, Geneva: World Health Organization, World Health Organization. World Malaria Report, 2017.

N. Minkeu, F. Vernick, and K. D. , A systematic review of the natural virome of anopheles mosquitoes, Viruses, vol.10, issue.5, p.222, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01830169

G. Rezza, R. Chen, and S. C. Weaver, O'nyong-nyong fever: a neglected mosquitoborne viral disease, Pathog Glob Health, vol.111, issue.6, pp.271-276, 2017.

G. Carissimo, K. Eiglmeier, J. Reveillaud, I. Holm, M. Diallo et al., Identification and characterization of two novel RNA viruses from anopheles gambiae species complex mosquitoes, PLoS One, vol.11, issue.5, p.153881, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01316516

A. Colmant, J. Hobson-peters, H. Bielefeldt-ohmann, A. F. Van-den-hurk, S. Hall-mendelin et al., A new clade of insect-specific flaviviruses from Australian anopheles mosquitoes displays species-specific host restriction, mSphere, vol.2, issue.4, pp.1-19, 2017.

J. R. Fauver, N. D. Grubaugh, B. J. Krajacich, J. Weger-lucarelli, S. M. Lakin et al., 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.

J. Villinger, M. K. Mbaya, D. Ouso, P. N. Kipanga, J. Lutomiah et al., Arbovirus and insect-specific virus discovery in Kenya by novel six genera multiplex highresolution melting analysis, Mol Ecol Resour, vol.17, issue.3, pp.466-80, 2017.

R. N. Tabue, P. Awono-ambene, J. Etang, J. Atangana, C. An et al., Role of Anopheles (Cellia) rufipes (Gough, 1910) and other local anophelines in human malaria transmission in the northern savannah of Cameroon: a cross-sectional survey, Parasit Vectors, vol.10, issue.1, p.22, 2017.

M. S. Alam, M. G. Khan, N. Chaudhury, S. Deloer, F. Nazib et al., Prevalence of anopheline species and their Plasmodium infection status in epidemic-prone border areas of Bangladesh, Malar J, vol.9, p.15, 2010.

L. Durnez, S. Mao, L. Denis, P. Roelants, T. Sochantha et al., Outdoor malaria transmission in forested villages of Cambodia, Malar J, vol.12, p.329, 2013.

N. Marasri, H. J. Overgaard, A. Sumarnrote, K. Thanispong, V. Corbel et al., Abundance and distribution of Anopheles mosquitoes in a malaria endemic area along the Thai-Lao border, J Vector Ecol, vol.42, issue.2, pp.325-359, 2017.

B. St-laurent, K. Oy, B. Miller, E. B. Gasteiger, E. Lee et al., Cow-baited tents are highly effective in sampling diverse Anopheles malaria vectors in Cambodia, Malar J, vol.15, issue.1, p.440, 2016.

M. W. Service, Mosquito ecology: field sampling methods, 1993.

C. X. Li, M. Shi, J. H. Tian, X. D. Lin, Y. J. Kang et al., Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses, Elife, vol.4, pp.1-26, 2015.

Y. Hagiwara-komoda, S. H. Choi, M. Sato, G. Atsumi, J. Abe et al., Truncated yet functional viral protein produced via RNA polymerase slippage implies underestimated coding capacity of RNA viruses, Sci Rep, vol.6, p.21411, 2016.

A. Olspert, B. Y. Chung, J. F. Atkins, J. P. Carr, and A. E. Firth, Transcriptional slippage in the positive-sense RNA virus family Potyviridae, EMBO Rep, vol.16, issue.8, pp.995-1004, 2015.

B. Y. Chung, A. E. Firth, and J. F. Atkins, Frameshifting in alphaviruses: a diversity of 3? stimulatory structures, J Mol Biol, vol.397, issue.2, pp.448-56, 2010.

A. E. Firth, B. J. Blitvich, N. M. Wills, C. L. Miller, and J. F. Atkins, Evidence for ribosomal frameshifting and a novel overlapping gene in the genomes of insectspecific flaviviruses, Virology, vol.399, issue.1, pp.153-66, 2010.

E. R. Aguiar, R. P. Olmo, S. Paro, F. V. Ferreira, I. J. De-faria et al., 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.

S. H. Lewis, K. A. Quarles, Y. Yang, M. Tanguy, L. Frezal et al., Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements, Nat Ecol Evol, vol.2, issue.1, pp.174-81, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01657238

P. Leger, E. Lara, B. Jagla, O. Sismeiro, Z. Mansuroglu et al., Dicer-2-and Piwi-mediated RNA interference in Rift Valley fever virus-infected mosquito cells, J Virol, vol.87, issue.3, pp.1631-1679, 2013.

U. Palatini, P. Miesen, R. Carballar-lejarazu, L. Ometto, E. Rizzo et al., 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.

E. M. Morazzani, M. R. Wiley, M. G. Murreddu, Z. N. Adelman, and K. M. Myles, Production of virus-derived ping-pong-dependent piRNA-like small RNAs in the mosquito soma, PLoS Pathog, vol.8, issue.1, p.1002470, 2012.

L. Castellano, E. Rizzi, J. Krell, D. Cristina, M. Galizi et al., The germline of the malaria mosquito produces abundant miRNAs, endo-siRNAs, piRNAs and 29-nt small RNAs, BMC Genomics, vol.16, p.100, 2015.

P. George, S. Jensen, R. Pogorelcnik, J. Lee, Y. Xing et al., Increased production of piRNAs from euchromatic clusters and genes in Anopheles gambiae compared with Drosophila melanogaster, Epigenetics Chromatin, vol.8, p.50, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01923991

C. Li, V. V. Vagin, S. Lee, J. Xu, S. Ma et al., Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies, Cell, vol.137, issue.3, pp.509-530, 2009.

M. Shi, X. D. Lin, J. H. Tian, L. J. Chen, X. Chen et al., Redefining the invertebrate RNA virosphere, Nature, vol.540, p.539, 2016.

C. L. Webster, F. M. Waldron, S. Robertson, D. Crowson, G. Ferrari et al., The discovery, distribution, and evolution of viruses associated with Drosophila melanogaster, PLoS Biol, vol.13, issue.7, p.1002210, 2015.

S. Cook, B. Y. Chung, D. Bass, G. Moureau, S. Tang et al., Novel virus discovery and genome reconstruction from field RNA samples reveals highly divergent viruses in dipteran hosts, PLoS One, vol.8, issue.11, p.80720, 2013.

R. A. Hall, H. Bielefeldt-ohmann, B. J. Mclean, C. A. O'brien, A. M. Colmant et al., Commensal viruses of mosquitoes: host restriction, transmission, and interaction with Arboviral pathogens, Evol Bioinformatics Online, vol.12, issue.2, pp.35-44, 2016.

E. Huhtamo, S. Cook, G. Moureau, N. Y. Uzcategui, T. Sironen et al., Novel flaviviruses from mosquitoes: mosquito-specific evolutionary lineages within the phylogenetic group of mosquito-borne flaviviruses, Virology, pp.320-329, 2014.

N. A. Broderick, N. Buchon, and B. Lemaitre, Microbiota-induced changes in drosophila melanogaster host gene expression and gut morphology, MBio, vol.5, issue.3, pp.1117-1121, 2014.

C. A. Lozupone, J. I. Stombaugh, J. I. Gordon, J. K. Jansson, and R. Knight, Diversity, stability and resilience of the human gut microbiota, Nature, vol.489, issue.7415, pp.220-250, 2012.

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. Hobson-peters, A. W. Yam, J. W. Lu, Y. X. Setoh, F. J. May et al., 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.8, issue.2, p.56534, 2013.

N. Buchon, N. A. Broderick, and B. Lemaitre, Gut homeostasis in a microbial world: insights from Drosophila melanogaster, Nat Rev Microbiol, vol.11, issue.9, pp.615-641, 2013.

Z. J. Whitfield, P. T. Dolan, M. Kunitomi, M. Tassetto, M. G. Seetin et al., The diversity, structure, and function of heritable adaptive immunity sequences in the Aedes aegypti genome, Curr Biol, vol.27, issue.22, pp.3511-3519, 2017.

M. Zakrzewski, G. Rasic, J. Darbro, L. Krause, Y. S. Poo et al., Mapping the virome in wild-caught Aedes aegypti from Cairns and Bangkok, Sci Rep, vol.8, issue.1, p.4690, 2018.

K. G. Frey, T. Biser, T. Hamilton, C. J. Santos, G. Pimentel et al., 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.

E. Atoni, Y. Wang, S. Karungu, C. Waruhiu, A. Zohaib et al., Metagenomic virome analysis of Culex mosquitoes from Kenya and China, Viruses, vol.10, issue.1, p.30, 2018.

M. Martin, Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnetjournal, vol.17, issue.1, p.3, 2011.

G. I. Giraldo-calderon, S. J. Emrich, R. M. Maccallum, G. Maslen, E. Dialynas et al., VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases, Nucleic Acids Res, vol.43, pp.707-720, 2015.

B. Langmead, C. Trapnell, M. Pop, and S. L. Salzberg, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol, vol.10, issue.3, p.25, 2009.

H. Li, Aligning sequence reads, clone sequences and assembly contigs with

E. Kopylova, L. Noe, and H. Touzet, SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data, Bioinformatics, vol.28, issue.24, pp.3211-3218, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00748990

S. Ratnasingham and P. D. Hebert, Bold: the barcode of life data system, Mol Ecol Notes, vol.7, issue.3, pp.355-64, 2007.

M. H. Schulz, D. R. Zerbino, M. Vingron, and E. Birney, Oases: robust de novo RNAseq assembly across the dynamic range of expression levels, Bioinformatics, vol.28, issue.8, pp.1086-92, 2012.

M. G. Grabherr, B. J. Haas, M. Yassour, J. Z. Levin, D. A. Thompson et al., Full-length transcriptome assembly from RNA-Seq data without a reference genome, Nat Biotechnol, vol.29, issue.7, pp.644-52, 2011.

W. Li and A. Godzik, Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences, Bioinformatics, vol.22, issue.13, pp.1658-1667, 2006.

S. F. Altschul, T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res, vol.25, issue.17, pp.3389-402, 1997.

D. H. Huson, S. Beier, I. Flade, A. Gorska, M. El-hadidi et al., MEGAN Community edition -interactive exploration and analysis of large-scale microbiome sequencing data, PLoS Comput Biol, vol.12, issue.6, p.1004957, 2016.

M. J. Sullivan, N. K. Petty, and S. A. Beatson, Easyfig: a genome comparison visualizer, Bioinformatics, vol.27, issue.7, pp.1009-1019, 2011.

W. Zhu, A. Lomsadze, and M. Borodovsky, Ab initio gene identification in metagenomic sequences, Nucleic Acids Res, vol.38, issue.12, p.132, 2010.

T. Seemann, Prokka: rapid prokaryotic genome annotation, Bioinformatics, vol.30, issue.14, pp.2068-2077, 2014.

P. Skewes-cox, T. J. Sharpton, K. S. Pollard, and J. L. Derisi, Profile hidden Markov models for the detection of viruses within metagenomic sequence data, PLoS One, vol.9, issue.8, p.105067, 2014.

S. Gotz, J. M. Garcia-gomez, J. Terol, T. D. Williams, S. H. Nagaraj et al., High-throughput functional annotation and data mining with the Blast2GO suite, Nucleic Acids Res, vol.36, issue.10, pp.3420-3455, 2008.

K. Rutherford, J. Parkhill, J. Crook, T. Horsnell, P. Rice et al., Artemis: sequence visualization and annotation, Bioinformatics, vol.16, issue.10, pp.944-949, 2000.

K. Katoh and D. M. Standley, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol Biol Evol, vol.30, issue.4, pp.772-80, 2013.

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.

A. Stamatakis, RAxML version 8: a tool for phylogenetic analysis and postanalysis of large phylogenies, Bioinformatics, vol.30, issue.9, pp.1312-1315, 2014.

E. Paradis, J. Claude, and K. Strimmer, APE: analyses of Phylogenetics and evolution in R language, Bioinformatics, vol.20, issue.2, pp.289-90, 2004.
URL : https://hal.archives-ouvertes.fr/ird-01887318

H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., Genome project data processing S: the sequence alignment/ map format and SAMtools, Bioinformatics, vol.25, issue.16, pp.2078-2087, 2009.

P. Rice, I. Longden, and A. Bleasby, EMBOSS: the European molecular biology open software suite, Trends Genet, vol.16, issue.6, pp.276-283, 2000.

K. P. Schliep, Phangorn: phylogenetic analysis in R, Bioinformatics, vol.27, issue.4, pp.592-595, 2011.

G. Carissimo, A. Pain, E. Belda, and K. D. Vernick, Highly focused transcriptional response of Anopheles coluzzii to O'nyong nyong arbovirus during the primary midgut infection, BMC Genomics, vol.19, issue.1, p.526, 2018.
URL : https://hal.archives-ouvertes.fr/pasteur-02009990

A. Dobin and T. R. Gingeras, Mapping RNA-seq reads with STAR, Curr Protoc Bioinformatics, vol.51, pp.11-14, 2015.

H. Thorvaldsdottir, J. T. Robinson, and J. P. Mesirov, Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration, Brief Bioinform, vol.14, issue.2, pp.178-92, 2013.

, R: A language and environment for statistical computing

, Publisher's Note

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