G. French-guiana and M. , the Americas, 2012.

S. Larrieu, Results from a seroprevalence study among blood donors, Trans R Soc Trop Med Hyg, vol.108, issue.1, pp.57-66, 2014.

P. Quénel, Contributions de la recherche virologique, clinique, épidémiologique, socio comportementale et en modélisation mathématique au contrôle de la dengue dans les DFA, Bulletin de veille sanitaire, vol.3, pp.1-16, 2009.

S. P. , Le chikungunya dans les Antilles Bulletin du 17, pp.1-6, 2014.

W. Van-bortel, Chikungunya outbreak in the Caribbean region, Euro Surveill, vol.19, issue.13, 2013.

S. P. , Situation épidémiologique du virus Zika aux Antilles et en Guyane. Point au 30 janvier 2017. Le Point épidémio N°1, INVS, pp.1-7, 2017.

, Pan American Health Organization / World Health Organization. Epidemiological Update: Yellow Fever, 2018.

P. S. Yen, Aedes aegypti mosquitoes from Guadeloupe (French West Indies) are able to transmit yellow fever virus, PLoS One, vol.13, issue.9, p.204710, 2018.
URL : https://hal.archives-ouvertes.fr/pasteur-01887187

J. R. Fauver, West African Anopheles gambiae mosquitoes harbor a taxonomically diverse virome including new insect-specific flaviviruses, mononegaviruses, and totiviruses, Virology, vol.498, pp.288-99, 2016.

E. Atoni, Metagenomic virome analysis of culex mosquitoes from Kenya and China, Viruses, vol.10, issue.1, 2018.

H. Xia, Comparative metagenomic profiling of viromes associated with four common mosquito species in China, Virol Sin, vol.33, issue.1, pp.59-66, 2018.

M. Sadeghi, Virome of >12 thousand Culex mosquitoes from throughout California, Virology, vol.523, pp.74-88, 2018.

K. G. Frey, Bioinformatic characterization of mosquito viromes within the eastern United States and Puerto Rico: discovery of novel viruses, Evol Bioinformatics Online, vol.12, issue.2, pp.1-12, 2016.

C. Shi, A metagenomic survey of viral abundance and diversity in mosquitoes from Hubei province, PLoS One, vol.10, issue.6, p.129845, 2015.

C. M. Roundy, Insect-specific viruses: a historical overview and recent developments, Adv Virus Res, vol.98, pp.119-165, 2017.

B. G. Bolling, Transmission dynamics of an insect-specific flavivirus in a naturally infected Culex pipiens laboratory colony and effects of co-infection on vector competence for West Nile virus, Virology, vol.427, issue.2, pp.90-97, 2012.

J. H. Erasmus, Utilization of an Eilat virus-based chimera for serological detection of chikungunya infection, PLoS Negl Trop Dis, vol.9, issue.10, p.4119, 2015.

R. M. Moll, Meconial peritrophic membranes and the fate of midgut bacteria during mosquito (Diptera: Culicidae) metamorphosis, J Med Entomol, vol.38, issue.1, pp.29-32, 2001.

G. Gimonneau, Composition of Anopheles coluzzii and Anopheles gambiae microbiota from larval to adult stages, Infect Genet Evol, vol.28, pp.715-739, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01546167

T. Chouin-carneiro, Differential susceptibilities of Aedes aegypti and Aedes albopictus from the Americas to Zika virus, PLoS Negl Trop Dis, vol.10, issue.3, p.4543, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01491874

S. L. Richards, S. L. Anderson, and C. C. Lord, Vector competence of Culex pipiens quinquefasciatus (Diptera: Culicidae) for West Nile virus isolates from Florida, Tropical Med Int Health, vol.19, issue.5, pp.610-617, 2014.

S. Crochu, Sequences of flavivirus-related RNA viruses persist in DNA form integrated in the genome of Aedes spp. mosquitoes, J Gen Virol, vol.85, pp.1971-80, 2004.

U. Palatini, Comparative genomics shows that viral integrations are abundant and express piRNAs in the arboviral vectors Aedes aegypti and Aedes albopictus, BMC Genomics, vol.18, issue.1, p.512, 2017.

M. Shi, Redefining the invertebrate RNA virosphere, Nature, vol.540, issue.7634, pp.539-582, 2016.

E. R. Aguiar, Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host, Nucleic Acids Res, vol.43, issue.13, pp.6191-206, 2015.

A. B. Allison, Cyclic avian mass mortality in the northeastern United States is associated with a novel orthomyxovirus, J Virol, vol.89, issue.2, pp.1389-403, 2015.

M. Shi, High-resolution metatranscriptomics reveals the ecological dynamics of mosquito-associated RNA viruses in Western Australia, J Virol, issue.17, p.91, 2017.

S. Katsuma, Novel macula-like virus identified in Bombyx mori cultured cells, J Virol, vol.79, issue.9, pp.5577-84, 2005.

S. Ratnasingham and P. D. Hebert, bold: the barcode of life data system, vol.7, pp.355-64, 2007.

D. E. Holmes, K. P. Nevin, and D. R. Lovley, Comparison of 16S rRNA, nifD, recA, gyrB, rpoB and fusA genes within the family Geobacteraceae fam, Int J Syst Evol Microbiol, vol.54, pp.1591-1600, 2004.

C. Richard, Chromobacterium violaceum, opportunist pathogenic bacteria in tropical and subtropical regions, Bull Soc Pathol Exot, vol.86, issue.3, pp.169-73, 1993.

M. Marchetti, Cupriavidus taiwanensis bacteroids in Mimosa pudica indeterminate nodules are not terminally differentiated, Appl Environ Microbiol, vol.77, issue.6, pp.2161-2165, 2011.

A. R. Chavshin, Malpighian tubules are important determinants of Pseudomonas transstadial transmission and longtime persistence in Anopheles stephensi, Parasit Vectors, vol.8, p.36, 2015.

C. Galiez, WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs, Bioinformatics, vol.33, pp.3113-3117, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01982199

S. M. Short, Amino acid metabolic signaling influences Aedes aegypti midgut microbiome variability, PLoS Negl Trop Dis, vol.11, issue.7, p.5677, 2017.

S. Van-tol and G. Dimopoulos, Chapter nine-influences of the mosquito microbiota on vector competence, Advances in insect physiology, vol.51, pp.243-91, 2016.

J. L. Ramirez, Reciprocal tripartite interactions between the Aedes aegypti midgut microbiota, innate immune system and dengue virus influences vector competence, PLoS Negl Trop Dis, vol.6, issue.3, p.1561, 2012.

N. Jupatanakul, S. Sim, and G. Dimopoulos, The insect microbiome modulates vector competence for arboviruses, Viruses, vol.6, issue.11, pp.4294-313, 2014.

D. Goindin, Screening of natural Wolbachia infection in Aedes aegypti, Aedes taeniorhynchus and Culex quinquefasciatus from Guadeloupe (French West Indies), Acta Trop, vol.185, pp.314-321, 2018.

R. L. Glaser and M. A. Meola, The native Wolbachia endosymbionts of Drosophila melanogaster and Culex quinquefasciatus increase host resistance to West Nile virus infection, PLoS One, vol.5, issue.8, p.11977, 2010.

G. Cheng, Mosquito defense strategies against viral infection, Trends Parasitol, vol.32, issue.3, pp.177-86, 2016.

X. Zhang, Discovery and high prevalence of Phasi Charoen-like virus in field-captured Aedes aegypti in South China, Virology, vol.523, pp.35-40, 2018.

M. J. Schultz, H. M. Frydman, and J. H. Connor, Dual insect specific virus infection limits arbovirus replication in Aedes mosquito cells, Virology, vol.518, pp.406-419, 2018.

J. D. Wuerth and F. Weber, Phleboviruses and the type i interferon response, Viruses, vol.8, issue.6, p.174, 2016.

S. Won, NSm protein of Rift Valley fever virus suppresses virus-induced apoptosis, J Virol, vol.81, issue.24, pp.13335-13380, 2007.

M. Marklewitz, Evolutionary and phenotypic analysis of live virus isolates suggests arthropod origin of a pathogenic RNA virus family, Proc Natl Acad Sci, vol.112, issue.24, pp.7536-7577, 2015.

R. J. Kent, M. B. Crabtree, and B. R. Miller, Transmission of West Nile virus by Culex quinquefasciatus say infected with Culex Flavivirus Izabal, PLoS Negl Trop Dis, vol.4, issue.5, p.671, 2010.

P. Burivong, Markedly reduced severity of dengue virus infection in mosquito cell cultures persistently infected with Aedes albopictus densovirus (AalDNV), Virology, vol.329, issue.2, pp.261-270, 2004.

A. R. Karpf, Superinfection exclusion of alphaviruses in three mosquito cell lines persistently infected with Sindbis virus, J Virol, vol.71, issue.9, pp.7119-7142, 1997.

B. G. Bolling, Insect-specific virus discovery: significance for the arbovirus community, Viruses, vol.7, issue.9, pp.4911-4939, 2015.

O. St, Mosquito-borne viruses and suppressors of invertebrate antiviral RNA silencing, Viruses, vol.6, issue.11, pp.4314-4345, 2014.

J. Xu and S. Cherry, Viruses and antiviral immunity in Drosophila, Dev Comp Immunol, vol.42, issue.1, pp.67-84, 2014.

C. Canchaya, Prophage genomics. Microbiol Mol Biol Rev, vol.67, issue.2, pp.238-76, 2003.

R. Stouthamer, J. A. Breeuwer, and G. D. Hurst, Wolbachia pipientis: microbial manipulator of arthropod reproduction, Annu Rev Microbiol, vol.53, pp.71-102, 1999.

J. A. Biliske, The bacteriophage WORiC is the active phage element in wRi of Drosophila simulans and represents a conserved class of WO phages, BMC Microbiol, vol.11, p.251, 2011.

M. Wu, Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements, PLoS Biol, vol.2, issue.3, p.69, 2004.

B. N. Kent, Complete bacteriophage transfer in a bacterial endosymbiont (Wolbachia) determined by targeted genome capture

, Genome Biol Evol, vol.3, pp.209-227, 2011.

N. Chauvatcharin, Bacteriophage WO-B and Wolbachia in natural mosquito hosts: infection incidence, transmission mode and relative density, Mol Ecol, vol.15, issue.9, pp.2451-61, 2006.

F. V. Theobald, A monograph of the Culicidae or mosquitoes. London: British Museum (Natural History), 1901.

S. Clark-gil and R. F. Darsie, The mosquitoes of Guatemala. Their identification, distribution and bionomics, with keys to adult females and larvae, Mosq Syst, vol.15, issue.3, pp.151-284, 1983.

N. Conceicao-neto, Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis, Sci Rep, vol.5, p.16532, 2015.

A. M. Bolger, M. Lohse, and B. Usadel, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, vol.30, issue.15, pp.2114-2134, 2014.

H. Li and R. Durbin, Fast and accurate short read alignment with burrowswheeler transform, Bioinformatics, vol.25, issue.14, pp.1754-60, 2009.

A. Bankevich, SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing, J Comput Biol, vol.19, issue.5, pp.455-77, 2012.

B. Buchfink, C. Xie, and D. H. Huson, Fast and sensitive protein alignment using DIAMOND, Nat Methods, vol.12, issue.1, pp.59-60, 2015.

B. D. Ondov, N. H. Bergman, and A. M. Phillippy, Interactive metagenomic visualization in a web browser, BMC Bioinf, vol.12, p.385, 2011.

S. F. Altschul, Basic local alignment search tool, J Mol Biol, vol.215, issue.3, pp.403-413, 1990.

V. I. Jurtz, MetaPhinder-identifying bacteriophage sequences in metagenomic data sets, PLoS One, vol.11, issue.9, p.163111, 2016.

S. Roux, VirSorter: mining viral signal from microbial genomic data, PeerJ, vol.3, p.985, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01557667

H. Wickham, ggplot2: elegant graphics for data analysis, 2016.

P. J. Mcmurdie and S. Holmes, phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data, PLoS One, vol.8, issue.4, p.61217, 2013.

J. N. Paulson, Differential abundance analysis for microbial marker-gene surveys, Nat Methods, vol.10, issue.12, pp.1200-1202, 2013.

P. Dixon, VEGAN, a package of R functions for community ecology, J Veg Sci, vol.14, issue.6, pp.927-957, 2003.

P. Stothard, The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences, Biotechniques, vol.28, issue.6, 2000.

K. Katoh, MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform, Nucleic Acids Res, vol.30, issue.14, pp.3059-66, 2002.

S. Capella-gutierrez, J. M. Silla-martinez, and T. Gabaldon, trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, vol.25, issue.15, pp.1972-1975, 2009.

D. Darriba, ProtTest 3: fast selection of best-fit models of protein evolution, Bioinformatics, vol.27, issue.8, pp.1164-1169, 2011.

S. Guindon, New algorithms and methods to estimate maximumlikelihood phylogenies: assessing the performance of PhyML 3.0, Syst Biol, vol.59, issue.3, pp.307-328, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511784

, Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations