Virome composition in marine fish revealed by meta-transcriptomics

Abstract

Identifying the components of host ecology that promote virus diversity is crucial for our understanding of the drivers of virus evolution and disease emergence. As the most species-rich group of vertebrates that exhibit diverse ecologies, fish provide an ideal model system to study the impacts of host ecology on the composition of their viromes. To better understand the factors that shape virome composition in marine fishes, we characterised the viromes of 23 fish species (19 from this study and four that were sampled previously (Geoghegan et al 2018a)) using unbiased bulk RNA-sequencing (meta-transcriptomics) together with both sequence and protein structural homology searches to identify divergent viruses that often evade characterisation. These data revealed that fish virome composition – that is, viral richness, abundance and diversity – were predominantly shaped by the phylogenetic history of their hosts, as reflected in taxonomic order. In addition, preferred mean water temperature, climate, habitat depth, community diversity and whether fish swim in schools or are solitary were identified as important ecological features that shaped virome diversity and abundance in these fish. Our analysis also identified 25 new virus transcripts that could be assigned to 11 different viral families, including the first fish virus in the Matonaviridae. Other viruses identified fell within the Astroviridae, Picornaviridae, Arenaviridae, Reoviridae, Hepadnaviridae, Paramyxoviridae, Rhabdoviridae, Hantaviridae, Filoviridae and Flaviviridae. Our results provide a better understanding of the ecological determinants of virome diversity and support the view that fish harbour a multitude of viruses, of which the vast majority are undescribed.

Metagenomic sequencing reveals a lack of virus exchange between native and invasive freshwater fish across the Murray-Darling Basin, Australia

“…A key observation of our study was the absence of Cyprinid herpesviruses, including CyHV-3, as well as other Alloherpesviridae, in any of the 36 RNA libraries. Similarly, although members of the Hepadnaviridae are commonly detected in fish [37,44,77,78] they were notably absent in our samples. The only DNA virus detected in this study was a novel poxvirus (Poxviridae) identified in western carp-gudgeon.…”

“…Their abundance primarily impacts smaller native fish (such as carp-gudgeon, rainbowfish and hardyheads) since they typically outcompete these species and disrupt food webs [62]. As well as being highly divergent, western carpgudgeon arenavirus formed a basal clade with a recently discovered arenavirus in the pygmy goby sampled from an Australian coral reef [37], a member of the same fish order (Gobiiformes). These data further suggest that arenaviruses may have been circulating in Gobiiform fishes (gobies and gudgeons) in Australia prior to the introduction of eastern mosquitofish.…”

“…Notably, we identified two novel arenaviruses that clustered with members of the newly formed Antennavirus genus that includes fish hosts [18,36]. Western carp-gudgeon arenavirus, found at Narrabri creek shared 36.9% amino acid sequence similarity with its closest relative, Wenling frogfish arenavirus 1 [18] and grouped with recently discovered arenaviruses from pygmy gobies (Eviota zebrina) sampled from an Australian coral reef [37]. Eastern mosquitofish arenavirus found in the Macquarie River shared 84.5% amino acid sequence similarity with its closest available relative, Wenling frogfish arenavirus 1 [18].…”

“…Tissue selection was based on previous studies [18,37,44], which show that liver and gill tissue serve as a rich source of viruses. To facilitate virus discovery, multiple individuals (1-10) were pooled according to species and the location in which they were captured (SI…”

A novel rubi-like virus in the Pacific electric ray (Tetronarce californica) reveals the complex evolutionary history of theMatonaviridae

“…It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted February 8, 2021. ; https://doi.org/10.1101/2021.02.08.430315 doi: bioRxiv preprint 2 of 12 survey of vertebrates in China and is highly divergent from RuV, sharing around 34% nucleotide similarity [10]. Tiger flathead matonavirus was identified through a meta-transcriptomic exploration of Australian marine fish [11], which, along with Guangdong Chinese water snake rubivirus, forms a sister clade to RuV. Even more recently, two novel rubella-like virus species were described: Rustrela virus, identified in several mammalian species close by and in a zoo in Germany, and Ruhugu virus from bats in Uganda [12].…”