M. Pallansch and R. Roos, Enteroviruses: Polioviruses, Coxsackieviruses, Echoviruses, and Newer Enteroviruses, Fields Virology. Philadelphia: Lippincott Williams and Wilkins, pp.839-894, 2007.

A. Boros, P. Pankovics, N. Knowles, and G. Reuter, Natural interspecies recombinant bovine/porcine enterovirus in sheep, Journal of General Virology, vol.93, issue.Pt_9, pp.1941-1951, 2012.
DOI : 10.1099/vir.0.041335-0

U. Blas-machado, J. Saliki, M. Boileau, S. Goens, and S. Caseltine, Fatal Ulcerative and Hemorrhagic Typhlocolitis in a Pregnant Heifer Associated with Natural Bovine Enterovirus Type-1 Infection, Veterinary Pathology, vol.7, issue.1, pp.110-115, 2007.
DOI : 10.1099/0022-1317-23-2-173

S. Nielsen, T. Mourier, U. Baandrup, T. Soland, and M. Bertelsen, Probable Transmission of Coxsackie B3 Virus from Human to Chimpanzee, Denmark, Emerging Infectious Diseases, vol.18, issue.7, pp.1163-1165, 2012.
DOI : 10.3201/eid1807.111689

C. Tapparel, F. Siegrist, T. Petty, and L. Kaiser, Picornavirus and enterovirus diversity with associated human diseases, Infection, Genetics and Evolution, vol.14, pp.282-293, 2013.
DOI : 10.1016/j.meegid.2012.10.016

J. Ayukekbong, J. Kabayiza, M. Lindh, T. Nkuo-akenji, and F. Tah, Shift of Enterovirus species among children in Cameroon ??? Identification of a new enterovirus, EV-A119, Journal of Clinical Virology, vol.58, issue.1, pp.227-232, 2013.
DOI : 10.1016/j.jcv.2013.07.005

M. Rakoto-andrianarivelo, D. Rousset, R. Razafindratsimandresy, S. Chevaliez, and S. Guillot, High Frequency of Human Enterovirus Species C Circulation in Madagascar, Journal of Clinical Microbiology, vol.43, issue.1, pp.242-249, 2005.
DOI : 10.1128/JCM.43.1.242-249.2005
URL : https://hal.archives-ouvertes.fr/pasteur-00319480

S. Sadeuh-mba, M. Bessaud, D. Massenet, M. Joffret, and M. Endegue, High Frequency and Diversity of Species C Enteroviruses in Cameroon and Neighboring Countries, Journal of Clinical Microbiology, vol.51, issue.3, pp.759-770, 2013.
DOI : 10.1128/JCM.02119-12

P. Silva, K. Stark, F. Mockenhaupt, K. Reither, and T. Weitzel, Molecular characterization of enteric viral agents from children in northern region of Ghana, Journal of Medical Virology, vol.346, issue.10, pp.1790-1798, 2008.
DOI : 10.1002/jmv.21231

N. Khetsuriani, A. Lamonte-fowlkes, S. Oberst, and M. Pallansch, Enterovirus surveillance?United States, MMWR Surveill Summ, vol.55, pp.1-20, 1970.

C. Tan, L. Ninove, J. Gaudart, A. Nougairede, and C. Zandotti, A Retrospective Overview of Enterovirus Infection Diagnosis and Molecular Epidemiology in the Public Hospitals of Marseille, France (1985???2005), PLoS ONE, vol.4, issue.3, p.18022, 1985.
DOI : 10.1371/journal.pone.0018022.s001

D. Antona, N. Leveque, J. Chomel, S. Dubrou, and D. Levy-bruhl, Surveillance of enteroviruses in France, 2000???2004, European Journal of Clinical Microbiology & Infectious Diseases, vol.84, issue.6, pp.403-412, 2000.
DOI : 10.1007/s10096-007-0306-4

C. Daleno, A. Piralla, A. Scala, F. Baldanti, and D. Greenberg, Full Genome Sequence of a Novel Human Enterovirus C (EV-C118) Isolated from Two Children with Acute Otitis Media and Community-Acquired Pneumonia in Israel, Genome Announcements, vol.1, issue.1, pp.121-00112, 2013.
DOI : 10.1128/genomeA.00121-12

A. Lukashev, J. Drexler, V. Kotova, E. Amjaga, and V. Reznik, Novel serotypes 105 and 116 are members of distinct subgroups of Human enterovirus C, Journal of General Virology, vol.93, issue.Pt_11, pp.2357-2362, 2012.
DOI : 10.1099/vir.0.043216-0

P. Pankovics, A. Boros, H. Szabo, G. Szekely, and K. Gyurkovits, Human enterovirus 109 (EV109) in acute paediatric respiratory disease in Hungary, Acta Microbiologica et Immunologica Hungarica, vol.59, issue.2, pp.285-290, 2012.
DOI : 10.1556/AMicr.59.2012.2.13

T. Smura, S. Blomqvist, T. Hovi, and M. Roivainen, The complete genome sequences for a novel enterovirus type, enterovirus 96, reflect multiple recombinations, Archives of Virology, vol.6, issue.7, pp.1157-1161, 2009.
DOI : 10.1007/s00705-009-0418-5

C. Tapparel, T. Junier, D. Gerlach, S. Van-belle, and L. Turin, New Respiratory Enterovirus and Recombinant Rhinoviruses among Circulating Picornaviruses, Emerging Infectious Diseases, vol.15, issue.5, pp.719-726, 2009.
DOI : 10.3201/eid1505.081286

M. Bessaud, S. Pillet, I. W. Joffret, M. Pozzetto, and B. , Molecular Characterization of Human Enteroviruses in the Central African Republic: Uncovering Wide Diversity and Identification of a New Human Enterovirus A71 Genogroup, Journal of Clinical Microbiology, vol.50, issue.5, pp.1650-1658, 2012.
DOI : 10.1128/JCM.06657-11

T. Bingjun, H. Yoshida, Y. W. Lin, L. Tsuji, and T. , Molecular typing and epidemiology of non-polio enteroviruses isolated from Yunnan Province, the People's Republic of China, Journal of Medical Virology, vol.11, issue.4, pp.670-679, 2008.
DOI : 10.1002/jmv.21122

H. Harvala, D. Van-nguyen, C. Mcintyre, S. Ahuka-mundeke, M. Ngole et al., Co-circulation of enteroviruses between apes and humans, Journal of General Virology, vol.95, issue.Pt_2, pp.59048-059040, 2013.
DOI : 10.1099/vir.0.059048-0

N. Junttila, N. Leveque, J. Kabue, G. Cartet, and F. Mushiya, New enteroviruses, EV-93 and EV-94, associated with acute flaccid paralysis in the Democratic Republic of the Congo, Journal of Medical Virology, vol.58, issue.4, pp.393-400, 2007.
DOI : 10.1002/jmv.20825

R. Fuentes-marins, A. Rodriguez, S. Kalter, A. Hellman, and R. Crandell, Isolation of enteroviruses from the ''normal'' baboon (papio doguera), J Bacteriol, vol.85, pp.1045-1050, 1963.

R. Heberling and F. Cheever, Characteristics of the Growth Cycles of Four Simian Enteroviruses (SV2, SV6, SV42, SV49)., Experimental Biology and Medicine, vol.120, issue.3, pp.825-828, 1965.
DOI : 10.3181/00379727-120-30666

W. Hoffert, M. Bates, and F. Cheever, Study of enteric viruses of simian origin, Am J Hyg, vol.68, pp.15-30, 1958.

R. Hull, J. Minner, and J. Smith, New viral agents recovered from tissue cultures of monkey kidney cells. I. Origin and properties of cytopathogenic agents S, Am J Hyg, vol.63, pp.204-215, 1956.

S. Kalter, Enteric Viruses of Nonhuman Primates, Veterinary Pathology, vol.19, issue.7 Suppl, pp.33-43, 1982.
DOI : 10.1177/030098588201907s05

A. Rodriguez, S. Kalter, R. Heberling, R. Helmke, and J. Guajardo, Viral infections of the captive Kenya baboon (Papio cynocephalus): a five-year epidemiologic study of an outdoor colony, Lab Anim Sci, vol.27, pp.356-371, 1977.

S. Kalter, C. Kim, and E. Sueltenfuss, Further Characterization of Agents Isolated from Normal Baboon (Papio Sp.), Journal of Infectious Diseases, vol.117, issue.4, pp.301-306, 1967.
DOI : 10.1093/infdis/117.4.301

H. Malherbe and R. Harwin, The cytopathic effects of vervet monkey viruses, S Afr Med J, vol.37, pp.407-411, 1963.

M. Oberste, K. Maher, and M. Pallansch, Molecular Phylogeny and Proposed Classification of the Simian Picornaviruses, Journal of Virology, vol.76, issue.3, pp.1244-1251, 2002.
DOI : 10.1128/JVI.76.3.1244-1251.2002

M. Oberste, K. Maher, and M. Pallansch, Genomic evidence that simian virus 2 and six other simian picornaviruses represent a new genus in Picornaviridae, Virology, vol.314, issue.1, pp.283-293, 2003.
DOI : 10.1016/S0042-6822(03)00420-3

N. Knowles, T. Hovi, T. Hyypiä, A. King, and A. Lindberg, Picornaviridae, Virus Taxonomy: Classification and Nomenclature of Viruses: Ninth Report of the International Committee on Taxonomy of Viruses, pp.855-880, 2012.

M. Oberste, K. Maher, and M. Pallansch, Complete genome sequences for nine simian enteroviruses, Journal of General Virology, vol.88, issue.12, pp.3360-3372, 2007.
DOI : 10.1099/vir.0.83124-0

H. Harvala, C. Sharp, E. Ngole, E. Delaporte, and M. Peeters, Detection and Genetic Characterization of Enteroviruses Circulating among Wild Populations of Chimpanzees in Cameroon: Relationship with Human and Simian Enteroviruses, Journal of Virology, vol.85, issue.9, pp.4480-4486, 2011.
DOI : 10.1128/JVI.02285-10

C. Neel, E. L. Li, Y. Takehisa, J. Rudicell, and R. , Molecular Epidemiology of Simian Immunodeficiency Virus Infection in Wild-Living Gorillas, Journal of Virology, vol.84, issue.3, pp.1464-1476, 2010.
DOI : 10.1128/JVI.02129-09

F. Van-heuverswyn, Y. Li, C. Neel, E. Bailes, and B. Keele, Human immunodeficiency viruses: SIV infection in wild gorillas, Nature, vol.18, issue.7116, p.164, 2006.
DOI : 10.1038/444164a

E. Bolanaki, C. Kottaridi, E. Dedepsidis, Z. Kyriakopoulou, and V. Pliaka, Direct extraction and molecular characterization of enteroviruses genomes from human faecal samples, Molecular and Cellular Probes, vol.22, issue.3, pp.156-161, 2008.
DOI : 10.1016/j.mcp.2007.12.001

W. Nix, B. Jiang, K. Maher, E. Strobert, and M. Oberste, Identification of Enteroviruses in Naturally Infected Captive Primates, Journal of Clinical Microbiology, vol.46, issue.9, pp.2874-2878, 2008.
DOI : 10.1128/JCM.00074-08

W. Nix, M. Oberste, and M. Pallansch, Sensitive, Seminested PCR Amplification of VP1 Sequences for Direct Identification of All Enterovirus Serotypes from Original Clinical Specimens, Journal of Clinical Microbiology, vol.44, issue.8, pp.2698-2704, 2006.
DOI : 10.1128/JCM.00542-06

S. Guillot, V. Caro, N. Cuervo, E. Korotkova, and M. Combiescu, Natural Genetic Exchanges between Vaccine and Wild Poliovirus Strains in Humans, Journal of Virology, vol.74, issue.18, pp.8434-8443, 2000.
DOI : 10.1128/JVI.74.18.8434-8443.2000

M. Bessaud, S. Jegouic, M. Joffret, C. Barge, and J. Balanant, Characterization of the genome of human enteroviruses: Design of generic primers for amplification and sequencing of different regions of the viral genome, Journal of Virological Methods, vol.149, issue.2, pp.277-284, 2008.
DOI : 10.1016/j.jviromet.2008.01.027
URL : https://hal.archives-ouvertes.fr/pasteur-00318628

M. Oberste, Complete genome sequences of all members of the species Human enterovirus A, Journal of General Virology, vol.85, issue.6, pp.1597-1607, 2004.
DOI : 10.1099/vir.0.79789-0

B. Keele, F. Van-heuverswyn, Y. Li, E. Bailes, and J. Takehisa, Chimpanzee Reservoirs of Pandemic and Nonpandemic HIV-1, Science, vol.313, issue.5786, pp.523-526, 2006.
DOI : 10.1126/science.1126531

A. Van-der-kuyl, C. Kuiken, J. Dekker, and J. Goudsmit, Phylogeny of African monkeys based upon mitochondrial 12S rRNA sequences, Journal of Molecular Evolution, vol.20, issue.2, pp.173-180, 1995.
DOI : 10.1007/BF00167111

B. Brown, K. Maher, M. Flemister, P. Naraghi-arani, and M. Uddin, Resolving ambiguities in genetic typing of human enterovirus species C clinical isolates and identification of enterovirus 96, 99 and 102, Journal of General Virology, vol.90, issue.7, pp.1713-1723, 2009.
DOI : 10.1099/vir.0.008540-0

K. Tamura, D. Peterson, N. Peterson, G. Stecher, and M. Nei, 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

S. Guindon, J. Dufayard, V. Lefort, M. Anisimova, and W. Hordijk, New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0, Systematic Biology, vol.59, issue.3, pp.307-321, 2010.
DOI : 10.1093/sysbio/syq010
URL : https://hal.archives-ouvertes.fr/lirmm-00511784

M. Kimura, A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, Journal of Molecular Evolution, vol.206, issue.5, Nov., pp.111-120, 1980.
DOI : 10.1007/BF01731581

M. Hasegawa, H. Kishino, and T. Yano, Dating of the human-ape splitting by a molecular clock of mitochondrial DNA, Journal of Molecular Evolution, vol.275, issue.3, pp.160-174, 1985.
DOI : 10.1007/BF02101694

M. Lee, P. Chiang, S. Luo, M. Huang, and G. Liou, Incidence rates of enterovirus 71 infections in young children during a nationwide epidemic in Taiwan, PLoS Negl Trop Dis, vol.6, pp.2008-2017, 2012.

X. Tan, X. Huang, S. Zhu, H. Chen, and Q. Yu, The Persistent Circulation of Enterovirus 71 in People's Republic of China: Causing Emerging Nationwide Epidemics Since 2008, PLoS ONE, vol.13, issue.9, p.25662, 2008.
DOI : 10.1371/journal.pone.0025662.s003

M. Bessaud, R. Razafindratsimandresy, A. Nougairede, M. Joffret, and J. Deshpande, Molecular Comparison and Evolutionary Analyses of VP1 Nucleotide Sequences of New African Human Enterovirus 71 Isolates Reveal a Wide Genetic Diversity, PLoS ONE, vol.91, issue.3, p.90624, 2014.
DOI : 10.1371/journal.pone.0090624.s005
URL : https://hal.archives-ouvertes.fr/pasteur-01078436

M. Bessaud, M. Joffret, B. Holmblat, R. Razafindratsimandresy, and F. Delpeyroux, Genetic Relationship between Cocirculating Human Enteroviruses Species C, PLoS ONE, vol.6, issue.Pt 10, p.24823, 2011.
DOI : 10.1371/journal.pone.0024823.t001
URL : https://hal.archives-ouvertes.fr/pasteur-00835576

M. Oberste, M. Feeroz, K. Maher, W. Nix, and G. Engel, Characterizing the picornavirus landscape among synanthropic nonhuman primates in Bangladesh, J Virol, vol.24, p.24, 2007.

M. Oberste, M. Feeroz, K. Maher, W. Nix, and G. Engel, Naturally acquired picornavirus infections in nonhuman primates at the Dhaka Zoo, J Virol, vol.24, p.24, 2012.

M. Oberste, K. Maher, S. Michele, G. Belliot, and M. Uddin, and 91 represent a novel group within the species Human enterovirus A, J Gen Virol, vol.76, issue.86, pp.90-445, 2005.

H. Harvala, C. Mcintyre, N. Imai, L. Clasper, and C. Djoko, High Seroprevalence of Enterovirus Infections in Apes and Old World Monkeys, Emerging Infectious Diseases, vol.18, issue.2, pp.283-286, 2012.
DOI : 10.3201/eid1802.111363

T. Smura, S. Blomqvist, A. Paananen, T. Vuorinen, and Z. Sobotova, Enterovirus surveillance reveals proposed new serotypes and provides new insight into enterovirus 5'-untranslated region evolution, Journal of General Virology, vol.88, issue.9, pp.2520-2526, 2007.
DOI : 10.1099/vir.0.82866-0