French guiana, Guadeloupe, and Martinique. Health in the Americas, 2012 Edition: Country Volume.
Larrieu S, et al. Dengue outbreaks: a constant risk for Reunion Island. Results from a seroprevalence study among blood donors. Trans R Soc Trop Med Hyg. 2014;108(1):57–9.
Article
PubMed
Google Scholar
Quénel P, et al. 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. 2009;3:1–16.
Google Scholar
INVS (Institut de Veille Sanitaire), S.p.F., Le chikungunya dans les Antilles Bulletin du 17 novembre au 14 décembre 2014. le point épidémio N°34/2014 2014: p. 1–6.
Van Bortel W, et al. Chikungunya outbreak in the Caribbean region, December 2013 to March 2014, and the significance for Europe. Euro Surveill. 2014;19(13).
INVS (Institut de Veille Sanitaire), S.p.F., Situation épidémiologique du virus Zika aux Antilles et en Guyane. Point au 30 janvier 2017. Le Point épidémio N° 1/2017, 2017: p. 1–7.
Pan American Health Organization / World Health Organization. Epidemiological Update: Yellow Fever. 20 March 2018. Washington DC: PAHO/WHO; 2018.
Google Scholar
Yen PS, et al. Aedes aegypti mosquitoes from Guadeloupe (French West Indies) are able to transmit yellow fever virus. PLoS One. 2018;13(9):e0204710.
Article
PubMed
PubMed Central
Google Scholar
Fauver JR, et al. West African Anopheles gambiae mosquitoes harbor a taxonomically diverse virome including new insect-specific flaviviruses, mononegaviruses, and totiviruses. Virology. 2016;498:288–99.
Article
CAS
PubMed
Google Scholar
Atoni E, et al. Metagenomic virome analysis of culex mosquitoes from Kenya and China. Viruses. 2018;10(1).
Article
PubMed Central
Google Scholar
Xia H, et al. Comparative metagenomic profiling of viromes associated with four common mosquito species in China. Virol Sin. 2018;33(1):59–66.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sadeghi M, et al. Virome of >12 thousand Culex mosquitoes from throughout California. Virology. 2018;523:74–88.
Article
CAS
PubMed
Google Scholar
Frey KG, et al. Bioinformatic characterization of mosquito viromes within the eastern United States and Puerto Rico: discovery of novel viruses. Evol Bioinformatics Online. 2016;12(Suppl 2):1–12.
Google Scholar
Shi C, et al. A metagenomic survey of viral abundance and diversity in mosquitoes from Hubei province. PLoS One. 2015;10(6):e0129845.
Article
PubMed
PubMed Central
Google Scholar
Roundy CM, et al. Insect-specific viruses: a historical overview and recent developments. Adv Virus Res. 2017;98:119–46.
Article
PubMed
Google Scholar
Bolling BG, et al. 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. 2012;427(2):90–7.
Article
CAS
PubMed
Google Scholar
Erasmus JH, et al. Utilization of an Eilat virus-based chimera for serological detection of chikungunya infection. PLoS Negl Trop Dis. 2015;9(10):e0004119.
Article
PubMed
PubMed Central
Google Scholar
Moll RM, et al. Meconial peritrophic membranes and the fate of midgut bacteria during mosquito (Diptera: Culicidae) metamorphosis. J Med Entomol. 2001;38(1):29–32.
Article
CAS
PubMed
Google Scholar
Gimonneau G, et al. Composition of Anopheles coluzzii and Anopheles gambiae microbiota from larval to adult stages. Infect Genet Evol. 2014;28:715–24.
Article
PubMed
Google Scholar
Chouin-Carneiro T, et al. Differential susceptibilities of Aedes aegypti and Aedes albopictus from the Americas to Zika virus. PLoS Negl Trop Dis. 2016;10(3):e0004543.
Article
PubMed
PubMed Central
Google Scholar
Richards SL, Anderson SL, Lord CC. Vector competence of Culex pipiens quinquefasciatus (Diptera: Culicidae) for West Nile virus isolates from Florida. Tropical Med Int Health. 2014;19(5):610–7.
Article
Google Scholar
Crochu S, et al. Sequences of flavivirus-related RNA viruses persist in DNA form integrated in the genome of Aedes spp. mosquitoes. J Gen Virol. 2004;85(Pt 7):1971–80.
Article
CAS
PubMed
Google Scholar
Palatini U, et al. Comparative genomics shows that viral integrations are abundant and express piRNAs in the arboviral vectors Aedes aegypti and Aedes albopictus. BMC Genomics. 2017;18(1):512.
Article
PubMed
PubMed Central
Google Scholar
Shi M, et al. Redefining the invertebrate RNA virosphere. Nature. 2016;540(7634):539–43.
Article
CAS
PubMed
Google Scholar
Aguiar ER, et al. Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host. Nucleic Acids Res. 2015;43(13):6191–206.
Article
CAS
PubMed
PubMed Central
Google Scholar
Allison AB, et al. Cyclic avian mass mortality in the northeastern United States is associated with a novel orthomyxovirus. J Virol. 2015;89(2):1389–403.
Article
PubMed
Google Scholar
Shi M, et al. High-resolution metatranscriptomics reveals the ecological dynamics of mosquito-associated RNA viruses in Western Australia. J Virol. 2017;91(17).
Katsuma S, et al. Novel macula-like virus identified in Bombyx mori cultured cells. J Virol. 2005;79(9):5577–84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ratnasingham S, Hebert PD. bold: the barcode of life data system (http://www.barcodinglife.org). Mol Ecol Notes. 2007;7(3):355–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Holmes DE, Nevin KP, Lovley DR. Comparison of 16S rRNA, nifD, recA, gyrB, rpoB and fusA genes within the family Geobacteraceae fam. Nov. Int J Syst Evol Microbiol. 2004;54(Pt 5):1591–9.
Article
CAS
PubMed
Google Scholar
Richard C. Chromobacterium violaceum, opportunist pathogenic bacteria in tropical and subtropical regions. Bull Soc Pathol Exot. 1993;86(3):169–73.
CAS
PubMed
Google Scholar
Marchetti M, et al. Cupriavidus taiwanensis bacteroids in Mimosa pudica indeterminate nodules are not terminally differentiated. Appl Environ Microbiol. 2011;77(6):2161–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chavshin AR, et al. Malpighian tubules are important determinants of Pseudomonas transstadial transmission and longtime persistence in Anopheles stephensi. Parasit Vectors. 2015;8:36.
Article
PubMed
PubMed Central
Google Scholar
Galiez C, et al. WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs. Bioinformatics. 2017;33(19):3113–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Short SM, et al. Amino acid metabolic signaling influences Aedes aegypti midgut microbiome variability. PLoS Negl Trop Dis. 2017;11(7):e0005677.
Article
PubMed
PubMed Central
Google Scholar
Van Tol S, Dimopoulos G. Chapter nine—influences of the mosquito microbiota on vector competence. In: Raikhel AS, editor. Advances in insect physiology, vol. 51; 2016. p. 243–91.
Google Scholar
Ramirez JL, et al. Reciprocal tripartite interactions between the Aedes aegypti midgut microbiota, innate immune system and dengue virus influences vector competence. PLoS Negl Trop Dis. 2012;6(3):e1561.
Article
PubMed
PubMed Central
Google Scholar
Jupatanakul N, Sim S, Dimopoulos G. The insect microbiome modulates vector competence for arboviruses. Viruses. 2014;6(11):4294–313.
Article
CAS
PubMed
PubMed Central
Google Scholar
Goindin D, et al. Screening of natural Wolbachia infection in Aedes aegypti, Aedes taeniorhynchus and Culex quinquefasciatus from Guadeloupe (French West Indies). Acta Trop. 2018;185:314–7.
Article
CAS
PubMed
Google Scholar
Glaser RL, Meola MA. The native Wolbachia endosymbionts of Drosophila melanogaster and Culex quinquefasciatus increase host resistance to West Nile virus infection. PLoS One. 2010;5(8):e11977.
Article
PubMed
PubMed Central
Google Scholar
Cheng G, et al. Mosquito defense strategies against viral infection. Trends Parasitol. 2016;32(3):177–86.
Article
PubMed
Google Scholar
Zhang X, et al. Discovery and high prevalence of Phasi Charoen-like virus in field-captured Aedes aegypti in South China. Virology. 2018;523:35–40.
Article
CAS
PubMed
Google Scholar
Schultz MJ, Frydman HM, Connor JH. Dual insect specific virus infection limits arbovirus replication in Aedes mosquito cells. Virology. 2018;518:406–13.
Article
CAS
PubMed
Google Scholar
Wuerth JD, Weber F. Phleboviruses and the type i interferon response. Viruses. 2016;8(6):174.
Article
PubMed Central
Google Scholar
Won S, et al. NSm protein of Rift Valley fever virus suppresses virus-induced apoptosis. J Virol. 2007;81(24):13335–45.
Article
CAS
PubMed
PubMed Central
Google Scholar
Marklewitz M, et al. Evolutionary and phenotypic analysis of live virus isolates suggests arthropod origin of a pathogenic RNA virus family. Proc Natl Acad Sci U S A. 2015;112(24):7536–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kent RJ, Crabtree MB, Miller BR. Transmission of West Nile virus by Culex quinquefasciatus say infected with Culex Flavivirus Izabal. PLoS Negl Trop Dis. 2010;4(5):e671.
Article
PubMed
PubMed Central
Google Scholar
Burivong P, et al. Markedly reduced severity of dengue virus infection in mosquito cell cultures persistently infected with Aedes albopictus densovirus (AalDNV). Virology. 2004;329(2):261–9.
Article
CAS
PubMed
Google Scholar
Karpf AR, et al. Superinfection exclusion of alphaviruses in three mosquito cell lines persistently infected with Sindbis virus. J Virol. 1997;71(9):7119–23.
CAS
PubMed
PubMed Central
Google Scholar
Bolling BG, et al. Insect-specific virus discovery: significance for the arbovirus community. Viruses. 2015;7(9):4911–28.
Article
CAS
PubMed
PubMed Central
Google Scholar
O'Neal ST, et al. Mosquito-borne viruses and suppressors of invertebrate antiviral RNA silencing. Viruses. 2014;6(11):4314–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xu J, Cherry S. Viruses and antiviral immunity in Drosophila. Dev Comp Immunol. 2014;42(1):67–84.
Article
PubMed
Google Scholar
Canchaya C, et al. Prophage genomics. Microbiol Mol Biol Rev. 2003;67(2):238–76. table of contents
Article
CAS
PubMed
PubMed Central
Google Scholar
Stouthamer R, Breeuwer JA, Hurst GD. Wolbachia pipientis: microbial manipulator of arthropod reproduction. Annu Rev Microbiol. 1999;53:71–102.
Article
CAS
PubMed
Google Scholar
Biliske JA, et al. The bacteriophage WORiC is the active phage element in wRi of Drosophila simulans and represents a conserved class of WO phages. BMC Microbiol. 2011;11:251.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wu M, et al. Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS Biol. 2004;2(3):E69.
Article
PubMed
PubMed Central
Google Scholar
Kent BN, et al. Complete bacteriophage transfer in a bacterial endosymbiont (Wolbachia) determined by targeted genome capture. Genome Biol Evol. 2011;3:209–18.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chauvatcharin N, et al. Bacteriophage WO-B and Wolbachia in natural mosquito hosts: infection incidence, transmission mode and relative density. Mol Ecol. 2006;15(9):2451–61.
Article
CAS
PubMed
Google Scholar
Theobald FV. A monograph of the Culicidae or mosquitoes. London: British Museum (Natural History); 1901.
Google Scholar
Clark-Gil S, Darsie RF. The mosquitoes of Guatemala. Their identification, distribution and bionomics, with keys to adult females and larvae. Mosq Syst. 1983;15(3):151–284.
Google Scholar
Conceicao-Neto N, et al. Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis. Sci Rep. 2015;5:16532.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H, Durbin R. Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics. 2009;25(14):1754–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bankevich A, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19(5):455–77.
Article
CAS
PubMed
PubMed Central
Google Scholar
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12(1):59–60.
Article
CAS
PubMed
Google Scholar
Ondov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a web browser. BMC Bioinf. 2011;12:385.
Article
Google Scholar
Altschul SF, et al. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–10.
Article
CAS
PubMed
Google Scholar
Jurtz VI, et al. MetaPhinder-identifying bacteriophage sequences in metagenomic data sets. PLoS One. 2016;11(9):e0163111.
Article
PubMed
PubMed Central
Google Scholar
Roux S, et al. VirSorter: mining viral signal from microbial genomic data. PeerJ. 2015;3:e985.
Article
PubMed
PubMed Central
Google Scholar
Wickham H. ggplot2: elegant graphics for data analysis. New York: Springer-Verlag; 2016.
Book
Google Scholar
McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8(4):e61217.
Article
CAS
PubMed
PubMed Central
Google Scholar
Paulson JN, et al. Differential abundance analysis for microbial marker-gene surveys. Nat Methods. 2013;10(12):1200–2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dixon P. VEGAN, a package of R functions for community ecology. J Veg Sci. 2003;14(6):927–30.
Article
Google Scholar
Stothard P. The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques. 2000;28(6):1102. 1104
Article
CAS
PubMed
Google Scholar
Katoh K, et al. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30(14):3059–66.
Article
CAS
PubMed
PubMed Central
Google Scholar
Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25(15):1972–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Darriba D, et al. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics. 2011;27(8):1164–5.
Article
CAS
PubMed
Google Scholar
Guindon S, et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59(3):307–21.
Article
CAS
PubMed
Google Scholar