M. Gaunt, A. Sall, X. De-lamballerie, A. Falconar, and T. Dzhivanian, Phylogenetic relationships of flaviviruses correlate with their epidemiology, disease association and biogeography, Journal of General Virology, vol.82, issue.8, pp.1867-1876, 2001.
DOI : 10.1099/0022-1317-82-8-1867

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

G. Grard, G. Moureau, R. Charrel, J. Lemasson, and J. Gonzalez, Genetic characterization of tick-borne flaviviruses: New insights into evolution, pathogenetic determinants and taxonomy, Virology, vol.361, issue.1, pp.80-92, 2007.
DOI : 10.1016/j.virol.2006.09.015

P. Zanotto, G. Gao, T. Gritsun, M. Marin, and W. Jiang, An Arbovirus Cline across the Northern Hemisphere, Virology, vol.210, issue.1, pp.152-159, 1995.
DOI : 10.1006/viro.1995.1326

S. Bhatt, P. Gething, O. Brady, J. Messina, and A. Farlow, The global distribution and burden of dengue, Nature, vol.62, issue.7446, p.24390349, 2013.
DOI : 10.1038/nature12060

C. Calisher and E. Gould, Taxonomy of the virus family Flaviviridae, Adv Virus Res, vol.59, pp.1-19, 2003.
DOI : 10.1016/S0065-3527(03)59001-7

G. Grard, G. Moureau, R. Charrel, E. Holmes, and E. Gould, Genomics and evolution of Aedes-borne flaviviruses, Journal of General Virology, vol.91, issue.1, 2010.
DOI : 10.1099/vir.0.014506-0

P. Zanotto, E. Gould, G. Gao, P. Harvey, and E. Holmes, Population dynamics of flaviviruses revealed by molecular phylogenies., Proceedings of the National Academy of Sciences, vol.93, issue.2, pp.548-553, 1996.
DOI : 10.1073/pnas.93.2.548

S. Cook and E. Holmes, A multigene analysis of the phylogenetic relationships among the flaviviruses (Family: Flaviviridae) and the evolution of vector transmission, Archives of Virology, vol.93, issue.2, p.16380812, 2005.
DOI : 10.1007/s00705-005-0626-6

X. De-lamballerie, S. Crochu, F. Billoir, J. Neyts, and P. De-micco, Genome sequence analysis of Tamana bat virus and its relationship with the genus Flavivirus, Journal of General Virology, vol.83, issue.10, pp.2443-2454, 2002.
DOI : 10.1099/0022-1317-83-10-2443

E. Gould, X. De-lamballerie, P. Zanotto, and E. Holmes, Origins, evolution, and vector???host coadaptations within the Genus Flavivirus, Adv Virus Res, vol.59, pp.277-314, 2003.
DOI : 10.1016/S0065-3527(03)59008-X

E. Huhtamo, N. Putkuri, S. Kurkela, T. Manni, and A. Vaheri, Characterization of a Novel Flavivirus from Mosquitoes in Northern Europe That Is Related to Mosquito-Borne Flaviviruses of the Tropics, Journal of Virology, vol.83, issue.18, pp.9532-9540, 2009.
DOI : 10.1128/JVI.00529-09

G. Grard, J. Lemasson, M. Sylla, A. Dubot, and S. Cook, Ngoye virus: a novel evolutionary lineage within the genus Flavivirus, Journal of General Virology, vol.87, issue.11, pp.3273-3277, 2006.
DOI : 10.1099/vir.0.82071-0

R. Charrel, A. Zaki, M. Fakeeh, A. Yousef, and R. De-chesse, Low Diversity of Alkhurma Hemorrhagic Fever Virus, Saudi Arabia, 1994???1999, Emerging Infectious Diseases, vol.11, issue.5, pp.683-688, 1994.
DOI : 10.3201/eid1105.041298

T. Bakonyi, E. Gould, J. Kolodziejek, H. Weissenbock, and N. Nowotny, Complete genome analysis and molecular characterization of Usutu virus that emerged in Austria in 2001, Virology, vol.328, issue.2, pp.301-310, 2004.
DOI : 10.1016/j.virol.2004.08.005

D. Nisbet, K. Lee, A. Van-den-hurk, C. Johansen, and G. Kuno, Identification of new flaviviruses in the Kokobera virus complex, Journal of General Virology, vol.86, issue.1, pp.121-124, 2005.
DOI : 10.1099/vir.0.80381-0

A. Vazquez, M. Sanchez-seco, G. Palacios, F. Molero, and N. Reyes, Novel Flaviviruses Detected in Different Species of Mosquitoes in Spain, Vector-Borne and Zoonotic Diseases, vol.12, issue.3, p.22141733, 2011.
DOI : 10.1089/vbz.2011.0687

S. Cook, S. Bennett, E. Holmes, D. Chesse, R. Moureau et al., Isolation of a new strain of the flavivirus cell fusing agent virus in a natural mosquito population from Puerto Rico, Journal of General Virology, vol.87, issue.4, pp.735-748, 2006.
DOI : 10.1099/vir.0.81475-0

S. Cook, G. Moureau, R. Harbach, L. Mukwaya, and K. Goodger, Isolation of a novel species of flavivirus and a new strain of Culex flavivirus (Flaviviridae) from a natural mosquito population in Uganda, Journal of General Virology, vol.90, issue.11, pp.2669-2678, 2009.
DOI : 10.1099/vir.0.014183-0

D. Kim, H. Guzman, R. Bueno, . Jr, J. Dennett et al., Characterization of Culex Flavivirus (Flaviviridae) strains isolated from mosquitoes in the United States and Trinidad, Virology, vol.386, issue.1, pp.154-159, 2009.
DOI : 10.1016/j.virol.2008.12.034

R. Sang, A. Gichogo, J. Gachoya, M. Dunster, and V. Ofula, Isolation of a new flavivirus related to Cell fusing agent virus (CFAV) from field-collected flood-water Aedes mosquitoes sampled from a dambo in central Kenya, Archives of Virology, vol.148, issue.6, pp.1085-1093, 2003.
DOI : 10.1007/s00705-003-0018-8

V. Stollar and V. Thomas, An agent in the Aedes aegypti cell line (Peleg) which causes fusion of Aedes albopictus cells, Virology, vol.64, issue.2, pp.367-377, 1975.
DOI : 10.1016/0042-6822(75)90113-0

S. Maruyama, L. Castro-jorge, J. Ribeiro, L. Gardinassi, and G. Garcia, Characterisation of divergent flavivirus NS3 and NS5 protein sequences detected in Rhipicephalus microplus ticks from Brazil, Mem??rias do Instituto Oswaldo Cruz, vol.109, issue.1, pp.38-50, 2014.
DOI : 10.1590/0074-0276130166

F. Billoir, R. De-chesse, H. Tolou, P. De-micco, and E. Gould, Phylogeny of the genus Flavivirus using complete coding sequences of arthropod-borne viruses and viruses with no known vector, Journal of General Virology, vol.81, issue.3, pp.781-790, 2000.
DOI : 10.1099/0022-1317-81-3-781

S. Crochu, S. Cook, H. Attoui, R. Charrel, D. Chesse et al., Sequences of flavivirus-related RNA viruses persist in DNA form integrated in the genome of Aedes spp. mosquitoes, Journal of General Virology, vol.85, issue.7, pp.1971-1980, 2004.
DOI : 10.1099/vir.0.79850-0

M. Gaunt and E. Gould, Rapid subgroup identification of the flaviviruses using degenerate primer E-gene RT-PCR and site specific restriction enzyme analysis, Journal of Virological Methods, vol.128, issue.1-2, pp.113-127, 2005.
DOI : 10.1016/j.jviromet.2005.04.006

G. Moureau, S. Temmam, J. Gonzalez, R. Charrel, and G. Grard, A Real-Time RT-PCR Method for the Universal Detection and Identification of Flaviviruses, Vector-Borne and Zoonotic Diseases, vol.7, issue.4, pp.467-477, 2007.
DOI : 10.1089/vbz.2007.0206

S. Emonet, G. Grard, N. Brisbarre, G. Moureau, and S. Temmam, LoPPS: A long PCR product sequencing method for rapid characterisation of long amplicons, Biochemical and Biophysical Research Communications, vol.344, issue.4, pp.1080-1085, 2006.
DOI : 10.1016/j.bbrc.2006.04.015

S. Emonet, G. Grard, N. Brisbarre, G. Moureau, and S. Temmam, Long PCR Product Sequencing (LoPPS): a shotgun-based approach to sequence long PCR products, Nature Protocols, vol.9, issue.2, pp.340-346, 2007.
DOI : 10.1038/nprot.2006.453

J. Rothberg, W. Hinz, T. Rearick, J. Schultz, and W. Mileski, An integrated semiconductor device enabling non-optical genome sequencing, Nature, vol.32, issue.7, pp.348-352, 2011.
DOI : 10.1038/nature10242

M. Larkin, G. Blackshields, N. Brown, R. Chenna, and P. Mcgettigan, Clustal W and Clustal X version 2.0, Bioinformatics, vol.23, issue.21, pp.2947-2948, 2007.
DOI : 10.1093/bioinformatics/btm404

URL : https://hal.archives-ouvertes.fr/hal-00206210

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

R. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004.
DOI : 10.1093/nar/gkh340

G. Talavera and J. Castresana, Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments, Systematic Biology, vol.56, issue.4, pp.564-577, 2007.
DOI : 10.1080/10635150701472164

J. Huelsenbeck and F. Ronquist, MRBAYES: Bayesian inference of phylogenetic trees, Bioinformatics, vol.17, issue.8, pp.754-755, 2001.
DOI : 10.1093/bioinformatics/17.8.754

A. Drummond and A. Rambaut, BEAST: Bayesian evolutionary analysis by sampling trees, BMC Evolutionary Biology, vol.7, issue.1, pp.214-17996036, 2007.
DOI : 10.1186/1471-2148-7-214

J. Reeder, P. Steffen, and R. Giegerich, pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows, Nucleic Acids Research, vol.35, issue.Web Server, pp.320-324, 2007.
DOI : 10.1093/nar/gkm258

URL : http://doi.org/10.1093/nar/gkm258

A. Firth, N. Wills, R. Gesteland, and J. Atkins, Stimulation of stop codon readthrough: frequent presence of an extended 3' RNA structural element, Nucleic Acids Research, vol.39, issue.15, pp.6679-6691, 2011.
DOI : 10.1093/nar/gkr224

A. Drummond, M. Suchard, D. Xie, and A. Rambaut, Bayesian Phylogenetics with BEAUti and the BEAST 1.7, Molecular Biology and Evolution, vol.29, issue.8, pp.1969-1973, 2012.
DOI : 10.1093/molbev/mss075

F. Abascal, R. Zardoya, and D. Posada, ProtTest: selection of best-fit models of protein evolution, Bioinformatics, vol.21, issue.9, pp.2104-2105, 2005.
DOI : 10.1093/bioinformatics/bti263

A. Drummond, S. Ho, M. Phillips, and A. Rambaut, Relaxed Phylogenetics and Dating with Confidence, PLoS Biology, vol.20, issue.5, pp.88-16683862, 2006.
DOI : 10.1371/journal.pbio.0040088.sd001

URL : http://doi.org/10.1371/journal.pbio.0040088

M. Gill, P. Lemey, N. Faria, A. Rambaut, and B. Shapiro, Improving Bayesian Population Dynamics Inference: A Coalescent-Based Model for Multiple Loci, Molecular Biology and Evolution, vol.30, issue.3, pp.713-724, 2013.
DOI : 10.1093/molbev/mss265

J. Bryant, E. Holmes, and A. Barrett, Out of Africa: A Molecular Perspective on the Introduction of Yellow Fever Virus into the Americas, PLoS Pathogens, vol.21, issue.5, pp.75-17511518, 2007.
DOI : 10.1371/journal.ppat.0030075.st001

W. Tabachnick, Evolutionary Genetics and Arthropod-borne Disease: The Yellow Fever Mosquito, American Entomologist, vol.37, issue.1, pp.14-24, 1991.
DOI : 10.1093/ae/37.1.14

M. Worobey, P. Telfer, S. Souquiere, M. Hunter, and C. Coleman, Island Biogeography Reveals the Deep History of SIV, Science, vol.329, issue.5998, p.20847261, 2010.
DOI : 10.1126/science.1193550

URL : https://hal.archives-ouvertes.fr/pasteur-00540189

P. Lemey, A. Rambaut, A. Drummond, and M. Suchard, Bayesian Phylogeography Finds Its Roots, PLoS Computational Biology, vol.90, issue.9, 2009.
DOI : 10.1371/journal.pcbi.1000520.s002

N. Karabatsos, International Catalogue of Arboviruses, 1985.

S. Cook, G. Moureau, A. Kitchen, E. Gould, and X. De-lamballerie, Molecular evolution of the insect-specific flaviviruses, Journal of General Virology, vol.93, issue.2, pp.223-234, 2012.
DOI : 10.1099/vir.0.036525-0

E. Huhtamo, G. Moureau, S. Cook, O. Julkunen, and N. Putkuri, Novel insect-specific flavivirus isolated from northern Europe, Virology, vol.433, issue.2, pp.471-478, 2012.
DOI : 10.1016/j.virol.2012.08.038

P. Liu, H. Lu, S. Li, G. Moureau, and Y. Deng, Genomic and antigenic characterization of the newly emerging Chinese duck egg-drop syndrome flavivirus: genomic comparison with Tembusu and Sitiawan viruses, Journal of General Virology, vol.93, issue.Pt_10, pp.2158-2170, 2012.
DOI : 10.1099/vir.0.043554-0

E. Huhtamo, S. Cook, G. Moureau, N. Uzcátegui, and T. Sironen, Novel flaviviruses from mosquitoes: Mosquito-specific evolutionary lineages within the phylogenetic group of mosquito-borne flaviviruses, Virology, vol.464, issue.465, 2014.
DOI : 10.1016/j.virol.2014.07.015

D. Lvov, Y. Tsyrkin, F. Karas, E. Timopheev, and V. Gromashevski, ?Sokuluk? virus, a new group B arbovirus isolated from Vespertilio pipistrellus Schreber, 1775, bat in the Kirghiz S.S.R., Archiv f???r die gesamte Virusforschung, vol.3, issue.3, pp.170-174, 1973.
DOI : 10.1007/BF01252762

I. Varelas-wesley and C. Calisher, Antigenic relationships of flaviviruses with undetermined arthropod-borne status, Am J Trop Med Hyg, vol.31, pp.1273-1284, 1982.

G. Kuno, Host Range Specificity of Flaviviruses: Correlation with In Vitro Replication, Journal of Medical Entomology, vol.44, issue.1, pp.93-101, 2007.
DOI : 10.1093/jmedent/41.5.93

J. Lee, N. Grubaugh, J. Kondig, M. Turell, and H. Kim, Isolation and genomic characterization of Chaoyang virus strain ROK144 from Aedes vexans nipponii from the Republic of Korea, Virology, vol.435, issue.2, pp.220-224, 2013.
DOI : 10.1016/j.virol.2012.10.020

S. Junglen, A. Kopp, A. Kurth, G. Pauli, and H. Ellerbrok, A New Flavivirus and a New Vector: Characterization of a Novel Flavivirus Isolated from Uranotaenia Mosquitoes from a Tropical Rain Forest, Journal of Virology, vol.83, issue.9, pp.4462-4468, 2009.
DOI : 10.1128/JVI.00014-09

J. Kolodziejek, K. Pachler, H. Bin, E. Mendelson, and L. Shulman, Barkedji virus, a novel mosquito-borne flavivirus identified in Culex perexiguus mosquitoes, Israel, 2011, Journal of General Virology, vol.94, issue.Pt_11, p.24362963, 2013.
DOI : 10.1099/vir.0.056200-0

J. Evangelista, C. Cruz, C. Guevara, H. Astete, and C. Carey, Characterization of a novel flavivirus isolated from Culex (Melanoconion) ocossa mosquitoes from Iquitos, Peru, Journal of General Virology, vol.94, issue.Pt_6, pp.1266-1272, 2013.
DOI : 10.1099/vir.0.050575-0

W. Batista, T. Gda, S. Vieira, D. Honda, E. Pereira et al., Notification of the first isolation of Cacipacore virus in a human in the State of Rond??nia, Brazil, Revista da Sociedade Brasileira de Medicina Tropical, vol.44, issue.4, pp.528-530, 2011.
DOI : 10.1590/S0037-86822011000400028

R. Williams, A. Vázquez, I. Asante, K. Bonney, and S. Odoom, Yaoundé-like virus in resident wild bird, Ghana. African Journal of Microbiology Research, vol.6, pp.1966-1969, 2012.

Z. Hubalek, J. Halouzka, and Z. Juricova, West Nile Fever in Czechland, Emerging Infectious Diseases, vol.5, issue.4, pp.594-595, 1999.
DOI : 10.3201/eid0504.990430

D. Lvov, A. Butenko, V. Gromashevsky, A. Kovtunov, and A. Prilipov, West Nile virus and other zoonotic viruses in Russia: examples of emerging-reemerging situations, Arch Virol, pp.85-96, 2004.
DOI : 10.1007/978-3-7091-0572-6_7

V. Bondre, R. Jadi, A. Mishra, P. Yergolkar, and V. Arankalle, West Nile virus isolates from India: evidence for a distinct genetic lineage, Journal of General Virology, vol.88, issue.3, pp.875-884, 2007.
DOI : 10.1099/vir.0.82403-0

F. May, C. Davis, R. Tesh, and A. Barrett, Phylogeography of West Nile Virus: from the Cradle of Evolution in Africa to Eurasia, Australia, and the Americas, Journal of Virology, vol.85, issue.6, pp.2964-2974, 2011.
DOI : 10.1128/JVI.01963-10

F. May, M. Lobigs, E. Lee, D. Gendle, and J. Mackenzie, Biological, antigenic and phylogenetic characterization of the flavivirus Alfuy, Journal of General Virology, vol.87, issue.2, pp.329-337, 2006.
DOI : 10.1099/vir.0.81252-0

M. Aguero, J. Fernandez-pinero, D. Buitrago, A. Sanchez, and M. Elizalde, Bagaza virus in partridges and pheasants, Spain, Emerg Infect Dis, vol.17, pp.1498-1501, 2010.

V. Gamino, A. Gutierrez-guzman, I. Fernandez-de-mera, J. Ortiz, and M. Duran-martin, Natural Bagaza virus infection in game birds in southern Spain, Veterinary Research, vol.43, issue.1, pp.65-75, 2012.
DOI : 10.1007/s11262-009-0343-4

V. Bondre, G. Sapkal, P. Yergolkar, P. Fulmali, and V. Sankararaman, Genetic characterization of Bagaza virus (BAGV) isolated in India and evidence of anti-BAGV antibodies in sera collected from encephalitis patients, Journal of General Virology, vol.90, issue.11, pp.2644-2649, 2009.
DOI : 10.1099/vir.0.012336-0

J. Fernandez-pinero, I. Davidson, M. Elizalde, S. Perk, and Y. Khinich, Bagaza virus and Israel turkey meningoencephalomyelitis virus are a single virus species, Journal of General Virology, vol.95, issue.4, p.25537376, 2014.
DOI : 10.1099/vir.0.061465-0

B. Pandey, N. Karabatsos, B. Cropp, M. Tagaki, and Y. Tsuda, Identification of a flavivirus isolated from mosquitos in Chiang Mai Thailand, Southeast Asian J Trop Med Public Health, vol.30, pp.161-165, 1999.

Y. Kono, K. Tsukamoto, A. Hamid, M. Darus, A. Lian et al., Encephalitis and retarded growth of chicks caused by Sitiawan virus, a new isolate belonging to the genus Flavivirus, Am J Trop Med Hyg, vol.63, pp.94-101, 2000.

J. Su, S. Li, X. Hu, X. Yu, and Y. Wang, Duck Egg-Drop Syndrome Caused by BYD Virus, a New Tembusu-Related Flavivirus, PLoS ONE, vol.9, issue.3, p.21455312, 2011.
DOI : 10.1371/journal.pone.0018106.t002

M. Dilcher, A. Sall, F. Hufert, and M. Weidmann, Full-length genome sequence of Ntaya virus, Virus Genes, vol.39, issue.Pt 1, pp.162-164, 2013.
DOI : 10.1007/s11262-012-0825-7

C. Boughton, R. Hawkes, and H. Naim, Illness caused by a Kokobera-like virus in south-eastern Australia. The Medical journal of, Australia, vol.145, pp.90-92, 1986.

F. May, D. Clark, K. Pham, S. Diviney, and D. Williams, Genetic divergence among members of the Kokobera group of flaviviruses supports their separation into distinct species, Journal of General Virology, vol.94, issue.Pt_7, pp.1462-1467, 2013.
DOI : 10.1099/vir.0.049940-0

J. Hobson-peters, A. Yam, J. Lu, Y. Setoh, and F. May, A New Insect-Specific Flavivirus from Northern Australia Suppresses Replication of West Nile Virus and Murray Valley Encephalitis Virus in Co-infected Mosquito Cells, PLoS ONE, vol.18, issue.2, p.23460804, 2013.
DOI : 10.1371/journal.pone.0056534.s001

K. Bloom, The Mississippi Valley's Great Yellow Fever Epidemic of 1878, Medical History LA, p.25510437, 1993.

D. Heinze, E. Gould, and N. Forrester, Revisiting the Clinal Concept of Evolution and Dispersal for the Tick-Borne Flaviviruses by Using Phylogenetic and Biogeographic Analyses, Journal of Virology, vol.86, issue.16, pp.8663-8671, 2012.
DOI : 10.1128/JVI.01013-12

K. Mcguire, E. Holmes, G. Gao, H. Reid, and E. Gould, Tracing the origins of louping ill virus by molecular phylogenetic analysis., Journal of General Virology, vol.79, issue.5, pp.981-988, 1998.
DOI : 10.1099/0022-1317-79-5-981

B. Mann, A. Mcmullen, D. Swetnam, and A. Barrett, Molecular Epidemiology and Evolution of West Nile Virus in North America, International Journal of Environmental Research and Public Health, vol.10, issue.10, pp.5111-5129, 2013.
DOI : 10.3390/ijerph10105111

G. Leonova, I. Kondratov, V. Ternovoi, E. Romanova, and E. Protopopova, Characterization of Powassan viruses from Far Eastern Russia, Archives of Virology, vol.288, issue.3, pp.811-820, 2009.
DOI : 10.1007/s00705-009-0376-y

T. Gritsun, P. Nuttall, and E. Gould, Tick-borne Flaviviruses, Adv Virus Res, vol.61, pp.317-371, 2003.
DOI : 10.1016/S0065-3527(03)61008-0

S. Telford, P. Armstrong, P. Katavolos, I. Foppa, and A. Garcia, A New Tick-borne Encephalitis-like Virus Infecting New England Deer Ticks, Ixodes dammini, Emerging Infectious Diseases, vol.3, issue.2, pp.165-170, 1997.
DOI : 10.3201/eid0302.970209

J. Pettersson and O. Fiz-palacios, Dating the origin of the genus Flavivirus in the light of Beringian biogeography, Journal of General Virology, vol.95, issue.Pt_9, p.25537376, 2014.
DOI : 10.1099/vir.0.065227-0

X. Gao, H. Liu, H. Wang, S. Fu, and Z. Guo, Southernmost Asia Is the Source of Japanese Encephalitis Virus (Genotype 1) Diversity from which the Viruses Disperse and Evolve throughout Asia, PLoS Neglected Tropical Diseases, vol.17, issue.24, p.24069502, 2013.
DOI : 10.1371/journal.pntd.0002459.s001

A. Firth and I. Brierley, Non-canonical translation in RNA viruses, Journal of General Virology, vol.93, issue.Pt_7, pp.1385-1409, 2012.
DOI : 10.1099/vir.0.042499-0

A. Firth and J. Atkins, A conserved predicted pseudoknot in the NS2A-encoding sequence of West Nile and Japanese encephalitis flaviviruses suggests NS1' may derive from ribosomal frameshifting, Virology Journal, vol.6, issue.1, p.14, 2009.
DOI : 10.1186/1743-422X-6-14

E. Melian, E. Hinzman, T. Nagasaki, A. Firth, and N. Wills, NS1' of Flaviviruses in the Japanese Encephalitis Virus Serogroup Is a Product of Ribosomal Frameshifting and Plays a Role in Viral Neuroinvasiveness, Journal of Virology, vol.84, issue.3, pp.1641-1647, 2010.
DOI : 10.1128/JVI.01979-09

A. Firth, B. Blitvich, N. Wills, C. Miller, and J. Atkins, Evidence for ribosomal frameshifting and a novel overlapping gene in the genomes of insect-specific flaviviruses, Virology, vol.399, issue.1, pp.153-166, 2010.
DOI : 10.1016/j.virol.2009.12.033

K. Clyde and E. Harris, RNA Secondary Structure in the Coding Region of Dengue Virus Type 2 Directs Translation Start Codon Selection and Is Required for Viral Replication, Journal of Virology, vol.80, issue.5, pp.2170-2182, 2006.
DOI : 10.1128/JVI.80.5.2170-2182.2006

K. Clyde, J. Barrera, and E. Harris, The capsid-coding region hairpin element (cHP) is a critical determinant of dengue virus and West Nile virus RNA synthesis, Virology, vol.379, issue.2, pp.314-323, 2008.
DOI : 10.1016/j.virol.2008.06.034

A. Groat-carmona, S. Orozco, P. Friebe, A. Payne, and L. Kramer, A novel coding-region RNA element modulates infectious dengue virus particle production in both mammalian and mosquito cells and regulates viral replication in Aedes aegypti mosquitoes, Virology, vol.432, issue.2, pp.511-526, 2012.
DOI : 10.1016/j.virol.2012.06.028

Y. Liu, E. Wimmer, and A. Paul, Cis-acting RNA elements in human and animal plus-strand RNA viruses, Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, vol.1789, issue.9-10, pp.495-517, 2009.
DOI : 10.1016/j.bbagrm.2009.09.007

A. Tuplin, D. Evans, A. Buckley, I. Jones, and E. Gould, Replication enhancer elements within the open reading frame of tick-borne encephalitis virus and their evolution within the Flavivirus genus, Nucleic Acids Research, vol.39, issue.16, pp.7034-7048, 2011.
DOI : 10.1093/nar/gkr237

A. Khromykh, H. Meka, K. Guyatt, and E. Westaway, Essential Role of Cyclization Sequences in Flavivirus RNA Replication, Journal of Virology, vol.75, issue.14, pp.6719-6728, 2001.
DOI : 10.1128/JVI.75.14.6719-6728.2001

L. Domier, N. Mccoppin, R. Larsen, D. Arcy, and C. , Nucleotide sequence shows that Bean leafroll virus has a Luteovirus-like genome organization, Journal of General Virology, vol.83, issue.7, pp.1791-1798, 2002.
DOI : 10.1099/0022-1317-83-7-1791

G. Loughran, A. Firth, and J. Atkins, Ribosomal frameshifting into an overlapping gene in the 2B-encoding region of the cardiovirus genome, Proceedings of the National Academy of Sciences, vol.108, issue.46, pp.1111-1119, 2011.
DOI : 10.1073/pnas.1102932108

Y. Fang, E. Treffers, Y. Li, A. Tas, and Z. Sun, Efficient -2 frameshifting by mammalian ribosomes to synthesize an additional arterivirus protein, Proceedings of the National Academy of Sciences, vol.109, issue.43, pp.2920-2928, 2012.
DOI : 10.1073/pnas.1211145109

P. Mattingly, II. Ecological aspects of the evolution of mosquito-borne virus diseases, Transactions of the Royal Society of Tropical Medicine and Hygiene, vol.54, issue.2, pp.97-112, 1960.
DOI : 10.1016/0035-9203(60)90046-8

G. Kuno and G. Chang, Biological Transmission of Arboviruses: Reexamination of and New Insights into Components, Mechanisms, and Unique Traits as Well as Their Evolutionary Trends, Clinical Microbiology Reviews, vol.18, issue.4, pp.608-637, 2005.
DOI : 10.1128/CMR.18.4.608-637.2005

D. Roiz, A. Vazquez, M. Seco, A. Tenorio, and A. Rizzoli, Detection of novel insect flavivirus sequences integrated in Aedes albopictus (Diptera: Culicidae) in Northern Italy, Virology Journal, vol.6, issue.1, p.93, 2009.
DOI : 10.1186/1743-422X-6-93

M. Sanchez-seco, A. Vazquez, X. Collao, L. Hernandez, and C. Aranda, Surveillance of Arboviruses in Spanish Wetlands: Detection of New Flavi- and Phleboviruses, Vector-Borne and Zoonotic Diseases, vol.10, issue.2, pp.203-206, 2009.
DOI : 10.1089/vbz.2008.0188

F. Edwards, On Some Malayan and Other Species of Culicoides, with a Note on the Genus Lasiohelea, Bulletin of Entomological Research, vol.13, issue.02, pp.161-167, 1922.
DOI : 10.1017/S0007485300028030

M. Laird, A ceratopogonine midge (Culicoides anophelis Edwards, 1922) sucking engorged blood from a mosquito (Armigeres lacuum Edwards, 1922) at Palmalmal, New Britain, Transactions and Proceedings of the Royal Society of New Zealand, vol.76, pp.158-161, 1946.

J. Chhilar and S. Chaudhry, First Report of a Biting Midge Culicoides Anophelis Parasitzing Mosquito Anopheles stephensi from North-Western India, 2011.

C. Reddy and M. Hafeez, Studies on certain aspects of prevalence of Culicoides species, 2011.

E. Gould, B. Coutard, H. Malet, B. Morin, S. Jamal et al., Understanding the alphaviruses: Recent research on important emerging pathogens and progress towards their control, Antiviral Research, vol.87, issue.2, 2009.
DOI : 10.1016/j.antiviral.2009.07.007

E. Gould, X. De-lamballerie, P. Zanotto, and E. Holmes, Evolution, epidemiology, and dispersal of flaviviruses revealed by molecular phylogenies, Adv Virus Res, vol.57, pp.71-103, 2001.
DOI : 10.1016/S0065-3527(01)57001-3

D. Gubler, Dengue and dengue hemorrhagic fever in the Americas, Puerto Rico health sciences journal, vol.6, pp.107-111, 1987.

G. Strode, Yellow Fever, 1951.

L. Kramer and L. Chandler, Phylogenetic analysis of the envelope gene of St. Louis encephalitis virus, Archives of Virology, vol.146, issue.12, pp.2341-2355, 2001.
DOI : 10.1007/s007050170007

E. Gould, S. Moss, and S. Turner, Evolution and dispersal of encephalitic flaviviruses, Arch Virol, pp.65-84, 2004.
DOI : 10.1007/978-3-7091-0572-6_6

O. Allicock, P. Lemey, A. Tatem, O. Pybus, and S. Bennett, Phylogeography and Population Dynamics of Dengue Viruses in the Americas, Molecular Biology and Evolution, vol.29, issue.6, pp.1533-1543, 2012.
DOI : 10.1093/molbev/msr320

D. Gubler, The emergence of dengue/dengue haemorrhagic fever as a global public health problem, Factors in the Emergence of Arbovirus Diseases, pp.83-92, 1997.

D. Gubler, Dengue/Dengue Haemorrhagic Fever: History and Current Status, Novartis Foundation Symposium, vol.277, pp.3-16, 2006.
DOI : 10.1002/0470058005.ch2

T. Briese, X. Jia, C. Huang, L. Grady, and W. Lipkin, Identification of a Kunjin/West Nile-like flavivirus in brains of patients with New York encephalitis, The Lancet, vol.354, issue.9186, pp.1261-1262, 1999.
DOI : 10.1016/S0140-6736(99)04576-6

R. Lanciotti, J. Roehrig, V. Deubel, J. Smith, and M. Parker, Origin of the West Nile Virus Responsible for an Outbreak of Encephalitis in the Northeastern United States, Science, vol.286, issue.5448, pp.2333-2337, 1999.
DOI : 10.1126/science.286.5448.2333

W. Reisen, Ecology of West Nile Virus in North America, Viruses, vol.5, issue.9, pp.2079-2105, 2013.
DOI : 10.3390/v5092079

J. Roehrig, M. Layton, P. Smith, G. Campbell, and R. Nasci, The Emergence of West Nile Virus in North America: Ecology, Epidemiology, and Surveillance, Curr Top Microbiol Immunol, vol.267, pp.223-240, 2002.
DOI : 10.1007/978-3-642-59403-8_11

W. Huanyu, W. Haiyan, F. Shihong, L. Guifang, and L. Hong, Isolation and identification of a distinct strain of Culex Flavivirus from mosquitoes collected in Mainland China, Virology Journal, vol.9, issue.1, pp.73-83, 2012.
DOI : 10.1080/10635150290102582

M. Morales-betoulle, M. Pineda, M. Sosa, S. Panella, N. Lopez et al., Culex Flavivirus Isolates from Mosquitoes in Guatemala, Journal of Medical Entomology, vol.45, issue.6, pp.1187-1190, 2008.
DOI : 10.1093/jmedent/45.6.1187

R. Harbach and I. Kitching, Phylogeny and classification of the Culicidae (Diptera), Systematic Entomology, vol.23, issue.4, pp.327-370, 1998.
DOI : 10.1046/j.1365-3113.1998.00072.x

R. Charrel, X. De-lamballerie, and C. Fulhorst, The Whitewater Arroyo Virus: Natural Evidence for Genetic Recombination among Tacaribe Serocomplex Viruses (Family Arenaviridae), Virology, vol.283, issue.2, pp.161-166, 2001.
DOI : 10.1006/viro.2001.0874

S. Engel, K. Hogan, J. Taylor, and S. Davis, Molecular Systematics and Paleobiogeography of the South American Sigmodontine Rodents, Molecular Biology and Evolution, vol.15, issue.2, pp.35-49, 1998.
DOI : 10.1093/oxfordjournals.molbev.a025918

A. Hughes and R. Friedman, Evolutionary Diversification of Protein-Coding Genes of Hantaviruses, Molecular Biology and Evolution, vol.17, issue.10, pp.1558-1568, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026254

C. Ramsden, E. Holmes, and M. Charleston, Hantavirus Evolution in Relation to Its Rodent and Insectivore Hosts: No Evidence for Codivergence, Molecular Biology and Evolution, vol.26, issue.1, pp.143-153, 2009.
DOI : 10.1093/molbev/msn234

C. Ramsden, F. Melo, L. Figueiredo, E. Holmes, and P. Zanotto, High Rates of Molecular Evolution in Hantaviruses, Molecular Biology and Evolution, vol.25, issue.7, pp.1488-1492, 2008.
DOI : 10.1093/molbev/msn093

J. Sun, Y. Yu, and V. Deubel, Japanese encephalitis virus NS1' protein depends on pseudoknot secondary structure and is cleaved by caspase during virus infection and cell apoptosis. Microbes and infection, Institut Pasteur, vol.14, p.22504173, 2012.

Q. Ye, X. Li, H. Zhao, S. Li, and Y. Deng, A single nucleotide mutation in NS2A of Japanese encephalitis-live vaccine virus (SA14-14-2) ablates NS1' formation and contributes to attenuation, Journal of General Virology, vol.93, issue.Pt_9, pp.1959-1964, 2012.
DOI : 10.1099/vir.0.043844-0