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There are rising concerns that emergent JEV genotype V (GV) is circulating in Asia, against which current vaccines may not be efficacious. To ascertain if JEV GV and other arboviruses are circulating in East Asia, we conducted next\u2010generation sequencing on 260 pools of <jats:italic>Culex tritaeniorhynchus<\/jats:italic> and <jats:italic>Culex bitaeniorhynchus<\/jats:italic> mosquitoes (6540 specimens) collected at Camp Humphreys, Republic of Korea (ROK) in 2018. Interrogation of our data revealed a highly abundant and diverse virosphere that contained sequences from 122 distinct virus species. Our statistical and hierarchical analysis uncovered correlates of potential health, virological, and ecological relevance. Furthermore, we obtained evidence that JEV GV was circulating in Pyeongtaek and, retrospectively, in Seoul in 2016 and placed these findings within the context of human and fowl reservoir activity. Sequence\u2010based analysis of JEV GV showed a divergent genotype that is the most distant from the GIII\u2010derived live attenuated SA14\u201014\u20102 vaccine strain and indicated regions probably responsible for reduced antibody affinity. These results emphasize recent concerns of shifting JEV genotype in East Asia and highlight the critical need for a vaccine proven efficacious against this re\u2010emergent virus. Together, our one\u2010health approach to <jats:italic>Culex<\/jats:italic> viral metagenomics uncovered novel insights into virus ecology and human health.<\/jats:p>","DOI":"10.1111\/mec.16133","type":"journal-article","created":{"date-parts":[[2021,8,21]],"date-time":"2021-08-21T20:31:49Z","timestamp":1629577909000},"page":"5470-5487","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":36,"title":["Metagenomic analysis reveals <i>Culex<\/i> mosquito virome diversity and Japanese encephalitis genotype V in the Republic of Korea"],"prefix":"10.1111","volume":"30","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5308-4680","authenticated-orcid":false,"given":"Mark A.","family":"Sanborn","sequence":"first","affiliation":[{"name":"Viral Diseases Branch Walter Reed Army Institute of Research Silver Spring MD USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kathryn 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