M. Pallansch and R. Roos, Enteroviruses: polioviruses, coxsackieviruses, echoviruses, and newer enteroviruses, Fields virology. Philadelphia: Lippincott Williams and Wilkins, pp.723-775, 2001.

P. Minor, The molecular biology of poliovaccines, Journal of General Virology, vol.73, issue.12, pp.3065-3077, 1992.
DOI : 10.1099/0022-1317-73-12-3065

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.3103-3110, 2002.
DOI : 10.1099/0022-1317-83-12-3103

H. Liu, D. Zheng, L. Zhang, M. Oberste, and O. Kew, Serial Recombination during Circulation of Type 1 Wild-Vaccine Recombinant Polioviruses in China, Journal of Virology, vol.77, issue.20, pp.10994-11005, 2003.
DOI : 10.1128/JVI.77.20.10994-11005.2003

N. Cuervo, S. Guillot, N. Romanenkova, M. Combiescu, and A. Aubert-combiescu, 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

M. Georgescu, F. Delpeyroux, M. Tardy-panit, J. Balanant, and M. Combiescu, High diversity of poliovirus strains isolated from the central nervous system from patients with vaccine-associated paralytic poliomyelitis, J Virol, vol.68, pp.8089-8101, 1994.

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

G. Lipskaya, A. Muzychenko, O. Kutitova, S. Maslova, and M. Equestre, Frequent isolation of intertypic poliovirus recombinants with serotype 2 specificity from vaccine-associated polio cases, Journal of Medical Virology, vol.75, issue.4, pp.290-296, 1991.
DOI : 10.1002/jmv.1890350415

B. Nkowane, S. Wassilak, and W. Orenstein, Vaccine-associated paralytic poliomyelitis. United States: 1973 through 1984, JAMA: The Journal of the American Medical Association, vol.257, issue.10, pp.1335-1340, 1987.
DOI : 10.1001/jama.257.10.1335

O. Kew, P. Wright, V. Agol, F. Delpeyroux, and H. Shimizu, 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

O. Kew, V. Morris-glasgow, M. Landaverde, C. Burns, and J. Shaw, Outbreak of Poliomyelitis in Hispaniola Associated with Circulating Type 1 Vaccine-Derived Poliovirus, Science, vol.296, issue.5566, pp.356-359, 2002.
DOI : 10.1126/science.1068284

X. Liang, Y. Zhang, W. Xu, N. Wen, and S. Zuo, An Outbreak of Poliomyelitis Caused by Type 1 Vaccine???Derived Poliovirus in China, The Journal of Infectious Diseases, vol.194, issue.5, pp.545-551, 2006.
DOI : 10.1086/506359

D. Rousset, M. Rakoto-andrianarivelo, R. Razafindratsimandresy, B. Randriamanalina, and S. Guillot, Recombinant Vaccine???Derived Poliovirus in Madagascar, Emerging Infectious Diseases, vol.9, issue.7, pp.885-887, 2003.
DOI : 10.3201/eid0907.020692

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

H. Shimizu, B. Thorley, F. Paladin, K. Brussen, and V. Stambos, Circulation of Type 1 Vaccine-Derived Poliovirus in the Philippines in 2001, Journal of Virology, vol.78, issue.24, pp.13512-13521, 2004.
DOI : 10.1128/JVI.78.24.13512-13521.2004

C. Yang, T. Naguib, S. Yang, E. Nasr, and J. Jorba, Circulation of Endemic Type 2 Vaccine-Derived Poliovirus in Egypt from 1983 to 1993, Journal of Virology, vol.77, issue.15, pp.8366-8377, 2003.
DOI : 10.1128/JVI.77.15.8366-8377.2003

O. Kew, R. Sutter, E. De-gourville, W. Dowdle, and M. Pallansch, VACCINE-DERIVED POLIOVIRUSES AND THE ENDGAME STRATEGY FOR GLOBAL POLIO ERADICATION, Annual Review of Microbiology, vol.59, issue.1, pp.587-635, 2005.
DOI : 10.1146/annurev.micro.58.030603.123625

V. Agol, Vaccine-derived polioviruses, Biologicals, vol.34, issue.2, pp.103-108, 2006.
DOI : 10.1016/j.biologicals.2006.02.007

URL : https://hal.archives-ouvertes.fr/pasteur-00319492

A. Bellmunt, G. May, R. Zell, P. Pring-akerblom, and W. Verhagen, Evolution of Poliovirus Type I during 5.5 Years of Prolonged Enteral Replication in an Immunodeficient Patient, Virology, vol.265, issue.2, pp.178-184, 1999.
DOI : 10.1006/viro.1999.0003

G. Gavrilin, E. Cherkasova, G. Lipskaya, O. Kew, and V. Agol, Evolution of Circulating Wild Poliovirus and of Vaccine-Derived Poliovirus in an Immunodeficient Patient: a Unifying Model, Journal of Virology, vol.74, issue.16, pp.7381-7390, 2000.
DOI : 10.1128/JVI.74.16.7381-7390.2000

J. Martin, G. Dunn, R. Hull, V. Patel, and P. Minor, Evolution of the Sabin Strain of Type 3 Poliovirus in an Immunodeficient Patient during the Entire 637-Day Period of Virus Excretion, Journal of Virology, vol.74, issue.7, pp.3001-3010, 2000.
DOI : 10.1128/JVI.74.7.3001-3010.2000

V. Patel, M. Ferguson, and P. Minor, Antigenic Sites on Type 2 Poliovirus, Virology, vol.192, issue.1, pp.361-364, 1993.
DOI : 10.1006/viro.1993.1044

P. Minor, M. Ferguson, D. Evans, J. Almond, and J. Icenogle, Antigenic Structure of Polioviruses of Serotypes 1, 2 and 3, Journal of General Virology, vol.67, issue.7, pp.1283-1291, 1986.
DOI : 10.1099/0022-1317-67-7-1283

H. Van-der-avoort, B. Hull, T. Hovi, M. Pallansch, and O. Kew, Comparative study of five methods for intratypic differentiation of polioviruses, J Clin Microbiol, vol.33, pp.2562-2566, 1995.

L. Shulman, Y. Manor, R. Handsher, F. Delpeyroux, and M. Mcdonough, Molecular and antigenic characterization of a highly evolved derivative of the type 2 oral poliovaccine strain isolated from sewage in Israel, J Clin Microbiol, vol.38, pp.3729-3734, 2000.

H. Horie, S. Koike, T. Kurata, Y. Satoyoshida, and I. Ise, Transgenic mice carrying the human poliovirus receptor: new animal model for study of poliovirus neurovirulence, J Virol, vol.68, pp.681-688, 1994.

P. Pipkin, D. Wood, V. Racaniello, and P. Minor, Characterisation of L cells expressing the human poliovirus receptor for the specific detection of polioviruses in vitro, Journal of Virological Methods, vol.41, issue.3, pp.333-340, 1993.
DOI : 10.1016/0166-0934(93)90022-J

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

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

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.

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.

B. Brown, M. Oberste, K. Maher, and M. Pallansch, Complete Genomic Sequencing Shows that Polioviruses and Members of Human Enterovirus Species C Are Closely Related in the Noncapsid Coding Region, Journal of Virology, vol.77, issue.16, pp.8973-8984, 2003.
DOI : 10.1128/JVI.77.16.8973-8984.2003

A. Smorodintsev, V. Ilyenko, M. Kurnosova, N. Goryev, and G. Zhilova, Virological and immunological characteristics of vaccinal infection in children inoculated per os with a live poliomyelitis vaccine made from the Sabin strains, Pan American Sanitary Bureau WDU, pp.312-323, 1959.

R. Aylward, D. Porta, L. Fiore, B. Ridolfi, and P. Chierchini, Unimmunized Gypsy Populations and Implications for the Eradication of Poliomyelitis in Europe, Journal of Infectious Diseases, vol.175, issue.Supplement 1, pp.86-88, 1997.
DOI : 10.1093/infdis/175.Supplement_1.S86

P. Fine and I. Carneiro, Transmissibility and Persistence of Oral Polio Vaccine Viruses: Implications for the Global Poliomyelitis Eradication Initiative, American Journal of Epidemiology, vol.150, issue.10, pp.1001-1021, 1999.
DOI : 10.1093/oxfordjournals.aje.a009924

Y. Maldonado, V. Pena-cruz, L. Sanchez, M. Logan, L. Blandon et al., Host and Viral Factors Affecting the Decreased Immunogenicity of Sabin Type 3 Vaccine after Administration of Trivalent Oral Polio Vaccine to Rural Mayan Children, Journal of Infectious Diseases, vol.175, issue.3, pp.545-553, 1997.
DOI : 10.1093/infdis/175.3.545

P. Strebel, R. Sutter, S. Cochi, R. Biellik, and E. Brink, Epidemiology of Poliomyelitis in the United States One Decade after the Last Reported Case of Indigenous Wild Virus-Associated Disease, Clinical Infectious Diseases, vol.14, issue.2, pp.568-579, 1992.
DOI : 10.1093/clinids/14.2.568

E. Korotkova, R. Park, E. Cherkasova, G. Lipskaya, and K. Chumakov, Retrospective Analysis of a Local Cessation of Vaccination against Poliomyelitis: a Possible Scenario for the Future, Journal of Virology, vol.77, issue.23, pp.12460-12465, 2003.
DOI : 10.1128/JVI.77.23.12460-12465.2003

F. Adu, J. Iber, D. Bukbuk, N. Gumede, and S. Yang, Isolation of recombinant type 2 vaccine-derived poliovirus (VDPV) from a Nigerian child, Virus Research, vol.127, issue.1, pp.17-25, 2007.
DOI : 10.1016/j.virusres.2007.03.009

G. Oprisan, M. Combiescu, S. Guillot, V. Caro, and A. Combiescu, Natural genetic recombination between co-circulating heterotypic enteroviruses, Journal of General Virology, vol.83, issue.9, pp.2193-2200, 2002.
DOI : 10.1099/0022-1317-83-9-2193

A. Lukashev, V. Lashkevich, O. Ivanova, G. Koroleva, and A. Hinkkanen, Recombination in Circulating Enteroviruses, Journal of Virology, vol.77, issue.19, pp.10423-10431, 2003.
DOI : 10.1128/JVI.77.19.10423-10431.2003

M. Oberste, K. Maher, and M. 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.855-867, 2004.
DOI : 10.1128/JVI.78.2.855-867.2004

S. Chevaliez, A. Szendroi, V. Caro, J. Balanant, and S. Guillot, 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

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

A. Mirand, C. Henquell, C. Archimbaud, H. Peigue-lafeuille, and J. Bailly, Emergence of recent echovirus 30 lineages is marked by serial genetic recombination events, Journal of General Virology, vol.88, issue.1, pp.166-176, 2007.
DOI : 10.1099/vir.0.82146-0

A. Lindberg, P. Andersson, C. Savolainen, M. 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.1223-1235, 2003.
DOI : 10.1099/vir.0.18971-0

M. Arita, S. Zhu, H. Yoshida, T. Yoneyama, and T. Miyamura, 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

M. Georgescu, F. Delpeyroux, and R. Crainic, Tripartite genome organization of a natural type 2 vaccine/nonvaccine recombinant poliovirus, Journal of General Virology, vol.76, issue.9, pp.2343-2348, 1995.
DOI : 10.1099/0022-1317-76-9-2343

P. Jiang, J. Faase, H. Toyoda, A. Paul, and E. Wimmer, Evidence for emergence of diverse polioviruses from C-cluster coxsackie A viruses and implications for global poliovirus eradication, Proceedings of the National Academy of Sciences, vol.104, issue.22, pp.9457-9462, 2007.
DOI : 10.1073/pnas.0700451104

G. Stanway, F. Brown, P. Christian, T. Hovi, and T. Hyypiä, Family Picornaviridae, Virus taxonomy: eighth report of the international committee on taxonomy of viruses, pp.757-778, 2005.

M. Combiescu, S. Guillot, A. Persu, A. Baicus, and D. Pitigoi, Circulation of a type 1 recombinant vaccine-derived poliovirus strain in a limited area in Romania, Archives of Virology, vol.77, issue.Suppl 1, pp.727-738, 2007.
DOI : 10.1007/s00705-006-0884-y

URL : https://hal.archives-ouvertes.fr/pasteur-00319082

N. Romanenkova, S. Guillot, N. Rozaeva, R. Crainic, and M. Bichurina, Use of a Multiple Restriction Fragment Length Polymorphism Method for Detecting Vaccine-Derived Polioviruses in Clinical Samples, Journal of Clinical Microbiology, vol.44, issue.11, pp.4077-4084, 2006.
DOI : 10.1128/JCM.00017-06

URL : https://hal.archives-ouvertes.fr/pasteur-00319463

J. Thompson, D. Higgins, and T. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Research, vol.22, issue.22, pp.4673-4680, 1994.
DOI : 10.1093/nar/22.22.4673

W. Pearson and D. Lipman, Improved tools for biological sequence comparison., Proceedings of the National Academy of Sciences, vol.85, issue.8, pp.2444-2448, 1988.
DOI : 10.1073/pnas.85.8.2444

J. Thompson, T. Gibson, F. Plewniak, F. Jeanmougin, and D. Higgins, The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools, Nucleic Acids Research, vol.25, issue.24, pp.4876-4882, 1997.
DOI : 10.1093/nar/25.24.4876

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

K. Strimmer and A. Von-haeseler, Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies, Molecular Biology and Evolution, vol.13, issue.7, pp.964-969, 1996.
DOI : 10.1093/oxfordjournals.molbev.a025664

M. Hasegawa, H. Kishino, T. Yano, M. Flemister, and M. Pallansch, 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

J. Felsenstein, PHYLIP: phylogeny inference package, version 3.6a3 [computer program]. Distributed by the author, 2000.

R. Page, TreeView: an application to display phylogenetic trees on personal computers, Comput Appl Biosci, vol.12, pp.357-358, 1996.

G. Perriere and M. Gouy, WWW-query: An on-line retrieval system for biological sequence banks, Biochimie, vol.78, issue.5, pp.364-369, 1996.
DOI : 10.1016/0300-9084(96)84768-7

URL : https://hal.archives-ouvertes.fr/hal-00435034

L. Reed and M. Muench, A simple method for estimating fifty percent endpoints, Amer J Hyg, vol.27, pp.493-497, 1938.

A. Macadam, S. Pollard, G. Ferguson, G. Dunn, and R. Skuce, The 5??? noncoding region of the type 2 poliovirus vaccine strain contains determinants of attenuation and temperature sensitivity, Virology, vol.181, issue.2, pp.451-458, 1991.
DOI : 10.1016/0042-6822(91)90877-E

A. Macadam, S. Pollard, G. Ferguson, R. Skuce, and D. Wood, Genetic Basis of Attenuation of the Sabin Type 2 Vaccine Strain of Poliovirus in Primates, Virology, vol.192, issue.1, pp.18-26, 1993.
DOI : 10.1006/viro.1993.1003

R. Ren, E. Moss, and V. Racaniello, Identification of two determinants that attenuate vaccine-related type 2 poliovirus, J Virol, vol.65, pp.1377-1382, 1991.

M. Yakovenko, E. Cherkasova, G. Rezapkin, O. Ivanova, and A. Ivanov, Antigenic Evolution of Vaccine-Derived Polioviruses: Changes in Individual Epitopes and Relative Stability of the Overall Immunological Properties, Journal of Virology, vol.80, issue.6, pp.2641-2653, 2006.
DOI : 10.1128/JVI.80.6.2641-2653.2006

K. Lentz, A. Smith, S. Geisler, S. Cox, and P. Buontempo, Structure of poliovirus type 2 Lansing complexed with antiviral agent SCH48973: comparison of the structural and biological properties of the three poliovirus serotypes, Structure, vol.5, issue.7, pp.961-978, 1997.
DOI : 10.1016/S0969-2126(97)00249-9

J. Hogle, M. Chow, and D. Filman, Three-dimensional structure of poliovirus at 2.9 A resolution, Science, vol.229, issue.4720, pp.1358-1365, 1985.
DOI : 10.1126/science.2994218