Virome composition in marine fish revealed by meta-transcriptomics

Abstract

Revealing the determinants of virome composition is central to placing disease emergence in a broader evolutionary context. Fish are the most species-rich group of vertebrates and so provide an ideal model system to study the factors that shape virome compositions and their evolution. We characterized the viromes of nineteen wild-caught species of marine fish using total RNA sequencing (meta-transcriptomics) combined with analyses of sequence and protein structural homology to identify divergent viruses that often evade characterization. From this, we identified twenty-five new vertebrate-associated viruses and a further twenty-two viruses likely associated with fish diet or their microbiomes. The vertebrate-associated viruses identified here included the first fish virus in the Matonaviridae (single-strand, negative-sense RNA virus). Other viruses fell within the Astroviridae, Picornaviridae, Arenaviridae, Reoviridae, Hepadnaviridae, Paramyxoviridae, Rhabdoviridae, Hantaviridae, Filoviridae, and Flaviviridae, and were sometimes phylogenetically distinct from known fish viruses. We also show how key metrics of virome composition-viral richness, abundance, and diversity-can be analysed along with host ecological and biological factors as a means to understand virus ecology. Accordingly, these data suggest that that the vertebrate-associated viromes of the fish sampled here are predominantly shaped by the phylogenetic history (i.e. taxonomic order) of their hosts, along with several biological factors including water temperature, habitat depth, community diversity and swimming behaviour. No such correlations were found for viruses associated with porifera, molluscs, arthropods, fungi, and algae, that are unlikely to replicate in fish hosts. Overall, these data indicate that fish harbour particularly large and complex viromes and the vast majority of fish viromes are undescribed.

Keywords: fish; host-jumping; metagenomics; virome; virus evolution.

Figure 1.

(A) Total standardized abundance of vertebrate-associated viruses (at the level of virus family) across the fish species examined. (B) Normalized viral abundance set out on a backbone of the fish host phylogeny at the order level. (C) Standardized number of total viral reads (black), vertebrate-associated viral reads (grey) and host reference gene ribosomal protein S13 (RPS13) (orange) in each species library.

Figure 2.

Phylogenetic relationships of likely vertebrate-associated viruses identified here. The maximum likelihood phylogenetic trees show the topological position of the newly discovered viruses (blue circles) and those identified in an earlier study (Geoghegan et al. 2018a), in the context of their closest phylogenetic relatives. Branches are highlighted to represent host class (fish = blue; mammals = red; birds, reptiles and amphibians = yellow; vector-borne (mammals and arthropods) = green). All branches are scaled according to the number of amino acid substitutions per site and trees were mid-point rooted for clarity only. An asterisk indicates node support of >70 per cent bootstrap support. See Supplementary Table S3 for all accession numbers.

Figure 3.

Significant explanatory variables in generalized linear models (GLM) for viral abundance and two measures of alpha diversity. Viral abundance is best explained by (A) fish host order and (B) mean preferred water temperature. Alpha diversity is best explained by (C) host order and (D) preferred habitat (Observed Richness) and by (E) host order and (F) host community diversity (Shannon Diversity). Stars indicate significant differences between groups determined by post hoc Tukey tests. Points represent different fish species and are coloured by host order.