{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T03:05:05Z","timestamp":1788923105735,"version":"build-2803163510"},"reference-count":101,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,1,22]],"date-time":"2026-01-22T00:00:00Z","timestamp":1769040000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    Outbreaks of mosquito-borne viruses are increasing in temperate regions, with West Nile and Usutu viruses now established in wide regions across Europe, and both detected in the UK. Current surveillance strategies focus on targeted approaches which are well suited for monitoring established threats but limited in their ability to detect recently described or neglected viruses. High throughput sequencing (HTS) provides an unbiased alternative, allowing simultaneous identification of well-recognised and overlooked arboviruses, alongside insect-specific viruses (ISVs) that may modulate vector competence of the insects transmitting these pathogens. This study presents the first comprehensive virome survey of\n                    <jats:italic>Culex<\/jats:italic>\n                    mosquitoes in the UK, analysing populations collected from 93 sites across England and Wales through HTS and a systematic virus discovery pipeline. Across these sites, 41 distinct viral taxa were identified, including 11 novel species. Most viruses were rare or confined to a few sites, with only three detected in more than one third of sites, suggesting the absence of a broad conserved virome across populations. Within this diversity, three arbovirus-related lineages were detected: Hedwig virus (\n                    <jats:italic>Peribunyaviridae<\/jats:italic>\n                    ), Umatilla virus (\n                    <jats:italic>Sedoreoviridae<\/jats:italic>\n                    ), and Atherstone virus (\n                    <jats:italic>Peribunyaviridae<\/jats:italic>\n                    ), the former two representing the first detections in the UK. These putative arboviruses were embedded in viral communities that showed minimal structuring by coarse land type but a modest decline in richness with latitude across rural sites, consistent with diversity gradients observed in other microbial systems. Together, these findings provide the first national-scale baseline of\n                    <jats:italic>Culex<\/jats:italic>\n                    mosquito-associated viral diversity in the UK, and demonstrate the value of metagenomic approaches in arbovirus preparedness.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2026.1749228","type":"journal-article","created":{"date-parts":[[2026,1,22]],"date-time":"2026-01-22T06:55:42Z","timestamp":1769064942000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Mosquito viromes across England and Wales reveal hidden arbovirus signals and limited ecological structuring"],"prefix":"10.3389","volume":"17","author":[{"given":"Jack","family":"Pilgrim","sequence":"first","affiliation":[{"name":"Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool","place":["Liverpool, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emma","family":"Widlake","sequence":"additional","affiliation":[{"name":"The School of Life Sciences and the Centre for Applied Entomology and Parasitology, Keele University","place":["Keele, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roksana","family":"Wilson","sequence":"additional","affiliation":[{"name":"Medical Entomology and Zoonoses Ecology Group, UK Health Security Agency","place":["Salisbury, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander G. C.","family":"Vaux","sequence":"additional","affiliation":[{"name":"Medical Entomology and Zoonoses Ecology Group, UK Health Security Agency","place":["Salisbury, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jolyon M.","family":"Medlock","sequence":"additional","affiliation":[{"name":"Medical Entomology and Zoonoses Ecology Group, UK Health Security Agency","place":["Salisbury, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alistair C.","family":"Darby","sequence":"additional","affiliation":[{"name":"Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool","place":["Liverpool, United Kingdom"]},{"name":"Faculty of Health and Life Sciences, Institute of Systems, Molecular and Integrative Biology, Centre for Genomic Research, University of Liverpool","place":["Liverpool, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew","family":"Baylis","sequence":"additional","affiliation":[{"name":"Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool","place":["Liverpool, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcus S. 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Dis."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"12","DOI":"10.7554\/eLife.66550","article-title":"Mosquito community composition shapes virus prevalence patterns along anthropogenic disturbance gradients","volume":"12","author":"Hermanns","year":"2023","journal-title":"eLife"},{"key":"ref35","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1093\/ismejo\/wrae145","article-title":"Temperature-dependent trophic associations modulate soil bacterial communities along latitudinal gradients","volume":"18","author":"Huang","year":"2024","journal-title":"ISME J."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"ref37","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1016\/j.cois.2018.05.009","article-title":"Densonucleosis viruses (\u2018densoviruses\u2019) for mosquito and pathogen control","volume":"28","author":"Johnson","year":"2018","journal-title":"Curr Opin Insect Sci"},{"key":"ref38","doi-asserted-by":"publisher","first-page":"e0214424","DOI":"10.1128\/jvi.02144-24","article-title":"Insect-specific Alphamesonivirus-1 (Mesoniviridae) in lymph node and lung tissues from two horses with acute respiratory syndrome","volume":"99","author":"Jurisic","year":"2025","journal-title":"J. Virol."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"372","DOI":"10.4269\/ajtmh.1978.27.372","article-title":"Supplement to international catalogue of arboviruses including certain other viruses of vertebrates","volume":"27","author":"Karabatsos","year":"1978","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"Katoh","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"ref41","author":"Kolde","year":"2018"},{"key":"ref42","doi-asserted-by":"publisher","first-page":"929","DOI":"10.3390\/v12090929","article-title":"Viral metagenomic analysis of Aedes albopictus mosquitos from southern Switzerland","volume":"12","author":"Kubacki","year":"2020","journal-title":"Viruses"},{"key":"ref43","doi-asserted-by":"publisher","first-page":"1259","DOI":"10.3390\/v12111259","article-title":"Superinfection exclusion in mosquitoes and its potential as an arbovirus control strategy","volume":"12","author":"Laureti","year":"2020","journal-title":"Viruses"},{"key":"ref44","doi-asserted-by":"publisher","first-page":"1544884","DOI":"10.3389\/fviro.2025.1544884","article-title":"West nile and Usutu viruses: current spreading and future threats in a warming northern Europe","volume":"5","author":"Laverdeur","year":"2025","journal-title":"Front. Virol."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"ref46","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1186\/s40168-023-01556-4","article-title":"Association of virome dynamics with mosquito species and environmental factors","volume":"11","author":"Liu","year":"2023","journal-title":"Microbiome"},{"key":"ref47","doi-asserted-by":"publisher","first-page":"e0012904","DOI":"10.1371\/journal.pntd.0012904","article-title":"Chikungunya virus in Europe: a retrospective epidemiology study from 2007 to 2023","volume":"19","author":"Liu","year":"2025","journal-title":"PLoS Negl. Trop. Dis."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"63","DOI":"10.3390\/pathogens14010063","article-title":"Introduction of vector-borne infections in Europe: emerging and re-emerging viral pathogens with potential impact on one health","volume":"14","author":"Logiudice","year":"2025","journal-title":"Pathogens"},{"key":"ref49","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"e1011880","DOI":"10.1371\/journal.ppat.1011880","article-title":"West Nile virus spread in Europe: phylogeographic pattern analysis and key drivers","volume":"20","author":"Lu","year":"2024","journal-title":"PLoS Pathog."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"2072","DOI":"10.1177\/15353702231209415","article-title":"Arbovirus surveillance in mosquitoes: historical methods, emerging technologies, and challenges ahead","volume":"248","author":"Maia","year":"2023","journal-title":"Exp. 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[R package]","author":"Massicotte","year":"2016"},{"key":"ref56","doi-asserted-by":"publisher","first-page":"2145","DOI":"10.3390\/ijerph15102145","article-title":"Assessment of the public health threats posed by vector-borne disease in the United Kingdom (UK)","volume":"15","author":"Medlock","year":"2018","journal-title":"Int. J. Environ. Res. Public Health"},{"key":"ref57","doi-asserted-by":"publisher","first-page":"466","DOI":"10.1017\/S0950268806007047","article-title":"Possible ecology and epidemiology of medically important mosquito-borne arboviruses in Great Britain","volume":"135","author":"Medlock","year":"2007","journal-title":"Epidemiol. Infect."},{"key":"ref58","doi-asserted-by":"publisher","first-page":"66","DOI":"10.3390\/v8030066","article-title":"Linking virus genomes with host taxonomy","volume":"8","author":"Mihara","year":"2016","journal-title":"Viruses"},{"key":"ref59","doi-asserted-by":"publisher","first-page":"777","DOI":"10.1038\/s41597-023-02676-0","article-title":"Monitoring the West Nile virus outbreaks in Italy using open access data","volume":"10","author":"Mingione","year":"2023","journal-title":"Sci Data"},{"key":"ref60","first-page":"498","article-title":"Umatilla virus in zoo-dwelling cape penguins with hepatitis, Germany","volume-title":"Emerg. Infect. 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Evol."},{"key":"ref64","doi-asserted-by":"publisher","first-page":"18","DOI":"10.2903\/j.efsa.2020.6041","article-title":"Rift Valley fever \u2013 epidemiological update and risk of introduction into Europe","volume":"18","author":"Nielsen","year":"2020","journal-title":"EFSA J."},{"key":"ref65","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/j.coviro.2018.07.006","article-title":"Insect-specific viruses: from discovery to potential translational applications","volume":"33","author":"Nouri","year":"2018","journal-title":"Curr. Opin. Virol."},{"key":"ref66","doi-asserted-by":"publisher","first-page":"2864","DOI":"10.1038\/ismej.2017.126","article-title":"dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication","volume":"11","author":"Olm","year":"2017","journal-title":"ISME J."},{"key":"ref67","doi-asserted-by":"publisher","first-page":"947","DOI":"10.1038\/s41559-024-02365-0","article-title":"Metagenomic analysis of individual mosquito viromes reveals the geographical patterns and drivers of viral diversity","volume":"8","author":"Pan","year":"2024","journal-title":"Nat. Ecol. Evol."},{"key":"ref68","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1016\/j.cois.2020.02.005","article-title":"Exploiting insect-specific viruses as a novel strategy to control vector-borne disease","volume":"39","author":"Patterson","year":"2020","journal-title":"Curr. Opin. Insect. Sci."},{"key":"ref69","article-title":"ViralQC: A tool for assessing completeness and contamination of predicted viral contigs","volume-title":"ArXiv","author":"Peng","year":"2025"},{"key":"ref70","doi-asserted-by":"publisher","first-page":"1701","DOI":"10.1093\/cid\/ciaa308","article-title":"Identification of umbre Orthobunyavirus as a novel zoonotic virus responsible for lethal encephalitis in 2 French patients with Hypogammaglobulinemia","volume":"72","author":"P\u00e9rot","year":"2021","journal-title":"Clin. Infect. Dis."},{"key":"ref71","doi-asserted-by":"publisher","first-page":"1033","DOI":"10.3390\/v11111033","article-title":"Meta-transcriptomic comparison of the RNA viromes of the mosquito vectors Culex pipiens and Culex torrentium in northern Europe","volume":"11","author":"Pettersson","year":"2019","journal-title":"Viruses"},{"key":"ref72","article-title":"Emergence risks from within? 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