P. Mcminn, Recent advances in the molecular epidemiology and control of human enterovirus 71 infection, Current Opinion in Virology, vol.2, issue.2, pp.199-205, 2012.
DOI : 10.1016/j.coviro.2012.02.009

M. Abzug, Enterovirus 71: emergence of the new poliomyelitis, South Afr J Epidemiol Infect, vol.24, pp.5-8, 2009.

M. Ooi, S. Wong, P. Lewthwaite, M. Cardosa, and T. Solomon, Clinical features, diagnosis, and management of enterovirus 71, The Lancet Neurology, vol.9, issue.11, pp.1097-1105, 2010.
DOI : 10.1016/S1474-4422(10)70209-X

T. Solomon, P. Lewthwaite, D. Perera, M. Cardosa, and P. Mcminn, Virology, epidemiology, pathogenesis, and control of enterovirus 71, The Lancet Infectious Diseases, vol.10, issue.11, pp.778-790, 2010.
DOI : 10.1016/S1473-3099(10)70194-8

Y. Li, Z. Liang, J. Xia, J. Wu, and L. Wang, Immunogenicity, Safety, and Immune persistence of A Novel Inactivated Human Enterovirus 71 (EV71) Vaccine: A Phase II, Randomized, Double-Blind, Placebo-Controlled trial, J Infect Dis, 2013.

F. Zhu, F. Meng, J. Li, X. Li, and Q. Mao, Efficacy, safety, and immunology of an inactivated alum-adjuvant enterovirus 71 vaccine in children in China: a multicentre, randomised, double-blind, placebo-controlled, phase 3 trial, The Lancet, vol.381, issue.9882, pp.2024-2032, 2013.
DOI : 10.1016/S0140-6736(13)61049-1

M. Oberste, K. Maher, D. Kilpatrick, and M. Pallansch, Molecular evolution of the human enteroviruses: correlation of serotype with VP1 sequence and application to picornavirus classification, J Virol, vol.73, pp.1941-1948, 1999.

C. Kottaridi, E. Bolanaki, N. Siafakas, and P. Markoulatos, Evaluation of seroneutralization and molecular diagnostic methods for echovirus identification, Diagnostic Microbiology and Infectious Disease, vol.53, issue.2, pp.113-119, 2005.
DOI : 10.1016/j.diagmicrobio.2005.06.016

A. Mirand, C. Henquell, C. Archimbaud, S. Ughetto, and D. Antona, Outbreak of hand, foot and mouth disease/herpangina associated with coxsackievirus A6 and A10 infections in 2010, France: a large citywide, prospective observational study, Clinical Microbiology and Infection, vol.18, issue.5, pp.110-118, 2012.
DOI : 10.1111/j.1469-0691.2012.03789.x

M. Oberste, K. Maher, D. Kilpatrick, M. Flemister, and B. Brown, Typing of human enteroviruses by partial sequencing of VP1, J Clin Microbiol, vol.37, pp.1288-1293, 1999.

B. Brown, M. Oberste, J. Alexander, J. Kennett, M. Pallansch et al., Molecular epidemiology and evolution of enterovirus 71 strains isolated from 1970 to 1998, J Virol, vol.73, pp.9969-9975, 1999.

H. Yu, W. Chen, H. Chang, R. Tang, and J. Zhao, Genetic analysis of the VP1 region of enterovirus 71 reveals the emergence of genotype A in central China in 2008, Virus Genes, vol.9, issue.1, pp.1-4, 2008.
DOI : 10.1007/s11262-010-0472-9

J. Zhu, Z. Luo, J. Wang, Z. Xu, and H. Chen, Phylogenetic Analysis of Enterovirus 71 Circulating in Beijing, China from 2007 to 2009, PLoS ONE, vol.49, issue.(9), p.56318, 2007.
DOI : 10.1371/journal.pone.0056318.s001

J. Deshpande, S. Nadkarni, and P. Francis, Enterovirus 71 isolated from a case of acute flaccid paralysis in India represents a new genotype, Current Science, vol.84, pp.1350-1353, 2003.

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

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

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

K. Lole, R. Bollinger, R. Paranjape, D. Gadkari, and S. Kulkarni, Full-length human immunodeficiency virus type 1 genomes from subtype Cinfected seroconverters in India, with evidence of intersubtype recombination, J Virol, vol.73, pp.152-160, 1999.

A. Drummond, S. Ho, M. Phillips, and A. Rambaut, Relaxed Phylogenetics and Dating with Confidence, PLoS Biology, vol.20, issue.5, p.88, 2006.
DOI : 10.1371/journal.pbio.0040088.sd001

A. Drummond and A. Rambaut, BEAST: Bayesian evolutionary analysis by sampling trees, BMC Evolutionary Biology, vol.7, issue.1, p.214, 2007.
DOI : 10.1186/1471-2148-7-214

B. Shapiro, A. Rambaut, and A. Drummond, Choosing Appropriate Substitution Models for the Phylogenetic Analysis of Protein-Coding Sequences, Molecular Biology and Evolution, vol.23, issue.1, pp.7-9, 2006.
DOI : 10.1093/molbev/msj021

A. Drummond, A. Rambaut, B. Shapiro, and O. Pybus, Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences, Molecular Biology and Evolution, vol.22, issue.5, pp.1185-1192, 2005.
DOI : 10.1093/molbev/msi103

V. Minin, E. Bloomquist, and M. Suchard, Smooth Skyride through a Rough Skyline: Bayesian Coalescent-Based Inference of Population Dynamics, Molecular Biology and Evolution, vol.25, issue.7, pp.1459-1471, 2008.
DOI : 10.1093/molbev/msn090

R. Kass and A. R. , Bayes Factors, Journal of the American Statistical Association, vol.2, issue.430, pp.773-795, 1995.
DOI : 10.1080/01621459.1995.10476572

M. Suchard, R. Weiss, and J. Sinsheimer, Bayesian Selection of Continuous-Time Markov Chain Evolutionary Models, Molecular Biology and Evolution, vol.18, issue.6, pp.1001-1013, 2001.
DOI : 10.1093/oxfordjournals.molbev.a003872

S. Shih, M. Ho, K. Lin, S. Wu, and Y. Chen, Genetic analysis of enterovirus 71 isolated from fatal and non-fatal cases of hand, foot and mouth disease during an epidemic in Taiwan, 1998, Virus Research, vol.68, issue.2, pp.127-136, 1998.
DOI : 10.1016/S0168-1702(00)00162-3

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

L. Bouslama, D. Nasri, L. Chollet, K. Belguith, and T. Bourlet, Natural Recombination Event within the Capsid Genomic Region Leading to a Chimeric Strain of Human Enterovirus B, Journal of Virology, vol.81, issue.17, pp.8944-8952, 2007.
DOI : 10.1128/JVI.00180-07

A. Lukashev, V. Lashkevich, O. Ivanova, G. Koroleva, and A. Hinkkanen, Recombination in circulating Human enterovirus B: independent evolution of structural and non-structural genome regions, Journal of General Virology, vol.86, issue.12, pp.3281-3290, 2005.
DOI : 10.1099/vir.0.81264-0

M. Oberste, S. Penaranda, and M. Pallansch, RNA Recombination Plays a Major Role in Genomic Change during Circulation of Coxsackie B Viruses, Journal of Virology, vol.78, issue.6, pp.2948-2955, 2004.
DOI : 10.1128/JVI.78.6.2948-2955.2004

P. Simmonds and J. Welch, Frequency and Dynamics of Recombination within Different Species of Human Enteroviruses, Journal of Virology, vol.80, issue.1, pp.483-493, 2006.
DOI : 10.1128/JVI.80.1.483-493.2006

C. Rao, P. Yergolkar, and K. Shankarappa, Antigenic Diversity of Enteroviruses Associated with Nonpolio Acute Flaccid Paralysis, India, 2007???2009, Emerging Infectious Diseases, vol.18, issue.11, pp.1833-1840, 2007.
DOI : 10.3201/eid1811.111457

N. Combelas, B. Holmblat, M. Joffret, F. Colbere-garapin, and F. Delpeyroux, Recombination between Poliovirus and Coxsackie A Viruses of Species C: A Model of Viral Genetic Plasticity and Emergence, Viruses, vol.3, issue.12, pp.1460-1484, 2011.
DOI : 10.3390/v3081460

A. Lukashev, Recombination among picornaviruses, Reviews in Medical Virology, vol.24, issue.Pt 3, pp.327-337, 2010.
DOI : 10.1002/rmv.660

C. Yip, S. Lau, J. Lo, K. Chan, and P. Woo, Genetic characterization of EV71 isolates from 2004 to 2010 reveals predominance and persistent circulation of the newly proposed genotype D and recent emergence of a distinct lineage of subgenotype C2 in Hong Kong, Virology Journal, vol.10, issue.1, p.222, 2013.
DOI : 10.1186/1471-2148-6-29

K. Tee, T. Lam, Y. Chan, J. Bible, and A. Kamarulzaman, Evolutionary Genetics of Human Enterovirus 71: Origin, Population Dynamics, Natural Selection, and Seasonal Periodicity of the VP1 Gene, Journal of Virology, vol.84, issue.7, pp.3339-3350, 2010.
DOI : 10.1128/JVI.01019-09

S. Van-der-sanden, H. Van-der-avoort, P. Lemey, G. Uslu, and M. Koopmans, Evolutionary trajectory of the VP1 gene of human enterovirus 71 genogroup B and C viruses, Journal of General Virology, vol.91, issue.8, pp.1949-1958, 2010.
DOI : 10.1099/vir.0.019695-0

A. Mirand, I. Schuffenecker, C. Henquell, G. Billaud, and G. Jugie, Phylogenetic evidence for a recent spread of two populations of human enterovirus 71 in European countries, Journal of General Virology, vol.91, issue.9, pp.2263-2277, 2010.
DOI : 10.1099/vir.0.021741-0