M. Vigilato, O. Cosivi, T. Knöbl, A. Clavijo, and H. Silva, Rabies Update for Latin America and the Caribbean, Emerging Infectious Diseases, vol.19, issue.4, pp.678-679, 2013.
DOI : 10.3201/eid1904.121482

L. Escobar, A. Peterson, M. Favi, V. Yung, and G. Medina-vogel, BAT-BORNE RABIES IN LATIN AMERICA, Revista do Instituto de Medicina Tropical de S??o Paulo, vol.57, issue.1, pp.63-72, 2015.
DOI : 10.1590/S0036-46652015000100009

D. Rosa, E. Kotait, I. Barbosa, T. Carrieri, M. Brandão et al., Bat-transmitted Human Rabies Outbreaks, Brazilian Amazon, Emerging Infectious Diseases, vol.12, issue.8, pp.1197-1202, 2006.
DOI : 10.3201/eid1208.050929

T. Barbosa, D. Medeiros, T. Da-rosa, E. Casseb, L. Medeiros et al., Molecular epidemiology of rabies virus isolated from different sources during a bat-transmitted human outbreak occurring in Augusto Correa municipality, Brazilian Amazon, Virology, vol.370, issue.2, pp.228-236, 2008.
DOI : 10.1016/j.virol.2007.10.005

M. Schneider, P. Romijn, W. Uieda, H. Tamayo, D. Da-silva et al., Rabies transmitted by vampire bats to humans: an emerging zoonotic disease in Latin America?, Revista Panamericana de Salud P??blica, vol.25, issue.3, pp.260-269, 2009.
DOI : 10.1590/S1020-49892009000300010

C. Rupprecht, C. Hanlon, and T. Hemachudha, Rabies re-examined, The Lancet Infectious Diseases, vol.2, issue.6, pp.327-343, 2002.
DOI : 10.1016/S1473-3099(02)00287-6

N. Johnson, N. Aréchiga-ceballos, and A. Aguilar-setien, Vampire Bat Rabies: Ecology, Epidemiology and Control, Viruses, vol.6, issue.5, pp.1911-1928, 2014.
DOI : 10.3390/v6051911

URL : http://doi.org/10.3390/v6051911

D. Streicker, A. Turmelle, M. Vonhof, I. Kuzmin, G. Mccracken et al., Host Phylogeny Constrains Cross-Species Emergence and Establishment of Rabies Virus in Bats, Science, vol.329, issue.5992, pp.676-679, 2010.
DOI : 10.1126/science.1188836

G. Salmón-mulanovich, A. Vásquez, C. Albújar, C. Guevara, V. Laguna-torres et al., Human Rabies and Rabies in Vampire and Nonvampire Bat Species, Southeastern Peru, 2007, Emerging Infectious Diseases, vol.15, issue.8, pp.1308-1310, 2007.
DOI : 10.3201/eid1508.081522

M. Sodré, A. Da-gama, and M. De-almeida, Updated list of bat species positive for rabies in Brazil, Revista do Instituto de Medicina Tropical de S??o Paulo, vol.52, issue.2, pp.75-81, 2010.
DOI : 10.1590/S0036-46652010000200003

M. De-almeida, L. Martorelli, M. Sodré, P. Katakoaka, and A. De-rosa, Rabies diagnosis and serology in bats from the State of S??o Paulo, Brazil, Revista da Sociedade Brasileira de Medicina Tropical, vol.44, issue.2, pp.140-145, 2011.
DOI : 10.1590/S0037-86822011005000011

L. Costa, F. Andrade, W. Uieda, L. Martorelli, and P. Kataoaka, Serological investigation of rabies virus neutralizing antibodies in bats captured in the eastern Brazilian Amazon, Transactions of the Royal Society of Tropical Medicine and Hygiene, vol.107, issue.11, pp.684-689, 2013.
DOI : 10.1093/trstmh/trt080

R. Condori-condori, D. Streicker, C. Cabezas-sanchez, and A. Velasco-villa, Enzootic and Epizootic Rabies Associated with Vampire Bats, Peru, Emerging Infectious Diseases, vol.19, issue.9, pp.1463-1469, 2013.
DOI : 10.3201/eid1909.130083

C. Torres, C. Lema, G. Dohmen, F. Beltran, F. Novaro et al., Phylodynamics of vampire bat-transmitted rabies in Argentina, Molecular Ecology, vol.44, issue.9, pp.2340-2352, 2014.
DOI : 10.1111/mec.12728

P. Vieira, L. , G. Pereira, S. Carnieli, P. Jr et al., Phylogeography of rabies virus isolated from herbivores and bats in the Esp??rito Santo State, Brazil, Virus Genes, vol.104, issue.2, pp.330-336, 2013.
DOI : 10.1007/s11262-012-0866-y

R. Oliveira, N. De-souza, S. Lobo, R. Castilho, J. Macedo et al., Rabies virus in insectivorous bats: Implications of the diversity of the nucleoprotein and glycoprotein genes for molecular epidemiology, Virology, vol.405, issue.2, p.20609456, 2010.
DOI : 10.1016/j.virol.2010.05.030

A. Albas, A. De-almeida-campos, B. Araujo, D. , S. Rodrigues et al., Molecular characterization of rabies virus isolated from non-haematophagous bats in Brazil, Revista da Sociedade Brasileira de Medicina Tropical, vol.44, issue.6, pp.678-683, 2011.
DOI : 10.1590/S0037-86822011000600006

H. Guarino, J. Castilho, J. Souto, R. Oliveira, N. Carrieri et al., Antigenic and genetic characterization of rabies virus isolates from Uruguay, Virus Research, vol.173, issue.2, pp.415-420, 2013.
DOI : 10.1016/j.virusres.2012.12.013

H. Delpietro, A. De-diaz, E. Fuenzalida, and J. Bell, Determination of the rate of rabies attack in bats, Bol Oficina Sanit Panam, vol.73, pp.222-230, 1972.

K. Mungrue and R. Mahabir, The Rabies Epidemic in Trinidad of 1923 to 1937: An Evaluation with a Geographic Information System, Wilderness & Environmental Medicine, vol.22, issue.1, pp.28-36, 2011.
DOI : 10.1016/j.wem.2010.11.001

J. Blackwood, D. Streicker, S. Altizer, and P. Rohani, Resolving the roles of immunity, pathogenesis, and immigration for rabies persistence in vampire bats, Proceedings of the National Academy of Sciences, vol.110, issue.51, pp.20837-20842, 2013.
DOI : 10.1073/pnas.1308817110

D. Streicker, S. Recuenco, W. Valderrama, J. Benavides, I. Vargas et al., Ecological and anthropogenic drivers of rabies exposure in vampire bats: implications for transmission and control, Proceedings of the Royal Society B: Biological Sciences, vol.19, issue.11, pp.3384-3392, 2012.
DOI : 10.1007/s00705-007-1033-y

D. George, C. Webb, M. Farnsworth, O. Shea, T. Bowen et al., Host and viral ecology determine bat rabies seasonality and maintenance, Proceedings of the National Academy of Sciences, vol.108, issue.25, pp.10208-10213, 2011.
DOI : 10.1073/pnas.1010875108

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3121824

D. Streicker, P. Lemey, A. Velasco-villa, and C. Rupprecht, Rates of Viral Evolution Are Linked to Host Geography in Bat Rabies, PLoS Pathogens, vol.26, issue.5, p.1002720, 2012.
DOI : 10.1371/journal.ppat.1002720.s008

J. Moreno and G. Baer, Experimental rabies in the vampire bat, Am J Trop Med Hyg, vol.29, pp.254-259, 1980.

A. Aguilar-setién, E. Loza-rubio, M. Salas-rojas, N. Brisseau, F. Cliquet et al., Salivary excretion of rabies virus by healthy vampire bats, Epidemiology and Infection, vol.133, issue.3, pp.517-522, 2005.
DOI : 10.1017/S0950268805003705

Y. Kobayashi, G. Sato, Y. Shoji, T. Sato, T. Itou et al., Molecular Epidemiological Analysis of Bat Rabies Viruses in Brazil, Journal of Veterinary Medical Science, vol.67, issue.7, pp.647-652, 2005.
DOI : 10.1292/jvms.67.647

A. Velasco-villa, L. Orciari, V. Juarez-islas, M. Gómez-sierra, I. Padilla-medina et al., Molecular Diversity of Rabies Viruses Associated with Bats in Mexico and Other Countries of the Americas, Journal of Clinical Microbiology, vol.44, issue.5, pp.1697-1710, 2006.
DOI : 10.1128/JCM.44.5.1697-1710.2006

D. Constantine, Bat rabies and other lyssavirus infections 68 Available from: National Wildlife Health Center, S. Geological Survey Circular, 1329.

U. Zargar, M. Chishti, F. Ahmad, and M. Rather, Does alteration in biodiversity really affect disease outcome? ??? A debate is brewing, Saudi Journal of Biological Sciences, vol.22, issue.1, pp.14-18, 2014.
DOI : 10.1016/j.sjbs.2014.05.004

M. Hansen, P. Potapov, R. Moore, M. Hancher, S. Turubanova et al., High-Resolution Global Maps of 21st-Century Forest Cover Change, Science, vol.342, issue.6160, pp.850-855, 2013.
DOI : 10.1126/science.1244693

M. Henry, J. Cosson, and J. Pons, Modelling multi-scale spatial variation in species richness from abundance data in a complex neotropical bat assemblage, Ecological Modelling, vol.221, issue.17, pp.2018-2027, 2010.
DOI : 10.1016/j.ecolmodel.2010.05.011

A. Gilbert, B. Petersen, S. Recuenco, M. Niezgoda, J. Gómez et al., Evidence of Rabies Virus Exposure among Humans in the Peruvian Amazon, American Journal of Tropical Medicine and Hygiene, vol.87, issue.2, pp.206-215, 2012.
DOI : 10.4269/ajtmh.2012.11-0689

D. General-de-epidemiologia, Brote de rabia silvestre en la comunidad nativa San Ramón-Yupicusa , distrito Imaza, provincia Bagua, Amazonas? 2011: Situación actual, Bol Epidemiol, vol.20, pp.138-139, 2011.

W. Fahl, P. Carnieli, . Jr, J. Castilho, M. Carrieri et al., Desmodus rotundus and Artibeus spp. bats might present distinct rabies virus lineages, The Brazilian Journal of Infectious Diseases, vol.16, issue.6, pp.545-551, 2012.
DOI : 10.1016/j.bjid.2012.07.002

M. Fernandes, L. Costa, F. Andrade, and L. Silva, Rabies in humans and non-human in the state of Par??, Brazilian Amazon, The Brazilian Journal of Infectious Diseases, vol.17, issue.2, pp.251-253, 2013.
DOI : 10.1016/j.bjid.2012.10.015

F. Berger, N. Desplanches, S. Baillargeaux, M. Joubert, M. Miller et al., Rabies Risk: Difficulties Encountered during Management of Grouped Cases of Bat Bites in 2 Isolated Villages in French Guiana, PLoS Neglected Tropical Diseases, vol.58, issue.10, pp.2258-23826400, 2013.
DOI : 10.1371/journal.pntd.0002258.s003

URL : https://hal.archives-ouvertes.fr/pasteur-01431423

J. Meynard, C. Flamand, C. Dupuy, A. Mahamat, F. Eltges et al., First Human Rabies Case in French Guiana, 2008: Epidemiological Investigation and Control, PLoS Neglected Tropical Diseases, vol.8, issue.6, p.22363830, 2012.
DOI : 10.1371/journal.pntd.0001537.s003

URL : https://hal.archives-ouvertes.fr/pasteur-01481637

R. Sikes, W. Gannon, and A. C. Mammalogists, Guidelines of the American Society of Mammalogists for the use of wild mammals in research, Journal of Mammalogy, vol.92, issue.1, pp.235-253, 2011.
DOI : 10.1644/10-MAMM-F-355.1

B. De-thoisy, C. Richard-hansen, B. Goguillon, P. Joubert, J. Obstancias et al., Rapid evaluation of threats to biodiversity: human footprint score and large vertebrate species responses in French Guiana, Biodiversity and Conservation, vol.3, issue.6, pp.1567-1584, 2010.
DOI : 10.1007/s10531-010-9787-z

V. Gond, V. Freycon, J. Molino, O. Brunaux, F. Ingrassia et al., Broad-scale spatial pattern of forest landscape types in the Guiana Shield, International Journal of Applied Earth Observation and Geoinformation, vol.13, issue.3, pp.357-367, 2011.
DOI : 10.1016/j.jag.2011.01.004

URL : https://hal.archives-ouvertes.fr/halsde-00676329

D. Paget, Etude de la diversité spatiale des écosystèmes forestiers guyanais, Thèse de Doctorat de l'ENGREF, 1999.

A. Borisenko, B. Lim, N. Ivanova, R. Hanner, and P. Hebert, DNA barcoding in surveys of small mammal communities: a field study in Suriname, Molecular Ecology Resources, vol.2, issue.3, pp.471-479, 2008.
DOI : 10.1111/j.1471-8286.2007.01998.x

P. Charles-dominique, A. Brosset, and S. Jouard, Les Chauves-souris de Guyane. Collection Patrimoines Naturels, p.172, 2001.

L. Dacheux, J. Reynes, P. Buchy, O. Sivuth, and B. Diop, A Reliable Diagnosis of Human Rabies Based on Analysis of Skin Biopsy Specimens, Clinical Infectious Diseases, vol.47, issue.11, pp.1410-1417, 2008.
DOI : 10.1086/592969

J. Ellison, S. Johnson, N. Kuzmina, A. Gilbert, W. Carson et al., Multidisciplinary Approach to Epizootiology and Pathogenesis of Bat Rabies Viruses in the United States, Zoonoses and Public Health, vol.91, issue.1, pp.46-57, 2013.
DOI : 10.1111/zph.12019

H. Bourhy, J. Reynes, E. Dunham, L. Dacheux, F. Larrous et al., The origin and phylogeography of dog rabies virus, Journal of General Virology, vol.89, issue.11, pp.2673-2681, 2008.
DOI : 10.1099/vir.0.2008/003913-0

O. Delmas, E. Holmes, C. Talbi, F. Larrous, L. Dacheux et al., Genomic Diversity and Evolution of the Lyssaviruses, PLoS ONE, vol.20, issue.10, p.18446239, 2008.
DOI : 10.1371/journal.pone.0002057.s003

C. Talbi, E. Holmes, P. De-benedictis, O. Faye, E. Nakouné et al., Evolutionary history and dynamics of dog rabies virus in western and central Africa, Journal of General Virology, vol.90, issue.4, pp.783-791, 2009.
DOI : 10.1099/vir.0.007765-0

K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei et al., MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods, Molecular Biology and Evolution, vol.28, issue.10, pp.2731-2739, 2011.
DOI : 10.1093/molbev/msr121

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203626

J. Nylander, MrModeltest v2. Program distributed by the author, Evolutionary Biology Centre, 2004.

F. Ronquist, M. Teslenko, P. Van-der-mark, D. Ayres, A. Darling et al., MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space, Systematic Biology, vol.61, issue.3, pp.539-542, 2012.
DOI : 10.1093/sysbio/sys029

H. Bourhy and P. Sureau, Rapid fluorescent focus inhibitions test (RFFIT) In: Commission des Laboratoires de Référence et d'Expertise, Méthodes de Laboratoire pour le Diagnostic de la Rage, pp.191-193, 1990.

J. Reynes, S. Molia, L. Audry, S. Hout, S. Ngin et al., Serologic Evidence of Lyssavirus Infection in Bats, Cambodia, Emerging Infectious Diseases, vol.10, issue.12, pp.2231-2234, 2004.
DOI : 10.3201/eid1012.040459

M. López-roig, H. Bourhy, R. Lavenir, and J. Serra-cobo, Seroprevalence Dynamics of European Bat Lyssavirus Type 1 in a Multispecies Bat Colony, Viruses, vol.6, issue.9, pp.3386-3399, 2014.
DOI : 10.3390/v6093386

M. Almeida, E. Massad, E. Aguiar, L. Martorelli, and A. Joppert, Neutralizing Antirabies Antibodies in Urban Terrestrial Wildlife in Brazil, Journal of Wildlife Diseases, vol.37, issue.2, pp.394-398, 2001.
DOI : 10.7589/0090-3558-37.2.394

M. East, H. Hofer, J. Cox, U. Wulle, H. Wiik et al., Regular exposure to rabies virus and lack of symptomatic disease in Serengeti spotted hyenas, Proceedings of the National Academy of Sciences, vol.98, issue.26, pp.15026-15031, 2001.
DOI : 10.1073/pnas.261411898

D. Araujo, L. Martorelli, A. Kataoka, A. Campos, C. Rodrigues et al., ANTIBODIES TO RABIES VIRUS IN TERRESTRIAL WILD MAMMALS IN NATIVE RAINFOREST ON THE NORTH COAST OF S??O PAULO STATE, BRAZIL, Journal of Wildlife Diseases, vol.50, issue.3, pp.469-77, 2014.
DOI : 10.7589/2013-04-099

R. Team, R: A language and environment for statistical computing. R Foundation for Statistical Computing, 2013.

A. Brosset, P. Charles-dominique, A. Cockle, J. Cosson, and D. Masson, Bat communities and deforestation in French Guiana, Canadian Journal of Zoology, vol.74, issue.11, pp.1974-1982, 1996.
DOI : 10.1139/z96-224

B. De-thoisy, A. Pavan, M. Delaval, A. Lavergne, T. Luglia et al., (Mormoopidae) in French Guiana and Brazilian Amapa, Acta Chiropterologica, vol.16, issue.1, pp.1-13, 2014.
DOI : 10.3161/150811014X683228

B. Kissi, N. Tordo, and H. Bourhy, Genetic Polymorphism in the Rabies Virus Nucleoprotein Gene, Virology, vol.209, issue.2, pp.526-537, 1995.
DOI : 10.1006/viro.1995.1285

R. Moratelli, D. Dias, and C. Bonvicino, Estrutura e analise zoogeografica de uma taxocenose de morcegos no norte do Estado do Amazonas, Brasil. Chiroptera Neotropical, vol.16, pp.661-671, 2010.

J. Price and C. Everard, RABIES VIRUS AND ANTIBODY IN BATS IN GRENADA AND TRINIDAD, Journal of Wildlife Diseases, vol.13, issue.2, pp.131-134, 1977.
DOI : 10.7589/0090-3558-13.2.131

N. Mochizuki, Y. Kobayashi, G. Sato, S. Hirano, T. Itou et al., Determination and Molecular Analysis of the Complete Genome Sequence of Two Wild-Type Rabies Viruses Isolated from a Haematophagous Bat and a Frugivorous Bat in Brazil, Journal of Veterinary Medical Science, vol.73, issue.6, pp.759-766, 2011.
DOI : 10.1292/jvms.10-0238

M. Salas-rojas, C. Sánchez-hernández, M. Romero-almaraz, G. Schnell, R. Schmid et al., Prevalence of rabies and LPM paramyxovirus antibody in non-hematophagous bats captured in the Central Pacific coast of Mexico, Transactions of the Royal Society of Tropical Medicine and Hygiene, vol.98, issue.10, pp.577-584, 2004.
DOI : 10.1016/j.trstmh.2003.10.019

M. Delaval and P. Charles-dominique, Edge effects on frugivorous and nectarivorous bat communities in a neotropical primary forest in French Guiana, Rev Ecol, vol.61, pp.343-352, 2006.

N. Gay, K. Olival, S. Bumrungsri, B. Siriaroonrat, M. Bourgarel et al., Parasite and viral species richness of Southeast Asian bats: Fragmentation of area distribution matters, International Journal for Parasitology: Parasites and Wildlife, vol.3, issue.2, pp.161-170, 2014.
DOI : 10.1016/j.ijppaw.2014.06.003

A. Turmelle and K. Olival, Correlates of Viral Richness in Bats (Order Chiroptera), EcoHealth, vol.17, issue.Suppl 5, pp.522-539, 2009.
DOI : 10.1007/s10393-009-0263-8

H. Bourhy, B. Kissi, M. Lafon, D. Sacramento, and N. J. Tordo, Antigenic and molecular characterization of bat rabies virus in Europe, Clin Microbiol, vol.30, pp.2419-2445, 1992.

K. Scheffer, M. Carrieri, A. Albas, H. Santos, I. Kotait et al., V??rus da raiva em quir??pteros naturalmente infectados no Estado de S??o Paulo, Brasil, Revista de Sa??de P??blica, vol.41, issue.3, pp.389-395, 2007.
DOI : 10.1590/S0034-89102007000300010

URL : http://doi.org/10.1590/s0034-89102007000300010

J. Serra-cobo, M. López-roig, M. Seguí, L. Sánchez, J. Nadal et al., Ecological Factors Associated with European Bat Lyssavirus Seroprevalence in Spanish Bats, PLoS ONE, vol.43, issue.5, p.23700480, 2013.
DOI : 10.1371/journal.pone.0064467.s002

URL : https://hal.archives-ouvertes.fr/pasteur-01481634

B. Amengual, H. Bourhy, M. López-roig, and J. Serra-cobo, Temporal Dynamics of European Bat Lyssavirus Type 1 and Survival of Myotis myotis Bats in Natural Colonies, PLoS ONE, vol.46, issue.10, pp.566-17593965, 2007.
DOI : 10.1371/journal.pone.0000566.s003

B. Amengual, H. Bourhy, M. López-roig, and J. Serra-cobo, Active monitoring of EBLV infection in natural colonies of the mouse-eared Bat (Myotis myotis), Dev Biol, vol.131, pp.547-553, 2008.

W. Kermack, G. A. Mckendrick, and A. , A contribution to the mathematical theory of epidemics. Part 3. In further studies of the problem of endemicity, Proc R Soc Lond (A) Mat, pp.92-122, 1927.

M. Galetti and R. Dirzo, Ecological and evolutionary consequences of living in a defaunated world, Biological Conservation, vol.163, pp.1-6, 2013.
DOI : 10.1016/j.biocon.2013.04.020

K. Logiudice, R. Ostfeld, K. Schmidt, and F. Keesing, The ecology of infectious disease: Effects of host diversity and community composition on Lyme disease risk, Proceedings of the National Academy of Sciences, vol.100, issue.2, pp.567-571, 2003.
DOI : 10.1073/pnas.0233733100

B. De-thoisy, C. Richard-hansen, and C. Peres, Impacts of subsistence game hunting on amazonian primates South American Primates: Comparative Perspectives in the Study of Behavior, Ecology, and Conservation, Book Series Developments in Primatology: Progress and Prospects, pp.389-412, 2009.