Detection and Characterisation of an Endogenous Betaretrovirus in Australian Wild Deer

Abstract

Endogenous retroviruses (ERVs) are the remnants of past retroviral infections that once invaded the host's germline and were vertically transmitted. ERV sequences have been reported in mammals, but their distribution and diversity in cervids are unclear. Using next-generation sequencing, we identified a nearly complete genome of an endogenous betaretrovirus in fallow deer (Dama dama). Further genomic analysis showed that this provirus, tentatively named cervid endogenous betaretrovirus 1 (CERV β1), has typical betaretroviral genome features (gag-pro-pol-env) and the betaretrovirus-specific dUTPase domain. In addition, CERV β1 pol sequences were detected by PCR in the six non-native deer species with wild populations in Australia. Phylogenetic analyses demonstrated that CERV β1 sequences from subfamily Cervinae clustered as sister taxa to ERV-like sequences in species of subfamily Muntiacinae. These findings, therefore, suggest that CERV β1 endogenisation occurred after the split of these two subfamilies (between 3.3 and 5 million years ago). Our results provide important insights into the evolution of betaretroviruses in cervids.

Keywords: betaretrovirus; class II retroviruses; deer; endogenous retroviruses; genetic characterisation.

Figure 1

Genomic structure of CERV β1. (a) The core retroviral genes gag, pro, pol, and env are blue, while coding regions and predicted conserved domains are green. The position of aberrant stop codons is denoted with red arrows. (b) Alignment of the four detected retroviral contigs. Sequences OL547611 and OL547612 are nearly complete proviruses, while sequences OL547609, OL0547610, and OL0547613 matched the gag gene. Genome alignments are represented by the outlined bars in grey, with divergent sites highlighted in black. The green bar above indicates the percentage identity among the sequences (green is the highest identity).

Figure 2

Phylogenetic analysis of CERV β1 sequences obtained by next-generation sequencing (in red), related sequences in deer genomes, and representative members of the genus Betaretrovirus. The tree was generated based on the gag protein by the maximum-likelihood method, and JTT + G + I substitution model with 1000 bootstrap replicates. Bootstrap values >70% are displayed at the tree branches. The scale bar indicates amino acid substitutions per site. ENTV: Enzootic nasal tumour virus.

Figure 3

Phylogenetic analysis of partial pol aa sequences. Translated sequences obtained by PCR in members of subfamily Cervinae are in red: chital deer (Axis axis), fallow deer (Dama dama), hog deer (Axis porcinus), red deer (Cervus elaphus), rusa deer (Rusa timorensis), and sambar deer (Rusa unicolor). Sequences of members of subfamily Muntiacinae are in blue. The tree was generated by the maximum-likelihood method based on JTT + G + I substitution model with 1000 bootstrap replicates. Bootstrap values >70% are displayed at the tree branches. The scale bar indicates amino acid substitutions per site.