Phylodynamics and Human-mediated dispersal of a zoonotic virus

PLoS Pathogens

Volumn 6, Issue 10, 2010, Pages

  Talbi, Chiraz ^a   Lemey, Philippe ^b   Suchard, Marc A ^c   Abdelatif, Elbia ^d   Elharrak, Mehdi ^e   Jalal, Nourlil ^f   Faouzi, Abdellah ^f   Echevarría, Juan E ^g   Morón, Sonia Vazquez ^g   Rambaut, Andrew ^h,i   Campiz, Nicholas ^j   Tatem, Andrew J ^j   Holmes, Edward C ^i,k   Bourhy, Hervé ^a  

^a INSTITUT PASTEUR   (France)

^b REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d Institut Pasteur d'Algerie   (Algeria)

^e Biopharma Laboratoire   (Morocco)

^f Institut Pasteur du Maroc   (Morocco)

^g INSTITUTO DE SALUD CARLOS III   (Spain)

^h UNIVERSITY OF EDINBURGH   (United Kingdom)

ⁱ NATIONAL INSTITUTES OF HEALTH   (United States)

^j UNIVERSITY OF FLORIDA   (United States)

^k PENNSYLVANIA STATE UNIVERSITY   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL VIRUS; ARTICLE; BAYES THEOREM; DOG; GENE FLOW; GEOGRAPHIC DISTRIBUTION; HUMAN; NONHUMAN; NORTH AFRICA; NUCLEOTIDE SEQUENCE; PATHOGENESIS; PHYLOGEOGRAPHY; PREDICTOR VARIABLE; RABIES; RABIES VIRUS; SIMULATION; VIRAL GENETICS; VIRUS TRANSMISSION; ALGERIA; ANIMAL; COMPUTER SIMULATION; DEMOGRAPHY; DISEASE TRANSMISSION; GENETICS; GEOGRAPHY; MOLECULAR EVOLUTION; MOROCCO; PHYLOGENY; PHYSIOLOGY; TUNISIA; VIROLOGY; ZOONOSIS;

ANIMALIA; CANIS FAMILIARIS; RABIES VIRUS;

ALGERIA; ANIMALS; COMPUTER SIMULATION; DEMOGRAPHY; DOGS; EVOLUTION, MOLECULAR; GENE FLOW; GEOGRAPHY; HUMANS; MOROCCO; PHYLOGENY; RABIES VIRUS; TUNISIA; ZOONOSES;

EID: 78449237743     PISSN: 15537366     EISSN: 15537374     Source Type: Journal    
DOI: 10.1371/journal.ppat.1001166     Document Type: Article

References (46)

1. Knobel DL, Cleaveland S, Coleman PG, Fevre EM, Meltzer MI, et al. (2005) Re-evaluating the burden of rabies in Africa and Asia. Bull World Health Organ 83: 360-368.
2. Cleaveland S, Meslin FX, Breiman R (2006) Dogs can play useful role as sentinel hosts for disease. Nature 440: 605.
3. Fevre EM, Kaboyo RW, Persson V, Edelsten M, Coleman PG, et al. (2005) The epidemiology of animal bite injuries in Uganda and projections of the burden of rabies. Trop Med Int Health 10: 790-798.
4. Ly S, Buchy P, Heng NY, Ong S, Chhor N, et al. (2009) Rabies situation in cambodia. PLoS Negl Trop Dis 3: e511.
5. Nel LH, Rupprecht CE (2007) Emergence of lyssaviruses in the Old World: the case of Africa. Curr Top Microbiol Immunol 315: 161-193.
6. Bourhy H, Reynes JM, Dunham EJ, Dacheux L, Larrous F, et al. (2008) The origin and phylogeography of dog rabies virus. J Gen Virol 89: 2673-2681.
7. Talbi C, Holmes EC, de Benedictis P, Faye O, Nakoune E, et al. (2009) Evolutionary history and dynamics of dog rabies virus in western and central Africa. J Gen Virol 90: 783-791.
8. Lemey P, Rambaut A, Drummond AJ, Suchard MA (2009) Bayesian phylogeography finds its roots. PLoS Comput Biol 5: e1000520.
9. Biek R, Henderson JC, Waller LA, Rupprecht CE, Real LA (2007) A highresolution genetic signature of demographic and spatial expansion in epizootic rabies virus. Proc Natl Acad Sci U S A 104: 7993-7998.
10. Bourhy H, Kissi B, Audry L, Smreczak M, Sadkowska-Todys M, et al. (1999) Ecology and evolution of rabies virus in Europe. J Gen Virol 80 (Pt 10): 2545-2557.
11. Real LA, Biek R (2007) Spatial dynamics and genetics of infectious diseases on heterogeneous landscapes. J R Soc Interface 4: 935-948.
12. Real LA, Henderson JC, Biek R, Snaman J, Jack TL, et al. (2005) Unifying the spatial population dynamics and molecular evolution of epidemic rabies virus. Proc Natl Acad Sci U S A 102: 12107-12111.
13. Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7: 214.
14. Ben Néfissa K, Moulin AM, Dellagi K (2007) La rage en Tunisie au XIX siècle: recrudescence ou émergence? Gesnerus 64: 173-192.
15. Wang TH, Donaldson YK, Brettle RP, Bell JE, S P (2001) Identification of shared populations of human immunodeficiency virus type 1 infecting microglia and tissue macrophages outside the central nervous system. J Virol 75: 11686-11699.
16. Gray RR, Tatem AJ, Lamers S, Hou W, Laeyendecker O, et al. (2009) Spatial phylodynamics of HIV-1 epidemic emergence in east Africa. Aids 23: F9-F17.
17. McRae BH, Beier P (2007) Circuit theory predicts gene flow in plant and animal populations. Proc Natl Acad Sci U S A 104: 19885-19890.
18. Balk DL, Deichmann U, Yetman G, Pozzi F, Hay SI, et al. (2006) Determining global population distribution: methods, applications and data. Adv Parasitol 62: 119-156.
19. Minin VN, Suchard M (2008) Counting labeled transitions in continuous-time Markov models of evolution. Journal of Mathematical Biology 56: 391-412.
20. Hampson K, Dushoff J, Bingham J, Bruckner G, Ali YH, et al. (2007) Synchronous cycles of domestic dog rabies in sub-Saharan Africa and the impact of control efforts. Proc Natl Acad Sci U S A 104: 7717-7722.
21. Hampson K, Dushoff J, Cleaveland S, Haydon DT, Kaare M, et al. (2009) Transmission dynamics and prospects for the elimination of canine rabies. PLoS Biol 7: e53.
22. Kitala PM, McDermott JJ, Coleman PG, Dye C (2002) Comparison of vaccination strategies for the control of dog rabies in Machakos District, Kenya. Epidemiol Infect 129: 215-222.
23. Wandeler AI, Matter HC, Kappeler A, Budde A (1993) The ecology of dogs and canine rabies: a selective review. Rev Sci Tech 12: 51-71.
24. Zinsstag J, Durr S, Penny MA, Mindekem R, Roth F, et al. (2009) Transmission dynamics and economics of rabies control in dogs and humans in an African city. Proc Natl Acad Sci U S A 106: 14996-15001.
25. Jenkins SR, Winkler WG (1987) Descriptive epidemiology from an epizootic of raccoon rabies in the Middle Atlantic States, 1982-1983. Am J Epidemiol 126: 429-437.
26. Windiyaningsih C, Wilde H, Meslin FX, Suroso T, Widarso HS (2004) The rabies epidemic on Flores Island, Indonesia (1998-2003). J Med Assoc Thai 87: 1389-1393.
27. Bourhy H, Dacheux L, Strady C, Mailles A (2005) Rabies in Europe in 2005. Euro Surveill 10: 213-216.
28. Cleaveland S, Kaare M, Tiringa P, Mlengeya T, Barrat J (2003) A dog rabies vaccination campaign in rural Africa: impact on the incidence of dog rabies and human dog-bite injuries. Vaccine 21: 1965-1973.
29. Coleman PG, Fevre EM, Cleaveland S (2004) Estimating the public health impact of rabies. Emerg Infect Dis 10: 140-142.
30. Kayali U, Mindekem R, Hutton G, Ndoutamia AG, Zinsstag J (2006) Costdescription of a pilot parenteral vaccination campaign against rabies in dogs in N'Djamena, Chad. Trop Med Int Health 11: 1058-1065.
31. Lardon Z, Watier F, Brunet A, Bernède C, Goudal M, et al. (2010) Imported Episodic Rabies Increases Patient Demand for and Physician Delivery of Antirabies Prophylaxis. Plos Neglected Tropical Diseases, in press.
32. Hufnagel L, Brockmann D, Geisel T (2004) Forecast and control of epidemics in a globalized world. Proc Natl Acad Sci U S A 101: 15124-15129.
33. Russell CA, Smith DL, Waller LA, Childs JE, Real LA (2004) A priori prediction of disease invasion dynamics in a novel environment. Proc Biol Sci 271: 21-25.
34. Henderson JC, Biek R, Hanlon CA, O'Dee S, Real LA (2008) Rabies virus in raccoons, Ohio, 2004. Emerg Infect Dis 14: 650-652.
35. Tatem AJ, Rogers DJ, Hay SI (2006) Global transport networks and infectious disease spread. Adv Parasitol 62: 293-343.
36. Kissi B, Tordo N, Bourhy H (1995) Genetic polymorphism in the rabies virus nucleoprotein gene. Virology 209: 526-537.
37. Delmas O, Holmes EC, Talbi C, Larrous F, Dacheux L, et al. (2008) Genomic diversity and evolution of the lyssaviruses. PLoS ONE 3: e2057.
38. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
39. Drummond AJ, Ho SY, Phillips MJ, Rambaut A (2006) Relaxed phylogenetics and dating with confidence. PLoS Biol 4: e88.
40. Drummond AJ, Rambaut A, Shapiro B, Pybus OG (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol 22: 1185-1192.
41. Suchard MA, Rambaut A (2009) Many-core algorithms for statistical phylogenetics. Bioinformatics 25: 1370-1376.
42. O'Brien JD, Minin VN, Suchard M (2009) Learning to count: robust estimates for labeled distances between molecular sequences. Molecular Biology and Evolution 26: 801-814.
43. Suchard M, Kitchen C, Sinsheimer J, Weiss R (2003) Hierarchical phylogenetic models for analyzing multipartite sequence data. Syst Biol 52: 649-664.
44. (2002) Road network data. VMAP0 (Vector Map Level 0). Highlands RanchColorado: LandInfo Worldwide Mapping.
45. Redelings BD, Suchard MA (2005) Joint Bayesian estimation of alignment and phylogeny. Syst Biol 54: 401-418.
46. Newton M, Raftery A (1994) Approximate Bayesian inference with the weighted likelihood bootstrap. Journal of the Royal Statistical Society Series B 56: 3-48.