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

Abstract

As the phylogenetic organization of mammalian polyomaviruses is complex and currently incompletely resolved, we aimed at a deeper insight into their evolution by identifying polyomaviruses in host orders and families that have either rarely or not been studied. Sixteen unknown and two known polyomaviruses were identified in animals that belong to 5 orders, 16 genera, and 16 species. From 11 novel polyomaviruses, full genomes could be determined. Splice sites were predicted for large and small T antigen (LTAg, STAg) coding sequences (CDS) and examined experimentally in transfected cell culture. In addition, splice sites of seven published polyomaviruses were analyzed. Based on these data, LTAg and STAg annotations were corrected for 10/86 and 74/86 published polyomaviruses, respectively. For 25 polyomaviruses, a spliced middle T CDS was observed or predicted. Splice sites that likely indicate expression of additional, alternative T antigens, were experimentally detected for six polyomaviruses. In contrast to all other mammalian polyomaviruses, three closely related cetartiodactyl polyomaviruses display two introns within their LTAg CDS. In addition, the VP2 of Glis glis (edible dormouse) polyomavirus 1 was observed to be encoded by a spliced transcript, a unique experimental finding within the Polyomaviridae family. Co-phylogenetic analyses based on LTAg CDS revealed a measurable signal of codivergence when considering all mammalian polyomaviruses, most likely driven by relatively recent codivergence events. Lineage duplication was the only other process whose influence on polyomavirus evolution was unambiguous. Finally, our analyses suggest that an update of the taxonomy of the family is required, including the creation of novel genera of mammalian and non-mammalian polyomaviruses.

Search for polyoma-, herpes-, and bornaviruses in squirrels of the family Sciuridae

“…This first description of PyVs, BHVs and GHVs in squirrels of different species increased our knowledge (e.g. [51,65] on the diversity of PyVs and HVs in rodents. In particular, some of these viruses represent novel highly divergent lineages or sublineages in the corresponding phylogenetic trees.…”

“…For three PyVs complete genomes were generated and splice sites were experimentally determined for one of these novel viruses. As reported earlier [65], such experimental determination is critically important for annotation of coding PyV sequences. The search for the reservoir of VSBV-1 within this study resulted in solely negative findings, although additional squirrel species were investigated.…”

“…3 (See legend on next page.) (Sciurus carolinensis polyomavirus 1 (this study) and Glis glis polyomavirus 1 [65]) or predicted in silico for Delphinus delphis polyomavirus 1, and Callosciurus prevostii polyomavirus 1 as the VP2 CDS of all clade members comprise highly conserved splice donor and acceptor motifs with high score (> 75) in the Human Splicing Finder 3.1. All three representatives of the novel CeryPyV1 cluster together within the genus Alphapolyomavirus.…”

“…The splice sites predicted for LTAg, STAg, and VP2 CDS of CprePyV1 (Table 5) were not studied experimentally because the CprePyV1 genome is closely related to that of ScarPyV1 (see phylogenetic tree analysis below) and the splice sites of both PyVs are conserved in position and sequence. Likewise, splice sites predicted for CeryPyV1 were not studied experimentally as they are conserved in position and sequence with those of the closely related Philantomba monticola PyV1, whose sites were experimentally confirmed earlier [65].…”

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

“…In the genome of the polyomavirus recovered from the Iberian hare samples, we identified all the polyomavirus ORFs. The large T-antigen, VP1 and genome-wide pairwise analysis of the Lepus polyomavirus (LepPyV) and those most closely related revealed that these two LepPyV isolates share >99% identity and are most closely related to the Glis glis polyomavirus (GenBank accession # MG701352) [39] sharing 60% (large T-antigen), 67% (VP1) and 64% (full genome) pairwise identity, shown in Figure 3. The large T-antigen of the hare-derived polyomaviruses recovered in this study is nested within a larger mammal clade but forms a distinct sub-clade.…”