S. Junglen and C. Drosten, Virus discovery and recent insights into virus diversity in arthropods, Curr. Opin. Microbiol, vol.16, pp.507-513, 2013.

S. Bovo, G. Mazzoni, A. Ribani, V. J. Utzeri, F. Bertolini et al., A viral metagenomic approach on a nonmetagenomic experiment: Mining next generation sequencing datasets from pig DNA identified several porcine parvoviruses for a retrospective evaluation of viral infections, PLoS ONE, vol.12, pp.1-17, 2017.

H. Liu, Y. Fu, J. Xie, J. Cheng, S. A. Ghabrial et al., Widespread Endogenization of Densoviruses and Parvoviruses in Animal and Human Genomes, J. Virol, vol.85, pp.9863-9876, 2011.

S. François, D. Filloux, P. Roumagnac, D. Bigot, P. Gayral et al., Discovery of parvovirus-related sequences in an unexpected broad range of animals, Sci. Rep, vol.6, pp.1-13, 2016.

B. C. Lister and A. Garcia, Climate-driven declines in arthropod abundance restructure a rainforest food web, Proc. Natl. Acad. Sci, vol.115, pp.10397-10406, 2018.

D. E. Walter, H. C. Proctor, and . Mites, Ecology, Evolution & Behaviour, 2013.

L. R. Jeppson, H. H. Keifer, and E. W. Baker, Mites Injurious to Economic Plants, 1975.

M. Grbi?, T. Van-leeuwen, R. M. Clark, S. Rombauts, P. Rouzé et al., The genome of Tetranychus urticae reveals herbivorous pest adaptations, Nature, vol.479, pp.487-492, 2011.

T. Van-leeuwen, J. Vontas, A. Tsagkarakou, W. Dermauw, and L. Tirry, Acaricide resistance mechanisms in the two-spotted spider mite Tetranychus urticae and other important Acari: A review, Insect Biochem. Mol. Biol, vol.40, pp.563-572, 2010.

J. B. Beavers and D. K. Reed, Susceptibility of seven tetranychids to the nonoccluded virus of the citrus red mite and the correlation of the carmine spider mite as a vector, J. Invertebr. Pathol, vol.20, pp.279-283, 1972.

D. K. Reed and P. R. Desjardins, Morphology of a non-occluded virus isolated from citrus red mite, Panonychus citri, Experientia, vol.38, pp.468-469, 1982.

R. Tokarz, S. H. Williams, S. Sameroff, M. Sanchez-leon, K. Jain et al., Virome analysis of Amblyomma americanum, Dermacentor variabilis, and Ixodes scapularis ticks reveals novel highly divergent vertebrate and invertebrate viruses, J. Virol, vol.88, pp.11480-11492, 2014.

S. Moutailler, I. Popovici, E. Devillers, M. Vayssier-taussat, and M. Eloit, Diversity of viruses in Ixodes ricinus, and characterization of a neurotropic strain of Eyach virus, New Microbes New Infect, vol.11, pp.71-81, 2016.

J. M. Sakamoto, T. F. Ng, Y. Suzuki, H. Tsujimoto, X. Deng et al., Bunyaviruses are common in male and female Ixodes scapularis ticks in central Pennsylvania, PeerJ, 2016.

H. Xia, C. Hu, D. Zhang, S. Tang, Z. Zhang et al., Metagenomic profile of the viral communities in rhipicephalus spp. ticks from Yunnan, China, PLoS ONE, vol.10, pp.1-16, 2015.

S. Levin, N. Sela, and N. Chejanovsky, Two novel viruses associated with the Apis mellifera pathogenic mite Varroa destructor, Sci. Rep, vol.6, pp.1-9, 2016.

F. Nazzi, S. P. Brown, D. Annoscia, F. Del-piccolo, G. Di-prisco et al., Synergistic parasite-pathogen interactions mediated by host immunity can drive the collapse of honeybee colonies, PLoS Pathog, vol.8, 2012.

E. Palanga, D. Filloux, D. P. Martin, E. Fernandez, Z. Bouda et al., Metagenomic-Based Screening and Molecular Characterization of Cowpea-Infecting Viruses in Burkina Faso, PLoS ONE, vol.11, 2016.

T. Matsuda, M. Morishita, N. Hinomoto, and T. Gotoh, Phylogenetic Analysis of the Spider Mite Sub-Family Tetranychinae (Acari: Tetranychidae) Based on the Mitochondrial COI Gene and the 18S and the 59 End of the 28S rRNA Genes Indicates That Several Genera Are Polyphyletic, PLoS ONE, vol.9, 2014.

T. Matsuda, T. Kozaki, K. Ishii, and T. Gotoh, Phylogeny of the spider mite sub-family Tetranychinae (Acari: Tetranychidae) inferred from RNA-Seq data, PLoS ONE, vol.13, 2018.

M. Van-munster, A. Janssen, A. Clérivet, . Van-den, and J. Heuvel, Can plants use an entomopathogenic virus as a defense against herbivores? Oecologia, vol.143, pp.396-401, 2005.

R. Uesugi, K. Goka, and M. Osakabe, Genetic basis of resistances to chlorfenapyr and etoxazole in the two-spotted spider mite (Acari: Tetranychidae), J. Econ. Entomol, vol.95, pp.1267-1274, 2002.

S. Wu and U. Manber, Agrep-A fast approximate pattern-matching tool, Conference Proceedings: USENIX Winter 1992 Technical Conference; USENIX Association, pp.153-162, 1992.

M. Martin, Cutadapt removes adapter sequences from high-throughput sequencing reads, vol.17, pp.10-12, 2011.
DOI : 10.14806/ej.17.1.200

D. R. Zerbino and E. Birney, Velvet: algorithms for de novo short read assembly using de Bruijn graphs, Genome Res, vol.18, pp.821-829, 2008.

B. Langmead, Aligning short sequencing reads with Bowtie, Curr. Protoc. Bioinforma, vol.32, pp.11-17, 2010.
DOI : 10.1002/0471250953.bi1107s32
URL : http://europepmc.org/articles/pmc3010897?pdf=render

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, J. Mol. Biol, vol.215, pp.403-410, 1990.
DOI : 10.1006/jmbi.1990.9999

R. C. Edgar and . Muscle, Multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, vol.32, pp.1792-1797, 2004.
DOI : 10.1093/nar/gkh340
URL : http://europepmc.org/articles/pmc390337?pdf=render

M. Kearse, R. Moir, A. Wilson, S. Stones-havas, M. Cheung et al., Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data, Bioinformatics, vol.28, pp.1647-1649, 2012.

A. Dereeper, V. Guignon, G. Blanc, S. Audic, S. Buffet et al., fr: robust phylogenetic analysis for the non-specialist, Nucleic Acids Res, vol.36, pp.465-469, 2008.
URL : https://hal.archives-ouvertes.fr/lirmm-00324099

S. Guindon, J. Dufayard, V. Lefort, M. Anisimova, W. Hordijk et al., New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0, Syst. Biol, vol.59, pp.307-321, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511784

F. Abascal, R. Zardoya, and D. Posada, ProtTest: Selection of best-fit models of protein evolution, Bioinformatics, vol.21, pp.2104-2105, 2005.

V. V. Dolja and E. V. Koonin, Metagenomics reshapes the concepts of RNA virus evolution by revealing extensive horizontal virus transfer, Virus Res, vol.244, pp.36-52, 2018.

S. F. Cotmore, M. Agbandje-mckenna, J. A. Chiorini, D. V. Mukha, D. J. Pintel et al., The family Parvoviridae. Arch. Virol, vol.159, pp.1239-1247, 2014.

S. F. Cotmore, P. Tattersall, and . Parvoviruses, Small Does Not Mean Simple, Annu. Rev. Virol, vol.1, pp.517-537, 2014.
DOI : 10.1146/annurev-virology-031413-085444

N. Conceição-neto, R. Godinho, F. Álvares, C. K. Yinda, W. Deboutte et al., Viral gut metagenomics of sympatric wild and domestic canids, and monitoring of viruses: Insights from an endangered wolf population, Ecol. Evol, vol.7, pp.4135-4146, 2017.

S. Duffy, L. A. Shackelton, and E. C. Holmes, Rates of evolutionary change in viruses: Patterns and determinants, Nat. Rev. Genet, vol.9, pp.267-276, 2008.

S. Duffy, Why are RNA virus mutation rates so damn high?, PLoS Biol, vol.16, pp.1-6, 2018.
DOI : 10.1371/journal.pbio.3000003
URL : https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.3000003&type=printable

P. Simmonds, P. Aiewsakun, and A. Katzourakis, Prisoners of war-host adaptation and its constraints on virus evolution, Nat. Rev. Microbiol, 2018.

G. Santos-matos, N. Wybouw, N. E. Martins, F. Zélé, M. Riga et al., Tetranychus urticae mites do not mount an induced immune response against bacteria, Proceedings. Biol. Sci, vol.284, 2017.
DOI : 10.1098/rspb.2017.0401
URL : https://royalsocietypublishing.org/doi/pdf/10.1098/rspb.2017.0401

M. Marklewitz, F. Zirkel, A. Kurth, C. Drosten, and S. Junglen, Evolutionary and phenotypic analysis of live virus isolates suggests arthropod origin of a pathogenic RNA virus family, Proc. Natl. Acad. Sci, vol.112, pp.7536-7541, 2015.

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

M. Shi, X. Lin, N. Vasilakis, J. Tian, C. Li et al., Divergent Viruses Discovered in Arthropods and Vertebrates Revise the Evolutionary History of the Flaviviridae and Related Viruses, J. Virol, vol.90, pp.659-669, 2016.

S. Halary, S. Temmam, D. Raoult, and C. Desnues, Viral metagenomics: are we missing the giants?, Curr. Opin. Microbiol, vol.31, pp.34-43, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01458400

M. Van-munster, A. M. Dullemans, M. Verbeek, . Van-den, J. F. Heuvel et al., Van Der Wilk, F. Characterization of a new densovirus infecting the green peach aphid Myzus persicae, J. Invertebr. Pathol, vol.84, pp.6-14, 2003.

P. Xu, Y. Liu, R. I. Graham, K. Wilson, and K. Wu, Densovirus Is a Mutualistic Symbiont of a Global Crop Pest (Helicoverpa armigera) and Protects against a Baculovirus and Bt Biopesticide, PLoS Pathog, vol.10, pp.2-12, 2014.

G. Clavijo, M. Van-munster, B. Monsion, N. Bochet, and V. Brault, Transcription of densovirus endogenous sequences in the Myzus persicae genome, J. Gen. Virol, vol.97, pp.1000-1009, 2016.

S. Alizon, J. C. De-roode, and Y. Michalakis, Multiple infections and the evolution of virulence, Ecol. Lett, vol.16, pp.556-567, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01567918

S. Francois, P. Bernardo, D. Filloux, P. Roumagnac, N. Yaverkovski et al., A Novel Itera-Like Densovirus Isolated by Viral Metagenomics from the Sea Barley Hordeum marinum, Genome Announc, vol.2, pp.1196-1210, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01837275

F. Zélé, M. Weill, and S. Magalhães, Identification of spider-mite species and their endosymbionts using multiplex PCR, Exp. Appl. Acarol, vol.74, pp.123-138, 2018.