The role of wild deer in the transmission of diseases of livestock


In Australia, wild deer, including Fallow, Sambar, Red, Rusa, Chital and Hog deer, can feed on agricultural landscapes and, therefore, pose a biosecurity risk to the agricultural sector as potential carriers of important livestock diseases such as foot-and-mouth disease (FMD). 

FMD is highly contagious and is the exotic disease of greatest significance to Australian agriculture. A large multi-state outbreak of FMD in Australia will result in an estimated direct economic loss of AU$52 billion over 10 years, with a current FMD freedom status underpinning a nationally significant annual trade in live animal and meat exports.  

A spatially explicit, multi-species model has been developed (Australian Animal Disease Spread Model; AADIS) to predict the movement of FMD virus through various Australian agricultural industries. However, this model currently does not include virus transmission between livestock and wildlife populations, including deer. The role of wildlife in the transmission of FMD has been demonstrated overseas, but has not been evaluated against wild deer populations within the unique farming systems and environment of Australia. 

This project will directly investigate the risk posed by deer to the livestock industry as hosts for exotic disease, using the transmission of endemic viral disease(s) between deer and livestock as an example.  This project will also evaluate the effectiveness of possible mitigation strategies should an outbreak occur. This will be achieved by estimating deer population density adjacent to farms, quantifying their level of interactions with livestock, the level of connectivity between local deer populations and by estimating the cross-species infection rate between deer and livestock species.  





  1. evaluating deer densities at the forest/farm interface  
  2. assessing the level of interactions between wild deer and domestic livestock and  
  3. quantifying the degree of connectivity between deer populations.

Project Leader

Dr Carlo Pacioni
Project Team
  • Dr Dave Ramsey, ARI
  • Dr Carlo Pacioni, ARI 
  • Mr Luke Woodford, ARI 
  • Dr Karla Jayne Helbig, LaTrobe University 
  • Dr Teresa Carvalho, LaTrobe University 
  • Dr Jaimie Hunnam DEDJTR VIC 
  • Dr Andrew Woolnough, DEDJTR VIC 
  • Dr Dave Forsyth, NSW DPI  
Project Partners
  • Arthur Rylah Institute (ARI), Victorian Government
  • Victorian Government Department of Economic Development, Jobs, Transport and Resources  (VIC DEDJTR)
  • NSW Department of Primary Industries (NSW DPI)
  • La Trobe University 

The project receives funding from the Australian Government Department of Agriculture, Water and the Environment


February 2021 update:

Betaretrovirus and Picobirnavirus has now been detected in wild fallow, rusa, sambar and chital deer. This virus has been considered an opportunistic gastrointestinal pathogen, however, reports of its detection in extra-intestinal sites have raised a debate regarding their actual site of infection. Respiratory tract samples are currently being screened.

August 2020 update:

The project is revealing that the risk posed by deer as hosts of exotic disease is real. Analysis has revealed the presence of novel Betaretrovirus and Picobirnavirus in serum samples from wild fallow, rusa, sambar and chital deer. The extent of the risk and likelihood of transference of these and other diseases from deer to livestock is subject to further investigation.

Screening is currently underway to determine the prevalence of these novel viruses in deer and livestock populations across Australia.

February 2020 update:

The majority of the laboratory work for the disease screening of the deer samples has been completed, while population genetics is still ongoing.

Sequences from two putative RNA viruses have been identified and completion of sequencing data and formal description is ongoing.

Two different strains of a gastro-intestinal protozoa have also been identified. Both are known to be able to infect livestock species and may have an impact for the industry.

August 2019 update:

A high-throughput sequencing system (Illumina Hiseq) was used to analyse five serum samples from wild Fallow deer. The sequencing depth was increased five-fold from initial sequencing analysis to provide a greater scope of detection. Preliminary evidence of viral genetic material was found in some samples with confirmation and further analysis ongoing.

Microscopic examination of blood smears from NSW has revealed the presence of several morphological forms, possibly compatible with blood-protozoa. DNA from each blood sample was tested for seven parasitic genera using PCR, returning a negative result for these parasite groups. Analysis of additional blood samples is ongoing.

Deeper analysis of the viral sequences found in the last trial of metagenomics is necessary. This will allow the development of specific primers to detect individual viruses using PCR. PCR analysis of the blood samples from NSW revealed negative results, despite microscopic analysis revealing evidence of possible presence of some microorganisms. Metagenomics analysis of a specific RNA region will help identify the microorganism and provide information to develop a screening tool.

February 2019 update: 

Faecal, blood and DNA samples have been collected from deer species across Australia and analysis undertaken to confirm species. 

Serum (blood) samples were screened for the presence of antigens and antibodies against Pestivirus and Bovine herpesvirus-1 using commercial serological tests. Antigens and antibodies against Pestivirus were detected in a very small number of the samples, while no serological evidence of Bovine herpesvirus-1 were detected in the samples. 

For a subset of the blood samples collected, blood smears were performed on site at the time of blood collection. Microscopy examination of 50 blood smears revealed the presence of several morphological forms, possibly compatible with blood-protozoan. The corresponding blood samples were screened by PCR for known blood parasites. Published primers targeting conserved regions of seven parasitic genera commonly infecting livestock species were selected for molecular identification. PCR conditions and protocols were optimised to enable large scale screening, and analysis is currently ongoing.  

Scientific publications:

  • Cripps J, Pacioni C, Scroggie M, Woolnough A and Ramsey D (2018) ‘Introduced deer and their potential role in disease transmission to livestock in Australia’, Mammal Review, 49:60–77.
  • Davies C, Wright W, Wedrowicz F, Pacioni C, and Hogan FE (2022) ‘Delineating genetic management units of sambar deer (Rusa unicolor) in south-eastern Australia, using opportunistic tissue sampling and targeted scat collection’, Wildlife Research, 49:147–157
  • Huaman Jose, Pacioni C, Forsyth D, Pople A, Hampton J, Helbig K and Carvalho T (2020) ‘Screening of Blood Parasites in Australian Wild Deer’, Authorea,
  • Huaman JL, Pacioni C, Forsyth DM, Pople A, Hampton JO, Carvalho TG and Helbig KJ (2020) ‘Serosurveillance and Molecular Investigation of Wild Deer in Australia Reveals Seroprevalence of Pestivirus Infection’, Viruses, 12
  • Huaman JL, Pacioni C, Forsyth DM, Pople A, Hampton JO, Carvalho TG, Helbig KJ (2022) ‘Detection and Characterisation of an Endogenous Betaretrovirus in Australian Wild Deer’, Viruses, 14(2):252,
  • Huaman Jose L., Pacioni C, Forsyth DM, Pople A, Hampton JO, Helbig KJ and Carvalho TG (2021) ‘Evaluation of haemoparasite and Sarcocystis infections in Australian wild deer’, International Journal for Parasitology: Parasites and Wildlife, 15:262-269.
  • Huaman JL, Pacioni C, Kenchington-Evans L, Doyle M, Helbig KJ and Carvalho TG (2022) ‘First Evidence of Entamoeba Parasites in Australian Wild Deer and Assessment of Transmission to Cattle’, Frontiers in Cellular and Infection Microbiology, 12,
  • Huaman J.L., Pacioni C, Sarker S, Doyle M, Forsyth DM, Pople A, Hampton JO, Carvalho TG and Helbig KJ (2021) ‘Molecular Epidemiology and Characterization of Picobirnavirus in Wild Deer and Cattle from Australia: Evidence of Genogroup I and II in the Upper Respiratory Tract’, Viruses, 13: 1492,
  • Huaman JL, Pacioni C, Sarker S, Doyle M, Forsyth DM, Pople A, Carvalho TG and Helbig KJ (2021) ‘Novel Picornavirus Detected in Wild Deer: Identification, Genomic Characterisation, and Prevalence in Australia’, Viruses, 13:2412,


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