{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T01:43:55Z","timestamp":1760060635445,"version":"build-2065373602"},"reference-count":86,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2025,9,16]],"date-time":"2025-09-16T00:00:00Z","timestamp":1757980800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>Nile tilapia (Oreochromis niloticus) is an indispensable source of high-quality protein worldwide. Along with the exponential expansion of tilapia aquaculture, several novel pathogenic viruses have emerged, and some cause significant economic losses. Unfortunately, there is scarce information on the biology and epidemiology of these viruses. This exploratory metagenomic study used Oxford Nanopore Technology (ONT) sequencing to profile the virome compositions of both wild and farmed Nile tilapia across five regions in Egypt. The Nile tilapia virome was dominated by two double-stranded DNA bacteriophages, Muvirus mu and M. sfmu, which constituted 79.8% of the detected sequences. Eukaryotic viruses, including members of the families Amnoonviridae, Peribunyaviridae, and Baculoviridae, were also identified. Two giant DNA viruses known to infect Acanthamoeba spp., Mollivirus sp., and Pandoravirus sp. were identified in the spleen virome of tilapia from a single sampling site. The diversity analysis showed no significant differences among tissue types or sampling sites. Phylogenetic analyses were performed on a single virus detected of potential pathogenicity, an amnoonvirus. The analyses demonstrated that the detected virus is a member of the family Amnoonviridae and placed it alongside members of the Tilapinevirus genus. The virus, however, was distinct from the other two members in the genus: T. tilapae and T. poikilos. This study underscores the usefulness of ONT in providing a foundational understanding of the Nile tilapia virome.<\/jats:p>","DOI":"10.3390\/pathogens14090935","type":"journal-article","created":{"date-parts":[[2025,9,16]],"date-time":"2025-09-16T11:19:31Z","timestamp":1758021571000},"page":"935","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Exploring the Virome of Nile Tilapia (Oreochromis niloticus) Using Metagenomic Analysis"],"prefix":"10.3390","volume":"14","author":[{"given":"Amira","family":"Ezzat","sequence":"first","affiliation":[{"name":"Department of Aquatic Animal Medicine, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3347-6075","authenticated-orcid":false,"given":"Ahmed","family":"Abd El Wahed","sequence":"additional","affiliation":[{"name":"Institute of Animal Hygiene and Veterinary Public Health, Faculty of Veterinary Medicine, University of Leipzig, An den Tierkliniken 43, D-04103 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-3219-8691","authenticated-orcid":false,"given":"Arianna","family":"Ceruti","sequence":"additional","affiliation":[{"name":"Institute of Animal Hygiene and Veterinary Public Health, Faculty of Veterinary Medicine, University of Leipzig, An den Tierkliniken 43, D-04103 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1623-6363","authenticated-orcid":false,"given":"Amel M.","family":"El Asely","sequence":"additional","affiliation":[{"name":"Department of Aquatic Animal Medicine, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7832-7412","authenticated-orcid":false,"given":"Mohamed Shawky","family":"Khalifa","sequence":"additional","affiliation":[{"name":"Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI 48824, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1439-9406","authenticated-orcid":false,"given":"Andrew D.","family":"Winters","sequence":"additional","affiliation":[{"name":"Department of Physiology, School of Medicine, Wayne State University, 656 West Kirby Street, Detroit, MI 48202, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Uwe","family":"Truyen","sequence":"additional","affiliation":[{"name":"Institute of Animal Hygiene and Veterinary Public Health, Faculty of Veterinary Medicine, University of Leipzig, An den Tierkliniken 43, D-04103 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adel A.","family":"Shaheen","sequence":"additional","affiliation":[{"name":"Department of Aquatic Animal Medicine, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5294-421X","authenticated-orcid":false,"given":"Mohamed","family":"Faisal","sequence":"additional","affiliation":[{"name":"Department of Aquatic Animal Medicine, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt"},{"name":"Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI 48824, USA"},{"name":"Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,9,16]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.9734\/arrb\/2019\/v31i330052","article-title":"Tilapia\u2014An excellent candidate species for world aquaculture: A Review","volume":"31","author":"Prabu","year":"2019","journal-title":"Annu. 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