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This study aimed to enhance understanding of viruses in CSF from children with clinically diagnosed meningitis and\/or encephalitis (M\/ME) of unknown aetiology using shotgun sequencing enhanced by hybrid capture\u00a0(HCSS).<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>A single-centre prospective study was conducted at Sant Joan de D\u00e9u University Hospital, Barcelona, involving 40\u00a0M\/ME episodes of unknown aetiology, recruited from May 2021 to July 2022. All participants had previously tested negative with the FilmArray Meningitis\/Encephalitis Panel.<\/jats:p>\n                <jats:p>HCSS was used to detect viral nucleic acid in the patients\u2019 CSF. Sequencing was performed on Illumina NovaSeq platform. Raw sequence data were analysed using CZ ID metagenomics and PikaVirus bioinformatics pipelines.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Forty episodes of M\/ME\u00a0of unknown aetiology in 39 children were analysed by HCSS. A significant viral detection in 30 CSF samples was obtained, including six parechovirus A, three enterovirus ACD, four polyomavirus 5, three HHV-7, two BKV, one HSV-1, one VZV, two CMV, one EBV, one influenza A virus, one rhinovirus, and 13 HERV-K113\u00a0detections. Of these, one sample with BKV, three with HHV-7, one with EBV, and all HERV-K113 were confirmed by specific PCR. The requirement for Intensive Care Unit admission was associated with HCSS detections.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>This study highlights HCSS as a powerful tool for the investigation of undiagnosed cases of M\/ME. Data generated must be carefully analysed and reasonable precautions must be taken before establishing association of clinical features with unexpected or novel virus findings.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1007\/s10096-024-04795-x","type":"journal-article","created":{"date-parts":[[2024,3,4]],"date-time":"2024-03-04T20:01:51Z","timestamp":1709582511000},"page":"863-873","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Hybrid capture shotgun sequencing detected unexpected viruses in the cerebrospinal fluid of children with acute meningitis and encephalitis"],"prefix":"10.1007","volume":"43","author":[{"given":"Cristian","family":"Launes","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan","family":"Camacho","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marina","family":"Pons-Espinal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"F. 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