In 2019, the gross tuna (Thunnus spp.) aquaculture industry was worth over $790 million USD worldwide due to its extreme popularity as food fish. Despite this, viruses in tuna are severely understudied compared the viruses of other livestock. However, viruses pose a significant threat to aquaculture industries, as seen with the Australian pilchard herpesvirus epidemics in 1995 and 1998, which killed millions of fish. It is therefore crucial to expand our knowledge of the fish virome to understand the viral threat and help prevent future epidemics.
RNA-sequencing datasets from 60 tuna transcriptomes from NCBI were analysed for the presence of viral sequences using a bioinformatic pipeline. A full-length novel virus from the Hepeviridae family was discovered in an Atlantic bluefin tuna (Thunnus thynnus) from Cartegena, Spain. Hepeviridae are known to cause hepatitis in mammals but recently, hepe-like viruses have also been discovered in aquatic animals. The novel Thunnus thynnus hepevirus (TTHV) showed signs of recombination, where the non-structural polyprotein shared 22.8% amino acid (aa) pairwise identity with the aquatic Wenzhou hepe-like virus 2, and the structural polyprotein was related (18.3% aa pairwise identity) to that of Pernambuco virus (unclassified viral family).
In the same fish, the partial genome (7,080 nt) of a novel Dicistroviridae was discovered. The novel Thunnus thynnus dicistrovirus (TTDV) phylogenetically clustered with the genus Cripavirus. Most Dicistroviridae are associated with insects, but TTDV is the first dicistrovirus to be discovered in a fish which suggests a potentially broader host range for Dicistroviridae and broader range of viral families in tuna.
The use of bioinformatic methods to screen full transcriptomes for novel viruses is a powerful tool used to discover the presence of two novel viruses herein and highlights the unsampled diversity of viruses in tuna. With the elucidated viral genomes, the pathogenicity of these viruses can now be assessed to prevent the impact of viral outbreaks among fish stocks worldwide.