Viromes of Freshwater Fish with Lacustrine and Diadromous Life Histories Differ in Composition

Abstract

Viruses that infect fish are understudied, yet they provide important evolutionary context to the viruses that infect terrestrial vertebrates. We surveyed gill tissue meta-transcriptomes collected from two species of native freshwater fish from Aotearoa New Zealand—Retropinna retropinna and Gobiomorphus cotidianus. A total of 64 fish were used for gill tissue meta-transcriptomic sequencing, from populations with contrasting life histories—landlocked (i.e., lacustrine) and diadromous—on the South Island and Chatham Islands. We observed that both viral richness and taxonomic diversity were significantly associated with life history and host species, with lacustrine R. retropinna characterised by higher viral alpha diversity than diadromous R. retropinna. Additionally, we observed transcripts of fish viruses from 12 vertebrate host-associated virus families, and phylogenetically placed eight novel RNA viruses and three novel DNA viruses in the Astroviridae, Paramyxoviridae, Orthomyxoviridae, Rhabdoviridae, Totiviridae, Poxviridae, Alloherpesviridae, and Adintoviridae in their evolutionary contexts. These results represent an important survey of the viruses that infect two widespread native fish species in New Zealand, and provide insight useful for future fish virus surveys.

Concurrent Detection of a Papillomatous Lesion and Sequence Reads Corresponding to a Member of the Family Adintoviridae in a Bell’s Hinge-Back Tortoise (Kinixys belliana)

“…However, adintoviruses have so far not been associated with diseases or tumours. On the contrary, transcripts from both adintovirus lineages were identified in the gill tissue of nondiseased freshwater fish by metatranscriptomic analyses [19].…”

Five Species of Wild Freshwater Sport Fish in Wisconsin, USA, Reveal Highly Diverse Viromes

“…Much of our current understanding of viruses infecting fish is based on the study of pathogenic viruses in symptomatic hosts. However, the recent rise of metagenomic sequencing has led to the discovery that fish harbor a greater number of viruses than any other class of vertebrates [ 1 , 2 , 3 , 4 , 5 , 6 , 7 ]. Most families of RNA viruses once thought to infect mammals have been described in bony fishes [ 1 ].…”

“…In most instances, such studies have been conducted in response to mortality events in wild fish [ 17 , 18 ] or in aquaculture settings [ 11 ]. We could only find a handful of broad virome surveys targeting wild freshwater fish, and none that had been conducted in the USA, to our knowledge [ 5 , 7 , 19 , 20 , 21 ]. This lack of data on wild freshwater fish viromes represents a potentially substantial knowledge gap.…”

Viromes of Antarctic fish resembles the diversity found at lower latitudes

“…Radiation of Antarctic fishes has also resulted in the highest rates of endemism of any isolated marine environment (Eastman & Clarke, 1998). Such species not only make for fascinating models of evolution (Seehausen, 2006;Thacker et al, 2021), but also for studying their associated microbial flora, particularly viruses (Costa, Ronco, et al, 2023;Perry et al, 2022). Still, much of the focus on the viruses of Antarctic species to date has revolved around birds, seals (Smeele et al, 2018;Varsani et al, 2017), environmental samples (Aguirre de Cárcer et al, 2016;Gong et al, 2018), as well as Trematomus fish (Kraberger et al, 2022) (Kraberger et al, 2022) (Kraberger et al, 2022).…”