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This deficiency limits our opportunity to use natural host-pathogen combinations in experimental studies, and may bias our understanding of the Drosophila virome. Here, we report fourteen DNA viruses detected in a metagenomic analysis of 6668 pool-sequenced Drosophila, sampled from forty-seven European locations between 2014 and 2016. These include three new nudiviruses, a new and divergent entomopoxvirus, a virus related to Leptopilina boulardi filamentous virus, and a virus related to Musca domestica salivary gland hypertrophy virus. We also find an endogenous genomic copy of galbut virus, a double-stranded RNA partitivirus, segregating at very low frequency. Remarkably, we find that Drosophila Vesanto virus, a small DNA virus previously described as a bidnavirus, may be composed of up to twelve segments and thus represent a new lineage of segmented DNA viruses. Two of the DNA viruses, Drosophila Kallithea nudivirus and Drosophila Vesanto virus are relatively common, found in 2 per cent or more of wild flies. The others are rare, with many likely to be represented by a single infected fly. We find that virus prevalence in Europe reflects the prevalence seen in publicly available datasets, with Drosophila Kallithea nudivirus and Drosophila Vesanto virus the only ones commonly detectable in public data from wild-caught flies and large population cages, and the other viruses being rare or absent. These analyses suggest that DNA viruses are at lower prevalence than RNA viruses in D.melanogaster, and may be less likely to persist in laboratory cultures. Our findings go some way to redressing an earlier bias toward RNA virus studies in Drosophila, and lay the foundation needed to harness the power of Drosophila as a model system for the study of DNA viruses.<\/jats:p>","DOI":"10.1093\/ve\/veab031","type":"journal-article","created":{"date-parts":[[2021,3,30]],"date-time":"2021-03-30T11:10:55Z","timestamp":1617102655000},"source":"Crossref","is-referenced-by-count":50,"title":["The discovery, distribution, and diversity of DNA viruses associated with<i>Drosophila melanogaster<\/i>in Europe"],"prefix":"10.1093","volume":"7","author":[{"given":"Megan A","family":"Wallace","sequence":"first","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK"}]},{"given":"Kelsey A","family":"Coffman","sequence":"additional","affiliation":[{"name":"Department of Entomology, University of Georgia, Athens, GA, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2131-7467","authenticated-orcid":false,"given":"Cl\u00e9ment","family":"Gilbert","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Universit\u00e9 Paris-Saclay, CNRS, IRD, UMR \u00c9volution, G\u00e9nomes, Comportement et \u00c9cologie, 91198 Gif-sur-Yvette, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0996-0262","authenticated-orcid":false,"given":"Sanjana","family":"Ravindran","sequence":"additional","affiliation":[{"name":"Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK"}]},{"given":"Gregory F","family":"Albery","sequence":"additional","affiliation":[{"name":"Department of Biology, Georgetown University, Washington, DC, USA"}]},{"given":"Jessica","family":"Abbott","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Department of Biology, Section for Evolutionary Ecology, Lund University, S\u00f6lvegatan 37, Lund 223 62, Sweden"}]},{"given":"Eliza","family":"Argyridou","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, Planegg, Germany"}]},{"given":"Paola","family":"Bellosta","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Department of Cellular, Computational and Integrative Biology, CIBIO University of Trento, Via Sommarive 9, Trento 38123, Italy"},{"name":"Department of Medicine & Endocrinology, NYU Langone Medical Center, 550 First Avenue, New York, NY 10016, USA"}]},{"given":"Andrea J","family":"Betancourt","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK"}]},{"given":"Herv\u00e9","family":"Colinet","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"UMR CNRS 6553 ECOBIO, Universit\u00e9 de Rennes1, Rennes, France"}]},{"given":"Katarina","family":"Eric","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Institute for Biological Research \u201cSinisa Stankovic\u201d, National Institute of Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, Serbia"}]},{"given":"Amanda","family":"Glaser-Schmitt","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, Planegg, Germany"}]},{"given":"Sonja","family":"Grath","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, Planegg, Germany"}]},{"given":"Mihailo","family":"Jelic","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, Serbia"}]},{"given":"Maaria","family":"Kankare","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Department of Biological and Environmental Science, University of Jyv\u00e4skyl\u00e4, Finland"}]},{"given":"Iryna","family":"Kozeretska","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"National Antarctic Scientific Center of Ukraine, 16 Shevchenko Avenue, Kyiv, 01601, Ukraine"}]},{"given":"Volker","family":"Loeschcke","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Department of Biology, Genetics, Ecology and Evolution, Aarhus University, Ny Munkegade 116, Aarhus C DK-8000, Denmark"}]},{"given":"Catherine","family":"Montchamp-Moreau","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Universit\u00e9 Paris-Saclay, CNRS, IRD, UMR \u00c9volution, G\u00e9nomes, Comportement et \u00c9cologie, 91198 Gif-sur-Yvette, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2679-625X","authenticated-orcid":false,"given":"Lino","family":"Ometto","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Department of Biology and Biotechnology, University of Pavia, Pavia 27100, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3003-248X","authenticated-orcid":false,"given":"Banu Sebnem","family":"Onder","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Department of Biology, Faculty of Science, Hacettepe University, Ankara, Turkey"}]},{"given":"Dorcas J","family":"Orengo","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Departament de Gen\u00e8tica, Microbiologia i Estad\u00edstica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain"}]},{"given":"John","family":"Parsch","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, Planegg, Germany"}]},{"given":"Marta","family":"Pascual","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Departament de Gen\u00e8tica, Microbiologia i Estad\u00edstica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5763-6294","authenticated-orcid":false,"given":"Aleksandra","family":"Patenkovic","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Institute for Biological Research \u201cSinisa Stankovic\u201d, National Institute of Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, Serbia"}]},{"given":"Eva","family":"Puerma","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Departament de Gen\u00e8tica, Microbiologia i Estad\u00edstica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain"}]},{"given":"Michael G","family":"Ritchie","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Centre for Biological Diversity, St Andrews University, St Andrews HY15 4SS, UK"}]},{"given":"Omar","family":"Rota-Stabelli","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Research and Innovation Center, Fondazione E. Mach, San Michele all\u2019Adige (TN) 38010, Italy"},{"name":"Centre Agriculture Food Environment, University of Trento, San Michele all\u2019Adige (TN) 38010, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5521-5269","authenticated-orcid":false,"given":"Mads Fristrup","family":"Schou","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Department of Biology, Section for Evolutionary Ecology, Lund University, S\u00f6lvegatan 37, Lund 223 62, Sweden"},{"name":"Department of Bioscience, Aarhus University, Aarhus, Denmark"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1875-3185","authenticated-orcid":false,"given":"Svitlana V","family":"Serga","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"National Antarctic Scientific Center of Ukraine, 16 Shevchenko Avenue, Kyiv, 01601, Ukraine"},{"name":"Taras Shevchenko National University of Kyiv, 64 Volodymyrska str, Kyiv 01601, Ukraine"}]},{"given":"Marina","family":"Stamenkovic-Radak","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, Serbia"}]},{"given":"Marija","family":"Tanaskovic","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Institute for Biological Research \u201cSinisa Stankovic\u201d, National Institute of Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, Serbia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8461-4373","authenticated-orcid":false,"given":"Marija Savic","family":"Veselinovic","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, Serbia"}]},{"given":"Jorge","family":"Vieira","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal"},{"name":"Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, University of Porto, i3S, Porto, Portugal"}]},{"given":"Cristina P","family":"Vieira","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal"},{"name":"Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, University of Porto, i3S, Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3810-0504","authenticated-orcid":false,"given":"Martin","family":"Kapun","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Department of Evolutionary Biology and Environmental Studies, University of Z\u00fcrich, Z\u00fcrich, Switzerland"},{"name":"Division of Cell & Developmental Biology, Medical University of Vienna, Vienna, Austria"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5990-1503","authenticated-orcid":false,"given":"Thomas","family":"Flatt","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Department of Biology, University of Fribourg, Fribourg CH-1700, Switzerland"}]},{"given":"Josefa","family":"Gonz\u00e1lez","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain"}]},{"given":"Fabian","family":"Staubach","sequence":"additional","affiliation":[{"name":"The European Drosophila Population Genomics Consortium (DrosEU)"},{"name":"Department of Evolution and Ecology, University of 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