I. Afonina, I. Ankoudinova, A. Mills, S. Lokhov, P. Huynh et al., Primers with 5??? flaps improve real-time PCR, BioTechniques, vol.43, issue.6, pp.770-773, 2007.
DOI : 10.2144/000112631

. Anonymous, Acute flaccid paralysis associated with circulating vaccine-derived poliovirus, Philippines, Wkly Epidemiol Rec, vol.76, pp.319-339, 2001.

. Anonymous, Circulation of a type 2 vaccine-derived poliovirus, Egypt, Wkly Epidemiol Rec, vol.76, pp.27-36, 2001.

. Anonymous, Titration of laboratory quality control standard In: WHO (Ed), Polio laboratory manual, World Health Organization, pp.75-78, 2004.

M. Arita, S. L. Zhu, H. Yoshida, T. Yoneyama, T. Miyamura et al., A Sabin 3-Derived Poliovirus Recombinant Contained a Sequence Homologous with Indigenous Human Enterovirus Species C in the Viral Polymerase Coding Region, Journal of Virology, vol.79, issue.20, pp.12650-12657, 2005.
DOI : 10.1128/JVI.79.20.12650-12657.2005

J. L. Bailly, A. Beguet, M. Chambon, C. Henquell, and H. Peigue-lafeuille, Nosocomial transmission of echovirus 30: molecular evidence by phylogenetic analysis of the VP1 encoding sequence, J Clin Microbiol, vol.38, pp.2889-92, 2000.

S. Blomqvist, A. L. Bruu, M. Stenvik, and T. Hovi, Characterization of a recombinant type 3/type 2 poliovirus isolated from a healthy vaccinee and containing a chimeric capsid protein VP1, Journal of General Virology, vol.84, issue.3, pp.573-80, 2003.
DOI : 10.1099/vir.0.18708-0

L. Bouslama, D. Nasri, L. Chollet, K. Belguith, T. Bourlet et al., 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.8944-52, 2007.
DOI : 10.1128/JVI.00180-07

V. Caro, S. Guillot, F. Delpeyroux, and R. Crainic, Molecular strategy for ???serotyping??? of human enteroviruses, Journal of General Virology, vol.82, issue.1, pp.79-91, 2001.
DOI : 10.1099/0022-1317-82-1-79

I. Casas, G. F. Palacios, G. Trallero, D. Cisterna, M. C. Freire et al., Molecular characterization of human enteroviruses in clinical samples: Comparison between VP2, VP1, and RNA polymerase regions using RT nested PCR assays and direct sequencing of products, Journal of Medical Virology, vol.65, issue.1, pp.138-186, 2001.
DOI : 10.1002/jmv.2013.abs

G. W. Chen, J. H. Huang, Y. L. Lo, K. C. Tsao, and S. C. Chang, Mosaic genome structure of echovirus type 30 that circulated in Taiwan in 2001, Archives of Virology, vol.44, issue.10, pp.1807-1824, 2001.
DOI : 10.1007/s00705-007-1018-x

S. Chevaliez, A. Szendroi, V. Caro, J. Balanant, S. Guillot et al., Molecular comparison of echovirus 11 strains circulating in Europe during an epidemic of multisystem hemorrhagic disease of infants indicates that evolution generally occurs by recombination, Virology, vol.325, issue.1, pp.56-70, 2004.
DOI : 10.1016/j.virol.2004.04.026

URL : https://hal.archives-ouvertes.fr/pasteur-00319483

N. Cuervo, S. Guillot, N. Romanenkova, M. Combiescu, A. Aubert-combiescu et al., Genomic Features of Intertypic Recombinant Sabin Poliovirus Strains Excreted by Primary Vaccinees, Journal of Virology, vol.75, issue.13, pp.5740-5751, 2001.
DOI : 10.1128/JVI.75.13.5740-5751.2001

G. Dahourou, S. Guillot, L. Gall, O. Crainic, and R. , Genetic recombination in wild-type poliovirus, Journal of General Virology, vol.83, issue.12, pp.3103-3113, 2002.
DOI : 10.1099/0022-1317-83-12-3103

T. Hyypia, T. Hovi, N. J. Knowles, and G. Stanway, Classification of enteroviruses based on molecular and biological properties., Journal of General Virology, vol.78, issue.1, pp.1-11, 1997.
DOI : 10.1099/0022-1317-78-1-1

H. Ishiko, Y. Shimada, M. Yonaha, O. Hashimoto, A. Hayashi et al., Molecular Diagnosis of Human Enteroviruses by Phylogeny???Based Classification by Use of the VP4 Sequence, The Journal of Infectious Diseases, vol.185, issue.6, pp.744-54, 2002.
DOI : 10.1086/339298

M. Iturriza-gomara, B. Megson, and J. Gray, Molecular detection and characterization of human enteroviruses directly from clinical samples using RT-PCR and DNA sequencing, Journal of Medical Virology, vol.32, issue.2, pp.243-53, 2006.
DOI : 10.1002/jmv.20533

N. Junttila, N. Leveque, J. P. Kabue, G. Cartet, F. Mushiya et al., 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

J. G. Kapsenberg, ECHO virus type 33 as a cause of meningitis, Archiv f???r die gesamte Virusforschung, vol.118, issue.1-2, pp.144-151, 1968.
DOI : 10.1007/BF01242122

O. M. Kew, P. F. Wright, V. I. Agol, F. Delpeyroux, H. Shimizu et al., Circulating vaccine-derived polioviruses: current state of knowledge, Bull World Health Organ, vol.82, pp.16-23, 2004.
URL : https://hal.archives-ouvertes.fr/pasteur-00319492

A. M. King, Preferred sites of recombination in poliovirus RNA: an analysis of 40 intertypic cross-over sequences, Nucleic Acids Research, vol.16, issue.24, pp.11705-11728, 1988.
DOI : 10.1093/nar/16.24.11705

C. Kottaridi, E. Bolanaki, Z. Kyriakopoulou, E. Dedepsidis, A. Pratti et al., Possible recombination and gene adaptation exchanges among clinical echovirus strains: crossing the temporal and topological barriers, Diagnostic Microbiology and Infectious Disease, vol.58, issue.4, pp.407-419, 2007.
DOI : 10.1016/j.diagmicrobio.2007.03.007

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, 2005.
DOI : 10.1016/j.diagmicrobio.2005.06.016

A. M. Lindberg, P. Andersson, C. Savolainen, M. N. Mulders, and T. Hovi, Evolution of the genome of Human enterovirus B: incongruence between phylogenies of the VP1 and 3CD regions indicates frequent recombination within the species, Journal of General Virology, vol.84, issue.5, pp.1223-1258, 2003.
DOI : 10.1099/vir.0.18971-0

A. N. Lukashev, Role of recombination in evolution of enteroviruses, Reviews in Medical Virology, vol.96, issue.3, pp.157-67, 2005.
DOI : 10.1002/rmv.457

A. N. Lukashev, V. A. Lashkevich, O. E. Ivanova, G. A. Koroleva, A. E. Hinkkanen et al., Recombination in Circulating Enteroviruses, Journal of Virology, vol.77, issue.19, pp.10423-10454, 2003.
DOI : 10.1128/JVI.77.19.10423-10431.2003

J. Martin, E. Samoilovich, G. Dunn, A. Lackenby, E. Feldman et al., Isolation of an Intertypic Poliovirus Capsid Recombinant from a Child with Vaccine-Associated Paralytic Poliomyelitis, Journal of Virology, vol.76, issue.21, pp.10921-10929, 2002.
DOI : 10.1128/JVI.76.21.10921-10928.2002

D. Nasri, L. Bouslama, S. Omar, H. Saoudin, T. Bourlet et al., Typing of Human Enterovirus by Partial Sequencing of VP2, Journal of Clinical Microbiology, vol.45, issue.8, pp.2370-2379, 2007.
DOI : 10.1128/JCM.00093-07

W. A. Nix, M. S. Oberste, and M. A. 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.2698-704, 2006.
DOI : 10.1128/JCM.00542-06

H. Norder, L. Bjerregaard, and L. O. Magnius, Homotypic echoviruses share aminoterminal VP1 sequence homology applicable for typing, Journal of Medical Virology, vol.12, issue.1, pp.35-44, 2001.
DOI : 10.1002/1096-9071(200101)63:1<35::AID-JMV1005>3.0.CO;2-Q

M. S. Oberste, K. Maher, D. R. Kilpatrick, and M. A. 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.

M. S. Oberste, K. Maher, and M. A. Pallansch, Evidence for Frequent Recombination within Species Human Enterovirus B Based on Complete Genomic Sequences of All Thirty-Seven Serotypes, Journal of Virology, vol.78, issue.2, pp.855-67, 2004.
DOI : 10.1128/JVI.78.2.855-867.2004

M. S. Oberste, W. A. Nix, K. Maher, and M. A. Pallansch, Improved molecular identification of enteroviruses by RT-PCR and amplicon sequencing, Journal of Clinical Virology, vol.26, issue.3, pp.375-382, 2003.
DOI : 10.1016/S1386-6532(03)00004-0

G. Oprisan, M. Combiescu, S. Guillot, V. Caro, A. Combiescu et al., Natural genetic recombination between co-circulating heterotypic enteroviruses, Journal of General Virology, vol.83, issue.9, pp.2193-200, 2002.
DOI : 10.1099/0022-1317-83-9-2193

G. Palacios and M. S. Oberste, Enteroviruses as agents of emerging infectious diseases, Journal of Neurovirology, vol.141, issue.5, 2005.
DOI : 10.1080/13550280591002531

M. Pallansch and R. Roos, Enteroviruses: polioviruses, coxsackieviruses, echoviruses, and newer enteroviruses, Fields Virology, pp.723-775, 2001.

M. Rakoto-andrianarivelo, S. Guillot, J. Iber, J. Balanant, B. Blondel et al., Co-Circulation and Evolution of Polioviruses and Species C Enteroviruses in a District of Madagascar, PLoS Pathogens, vol.229, issue.12, p.191, 2007.
DOI : 10.1371/journal.ppat.0030191.sg001

URL : https://hal.archives-ouvertes.fr/pasteur-00318673

G. M. Rossolini, S. Cresti, A. Ingianni, P. Cattani, M. L. Riccio et al., Use of deoxyinosine-containing primers vs degenerate primers for polymerase chain reaction based on ambiguous sequence information, Molecular and Cellular Probes, vol.8, issue.2, pp.91-99, 1994.
DOI : 10.1006/mcpr.1994.1013

D. Rousset, M. Rakoto-andrianarivelo, R. Razafindratsimandresy, B. Randriamanalina, S. Guillot et al., Recombinant Vaccine???Derived Poliovirus in Madagascar, Emerging Infectious Diseases, vol.9, issue.7, pp.885-892, 2003.
DOI : 10.3201/eid0907.020692

URL : https://hal.archives-ouvertes.fr/pasteur-00316067

J. Santti, T. Hyypia, L. Kinnunen, and M. Salminen, Evidence of recombination among enteroviruses, J Virol, vol.73, pp.8741-8750, 1999.

P. Simmonds and J. Welch, Frequency and Dynamics of Recombination within Different Species of Human Enteroviruses, Journal of Virology, vol.80, issue.1, pp.483-93, 2006.
DOI : 10.1128/JVI.80.1.483-493.2006