G. Liang, X. Gao, and E. A. Gould, Factors responsible for the emergence of arboviruses; strategies, challenges and limitations for their control, Emerging Microbes & Infections, vol.4, issue.1, pp.1-5, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01217372

S. Bhatt, P. W. Gething, O. J. Brady, J. P. Messina, A. W. Farlow et al., The global distribution and burden of dengue, Nature, vol.496, issue.7446, pp.504-507, 2013.

C. H. Calisher, N. Karabatsos, J. M. Dalrymple, R. E. Shope, J. S. Porterfield et al., Antigenic Relationships between Flaviviruses as Determined by Cross-neutralization Tests with Polyclonal Antisera, Journal of General Virology, vol.70, issue.1, pp.37-43, 1989.

M. G. Guzman and E. Harris, Dengue, The Lancet, vol.385, issue.9966, pp.453-465, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01873838

. Anon, The dengue epidemic in Greece, Leag. Nations Mon. Epidemiol. Rep, vol.7, p.334, 1928.

G. Rezza, Dengue and chikungunya: long-distance spread and outbreaks in naïve areas, Pathogens and Global Health, vol.108, issue.8, pp.349-355, 2014.

T. J. Curtin, Status of Aedes Aegypti In The Eastern Mediterranean, Journal of Medical Entomology, vol.4, issue.1, pp.48-50, 1967.

G. La-ruche, First two autochthonous dengue virus infections in metropolitan France, European Communicable Disease Bulletin, vol.15, p.19676, 2010.

I. Gjenero-margan, Colloque Européen démographique, European Demographic Information Bulletin, vol.3, issue.2, pp.111-111, 1972.

E. Marchand, C. Prat, C. Jeannin, E. Lafont, T. Bergmann et al., Autochthonous case of dengue in France, October 2013, Eurosurveillance, vol.18, issue.50, p.20661, 2013.

S. Giron, Réunion des archéologues de la région Provence-Alpes-Côte d'Azur du 14 octobre 1981, Les Nouvelles de l'archéologie, vol.7, issue.1, pp.79-81, 1982.

T. Succo, I. Leparc-goffart, J. Ferré, D. Roiz, B. Broche et al., Autochthonous dengue outbreak in Nîmes, South of France, July to September 2015, Eurosurveillance, vol.21, issue.21, pp.5-11, 2016.

F. Franke, S. Giron, C. Jeannin, I. Leparc-goffart, H. De-valk et al., Emergences de dengue, de chikungunya et de zika en France métropolitaine, 2006?2019, Médecine et Maladies Infectieuses, vol.50, issue.6, p.S109, 2020.

F. Santé-publique, Chikungunya, dengue et zika -Données de la surveillance renforcée en France métropolitaine en 2020, 2020.

J. Adhami and P. Reiter, Introduction and establishment of Aedes (Stegomyia) albopictus skuse (Diptera: Culicidae) in Albania, J. Am. Mosq. Control Assoc, vol.14, pp.340-343, 1998.

A. Sabatini, V. Raineri, G. Trovato, and M. Coluzzi, Aedes albopictus in Italy and possible diffusion of the species into the Mediterranean area, Parassitologia, vol.32, pp.301-304, 1990.

J. M. Medlock, K. M. Hansford, V. Versteirt, B. Cull, H. Kampen et al., An entomological review of invasive mosquitoes in Europe, Bulletin of Entomological Research, vol.105, issue.6, pp.637-663, 2015.

L. P. Lounibos and L. D. Kramer, Invasiveness ofAedes aegyptiandAedes albopictusand Vectorial Capacity for Chikungunya Virus, Journal of Infectious Diseases, vol.214, issue.suppl 5, pp.S453-S458, 2016.

L. Lambrechts, T. W. Scott, and D. J. Gubler, Consequences of the Expanding Global Distribution of Aedes albopictus for Dengue Virus Transmission, PLoS Neglected Tropical Diseases, vol.4, issue.5, p.e646, 2010.
URL : https://hal.archives-ouvertes.fr/pasteur-02011027

A. Vega-rua, K. Zouache, V. Caro, L. Diancourt, P. Delaunay et al., High Efficiency of Temperate Aedes albopictus to Transmit Chikungunya and Dengue Viruses in the Southeast of France, PLoS ONE, vol.8, issue.3, p.e59716, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-01718113

C. Paupy, H. Delatte, L. Bagny, V. Corbel, and D. Fontenille, Aedes albopictus, an arbovirus vector: From the darkness to the light, Microbes and Infection, vol.11, issue.14-15, pp.1177-1185, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02958368

D. Metselaar, An outbreak of type 2 dengue fever in the Seychelles, probably transmitted by Aedes albopictus (Skuse), Bull. World Health Organ, vol.58, pp.937-943, 1980.

A. B. Sabin, Research on Dengue during World War II 1, The American Journal of Tropical Medicine and Hygiene, vol.1, issue.1, pp.30-50, 1952.

P. Coulanges, Y. Clercy, F. X. Jousset, F. Rodhain, and C. Hannoun, Dengue at Reunion: isolation of a strain at the Pasteur Institute of Madagascar, Bull. Soc. Pathol. Exot, vol.72, pp.205-209, 1979.

P. V. Effler, L. Pang, P. Kitsutani, V. Vorndam, M. Nakata et al., Dengue Fever, Hawaii, 2001?2002, Emerging Infectious Diseases, vol.11, issue.5, pp.742-749, 2005.

E. Wang, H. Ni, R. Xu, A. D. Barrett, S. J. Watowich et al., Evolutionary Relationships of Endemic/Epidemic and Sylvatic Dengue Viruses, Journal of Virology, vol.74, issue.7, pp.3227-3234, 2000.

G. Manokaran, E. Finol, C. Wang, J. Gunaratne, J. Bahl et al., Dengue subgenomic RNA binds TRIM25 to inhibit interferon expression for epidemiological fitness, Science, vol.350, issue.6257, pp.217-221, 2015.

A. Slonchak, L. E. Hugo, M. E. Freney, S. Hall-mendelin, A. A. Amarilla et al., Zika virus noncoding RNA suppresses apoptosis and is required for virus transmission by mosquitoes, Nature Communications, vol.11, issue.1, 2020.

G. P. Göertz, J. W. Van-bree, A. Hiralal, B. M. Fernhout, C. Steffens et al., Subgenomic flavivirus RNA binds the mosquito DEAD/H-box helicase ME31B and determines Zika virus transmission by Aedes aegypti, Proceedings of the National Academy of Sciences, vol.116, issue.38, pp.19136-19144, 2019.

S. C. Yeh and J. Pompon, Flaviviruses Produce a Subgenomic Flaviviral RNA That Enhances Mosquito Transmission, DNA and Cell Biology, vol.37, issue.3, pp.154-159, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01937761

J. Pompon, M. Manuel, G. K. Ng, B. Wong, C. Shan et al., Dengue subgenomic flaviviral RNA disrupts immunity in mosquito salivary glands to increase virus transmission, PLOS Pathogens, vol.13, issue.7, p.e1006535, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02013864

G. P. Göertz, J. J. Fros, P. Miesen, C. B. Vogels, M. L. Van-der-bent et al., Noncoding Subgenomic Flavivirus RNA Is Processed by the Mosquito RNA Interference Machinery and Determines West Nile Virus Transmission by Culex pipiens Mosquitoes, Journal of Virology, vol.90, issue.22, pp.10145-10159, 2016.

C. V. Filomatori, J. M. Carballeda, S. M. Villordo, S. Aguirre, H. M. Pallarés et al., Dengue virus genomic variation associated with mosquito adaptation defines the pattern of viral non-coding RNAs and fitness in human cells, PLOS Pathogens, vol.13, issue.3, p.e1006265, 2017.

H. M. Pallarés, G. S. Costa-navarro, S. M. Villordo, F. Merwaiss, L. De-borba et al., Zika Virus Subgenomic Flavivirus RNA Generation Requires Cooperativity between Duplicated RNA Structures That Are Essential for Productive Infection in Human Cells, Journal of Virology, vol.94, issue.18, 2020.

I. Schuffenecker, I. Iteman, A. Michault, S. Murri, L. Frangeul et al., Genome Microevolution of Chikungunya Viruses Causing the Indian Ocean Outbreak, PLoS Medicine, vol.3, issue.7, p.e263, 2006.
URL : https://hal.archives-ouvertes.fr/pasteur-01659363

K. A. Tsetsarkin, D. L. Vanlandingham, C. E. Mcgee, and S. Higgs, A Single Mutation in Chikungunya Virus Affects Vector Specificity and Epidemic Potential, PLoS Pathogens, vol.3, issue.12, p.e201, 2007.

M. Vazeille, S. Moutailler, D. Coudrier, C. Rousseaux, H. Khun et al., Two Chikungunya Isolates from the Outbreak of La Reunion (Indian Ocean) Exhibit Different Patterns of Infection in the Mosquito, Aedes albopictus, PLoS ONE, vol.2, issue.11, p.e1168, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00196860

J. A. Roby, G. P. Pijlman, J. Wilusz, and A. A. Khromykh, Noncoding Subgenomic Flavivirus RNA: Multiple Functions in West Nile Virus Pathogenesis and Modulation of Host Responses, Viruses, vol.6, issue.2, pp.404-427, 2014.

G. P. Göertz and G. P. Pijlman, Dengue Non-coding RNA: TRIMmed for Transmission, Cell Host & Microbe, vol.18, issue.2, pp.133-134, 2015.

S. M. Villordo, C. V. Filomatori, I. Sánchez-vargas, C. D. Blair, and A. V. Gamarnik, Dengue Virus RNA Structure Specialization Facilitates Host Adaptation, PLOS Pathogens, vol.11, issue.1, p.e1004604, 2015.

G. P. Pijlman, A. Funk, N. Kondratieva, J. Leung, S. Torres et al., A Highly Structured, Nuclease-Resistant, Noncoding RNA Produced by Flaviviruses Is Required for Pathogenicity, Cell Host & Microbe, vol.4, issue.6, pp.579-591, 2008.

A. Schuessler, A. Funk, H. M. Lazear, D. A. Cooper, S. Torres et al., West Nile Virus Noncoding Subgenomic RNA Contributes to Viral Evasion of the Type I Interferon-Mediated Antiviral Response, Journal of Virology, vol.86, issue.10, pp.5708-5718, 2012.

C. B. Vogels, L. J. Van-de-peppel, A. J. Van-vliet, M. Westenberg, A. Ibañez-justicia et al., Winter Activity and Aboveground Hybridization Between the Two Biotypes of the West Nile Virus VectorCulex pipiens, Vector-Borne and Zoonotic Diseases, vol.15, issue.10, pp.619-626, 2015.

J. Pompon, R. Morales-vargas, M. Manuel, C. Huat-tan, T. Vial et al., A Zika virus from America is more efficiently transmitted than an Asian virus by Aedes aegypti mosquitoes from Asia, Scientific Reports, vol.7, issue.1, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02013884

E. G. Chapman, S. L. Moon, J. Wilusz, and J. S. Kieft, RNA structures that resist degradation by Xrn1 produce a pathogenic Dengue virus RNA, eLife, vol.3, 2014.

M. Manni, C. R. Guglielmino, F. Scolari, A. Vega-rúa, A. Failloux et al., Genetic evidence for a worldwide chaotic dispersion pattern of the arbovirus vector, Aedes albopictus, PLOS Neglected Tropical Diseases, vol.11, issue.1, p.e0005332, 2017.
URL : https://hal.archives-ouvertes.fr/pasteur-01468191

S. Sherpa, D. Rioux, C. Pougnet-lagarde, and L. Després, Genetic diversity and distribution differ between long-established and recently introduced populations in the invasive mosquito Aedes albopictus, Infection, Genetics and Evolution, vol.58, pp.145-156, 2018.

N. Vasilakis, E. R. Deardorff, J. L. Kenney, S. L. Rossi, K. A. Hanley et al., Mosquitoes Put the Brake on Arbovirus Evolution: Experimental Evolution Reveals Slower Mutation Accumulation in Mosquito Than Vertebrate Cells, PLoS Pathogens, vol.5, issue.6, p.e1000467, 2009.

K. A. Stapleford, L. L. Coffey, S. Lay, A. V. Bordería, V. Duong et al., Emergence and Transmission of Arbovirus Evolutionary Intermediates with Epidemic Potential, Cell Host & Microbe, vol.15, issue.6, pp.706-716, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-01680236

R. Bellone, S. Lequime, H. Jupille, G. P. Göertz, F. Aubry et al., Experimental adaptation of dengue virus 1 to Aedes albopictus mosquitoes by in vivo selection, Scientific Reports, vol.10, issue.1, p.18404, 2020.
URL : https://hal.archives-ouvertes.fr/pasteur-02989626

A. Funk, K. Truong, T. Nagasaki, S. Torres, N. Floden et al., RNA Structures Required for Production of Subgenomic Flavivirus RNA, Journal of Virology, vol.84, issue.21, pp.11407-11417, 2010.

B. M. Akiyama, D. Eiler, and J. S. Kieft, Structured RNAs that evade or confound exonucleases: function follows form, Current Opinion in Structural Biology, vol.36, pp.40-47, 2016.

E. G. Chapman, D. A. Costantino, J. L. Rabe, S. L. Moon, J. Wilusz et al., The Structural Basis of Pathogenic Subgenomic Flavivirus RNA (sfRNA) Production, Science, vol.344, issue.6181, pp.307-310, 2014.

B. M. Akiyama, H. M. Laurence, A. R. Massey, D. A. Costantino, X. Xie et al., Zika virus produces noncoding RNAs using a multi-pseudoknot structure that confounds a cellular exonuclease, Science, vol.354, issue.6316, pp.1148-1152, 2016.

S. L. Moon, B. J. Dodd, D. E. Brackney, C. J. Wilusz, G. D. Ebel et al., Flavivirus sfRNA suppresses antiviral RNA interference in cultured cells and mosquitoes and directly interacts with the RNAi machinery, Virology, vol.485, pp.322-329, 2015.

E. Schnettler, M. G. Sterken, J. Y. Leung, S. W. Metz, C. Geertsema et al., Noncoding Flavivirus RNA Displays RNA Interference Suppressor Activity in Insect and Mammalian Cells, Journal of Virology, vol.86, issue.24, pp.13486-13500, 2012.

K. A. Tsetsarkin, C. E. Mcgee, S. M. Volk, D. L. Vanlandingham, S. C. Weaver et al., Epistatic Roles of E2 Glycoprotein Mutations in Adaption of Chikungunya Virus to Aedes Albopictus and Ae. Aegypti Mosquitoes, PLoS ONE, vol.4, issue.8, p.e6835, 2009.

K. A. Tsetsarkin, R. Chen, M. B. Sherman, and S. C. Weaver, Chikungunya virus: evolution and genetic determinants of emergence, Current Opinion in Virology, vol.1, issue.4, pp.310-317, 2011.

A. Syenina, D. Vijaykrishna, E. S. Gan, H. C. Tan, M. M. Choy et al., Positive epistasis between viral polymerase and the 3? untranslated region of its genome reveals the epidemiologic fitness of dengue virus, Proceedings of the National Academy of Sciences, vol.117, issue.20, pp.11038-11047, 2020.

D. E. Brackney, J. C. Scott, F. Sagawa, J. E. Woodward, N. A. Miller et al., C6/36 Aedes albopictus Cells Have a Dysfunctional Antiviral RNA Interference Response, PLoS Neglected Tropical Diseases, vol.4, issue.10, p.e856, 2010.

M. Grandadam, V. Caro, S. Plumet, J. Thiberge, Y. Souarès et al., Chikungunya Virus, Southeastern France, Emerging Infectious Diseases, vol.17, issue.5, pp.910-913, 2011.
URL : https://hal.archives-ouvertes.fr/pasteur-01681259

T. Fansiri, A. Fontaine, L. Diancourt, V. Caro, B. Thaisomboonsuk et al., Genetic Mapping of Specific Interactions between Aedes aegypti Mosquitoes and Dengue Viruses, PLoS Genetics, vol.9, issue.8, p.e1003621, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-00854586

J. G. Christenbury, P. P. Aw, S. H. Ong, M. J. Schreiber, A. Chow et al., A method for full genome sequencing of all four serotypes of the dengue virus, Journal of Virological Methods, vol.169, issue.1, pp.202-206, 2010.

A. M. Bolger, M. Lohse, and B. Usadel, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, vol.30, issue.15, pp.2114-2120, 2014.

S. Boisvert, F. Raymond, É. Godzaridis, F. Laviolette, and J. Corbeil, Ray Meta: scalable de novo metagenome assembly and profiling, Genome Biology, vol.13, issue.12, p.R122, 2012.

B. Langmead and S. L. Salzberg, Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-359, 2012.

H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, issue.16, pp.2078-2079, 2009.

A. R. Quinlan and I. M. Hall, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, vol.26, issue.6, pp.841-842, 2010.

A. Wilm, P. P. Aw, D. Bertrand, G. H. Yeo, S. H. Ong et al., LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets, Nucleic Acids Research, vol.40, issue.22, pp.11189-11201, 2012.

C. W. Nelson, L. H. Moncla, and A. L. Hughes, SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data: Table 1., Bioinformatics, vol.31, p.btv449, 2015.

M. Zuker, Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acids Research, vol.31, issue.13, pp.3406-3415, 2003.

K. Darty, A. Denise, and Y. Ponty, VARNA: Interactive drawing and editing of the RNA secondary structure, Bioinformatics, vol.25, issue.15, pp.1974-1975, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00432548

S. M. Villordo, J. M. Carballeda, C. V. Filomatori, and A. V. Gamarnik, RNA Structure Duplications and Flavivirus Host Adaptation, Trends in Microbiology, vol.24, issue.4, pp.270-283, 2016.

F. Aubry, A. Nougairède, L. De-fabritus, G. Querat, E. A. Gould et al., Single-stranded positive-sense RNA viruses generated in days using infectious subgenomic amplicons, Journal of General Virology, vol.95, issue.11, pp.2462-2467, 2014.

S. Holm, Correction: An Improved Sequentially Rejective Bonferroni Test Procedure, Biometrics, vol.43, issue.3, p.737, 1987.