Molecular Characterization of a Novel Gammaretrovirus in Killer Whales ( Orcinus orca )

Abstract

There are currently no published data documenting the presence of retroviruses in cetaceans, though the occurrences of cancers and immunodeficiency states suggest the potential. We examined tissues from adult killer whales and detected a novel gammaretrovirus by degenerate PCR. Reverse transcription-PCR also demonstrated tissue and serum expression of retroviral mRNA. The full-length sequence of the provirus was obtained by PCR, and a TaqMan-based copy number assay did not demonstrate evidence of productive infection. PCR on blood samples from 11 healthy captive killer whales and tissues from 3 free-ranging animals detected the proviral DNA in all tissues examined from all animals. A survey of multiple cetacean species by PCR for gag, pol, and env sequences showed homologs of this virus in the DNA of eight species of delphinids, pygmy and dwarf sperm whales, and harbor porpoises, but not in beluga or fin whales. Analysis of the bottlenose dolphin genome revealed two full-length proviral sequences with 97.4% and 96.9% nucleotide identity to the killer whale gammaretrovirus. The results of single-cell PCR on killer whale sperm and Southern blotting are also consistent with the conclusion that the provirus is endogenous. We suggest that this gammaretrovirus entered the delphinoid ancestor's genome before the divergence of modern dolphins or that an exogenous variant existed following divergence that was ultimately endogenized. However, the transcriptional activity demonstrated in tissues and the nearly intact viral genome suggest a more recent integration into the killer whale genome, favoring the latter hypothesis. The proposed name for this retrovirus is killer whale endogenous retrovirus.

Broad-scale phylogenomics provides insights into retrovirus–host evolution

“…These sequences cluster with the recently indentified killer whale ERV (26), and here we also recover an adjacent dolphin sequence (Fig. S1, V, Killer whale).…”

Endogenous viruses: Connecting recent and ancient viral evolution

“…Terrestrial boreoeutherians, marsupials, and birds Marine and terrestrial boreoeutherians, marsupials, birds, reptiles, and amphibians (Anai et al, 2012;Bamunusinghe et al, 2013;Bolisetty et al, 2012;Elleder et al, 2012;Fiebig et al, 2006;Hanger et al, 2000;Jaratlerdsiri et al, 2009;Lamere et al, 2009;Martin et al, 1999;Patience et al, 2001;Tarlinton et al, 2013;Tristem et al, 1996;Wang et al, (Bertsch et al, 2009;Gayral et al, 2008;Iskra-Caruana et al, 2010;Kunii et al, 2004;Staginnus and Richert-Pöggeler, 2006) Furthermore, there is also a tendency for non-agriculturally and medically important viruses to be overlooked. As a result, it could thus be that the actual viral host range is much broader than surveillance of existing viruses alone could reveal.…”

De novo Assembly of the Indo-Pacific Humpback Dolphin Leucocyte Transcriptome to Identify Putative Genes Involved in the Aquatic Adaptation and Immune Response

“…It is explicit that environmental contaminants and microparasites, including viruses, bacteria and protozoans, may constrain the growth of wild animal populations [29]. To date, many microparasites have been detected in marine animals, including Paramyxoviridae, Poxviridae, HerpesvIridae, Adenoviridae, and Caliciviridae [30], [31]. These microparasites interfered with population abundance by inducing high mortalities, lowering reproductive success or synergistically increasing the virulence of other diseases.…”