A novel endogenous betaretrovirus group characterized from polar bears (Ursus maritimus) and giant pandas (Ailuropoda melanoleuca)

Abstract

Transcriptome analysis of polar bears (Ursus maritimus) yielded sequences with highest similarity to the human endogenous retrovirus group HERV-K(HML-2). Further analysis of the polar bear draft genome identified an endogenous betaretrovirus group comprising 26 proviral copies and 231 solo LTRs. Molecular dating indicates the group originated before the divergence of bears from a common ancestor but is not present in all carnivores. Closely related sequences were identified in the giant panda (Ailuropoda melanoleuca) and characterized from its genome. We have designated the polar bear and giant panda sequences Ursus maritimus endogenous retrovirus (UmaERV) and Ailuropoda melanoleuca endogenous retrovirus (AmeERV), respectively. Phylogenetic analysis demonstrated that the bear virus group is nested within the HERV-K supergroup among bovine and bat endogenous retroviruses suggesting a complex evolutionary history within the HERV-K group. All individual remnants of proviral sequences contain numerous frameshifts and stop codons and thus, the virus is likely non-infectious.

Endogenous viruses: Connecting recent and ancient viral evolution

“…Boreoeutherians, marsupials, and birds (Arnaud et al, 2008;Baba et al, 2011;Baillie and Wilkins, 2001;Baillie et al, 2004;Bolisetty et al, 2012;Ericsson et al, 2001;Gifford et al, 2005;Hayward et al, 2013;Herniou et al, 1998;Lavie et al, 2004;Mayer et al, 2013;; Van der Kuyl, 2011) VI/RT-RNA virus Retroviridae (Gammaretroviruses)…”

Anti-NMDA Receptor Encephalitis in the Polar Bear (Ursus maritimus) Knut

“…An exceptionally extensive investigation for infectious causes for a single animal failed to demonstrate a bacterial, viral or parasitic cause for the encephalitis. Highly detailed pathological investigations, histology, extensive serology, thirty five pan-PCR assays, two pathogen microarray systems, and shotgun sequencing on both the GSF FLX and Illumina HiSeq systems only revealed a serological response to influenza A and a novel endogenous retroviral group, neither of which would have been responsible for Knut’s symptoms 1 2 . Thus, a diagnosis of “encephalitis of unknown etiology” was established.…”

A Novel Endogenous Betaretrovirus in the Common Vampire Bat (Desmodus rotundus) Suggests Multiple Independent Infection and Cross-Species Transmission Events

“…Little is known about retroviruses in bats from the neotropics, and nothing is known about those in vampire bats. Endogenous retroviruses (ERVs) are present in the genomes of all vertebrates examined (2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13). As different species may share ERV sequences, it is assumed that, in many cases, an exogenous retrovirus infected the common ancestor of multiple species and became fixed in the genome prior to species divergence (14)(15)(16).…”

“…At the time of integration, retroviral LTR sequences are identical, but after integration, they behave as paralog sequences evolving at the same rate as the host's genome. Therefore, it is possible to estimate the date of a provirus insertion based on the LTR's divergence using the formula T ϭ (D/R)/2, were T is the invasion time (million years), D is the 5= and 3= LTR divergence given as the number of differences per nucleotide per site (overall nucleotide divergence) (34), and R is the genomic substitution rate per site per year (35), although there are some reservations about this dating method (6,12,36). For the DrERV_824 and DrERV_216 variants, an integration time of 17.9 and 16.0 million years ago (mya) was estimated, while for CpERV, a date of 7.7 mya was obtained ( Table 1).…”