R. Moratelli and C. Calisher, Bats and zoonotic viruses: can we confidently link bats with emerging deadly viruses?, Mem??rias do Instituto Oswaldo Cruz, vol.9, issue.1, pp.1-22, 2015.
DOI : 10.1128/JVI.00723-12
URL : http://www.scielo.br/pdf/mioc/v110n1/0074-0276-mioc-110-01-00001.pdf

K. Olival, C. Weekley, and P. Daszak, Are Bats Really ???Special??? as Viral Reservoirs? What We Know and Need to Know, Bats and Viruses, pp.281-294, 2015.
DOI : 10.1016/j.coviro.2011.10.013

K. Olival, P. Hosseini, C. Zambrana-torrelio, N. Ross, T. Bogich et al., Host and viral traits predict zoonotic spillover from mammals, Nature, vol.20, issue.7660, pp.646-650, 2017.
DOI : 10.1111/j.1466-8238.2010.00587.x

C. Brook and A. Dobson, Bats as ???special??? reservoirs for emerging zoonotic pathogens, Trends in Microbiology, vol.23, issue.3, pp.172-180, 2015.
DOI : 10.1016/j.tim.2014.12.004

A. Luis, O. Shea, T. Hayman, D. Wood, J. Cunningham et al., Network analysis of host-virus communities in bats and rodents reveals determinants of cross-species transmission, Ecology Letters, vol.9, issue.11, pp.1153-1162, 2015.
DOI : 10.1371/journal.ppat.1003657

R. Plowright, P. Eby, P. Hudson, I. Smith, D. Westcott et al., Ecological dynamics of emerging bat virus spillover, Proceedings of the Royal Society B: Biological Sciences, vol.6, issue.8, pp.20142124-20142124, 2014.
DOI : 10.1890/070086
URL : http://rspb.royalsocietypublishing.org/content/royprsb/282/1798/20142124.full.pdf

K. Schneeberger and C. Voigt, Zoonotic Viruses and Conservation of Bats Bats in the Anthropocene: Conservation of Bats in a Changing World, pp.263-292, 2016.

E. Donaldson, A. Haskew, J. Gates, J. Huynh, C. Moore et al., Metagenomic Analysis of the Viromes of Three North American Bat Species: Viral Diversity among Different Bat Species That Share a Common Habitat, Journal of Virology, vol.84, issue.24, pp.13004-13018, 2010.
DOI : 10.1128/JVI.01255-10

L. Li, J. Victoria, C. Wang, M. Jones, G. Fellers et al., Bat Guano Virome: Predominance of Dietary Viruses from Insects and Plants plus Novel Mammalian Viruses, Journal of Virology, vol.84, issue.14, pp.6955-6965, 2010.
DOI : 10.1128/JVI.00501-10
URL : http://jvi.asm.org/content/84/14/6955.full.pdf

M. Canuti, A. Eis-huebinger, M. Deijs, M. De-vries, J. Drexler et al., Two Novel Parvoviruses in Frugivorous New and Old World Bats, PLoS ONE, vol.45, issue.1, p.22216187, 2011.
DOI : 10.1371/journal.pone.0029140.t003
URL : https://doi.org/10.1371/journal.pone.0029140

X. Ge, Y. Li, X. Yang, H. Zhang, P. Zhou et al., Metagenomic Analysis of Viruses from Bat Fecal Samples Reveals Many Novel Viruses in Insectivorous Bats in China, Journal of Virology, vol.86, issue.8, pp.4620-4630, 2012.
DOI : 10.1128/JVI.06671-11

H. Tse, A. Tsang, H. Tsoi, A. Leung, C. Ho et al., Identification of a Novel Bat Papillomavirus by Metagenomics, PLoS ONE, vol.7, issue.8, pp.43986-22937142, 2012.
DOI : 10.1371/journal.pone.0043986.s003

Z. Wu, X. Ren, L. Yang, Y. Hu, Y. J. He et al., Virome Analysis for Identification of Novel Mammalian Viruses in Bat Species from Chinese Provinces, Journal of Virology, vol.86, issue.20, pp.10999-11012, 2012.
DOI : 10.1128/JVI.01394-12

B. He, Z. Li, F. Yang, J. Zheng, Y. Feng et al., Virome Profiling of Bats from Myanmar by Metagenomic Analysis of Tissue Samples Reveals More Novel Mammalian Viruses, PLoS ONE, vol.8, p.23630620, 2013.

L. Dacheux, M. Cervantes-gonzalez, G. Guigon, J. Thiberge, M. Vandenbogaert et al., A Preliminary Study of Viral Metagenomics of French Bat Species in Contact with Humans: Identification of New Mammalian Viruses, PLoS ONE, vol.6, issue.1, pp.87194-24489870, 2014.
DOI : 10.1371/journal.pone.0087194.s006
URL : https://hal.archives-ouvertes.fr/pasteur-01430485

D. Hu, C. Zhu, Y. Wang, A. L. Yang, L. Ye et al., Virome analysis for identification of novel mammalian viruses in bats from Southeast China, Scientific Reports, vol.30, issue.1, p.28883450, 2017.
DOI : 10.1093/molbev/mst197

Z. Wu, L. Yang, X. Ren, G. He, J. Zhang et al., Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases, The ISME Journal, vol.111, issue.3, pp.609-620, 2016.
DOI : 10.1073/pnas.1405889111

C. Calisher, Viruses in Bats, p.23, 2015.
DOI : 10.1128/JVI.00892-13

S. Cibulski, T. Teixeira, F. De-sales-lima, H. Santos, A. Franco et al., A Novel Anelloviridae Species Detected in Tadarida brasiliensis Bats: First Sequence of a Chiropteran Anellovirus, Genome Announcements, vol.83, issue.6
DOI : 10.1128/JVI.01946-08

F. Lima, S. Cibulski, D. Bello, A. Mayer, F. Witt et al., A Novel Chiropteran Circovirus Genome Recovered from a Brazilian Insectivorous Bat Species, Genome Announcements, vol.3, issue.6, pp.1393-1408, 2015.
DOI : 10.1128/JVI.01394-12
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4661317/pdf

F. Lima, S. Cibulski, H. Santos, T. Teixeira, A. Varela et al., Genomic Characterization of Novel Circular ssDNA Viruses from Insectivorous Bats in Southern Brazil, PLOS ONE, vol.19, issue.2, p.25688970, 2015.
DOI : 10.1371/journal.pone.0118070.t003

J. Drexler, V. Corman, M. Müller, G. Maganga, P. Vallo et al., Bats host major mammalian paramyxoviruses, Nature Communications, vol.16, pp.796-22531181, 2012.
DOI : 10.1126/science.1108871
URL : https://hal.archives-ouvertes.fr/pasteur-00700110

S. Tong, X. Zhu, Y. Li, M. Shi, J. Zhang et al., New World Bats Harbor Diverse Influenza A Viruses, PLoS Pathogens, vol.94, issue.10, pp.1003657-24130481, 2013.
DOI : 10.1371/journal.ppat.1003657.s021
URL : https://doi.org/10.1371/journal.ppat.1003657

F. Lima, S. Cibulski, A. Witt, A. Franco, and P. Roehe, Genomic characterization of two novel polyomaviruses in Brazilian insectivorous bats, Archives of Virology, vol.86, issue.7, pp.1831-1836, 2015.
DOI : 10.1128/JVI.00723-12

A. Brosset, P. Charles-dominique, A. Cockle, J. Cosson, and D. Masson, Bat communities and deforestation in French Guiana, Canadian Journal of Zoology, vol.42, issue.11, pp.1974-1982, 1996.
DOI : 10.2307/1933691

M. Delaval and P. Charles-dominique, Edge effects on frugivorous and nectarivorous bat communities in a neotropical primary forest in French Guiana. Revue d'e ´cologie, pp.343-352, 2006.

K. Jung and C. Threlfall, Urbanisation and Its Effects on Bats?A Global Meta-Analysis Bats in the Anthropocene: Conservation of Bats in a Changing World, pp.13-33978

B. De-thoisy, H. Bourhy, M. Delaval, D. Pontier, L. Dacheux et al., Bioecological Drivers of Rabies Virus Circulation in a Neotropical Bat Community, PLOS Neglected Tropical Diseases, vol.15, issue.1, pp.4378-26808820, 2016.
DOI : 10.1371/journal.pntd.0004378.s002
URL : https://hal.archives-ouvertes.fr/pasteur-01429578

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

G. Wilkinson, The social organization of the common vampire bat, Behav Ecol Sociobiol, vol.17, pp.123-134, 1985.

G. Wilkinson, The social organization of the common vampire bat, Behav Ecol Sociobiol, vol.17, pp.111-121, 1985.

N. Johnson, N. Aréchiga-ceballos, and A. Aguilar-setien, Vampire Bat Rabies: Ecology, Epidemiology and Control, Viruses, vol.26, issue.5, pp.1911-1928, 2014.
DOI : 10.2307/1376270
URL : http://www.mdpi.com/1999-4915/6/5/1911/pdf

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.439, issue.7078, pp.20837-20842, 2013.
DOI : 10.1038/nature04454

A. Turmelle and K. Olival, Correlates of Viral Richness in Bats (Order Chiroptera), EcoHealth, vol.17, issue.Suppl 5, pp.522-539, 2009.
DOI : 10.1111/j.1469-1809.1949.tb02451.x

D. Dechmann, B. Kranstauber, D. Gibbs, and M. Wikelski, Group Hunting???A Reason for Sociality in Molossid Bats?, PLoS ONE, vol.5, issue.2, pp.9012-20140247, 2010.
DOI : 10.1371/journal.pone.0009012.g005

R. Sikes and W. Gannon, 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

J. Victoria, A. Kapoor, L. Li, O. Blinkova, B. Slikas et al., Metagenomic Analyses of Viruses in Stool Samples from Children with Acute Flaccid Paralysis, Journal of Virology, vol.83, issue.9, pp.4642-4651, 2009.
DOI : 10.1128/JVI.02301-08

L. Prescott, L. Sherwood, and C. Woolverton, Les virus : introduction et caractères généraux. Microbiologie, 2010.

T. Allander, S. Emerson, R. Engle, R. Purcell, and J. Bukh, A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species, Proceedings of the National Academy of Sciences, vol.38, issue.5, pp.11609-11614, 2001.
DOI : 10.1002/hep.510300118

N. Berthet, A. Reinhardt, I. Leclercq, S. Van-ooyen, C. Batéjat et al., Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR, BMC Molecular Biology, vol.9, issue.1, pp.77-18771595, 2008.
DOI : 10.1186/1471-2199-9-77

A. Bolger, M. Lohse, and B. Usadel, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, vol.30, issue.15, pp.2114-2120, 2014.
DOI : 10.1093/bioinformatics/btu170
URL : https://academic.oup.com/bioinformatics/article-pdf/30/15/2114/17143152/btu170.pdf

C. Brown, A. Howe, Q. Zhang, A. Pyrkosz, and T. Brom, A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data. arXiv:12034802 [q-bio], 2012.

M. Crusoe, H. Alameldin, S. Awad, E. Boucher, A. Caldwell et al., The khmer software package: enabling efficient nucleotide sequence analysis, F1000Research, vol.https, p.26535114, 2015.
DOI : 10.12688/f1000research.6924.1
URL : https://doi.org/10.12688/f1000research.6924.1

K. Baker, R. Leggett, N. Bexfield, A. M. Daly, G. Todd et al., Metagenomic study of the viruses of African straw-coloured fruit bats: Detection of a chiropteran poxvirus and isolation of a novel adenovirus, Virology, vol.441, issue.2, pp.95-106, 2013.
DOI : 10.1016/j.virol.2013.03.014

D. Zerbino and E. Birney, Velvet: Algorithms for de novo short read assembly using de Bruijn graphs, Genome Research, vol.18, issue.5, pp.821-829, 2008.
DOI : 10.1101/gr.074492.107
URL : http://genome.cshlp.org/content/18/5/821.full.pdf

A. Bankevich, S. Nurk, D. Antipov, A. Gurevich, M. Dvorkin et al., SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing, Journal of Computational Biology, vol.19, issue.5, pp.455-477, 2012.
DOI : 10.1089/cmb.2012.0021
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3342519/pdf

R. Edgar, Search and clustering orders of magnitude faster than BLAST, Bioinformatics, vol.26, issue.19, pp.2460-2461, 2010.
DOI : 10.1093/bioinformatics/btq461
URL : https://academic.oup.com/bioinformatics/article-pdf/26/19/2460/16896486/btq461.pdf

M. Kearse, R. Moir, A. Wilson, S. Stones-havas, M. Cheung et al., Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data, Bioinformatics, vol.28, issue.12, pp.1647-1649, 2012.
DOI : 10.1093/bioinformatics/bts199

K. Katoh, K. Misawa, K. Kuma, and T. Miyata, MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform, Nucleic Acids Research, vol.30, issue.14, pp.3059-3066, 2002.
DOI : 10.1093/nar/gkf436
URL : https://academic.oup.com/nar/article-pdf/30/14/3059/9488148/gkf436.pdf

D. Darriba, G. Taboada, R. Doallo, and D. Posada, jModelTest 2: more models, new heuristics and parallel computing, Nature Methods, vol.9, issue.8, pp.772-772, 2012.
DOI : 10.1109/TAC.1974.1100705
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4594756/pdf

D. Darriba, G. Taboada, R. Doallo, and D. Posada, ProtTest 3: fast selection of best-fit models of protein evolution, Bioinformatics, vol.27, issue.8, pp.1164-1165, 2011.
DOI : 10.1093/bioinformatics/btr088

A. Rambaut, M. Suchard, D. Xie, and A. Drummond, Tracer v1

L. Li, A. Kapoor, B. Slikas, O. Bamidele, C. Wang et al., Multiple Diverse Circoviruses Infect Farm Animals and Are Commonly Found in Human and Chimpanzee Feces, Journal of Virology, vol.84, issue.4, pp.1674-1682, 2010.
DOI : 10.1128/JVI.02109-09
URL : https://hal.archives-ouvertes.fr/pasteur-01375296

X. Ge, J. Li, C. Peng, L. Wu, X. Yang et al., Genetic diversity of novel circular ssDNA viruses in bats in China, Journal of General Virology, vol.92, issue.11, pp.2646-2653, 2011.
DOI : 10.1099/vir.0.034108-0

S. Murray, Foamy virus infection in primates, Journal of Medical Primatology, vol.73, issue.4-5, pp.225-235, 2006.
DOI : 10.1034/j.1600-065X.2002.18511.x

A. Voevodin and M. P. Spumaviruses, Simian Virology, pp.217-233, 2009.
DOI : 10.1002/9780813809793

A. Mouinga-ondémé, M. Caron, D. Nkoghé, P. Telfer, P. Marx et al., Cross-Species Transmission of Simian Foamy Virus to Humans in Rural Gabon, Central Africa, Journal of Virology, vol.86, issue.2, pp.1255-1260, 2012.
DOI : 10.1128/JVI.06016-11

A. Blasse, S. Calvignac-spencer, K. Merkel, A. Goffe, C. Boesch et al., Mother-Offspring Transmission and Age-Dependent Accumulation of Simian Foamy Virus in Wild Chimpanzees, Journal of Virology, vol.87, issue.9, pp.5193-5204, 2013.
DOI : 10.1128/JVI.02743-12

W. Liu, M. Worobey, Y. Li, B. Keele, F. Bibollet-ruche et al., Molecular Ecology and Natural History of Simian Foamy Virus Infection in Wild-Living Chimpanzees, PLoS Pathogens, vol.373, issue.10, p.18604273, 2008.
DOI : 10.1371/journal.ppat.1000097.s003

C. Muniz, H. Jia, A. Shankar, L. Troncoso, A. Augusto et al., An expanded search for simian foamy viruses (SFV) in Brazilian New World primates identifies novel SFV lineages and host age-related infections, Retrovirology, vol.87, issue.7548, pp.94-26576961, 2015.
DOI : 10.1128/JVI.02743-12

R. García-pérez, C. Ibáñez, J. Godínez, N. Aréchiga, I. Garin et al., Novel Papillomaviruses in Free-Ranging Iberian Bats: No Virus???Host Co-evolution, No Strict Host Specificity, and Hints for Recombination, Genome Biology and Evolution, vol.6, issue.1, pp.94-104, 2014.
DOI : 10.1093/gbe/evt211

C. Phillips, G. Phelan, S. Dowd, M. Mcdonough, A. Ferguson et al., Microbiome analysis among bats describes influences of host phylogeny, life history, physiology and geography, Molecular Ecology, vol.73, issue.11, pp.2617-2627, 2012.
DOI : 10.1128/AEM.00062-07

M. Carrillo-araujo, N. Ta?, R. Alcántara-hernández, O. Gaona, J. Schondube et al., Phyllostomid bat microbiome composition is associated to host phylogeny and feeding strategies, Frontiers in Microbiology, vol.73, issue.267, pp.447-26042099, 2015.
DOI : 10.1128/AEM.00062-07
URL : http://journal.frontiersin.org/article/10.3389/fmicb.2015.00447/pdf

J. Drexler, A. Seelen, V. Corman, A. Tateno, V. Cottontail et al., Bats Worldwide Carry Hepatitis E Virus-Related Viruses That Form a Putative Novel Genus within the Family Hepeviridae, Journal of Virology, vol.86, issue.17, pp.9134-9147, 2012.
DOI : 10.1128/JVI.00800-12

G. Wibbelt, A. Kurth, N. Yasmum, M. Bannert, S. Nagel et al., Discovery of herpesviruses in bats, Journal of General Virology, vol.88, issue.10, pp.2651-2655, 2007.
DOI : 10.1099/vir.0.83045-0

V. Molnár, M. Jánoska, B. Harrach, R. Glávits, N. Pálmai et al., Detection of a novel bat gammaherpesvirus in Hungary, Acta Veterinaria Hungarica, vol.56, issue.4, pp.529-538, 2008.
DOI : 10.1556/AVet.56.2008.4.10

R. Razafindratsimandresy, E. Jeanmaire, D. Counor, P. Vasconcelos, A. Sall et al., Partial molecular characterization of alphaherpesviruses isolated from tropical bats, Journal of General Virology, vol.90, issue.1, pp.44-47, 2009.
DOI : 10.1099/vir.0.006825-0
URL : https://hal.archives-ouvertes.fr/pasteur-00592600

S. Watanabe, N. Ueda, K. Iha, J. Masangkay, H. Fujii et al., Detection of a new bat gammaherpesvirus in the Philippines, Virus Genes, vol.24, issue.1, p.90, 2009.
DOI : 10.1007/s11262-009-0368-8

K. Sano, S. Okazaki, S. Taniguchi, J. Masangkay, R. Puentespina et al., Detection of a novel herpesvirus from bats in the Philippines, Virus Genes, vol.88, issue.1, pp.136-139, 2015.
DOI : 10.1128/JVI.03405-13

K. Host and B. Damania, Discovery of a Novel Bat Gammaherpesvirus. mSphere, p.27303690, 2016.

X. Zheng, M. Qiu, S. Chen, X. J. Ma, L. Liu et al., High prevalence and diversity of viruses of the subfamily Gammaherpesvirinae, family Herpesviridae, in fecal specimens from bats of different species in southern China, Archives of Virology, vol.22, issue.2, pp.135-140, 2016.
DOI : 10.5604/12321966.1152063

A. Ishii, K. Ueno, Y. Orba, M. Sasaki, L. Moonga et al., A nairovirus isolated from African bats causes haemorrhagic gastroenteritis and severe hepatic disease in mice, Nature Communications, vol.848, pp.6651-25451856, 2014.
DOI : 10.1016/S0006-8993(99)01909-5
URL : http://www.nature.com/articles/ncomms6651.pdf

P. Walker, S. Widen, C. Firth, K. Blasdell, T. Wood et al., Genomic Characterization of Yogue, Kasokero, Issyk-Kul, Keterah, Gossas, and Thiafora Viruses: Nairoviruses Naturally Infecting Bats, Shrews, and Ticks, The American Journal of Tropical Medicine and Hygiene, vol.93, issue.5, pp.1041-1051, 2015.
DOI : 10.4269/ajtmh.15-0344
URL : http://www.ajtmh.org/deliver/fulltext/14761645/93/5/1041.pdf?itemId=/content/journals/10.4269/ajtmh.15-0344&mimeType=pdf&containerItemId=content/journals/14761645

D. Lvov, F. Karas, E. Timofeev, Y. Tsyrkin, S. Vargina et al., ?Issyk-Kul? virus, a new arbovirus isolated from bats and argas (Carios) vespertilionis (Latr., 1802) in the Kirghiz S.S.R., Archiv f???r die gesamte Virusforschung, vol.96, issue.2, pp.207-209, 1973.
DOI : 10.3181/00379727-96-23483

M. Müller, S. Devignot, E. Lattwein, V. Corman, G. Maganga et al., Evidence for widespread infection of African bats with Crimean-Congo hemorrhagic fever-like viruses, Scientific Reports, vol.13, issue.14, pp.26637-27217069, 2016.
DOI : 10.3201/eid1309.070342

J. Duboscq and P. Heeb, Pathogènes, parasites et réseaux dans les sociétés animales Analyse des réseaux sociaux appliquée à l'e ´thologie et l'e ´cologie, Editions Matériologiques, pp.343-358, 2015.