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.

Single-Stranded DNA Viruses in Antarctic Cryoconite Holes

“…Yau and Seth-Pasricha [31] and Smeele, et al [32] provide comprehensive reviews on our current knowledge of Antarctic virology. DNA viruses have been described from continental Antarctica [9] in soils [33,34,35], microbial mats [36,37], and lakes [38,39,40,41,42], and associated with various Antarctic animals [32,43,44,45] including fish [46,47]. Many of the viruses discovered in Antarctic aquatic ecosystems have single-stranded DNA (ssDNA) viral genomes [37,38,39].…”

Novel Polyomaviruses in Mammals from Multiple Orders and Reassessment of Polyomavirus Evolution and Taxonomy

“…This scheme would allow that all mammalian polyomavirus species are assigned to a genus, following the current ICTV guidelines (New Rule 3.24. ratified by the ICTV in 2018 [79]). Such a taxonomy update should be extended to also assign currently unclassified invertebrate and fish polyomaviruses to genera of their own and possibly create higher taxa [80].…”

Coinfections of Novel Polyomavirus, Anelloviruses and a Recombinant Strain of Myxoma Virus-MYXV-Tol Identified in Iberian Hares

“…First identified in humans in 1997 [15], anelloviruses have been found in a wide range of animals, including pigs, non-human primates, seals, bats and horses [16,[18][19][20][21], and are largely host species-specific. Polyomaviruses on the other hand are circular double-stranded DNA viruses of~4-7 kb that, like anelloviruses, are host specific and have been identified in various animals [22][23][24]. In our analysis of various sample types from 11 hares, we identified 14 viruses belonging to two new species of anelloviruses and two viruses belonging to a new species of polyomavirus.…”

“…The aligned amino acid sequences of the large T-antigen was used to infer a maximum likelihood phylogenetic tree using PHYML [31] with the rtREV + G + I substitution model, determined as the best fit model using ProtTest [32]. Branches with <0.8 aLRT support were collapsed using TreeGraph2 [33] and the resulting phylogenetic tree was rooted with large T-antigen sequences of fish polyomaviruses [22]. The genome-wide nucleotide, the large T-antigen and the VP1 amino acid sequence pairwise identities were determined using SDT v1.2 [30].…”