J. A. Adeniji and T. O. Faleye, Isolation and identification of enteroviruses from sewage and sewage-contaminated water in, Food Environ. Virol, vol.6, issue.2, 2014.

D. Antona, M. Kossorotoff, I. Schuffenecker, A. Mirand, M. Leruez-ville et al., Severe paediatric conditions linked with EV-A71 and EV-D68, France, Euro Surveill, vol.21, issue.46, p.30402, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01883166

L. N. Apostol, T. Imagawa, A. Suzuki, Y. Masago, S. Lupisan et al., Genetic diversity and molecular characterization of enteroviruses from sewage-polluted urban and rural rivers in the Philippines, Virus Genes, vol.45, issue.2, 2012.

C. Barnadas, S. E. Midgley, M. N. Skov, L. Jensen, M. W. Poulsen et al., An enhanced Enterovirus surveillance system allows identification and characterization of rare and emerging respiratory enteroviruses in Denmark, 2015-16, J. Clin. Virol, vol.93, 2017.

K. S. Benschop, H. G. Van-der-avoort, E. Jusic, H. Vennema, R. Van-binnendijk et al., Polio and measles down the drain: environmental enterovirus surveillance in The Netherlands, Appl. Environ. Microbiol, vol.83, 2005.

Y. Berchenko, Y. Manor, L. S. Freedman, E. Kaliner, I. Grotto et al., Estimation of polio infection prevalence from environmental surveillance data, Sci. Transl. Med, vol.9, issue.383, 2017.

M. Bessaud, M. Joffret, B. Holmblat, R. Razafindratsimandresy, and F. Delpeyroux, Genetic relationship between cocirculating human enteroviruses species C, PLoS One, vol.6, issue.9, 2011.
URL : https://hal.archives-ouvertes.fr/pasteur-00835576

L. Bian, Y. Wang, X. Yao, Q. Mao, M. Xu et al., Coxsackievirus A6: a new emerging pathogen causing hand, foot and mouth disease outbreaks worldwide, Expert Rev. Anti Infect. Ther, vol.13, issue.9, 2015.

M. Bisseux, J. Colombet, A. Mirand, A. Roque-afonso, F. Abravanel et al., Monitoring human enteric viruses in wastewater and relevance to infections encountered in the clinical setting: a one-year experiment in central France, Euro Surveill, vol.23, issue.7, pp.17-00237, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01734503

N. E. Brinkman, G. S. Fout, and S. P. Keely, Retrospective surveillance of wastewater to examine seasonal dynamics of enterovirus infections, vol.2, 2017.

D. Casas-alba, M. F. De-sevilla, A. Valero-rello, C. Fortuny, J. García-garcía et al., Outbreak of brainstem encephalitis associated with enterovirus-A71 in Catalonia, Spain (2016): a clinical observational study in a children's reference centre in Catalonia, Clin. Microbiol. Infect, 2017.

T. L. Cowger, C. C. Burns, S. Sharif, H. E. Gary, J. Iber et al., The role of supplementary environmental surveillance to complement acute flaccid paralysis surveillance for wild poliovirus in Pakistan, PLoS One, vol.12, issue.7, 2011.

R. Delogu, A. Battistone, G. Buttinelli, S. Fiore, S. Fontana et al., Poliovirus and other enteroviruses from environmental surveillance in Italy, Food Environ. Virol, vol.10, issue.4, 2009.

P. Esling, F. Lejzerowicz, and J. Pawlowski, Accurate multiplexing and filtering for high-throughput amplicon-sequencing, Nucleic Acids Res, vol.43, issue.5, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01279130

M. Galan, M. Razzauti, E. Bard, M. Bernard, C. Brouat et al., 16S rRNA amplicon sequencing for epidemiological surveys of bacteria in wildlife, vol.1, pp.32-48, 2016.

H. Harvala, J. Calvert, D. Van-nguyen, L. Clasper, N. Gadsby et al., Comparison of diagnostic clinical samples and environmental sampling for enterovirus and parechovirus surveillance in Scotland, Euro Surveill, vol.19, issue.15, p.20772, 2010.

C. Hassel, A. Mirand, A. Farkas, S. Diedrich, H. P. Huemer et al., Phylogeography of coxsackievirus A16 reveals global transmission pathways and recent emergence and spread of a recombinant genogroup, J. Virol, vol.91, issue.18, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01882287

C. Hassel, A. Mirand, A. Lukashev, E. Terletskaialadwig, A. Farkas et al., Transmission patterns of human enterovirus 71 to, from and among European countries, Euro Surveill, vol.20, issue.34, p.30005, 2003.
URL : https://hal.archives-ouvertes.fr/hal-01885350

C. Henquell, A. Mirand, J. Richter, I. Schuffenecker, B. B?-ottiger et al., Phylogenetic patterns of human coxsackievirus B5 arise from population dynamics between two genogroups and reveal evolutionary factors of molecular adaptation and transmission, J. Virol, vol.87, issue.22, pp.12249-12259, 2013.

C. C. Holm-hansen, S. E. Midgley, and T. K. Fischer, Global emergence of enterovirus D68: a systematic review, Lancet Infect. Dis, vol.16, issue.5, 2016.

N. Khetsuriani, I. Perehinets, D. Nitzan, D. Popovic, T. Moran et al., Responding to a cVDPV1 outbreak in Ukraine: implications, challenges and opportunities, Vaccine, vol.35, issue.36, 2017.

M. Lang, A. Mirand, N. Savy, C. Henquell, S. Maridet et al., Acute flaccid paralysis following enterovirus D68 associated pneumonia, Euro Surveill, vol.19, issue.44, p.20952, 2014.

Y. Manor, L. M. Shulman, E. Kaliner, M. Hindiyeh, D. Ram et al., Intensified environmental surveillance supporting the response to wild poliovirus type 1 silent circulation in Israel, Euro Surveill, vol.19, issue.7, p.20708, 2013.

A. Mirand, C. Archimbaud, C. Henquell, Y. Michel, M. Chambon et al., Prospective identification of HEV-B enteroviruses during the 2005 outbreak, J. Med. Virol, vol.78, issue.12, 2006.

A. Mirand, C. Henquell, C. Archimbaud, M. Chambon, F. Charbonne et al., Prospective identification of enteroviruses involved in meningitis in 2006 through direct genotyping in cerebrospinal fluid, J. Clin. Microbiol, vol.46, issue.1, 2008.

A. Mirand, F. V. Le-sage, B. Pereira, R. Cohen, C. Levy et al., Ambulatory pediatric surveillance of hand, foot and mouth disease as signal of an outbreak of coxsackievirus A6 infections, Emerg. Infect. Dis, vol.22, issue.11, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01883171

A. Mirand, I. Schuffenecker, C. Henquell, G. Billaud, G. Jugie et al., Phylogenetic evidence for a recent spread of two populations of human enterovirus 71, 2010.

, J. Gen. Virol, vol.91

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, J. Clin. Microbiol, vol.44, issue.8, 2006.

I. Othman, A. Mirand, I. Slama, M. Mastouri, H. Peigue-lafeuille et al., Enterovirus migration patterns between France and Tunisia, Polio Eradication & Endgame Strategic Plan, vol.10, issue.12, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01885357

M. N. Price, P. S. Dehal, and A. P. Arkin, FastTree 2-approximately maximumlikelihood trees for large alignments, PLoS One, vol.5, issue.3, 2010.

I. B. Schnell, K. Bohmann, and M. T. Gilbert, Tag jumps illuminated-reducing sequence-to-sample misidentifications in metabarcoding studies, Mol. Ecol. Resour, vol.15, issue.6, 2015.

I. Schuffenecker, A. Mirand, L. Josset, C. Henquell, D. Hecquet et al., Epidemiological and clinical characteristics of patients infected with enterovirus D68, Euro Surveill, vol.21, p.30226, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01883183

N. Taib, J. Mangot, I. Domaizon, G. Bronner, and D. Debroas, Phylogenetic affiliation of SSU rRNA genes generated by massively parallel sequencing: new insights into the freshwater protist diversity, PLoS One, vol.8, issue.3, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00840867

K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei et al., MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol. Biol. Evol, vol.28, issue.10, 2011.

R. H. Tangermann, C. Lamoureux, G. Tallis, and A. Goel, The critical role of acute flaccid paralysis surveillance in the Global Polio Eradication Initiative, Int. Health, vol.9, issue.3, 2017.

C. C. Van-leer-buter, R. Poelman, R. Borger, and H. G. Niesters, Newly identified enterovirus C genotypes, identified in The Netherlands through routine sequencing of all enteroviruses detected in clinical materials from 2008 to 2015, J. Clin. Microbiol, vol.54, issue.9, 2016.

R. Volle, C. Nourrisson, A. Mirand, C. Regagnon, M. Chambon et al., Quantitative real-time RT-PCR assay for research studies on enterovirus infections in the central nervous system, J. Virol. Methods, vol.185, issue.1, 2012.

W. Xing, Q. Liao, C. Viboud, J. Zhang, J. Sun et al., Hand, foot, and mouth disease in China, 2008-12: an epidemiological study, Lancet Infect. Dis, vol.14, issue.4, pp.70342-70348, 2014.