Fish polyomaviruses belong to two distinct evolutionary lineages

Abstract

The Polyomaviridae is a diverse family of circular double-stranded DNA viruses. Polyomaviruses have been isolated from a wide array of animal hosts. An understanding of the evolutionary and ecological dynamics of these viruses is essential to understanding the pathogenicity of polyomaviruses. Using a high throughput sequencing approach, we identified a novel polyomavirus in an emerald notothen (Trematomus bernacchii) sampled in the Ross sea (Antarctica), expanding the known number of fish-associated polyomaviruses. Our analysis suggests that polyomaviruses belong to three main evolutionary clades; the first clade is made up of all recognized terrestrial polyomaviruses. The fish-associated polyomaviruses are not monophyletic, and belong to two divergent evolutionary lineages. The fish viruses provide evidence that the evolution of the key viral large T protein involves gain and loss of distinct domains.

Keywords: Antarctica; Polyomaviridae; Trematomus bernacchii; emerald notothen.

Fig. 1.

Genome structure of the fish-associated PyVs. Neighbour-joining (NJ) phylogenetic tree inferred from alignments of the complete viral genome sequences of the known fish PyVs and SV40. English host names are used to refer to the associated fish PyVs. The novel virus identified in this work is underlined. Numbers at the nodes represent the bootstrap support for the NJ tree. To the right of the tree the (linearized) genome organization for each genotype is shown, highlighting the VP2 (red), VP1 (yellow) and T-Ag (green) ORFs. Numbers refer to the genome size. Grey ORFs in the SV40 diagram refer to (from left to right) Agno, VP3, Alto and t-Ag. The eel-associated viruses are also shown for reference (Fig. S1, available in the online version of this article shows fully annotated versions of the eel virus genomes).

Fig. 2.

Fish viral proteins are evolutionarily divergent (a) maximum likelihood phylogenetic trees of individual protein trees. English host names are used to refer to the fish-associated PyVs. Trees were rooted using SV40, and the remaining (n=114) amniote PyVs were removed to improve visualization (complete trees available in Fig. S2). Symbols indicate bootstrap support (square=100; diamond >90; circle >80). Nodes with bootstrap support less than 70 % were collapsed. Heat maps to the right of the tree show the pairwise sequence similarity. (b) Graphs comparing the percentage pairwise similarity of different PyV proteins. The black line shows the distribution of pairwise comparisons of fish PyVs. The grey plot represents comparisons between fish and amniote PyV, while the red plots show comparisons between amniote PyV. This data shows that amniote PyVs are more similar to other amniote PyVs than fish PyVs are to each other. (c) Bar graphs showing average and sd of the curves in (b).

Fig. 3.

Species tree of the fish-associated PyVs. (a) Unrooted Bayesian species tree was based on the T-Ag, VP1 and VP2 protein sequences. Nodes with posterior support less than 0.7 were collapsed. English host names are used to refer to the associated fish PyVs. (b) DensiTree representation of the tree in (a) shows the highly uncertain evolutionary history of the perciform fish PyVs. The solid blue line represents the root canal, which helps to focus on the main features of the tree set.

Fig. 4.

Evolutionary analysis of the T-Ag protein. (a) Diagram of the SV40 T-Ag protein (708 aa). The J-domain, with embedded HPDKGG hexapeptide, Rb binding motif, nuclear localization signal (NLS), and helicase domains are indicated. The helicase domain is divided into a zinc (Zn) domain and the ATPase. (b) Maximum likelihood phylogenetic tree of the T-Ag protein. Trees were rooted using SV40, and the remaining (n=114) amniote PyVs were removed to improve visualization (complete trees available in Fig. S2). Nodes with bootstrap support less than 70 % were collapsed. Diagrams to the right of the tree show the individual domains in T-Ag DnaJ (grey), the HPDKGG hexapeptide (black diamond). Origin binding domain (blue) and helicase domain (purple). English host names are used to refer to the associated fish PyVs. (c) Homology models of the different PyV DnaJ domains homology modelled on the murine PyV DnaJ domain (1FAF [42]). Models for SV40 (purple), the guitarfish (blue), marbled (green) and Japanese (yellow) eel viruses were visualized and analysed using Chimera version 1.11.2 [43]. (d) Merged overlay of the models shown in (c). The black arrow head points towards the conserved HPDKGG hexapeptide.