Exploring the Virome of Nile Tilapia (Oreochromis niloticus) Using Metagenomic Analysis

Nile tilapia (<i>Oreochromis niloticus</i>) 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, <i>Muvirus mu</i> and <i>M. sfmu</i>, which constituted 79.8% of the detected sequences. Eukaryotic viruses, including members of the families <i>Amnoonviridae</i>, <i>Peribunyaviridae</i>, and <i>Baculoviridae</i>, were also identified. Two giant DNA viruses known to infect <i>Acanthamoeba</i> spp., <i>Mollivirus</i> sp., and <i>Pandoravirus</i> 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 <i>Amnoonviridae</i> and placed it alongside members of the <i>Tilapinevirus</i> genus. The virus, however, was distinct from the other two members in the genus: <i>T. tilapae</i> and <i>T. poikilos</i>. This study underscores the usefulness of ONT in providing a foundational understanding of the Nile tilapia virome.