Metavirome survey of eight ray-finned fishes: Domination of giant viral members from pandoravirus and megaviricetes

Background: Fish are an essential source of food worldwide. Most microbial diversity in marine ecosystems remains uncharacterized, with viruses accounting for most of the remaining diversity. This poses a potential major threat to public health, making it critical to understand the variety of viruses in marine ecosystems. Our objective was to assess the virome of ray-finned fishes in terms of diversity and its potential relation to human diseases. Methods: Metagenomic data from a BioProject on ray-finned fishes, with the accession number PRJNA493014 containing eight Sequence Read Archive (SRA) experiments, were retrieved from the SRA. Sequencing data were trimmed and assembled using Unicycler. Reads from each sequencing run were mapped to the reference using Kraken. Unassigned viral reads from the genomes of the eight ray-finned fish species were used to find giant viral fingerprints. Results: We found 2,228,888 sequence reads among ray-finned fishes representing viral kingdom fingerprints. The pooled genome assay of ray-finned fishes revealed a significant abundance of viruses in three clades: the genus Pandoravirus (31%), the order Herpesvirales (23%), and the kingdom Bamfordvirae (10%). Additionally, 432,281 out of 2,031,445 reads (21%) remained unassigned as viruses. According to findings from GiantVirusFinder, 17,931 hits (4.15%) were mapped to the genomes of known giant viruses. Conclusion: Considering that humans regularly consume seafood as a primary part of their diet, it is essential to note that ray-finned fishes serve as hosts to various giant DNA viruses with extensive evolutionary histories. As demonstrated here, there is a need to screen fish for viral infections that may be linked to human illnesses.