Unravelling transmission trees of infectious diseases by combining genetic and epidemiological data

Proceedings of the Royal Society B: Biological Sciences

Volumn 279, Issue 1728, 2012, Pages 444-450

  Ypma, R J F ^a,b   Bataille, A M A ^c,d   Stegeman, A ^c   Koch, G ^d   Wallinga, J ^a,b   van Ballegooijen, W M ^a  

^a NATIONAL INSTITUTE FOR PUBLIC HEALTH AND THE ENVIRONMENT   (Netherlands)

^b UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^c UTRECHT UNIVERSITY   (Netherlands)

^d WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

Avian influenza; Molecular epidemiology; Transmission tree

Indexed keywords

AVIAN INFLUENZA; DATA SET; DISEASE TRANSMISSION; EPIDEMIC; EPIDEMIOLOGY; GENETIC ANALYSIS; GENETIC VARIATION; INFECTIOUS DISEASE; MOLECULAR ANALYSIS; PATHOGEN; POULTRY;

NETHERLANDS;

EID: 84055176877     PISSN: 09628452     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rspb.2011.0913     Document Type: Article

References (22)

1. Keeling, M.J., Woolhouse, M.E., May, R.M., Davies, G. & Grenfell, B. T. 2003 Modelling vaccination strategies against foot-and-mouth disease. Nature 421, 136-142. (doi:10.1038/nature01343)
2. Ferguson, N. M., Donnelly, C. A. & Anderson, R. M. 2001 Transmission intensity and impact of control policies on the foot and mouth epidemic in Great Britain. Nature 413, 542-548. (doi:10.1038/35097116)
3. Heijne, J. C., Teunis, P., Morroy, G., Wijkmans, C., Oostveen, S., Duizer, E., Kretzschmar, M. & Wallinga, J. 2009 Enhanced hygiene measures and norovirus transmission during an outbreak. Emerg. Infect. Dis. 15, 24-30. (doi:10.3201/1501.080299)
4. Wallinga, J. & Teunis, P. 2004 Different epidemic curves for severe acute respiratory syndrome reveal similar impacts of control measures. Am. J. Epidemiol. 160, 509-516. (doi:10.1093/aje/kwh255)
5. Lloyd-Smith, J. O., Schreiber, S. J., Kopp, P. E. & Getz, W. M. 2005 Superspreading and the effect of individual variation on disease emergence. Nature 438, 355-359. (doi:10.1038/nature04153)
6. Spada, E., Sagliocca, L., Sourdis, J., Garbuglia, A. R., Poggi, V., De Fusco, C. & Mele, A. 2004 Use of the minimum spanning tree model for molecular epidemiological investigation of a nosocomial outbreak of hepatitis C virus infection. J. Clin. Microbiol. 42, 4230-4236. (doi:10.1128/JCM.42.9.4230-4236.2004)
7. Zhang, L., Diaz, R. S., Ho, D. D., Mosley, J. W., Busch, M. P. & Mayer, A. 1997 Host-specific driving force in human immunodeficiency virus type 1 evolution in vivo. J. Virol. 71, 2555-2561.
8. Leitner, T. & Albert, J. 1999 The molecular clock of HIV-1 unveiled through analysis of a known transmission history. Proc. Natl Acad. Sci. USA 96, 10 752-10 757. (doi:10.1073/pnas.96.19.10752)
9. Pybus, O. G. & Rambaut, A. 2009 Evolutionary analysis of the dynamics of viral infectious disease. Nat. Rev. Genet. 10, 540-550. (doi:10.1038/nrg2583)
10. Cottam, E. M., Thebaud, G., Wadsworth, J., Gloster, J., Mansley, L., Paton, D. J., King, D. P. & Haydon, D. T. 2008 Integrating genetic and epidemiological data to determine transmission pathways of foot-and-mouth disease virus. Proc. R. Soc. B 275, 887-895. (doi:10.1098/ rspb.2007.1442)
11. Jombart, T., Eggo, R. M., Dodd, P. J. & Balloux, F. 2011 Reconstructing disease outbreaks from genetic data: a graph approach. Heredity 106, 383-390. (doi:10.1038/ hdy.2010.78)
12. Stegeman, A., Bouma, A., Elbers, A. R., de Jong, M. C., Nodelijk, G., de Klerk, F., Koch, G. & van Boven, M. 2004 Avian influenza A virus (H7N7) epidemic in The Netherlands in 2003: course of the epidemic and effectiveness of control measures. J. Infect. Dis. 190, 2088- 2095. (doi:10.1086/425583)
13. Fouchier, R. A. et al. 2004 Avian influenza A virus (H7N7) associated with human conjunctivitis and a fatal case of acute respiratory distress syndrome. Proc. Natl Acad. Sci. USA 101, 1356-1361. (doi:10.1073/ pnas.0308352100)
14. Koopmans, M. et al. 2004 Transmission of H7N7 avian influenza A virus to human beings during a large outbreak in commercial poultry farms in the Netherlands. Lancet 363, 587-593. (doi:10.1016/S0140-6736(04)15589-X)
15. Boender, G. J., Hagenaars, T. J., Bouma, A., Nodelijk, G., Elbers, A. R., de Jong, M. C. & van Boven, M. 2007 Risk maps for the spread of highly pathogenic avian influenza in poultry. PLoS Comput. Biol. 3, e71. (doi:10.1371/journal. pcbi.0030071)
16. Bavinck, V., Bouma, A., van Boven, M., Bos, M. E., Stassen, E. & Stegeman, J. A. 2009 The role of backyard poultry flocks in the epidemic of highly pathogenic avian influenza virus (H7N7) in the Netherlands in 2003. Prev. Vet. Med. 88, 247-254. (doi:10.1016/j.prevetmed.2008. 10.007)
17. Bessell, P. R., Shaw, D. J., Savill, N. J. & Woolhouse, M. E. 2010 Estimating risk factors for farm-level transmission of disease: foot and mouth disease during the 2001 epidemic in Great Britain. Epidemics 2, 109-115. (doi:10.1016/j.epidem.2010.06.002)
18. Bos, M. E., van Boven, M., Nielen, M., Bouma, A., Elbers, A. R., Nodelijk, G., Koch, G., Stegeman, A. & de Jong, M. C. 2007 Estimating the day of highly pathogenic avian influenza (H7N7) virus introduction into a poultry flock based on mortality data. Vet. Res. 38, 493-504. (doi:10.1051/vetres:2007008)
19. Bataille, A., van de Meer, F., Koch, G. & Stegeman, A. 2011 Evolutionary analysis of inter-farm transmission dynamics in a highly pathogenic avian influenza outbreak. PLoS Pathog.
20. de Jong, M. C., Stegeman, A., van der Goot, J. & Koch, G. 2009 Intra- and interspecies transmission of H7N7 highly pathogenic avian influenza virus during the avian influenza epidemic in The Netherlands in 2003. Rev. Sci. Tech. 28, 333-340.
21. Spekreijse, D., Bouma, A., Stegeman, J. A., Koch, G. & de Jong, M. C. M. 2010 The effect of inoculation dose of a highly pathogenic avian influenza virus strain H5N1 on the infectiousness of chickens. Vet. Microbiol. 147, 59-66. (doi:10.1016/j.vetmic.2010.06.012)
22. Mossong, J. et al. 2008 Social contacts and mixing patterns relevant to the spread of infectious diseases. PLoS Med. 5, e74. (doi:10.1371/journal.pmed.0050074)