaria movement and migration patterns in East Africa. Malar. J. 12, 397. (doi:10.1186/1475-2875-12-397)
25. Danon L, House T, Keeling MJ. 2009 The role of routine versus random movements on the spread of disease in Great Britain. Epidemics 1, 250–258. (doi:10.1016/j.epidem.2009.11.002)
26. González M, Hildago C, Barabási A. 2008 Understanding individual human mobility patterns. Nature 453, 779–782. (doi:10.1038/nature06958)
27. Tizzoni M, Bajardi P, Decuyper A, Kon Kam King G, Schneider CM, Blondel V, Smoreda Z, González MC, Colizza V. 2014 On the use of human mobility proxies for modeling epidemics. PLoS Comput. Biol. 10, e1003716. (doi:10.1371/journal.pcbi.1003716)
28. Stumpf MPH, Wiuf C, May R. 2005 Subnets of scalefree networks are not scale-free: sampling properties of networks. Proc. Natl Acad. Sci. USA 102, 4221–4224. (doi:10.1073/pnas.0501179102)
29. Goodman LA. 1961 Snowball sampling. Ann. Math. Stat. 32, 148–170. (doi:10.1214/aoms/1177705148)
30. Kendall C, Kerr LRFS, Gondim RC, Werneck GL, Hermelinda Maia Macena R, Pontes MK, Johnston LG, Sabin K, McFarland W. 2008 An empirical comparison of respondent-driven sampling, time location sampling, and snowball sampling for behavioral surveillance in men who have sex with men, Fortaleza, Brazil. AIDS Behav. 12, S97–S104. (doi:10.1007/s10461-008-9390-4)
31. Fumanelli L, Ajelli M, Manfredi P. 2012 Inferring the structure of social contacts from demographic data in the analysis of infectious diseases spread. PLoS Comput. Biol. 8, e1002775. (doi:10.1371/journal.pcbi.1002673)
32. Tildesley MJ, House TA, Bruhn MC, Curry RJ, O’Neil M, Allpress JLE, Smith G, Keeling MJ. 2010 Impact of spatial clustering on disease transmission and optimal control. Proc. Natl Acad. Sci. USA 106, 1041–1046. (doi:10.1073/pnas.0909047107)
33. Kiss IZ, Green DM, Kao RR. 2006 The network of sheep movements within Great Britain: network properties and their implications for infectious disease spread. J. R. Soc. Interface 3, 669–677. (doi:10.1098/rsif.2006.0129)
34. Szmaragd C, Wilson AJ, Carpenter S, Wood JLN, Mellor PS, Gubbins S. 2009 A modeling framework to describe the transmission of bluetongue virus within and between farms in Great Britain. PLoS ONE 4, e7741. (doi:10.1371/journal.pone.0007741)
35. Ensoy C, Aerts M, Welby S, Van der Stede Y, Faes C. 2013 A dynamic spatio-temporal model to investigate the effect of cattle movements on the spread of bluetongue BTV-8 in Belgium. PLoS ONE 8, e78591. (doi:10.1371/journal.pone.0078591)
36. Kolaczyk ED. 2009 Statistical analysis of network data. 1st edn. New York: Springer.
37. Robinson SE, Christley RM. 2007 Exploring the role of auction markets in cattle movements in Great Britain. Prev. Vet. Med. 81, 21–37. (doi:10.1016/j.prevetmed.2007.04.011)
38. Vernon MC, Keeling MJ. 2009 Representing the UK’s cattle herd as static and dynamic networks. Proc. R. Soc. B 276, 469–476. (doi:10.1098/rspb.2008.1009)
39. Keeling MJ. 2004 The implications of network structure for epidemic dynamics. Theor. Popul. Biol. 67, 1–8. (doi:10.1016/j.tpb.2004.08.002)
40. Newman MEJ. 2010 Networks. 1st edn. Oxford, UK: Oxford University Press.
41. Foster JG, Foster DV, Grassberger P, Paczuski M. 2010 Edge direction and the structure of networks. Proc. Natl Acad. Sci. USA 107, 10 815–10 820. (doi:10.1073/pnas.0912671107)
42. DEFRA. 2012 Livestock at farm shows and markets: welfare regulations. See https://www.gov.uk/farmed-animal-welfare-at-shows-and-markets.
43. Lindström T, Grear DA, Buhnerkempe M, Webb CT, Miller RS, Portacci K, Wennergren U. 2013 A Bayesian approach for modeling cattle movements in the United States: scaling up a partially observed network. PLoS ONE 8, e53432. (doi:10.1371/journal.pone.0053432)
44. Bajardi P, Barrat A, Savini L, Colizza V. 2013 Optimizing surveillance for livestock disease spreading through animal movements. J. R. Soc. Interface 9, 2814–2825. (doi:10.1098/rsif.2012.0289)
45. Nöremark M, Håkansson N, Lindström T, Wennergren U, Lewerin S. 2009 Spatial and temporal investigations of reported movements, births and deaths of cattle and pigs in Sweden. Acta Vet. Scand. 51, 37. (doi:10.1186/1751-0147-51-37)
46. Rautureau S, Dufour B, Durand B. 2012 Structuring the passive surveillance network improves epizootic detection and control efficacy: a simulation study on foot-and-mouth disease in France. Transbound. Emerging Dis. 59, 311–322. (doi:10.1111/j.1865-1682.2011.01271.x)
47. Odden M, Athreya V, Rattan S, Linnell JDC. 2014 Adaptable neighbours: movement patterns of GPScollared leopards in human dominated landscapes in India. PLoS ONE 9, e112044. (doi:10.1371/journal.pone.0112044)
48. Robinson PM et al. 2012 Foraging behavior and success of a mesopelagic predator in the northeast Pacific Ocean: insights from a data-rich species, the northern elephant seal. PLoS ONE 7, e36728. (doi:10.1371/journal.pone.0036728)
49. Kao RR, Green DM, Johnson J, Kiss IZ. 2007 Disease dynamics over very different times-scales: foot-andmouth disease and scarpie on the network of livestock movements in the UK. J. R. Soc. Interface 4, 907–916. (doi:10.1098/rsif.2007.1129)