M. Guzman, S. Halstead, H. Artsob, P. Buchy, J. Farrar et al., Dengue: a continuing global threat, Nature Reviews Microbiology, vol.11, issue.12, pp.7-16, 2010.
DOI : 10.4161/hv.2.2.2555

R. Lanciotti, J. Roehrig, V. Deubel, J. Smith, M. Parker et al., Origin of the West Nile Virus Responsible for an Outbreak of Encephalitis in the Northeastern United States, Science, vol.286, issue.5448, pp.2333-2340, 1999.
DOI : 10.1126/science.286.5448.2333

E. Gould, T. Solomon, and . Pmid, Pathogenic flaviviruses, The Lancet, vol.371, issue.9611, pp.500-509, 2008.
DOI : 10.1016/S0140-6736(08)60238-X

K. Kretsinger, A. Gasasira, A. Poy, K. Porter, J. Everts et al., Polio Eradication in the World Health Organization African Region, 2008-2012, Journal of Infectious Diseases, vol.62, issue.19, pp.23-39, 2008.
DOI : 10.1093/infdis/jiq140

D. Henderson, Principles and lessons from the smallpox eradication programme. Bull World Health Organ, Epub PMID, vol.65, issue.4, pp.535-581, 1987.

F. Cutts, A. Henao-restrepo, and J. Olive, Measles elimination: progress and challenges, Vaccine, vol.17, issue.11, pp.47-52, 1999.
DOI : 10.1016/S0264-410X(99)00309-6

T. Reichert, N. Sugaya, D. Fedson, W. Glezen, L. Simonsen et al., The Japanese Experience with Vaccinating Schoolchildren against Influenza, New England Journal of Medicine, vol.344, issue.12, pp.889-96, 2001.
DOI : 10.1056/NEJM200103223441204

F. Heinz and K. Stiasny, Flaviviruses and flavivirus vaccines, Vaccine, vol.30, issue.29, pp.4301-4307, 2012.
DOI : 10.1016/j.vaccine.2011.09.114

S. Kitchener, Viscerotropic and neurotropic disease following vaccination with the 17D yellow fever vaccine, ARILVAX??, Vaccine, vol.22, issue.17-18, pp.17-18, 2004.
DOI : 10.1016/j.vaccine.2004.01.026

A. Barrett, Current Status of Flavivirus Vaccines, Annals of the New York Academy of Sciences, vol.4, issue.Suppl. 2, pp.262-71, 2001.
DOI : 10.1093/infdis/170.6.1448

J. Coffin, Attenuation by a Thousand Cuts, New England Journal of Medicine, vol.359, issue.21, pp.2283-52283, 2008.
DOI : 10.1056/NEJMcibr0805820

J. Meng, S. Lee, A. Hotard, and M. Moore, Refining the Balance of Attenuation and Immunogenicity of Respiratory Syncytial Virus by Targeted Codon Deoptimization of Virulence Genes, mBio, vol.5, issue.5, p.25249281, 2014.
DOI : 10.1128/mBio.01704-14

L. Nouen, C. Brock, L. Luongo, C. Mccarty, T. Yang et al., Attenuation of human respiratory syncytial virus by genome-scale codon-pair deoptimization, Proceedings of the National Academy of Sciences, vol.247, issue.2, pp.13169-74, 2014.
DOI : 10.1006/viro.1998.9248

Y. Ni, Z. Zhao, T. Opriessnig, S. Subramaniam, L. Zhou et al., Computer-aided codon-pairs deoptimization of the major envelope GP5 gene attenuates porcine reproductive and respiratory syndrome virus, Virology, vol.450, issue.451, pp.450-451132, 2014.
DOI : 10.1016/j.virol.2013.12.009

G. Martrus, M. Nevot, C. Andres, B. Clotet, and M. Martinez, Changes in codon-pair bias of human immunodeficiency virus type 1 have profound effects on virus replication in cell culture, Retrovirology, vol.10, issue.1, pp.78-3726367, 2013.
DOI : 10.1128/JVI.01594-06

C. Burns, J. Shaw, R. Campagnoli, J. Jorba, A. Vincent et al., Modulation of Poliovirus Replicative Fitness in HeLa Cells by Deoptimization of Synonymous Codon Usage in the Capsid Region, Journal of Virology, vol.80, issue.7, pp.3259-72, 2006.
DOI : 10.1128/JVI.80.7.3259-3272.2006

S. Mueller, D. Papamichail, J. Coleman, S. Skiena, and E. Wimmer, Reduction of the Rate of Poliovirus Protein Synthesis through Large-Scale Codon Deoptimization Causes Attenuation of Viral Virulence by Lowering Specific Infectivity, Journal of Virology, vol.80, issue.19, pp.9687-96, 2006.
DOI : 10.1128/JVI.00738-06

J. Coleman, D. Papamichail, S. Skiena, B. Futcher, E. Wimmer et al., Virus Attenuation by Genome-Scale Changes in Codon Pair Bias, Science, vol.67, issue.6, pp.1784-1791, 2008.
DOI : 10.1158/0008-5472.CAN-06-3713

S. Mueller, J. Coleman, D. Papamichail, C. Ward, A. Nimnual et al., Live attenuated influenza virus vaccines by computer-aided rational design, Nature Biotechnology, vol.79, issue.7, pp.723-729, 2010.
DOI : 10.1093/infdis/150.6.834

C. Burns, R. Campagnoli, J. Shaw, A. Vincent, J. Jorba et al., Genetic Inactivation of Poliovirus Infectivity by Increasing the Frequencies of CpG and UpA Dinucleotides within and across Synonymous Capsid Region Codons, Journal of Virology, vol.83, issue.19, pp.9957-69, 2009.
DOI : 10.1128/JVI.00508-09

A. Nougairede, D. Fabritus, L. , A. F. Gould, E. Holmes et al., Random Codon Re-encoding Induces Stable Reduction of Replicative Fitness of Chikungunya Virus in Primate and Mosquito Cells, PLoS Pathogens, vol.79, issue.Pt 11, pp.1003172-3578757, 2013.
DOI : 10.1371/journal.ppat.1003172.s003

L. De-fabritus, A. Nougairede, F. Aubry, E. Gould, and X. De-lamballerie, Attenuation of Tick-Borne Encephalitis Virus Using Large-Scale Random Codon Re-encoding, PLOS Pathogens, vol.27, issue.Suppl
DOI : 10.1371/journal.ppat.1004738.s001
URL : https://hal.archives-ouvertes.fr/hal-01218538

I. Takashima, K. Morita, M. Chiba, D. Hayasaka, T. Sato et al., A case of tick-borne encephalitis in Japan and isolation of the the virus, J Clin Microbiol. PMID, vol.35, issue.8, pp.1943-1950, 1997.

D. Hayasaka, T. Gritsun, K. Yoshii, T. Ueki, A. Goto et al., Amino acid changes responsible for attenuation of virus neurovirulence in an infectious cDNA clone of the Oshima strain of Tick-borne encephalitis virus, Journal of General Virology, vol.85, issue.4, pp.1007-1025, 2004.
DOI : 10.1099/vir.0.19668-0

B. Tigabu, T. Juelich, J. Bertrand, and M. Holbrook, Clinical evaluation of highly pathogenic tick-borne flavivirus infection in the mouse model, Journal of Medical Virology, vol.3, issue.7, pp.1261-1270, 2009.
DOI : 10.4049/jimmunol.167.5.2869

F. Aubry, A. Nougairede, L. De-fabritus, G. Querat, E. Gould et al., Single-stranded positive-sense RNA viruses generated in days using infectious subgenomic amplicons, Journal of General Virology, vol.96, issue.2, pp.2462-2469, 2014.
DOI : 10.1016/S0166-0934(01)00331-7

S. Zhang, G. Zubay, and E. Goldman, Low-usage codons in Escherichia coli, yeast, fruit fly and primates, Gene, vol.105, issue.1, pp.61-72, 1991.
DOI : 10.1016/0378-1119(91)90514-C

J. Zhou, J. Zhang, H. Chen, L. Ma, and Y. Liu, Analysis of synonymous codon usage in foot-and-mouth disease virus, Veterinary Research Communications, vol.368, issue.4, pp.393-404, 2010.
DOI : 10.1099/0022-1317-83-10-2455

J. Peden, CodonW v1.3. Laboratory of Paul Sharp at the University of Nottingham, 1997.

L. Ninove, A. Nougairede, C. Gazin, L. Thirion, I. Delogu et al., RNA and DNA Bacteriophages as Molecular Diagnosis Controls in Clinical Virology: A Comprehensive Study of More than 45,000 Routine PCR Tests, PLoS ONE, vol.45, issue.2, pp.16142-3036576, 2011.
DOI : 10.1371/journal.pone.0016142.s004

S. Ding, M. Chi, B. Scull, R. Rigby, N. Schwerbrock et al., High-Fat Diet: Bacteria Interactions Promote Intestinal Inflammation Which Precedes and Correlates with Obesity and Insulin Resistance in Mouse, PLoS ONE, vol.10, issue.10, p.2922379, 2010.
DOI : 10.1371/journal.pone.0012191.t005

L. Reed and H. Muench, A simple method of estimating fifty per cent endpoints, Am J Hyg, vol.27, pp.493-500, 1938.

L. De-fabritus, A. Nougairede, F. Aubry, E. Gould, and X. De-lamballerie, Attenuation of Tick-Borne Encephalitis Virus Using Large-Scale Random Codon Re-encoding, PLOS Pathogens, vol.27, issue.Suppl, p.4348424, 2015.
DOI : 10.1371/journal.ppat.1004738.s001
URL : https://hal.archives-ouvertes.fr/hal-01218538

D. Hayasaka, N. Nagata, Y. Fujii, H. Hasegawa, T. Sata et al., Mortality following peripheral infection with Tick-borne encephalitis virus results from a combination of central nervous system pathology, systemic inflammatory and stress responses, Virology, vol.390, issue.1, pp.139-50, 2009.
DOI : 10.1016/j.virol.2009.04.026

T. Kimura, M. Sasaki, M. Okumura, E. Kim, and H. Sawa, Flavivirus Encephalitis, Veterinary Pathology, vol.22, issue.5, pp.806-824, 2010.
DOI : 10.3201/eid0704.017420

B. Christenson and M. Bottiger, Measles antibody: comparison of long-term vaccination titres, early vaccination titres and naturally acquired immunity to and booster effects on the measles virus, Vaccine, vol.12, issue.2, pp.129-162, 1994.
DOI : 10.1016/0264-410X(94)90049-3

Y. Zhu, J. Heath, J. Collins, T. Greene, L. Antipa et al., Experimental Measles. II. Infection and Immunity in the Rhesus Macaque, Virology, vol.233, issue.1, pp.85-92, 1997.
DOI : 10.1006/viro.1997.8575

T. Gritsun, V. Lashkevich, and E. Gould, Tick-borne encephalitis, Antiviral Research, vol.57, issue.1-2, pp.129-175, 2003.
DOI : 10.1016/S0166-3542(02)00206-1