Evaluation of haemoparasite and Sarcocystis infections in Australian wild deer

Evidence of Australian wild deer exposure to N. caninum infection and potential implications for the maintenance of N. caninum sylvatic cycle

Infections with the coccidian parasite Neospora caninum affect domestic and wild animals worldwide. In Australia, N. caninum infections cause considerable losses to the cattle industry with seroprevalence of 8.7% in beef and 10.9% in dairy cattle. Conversely, the role of wild animals, in maintaining the parasite cycle is also unclear. It is possible that native or introduced herbivorous species could be reservoir hosts of N. caninum in Australia, but to date, this has not been investigated. We report here the first large-scale screening of N. caninum antibodies in Australian wild deer, spanning three species (fallow, red and sambar deer). Consequently, we also assessed two commercial cELISA tests validated for detecting N. caninum in cattle for their ability to detect N. caninum antibodies in serum samples of wild deer. N. caninum antibodies were detected in 3.7% (7/189, 95% CI 1.8 - 7.45) of the wild deer serum samples collected in south-eastern Australia (n = 189), including 97 fallow deer (Dama dama), 14 red deer (Cervus elaphus), and 78 sambar deer (Rusa unicolor). Overall, our study provides the first detection of N. caninum antibodies in wild deer and quantifies deer's potential role in the sylvatic cycle of N. caninum.

A survey of piroplasms in white-tailed deer (Odocoileus virginianus) in the southeastern United States to determine their possible role as Theileria orientalis hosts

In 2017, clinical disease and mortality in cattle associated with Theileria orientalis Ikeda was reported in Virginia, U.S. The exotic tick, Haemaphysalis longicornis, is a competent vector for this species. White-tailed deer (Odocoileus virginianus) are commonly infested with H. longicornis in the eastern U.S. and are also infected with several genotypes of piroplasms such as a Theileria sp. (often called Theileria cervi-like), Babesia odocoilei, and Babesia sp. H10. However, it is currently unknown if deer are susceptible to T. orientalis and can act as potential hosts. In this study, we tested 552 white-tailed deer samples from the southeastern U.S. to determine the presence of T. orientalis. We used a PCR-RFLP to test 293 (53%) of these samples to distinguish between piroplasm genera. A total of 189 white-tailed deer were positive with Theileria, 47 were positive with Babesia, and 57 did not amplify. Because this assay does not determine species, we sequenced 30 random samples targeting a fragment of the 18S rRNA gene. Although a high diversity of Theileria and Babesia spp. were detected, none were T. orientalis. All 552 samples were then screened with a T. orientalis specific real-time PCR protocol, but none were positive for T. orientalis. Our data suggests that white-tailed deer are commonly infected with piroplasm species but not T. orientalis.

•

Piroplasm parasites of 552 white-tailed deer were surveyed in the Eastern U.S.

•

A high prevalence and diversity of Theileria and Babesia species were observed.

•

No infections with exotic Theileria orientalis Ikeda was detected in white-tailed deer.

First Evidence of Entamoeba Parasites in Australian Wild Deer and Assessment of Transmission to Cattle

Australian wild deer populations have significantly expanded in size and distribution in recent decades. Due to their role in pathogen transmission, these deer populations pose a biosecurity risk to the livestock industry. However, little is known about the infection status of wild deer in Australia. The intestinal parasite Entamoeba bovis has been previously detected in farm and wild ruminants worldwide, but its epidemiology and distribution in wild ruminants remain largely unexplored. To investigate this knowledge gap, faecal samples of wild deer and domestic cattle from south-eastern Australia were collected and analysed for the presence of Entamoeba spp. using PCR and phylogenetic analysis of the conserved 18S rRNA gene. E. bovis parasites were detected at high prevalence in cattle and wild deer hosts, and two distinct Entamoeba ribosomal lineages (RLs), RL1 and RL8, were identified in wild deer. Phylogenetic analysis further revealed the existance of a novel Entamoeba species in sambar deer and a novel Entamoeba RL in fallow deer. While we anticipated cross-species transmission of E. bovis between wild deer and cattle, the data generated in this study demonstrated transmission is yet to occur in Australia. Overall, this study has identified novel variants of Entamoeba and constitutes the first report of Entamoeba in fallow deer and sambar deer, expanding the host range of this parasite. Epidemiological investigations and continued surveillance of Entamoeba parasites in farm ruminants and wild animals will be required to evaluate pathogen emergence and transmission to livestock.

Detection and Characterisation of an Endogenous Betaretrovirus in Australian Wild Deer

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.

Novel Picornavirus Detected in Wild Deer: Identification, Genomic Characterisation, and Prevalence in Australia

The use of high-throughput sequencing has facilitated virus discovery in wild animals and helped determine their potential threat to humans and other animals. We report the complete genome sequence of a novel picornavirus identified by next-generation sequencing in faeces from Australian fallow deer. Genomic analysis revealed that this virus possesses a typical picornavirus-like genomic organisation of 7554 nt with a single open reading frame (ORF) encoding a polyprotein of 2225 amino acids. Based on the amino acid identity comparison and phylogenetic analysis of the P1, 2C, 3CD, and VP1 regions, this novel picornavirus was closely related to but distinct from known bopiviruses detected to date. This finding suggests that deer/bopivirus could belong to a novel species within the genus Bopivirus, tentatively designated as "Bopivirus C". Epidemiological investigation of 91 deer (71 fallow, 14 sambar and 6 red deer) and 23 cattle faecal samples showed that six fallow deer and one red deer (overall prevalence 7.7%, 95% confidence interval [CI] 3.8-15.0%) tested positive, but deer/bopivirus was undetectable in sambar deer and cattle. In addition, phylogenetic and sequence analyses indicate that the same genotype is circulating in south-eastern Australia. To our knowledge, this study reports for the first time a deer-origin bopivirus and the presence of a member of genus Bopivirus in Australia. Further epidemiological and molecular studies are needed to investigate the geographic distribution and pathogenic potential of this novel Bopivirus species in other domestic and wild animal species.