– ABOUT
AUSTRALIAN ANIMAL DISEASE GENOMICS INITIATIVE
Animal diseases pose a significant threat to Australia’s agricultural industries, resulting in livestock productivity losses, trade restrictions, and increased disease control costs. Despite Australia’s strong animal health status, this is increasingly challenged by environmental changes that affect pest and disease spread, as well as the rising frequency of extreme weather events. The movement of people, livestock, and wildlife further heightens the risk of pest and disease entry into Australia, intensifying pressures to maintain disease-free claims from trading partners and the World Organisation for Animal Health (WOAH).
In addition to impacting food systems, animal diseases threaten native wildlife and pose zoonotic risks, with over 30 new human pathogens identified in the past three decades, at least 75% of which originated in animals. The emergence of zoonotic diseases is a major threat to global health security, livelihoods, and economies. Addressing these challenges requires a concerted effort to understand viral diversity and the factors driving disease outbreaks.
This Initiative is creating high-quality reference data on known and novel pathogens and parasites to support fundamental research and disease control efforts, including surveillance, diagnostics, epidemiological studies, tracking antimicrobial resistance, and informing vaccine development.
OBJECTIVES
In collaboration with the animal health community, this initiative enhances disease research and biosecurity through two key efforts:
1) Reference Genome Library – Sequencing and annotating high-quality genomes of priority animal pathogens, including bacteria, fungi, viruses, and parasites. These resources will be openly available to support disease understanding and management.
2) Animal Virome Atlas – Metagenomic sequencing to map virus diversity in animals, exploring how virome structures change and assessing ecological and evolutionary disease drivers.
By generating open-access genomic data, this initiative strengthens Australia’s ability to understand, monitor, manage, and respond to animal disease threats.
Request for Partnership now open
PROJECTS
| Scientific name | Project Summary | Data Strategy | Project Lead | Partners | |
|---|---|---|---|---|---|
| Theme 1: Reference Genome Library | Coxiella burnetii (Q fever) | Generate complete genome sequences for C. burnetii isolates to improve understanding of strain diversity and transmission pathways in humans and livestock. The data will enhance detection methods and strengthen surveillance and research into vaccine and disease control strategies. | Reference genome (PacBio HiFi) | Tarka Raj Bhatta | Barwon Health, Australian Rickettsial Reference Laboratory; Deakin University; The University of Melbourne; Monash University |
| Theme 1: Reference Genome Library | Moraxella spp. | Produce genomic data on Moraxella strains associated with pinkeye in cattle. The project will assess antimicrobial resistance and strain variation to improve diagnostic precision and inform management practices in the livestock sector. | Reference genome (ONT) | Barbara Brito | NSW Department of Primary Industries and Regional Development; University of Technology Sydney; The University of Sydney |
| Theme 1: Reference Genome Library | Vibrio spp. | Create genomic references for Vibrio species affecting farmed aquatic animals. The data will support improved diagnostics, monitoring of disease spread, and management decisions to protect aquaculture productivity. | Reference genome (ONT) | Mei Ooi | Department of Natural Resources and Environment Tasmania - Animal Health Laboratory |
| Theme 1: Reference Genome Library | Trypanosoma spp. | Generate genomic assemblies of newly discovered trypanosome species. The project will clarify parasite life cycles, improve understanding of transmission pathways, and identify biological vulnerabilities that can inform treatment and management strategies for wildlife, livestock, and potential human infections. | Reference genome (PacBio HiFi, Illumina), Transcriptomics (Illumina) | Alexander Maier | The Australian National University |
| Theme 1: Reference Genome Library | Teladorsagia circumcincta (Brown stomach worm) | Develop a reference genome for T. circumcincta to investigate population structure and resistance mechanisms. The data will advance diagnostic capability, support vaccine development, and underpin improved parasite control in Australian sheep industries. | Reference genome (PacBio HiFi, Hi-C) | Annaleise Wilson | CSIRO |
| Theme 1: Reference Genome Library | Marteilia sydneyi (QX disease) | Generate genomic resources for M. sydneyi, the causative agent of QX disease in oysters. The genome data will enhance diagnostic tools, inform selective breeding for resistance, and strengthen management of aquaculture biosecurity risks. | Reference genome (PacBio HiFi, ONT, Hi-C), Transcriptomics (Iso-seq) | Ido Bar | Griffith University; NSW Department of Primary Industries and Regional Development; QLD Department of Agriculture and Fisheries; University of St Andrews (Scotland) |
| Theme 2: Animal Virome Atlas | Honeybee virome (Apis mellifera & Varroa destructor | Tracks changes in the viral landscape of honey bees (Apis mellifera) tracking how the honey bee virome shifts before, during, and after Varroa invasion in specific NSW regions. Focuses on novel virus discovery, diagnostic development, and understanding Varroa-vectored viral emergence. | Virome sequencing (short read) | Emily Remnant | The University of Sydney |
| Theme 2: Animal Virome Atlas | Native stingless bee virome (Tetragonula carbonaria) | Surveys viral diversity in wild and managed colonies of Tetragonula carbonaria across Queensland and New South Wales. Compares viromes between wild, managed, and co-located hives with honey bees to assess viral spillover risk and inform pollinator biosecurity and management. | Virome sequencing (short read) | Emily Remnant | The University of Sydney; Macquarie University |
| Theme 2: Animal Virome Atlas | Tick virome (Ixodes spp.) | Profiles viruses from five Sternalixodes tick species collected in Queensland and northern New South Wales using museum and field samples. Identifies shared and unique viral signatures to improve understanding of tick-borne virus ecology and zoonotic disease potential. | Virome sequencing (short read) | Rhys Parry | The University of Queensland |
| Theme 2: Animal Virome Atlas | Dragon lizard virome (Agamidae spp.) | Characterises viruses in wild and captive dragon lizards from multiple regions. Compares healthy and diseased animals, including threatened species, to identify novel viruses and inform reptile disease monitoring and conservation management. | Virome sequencing (short read) | Julien Melade | The University of Sydney; University of Canberra |
| Theme 2: Animal Virome Atlas | Koala virome (Phascolarctos cinereus) | Characterises the respiratory virome of koalas by integrating viral, bacterial, fungal, and host immune data to identify drivers of disease susceptibility and potential biomarkers of infection risk. Outputs include novel RNA virus discovery, ecological and evolutionary analysis of viral communities, and insights into microbiome–virome–immunity interactions that inform wildlife health and conservation strategies. | Virome sequencing (short read) | Kosuke Takada | The University of Sydney |
| Theme 2: Animal Virome Atlas | Marsupials virome (multiple species) | Uses archived diagnostic samples from Victorian marsupials (including wombats, koalas, kangaroos, and wallabies) to detect known and novel viruses. Links viral presence to disease presentation, improving diagnostic capability and clinical management for wildlife health programs. | Virome sequencing (short read) | Alistair Legione | The University of Melbourne (Asia-Pacific Centre for Animal Health) |
| Theme 2: Animal Virome Atlas | Endangered marsupial virome | Examines viruses in two endangered marsupials (Lasiorhinus krefftii and Perameles bougainville) from Western Australia and Queensland to identify novel viral species and assess ecological and evolutionary patterns. Data will inform conservation strategies, early disease detection, and translocation management. | Virome sequencing (short read) | Ayda Susana Ortiz Baez | The University of Sydney |
| Theme 2: Animal Virome Atlas | Wildlife–Domestic interface virome | Explores virome diversity across domestic and wild species (including kangaroos, ducks, and dogs) to identify viral families shared among taxa and better understand potential cross-species transmission pathways. | Virome sequencing (short read) | Subir Sarker | James Cook University |
| Theme 2: Animal Virome Atlas | Queensland Wildlife Virome (multiple species) | Samples a wide range of native mammals (e.g. kangaroos, possums, quolls) and birds admitted to the Australia Zoo Wildlife Hospital in Queensland to characterise both known and novel viruses. The project generates high-quality virome datasets to assess host–virus dynamics, zoonotic potential, and viral diversity, strengthening wildlife disease surveillance and One Health biosecurity outcomes. | Virome sequencing (short read) | Subir Sarker | James Cook University; University of the Sunshine Coast |
PARTNERS
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advisory committee members
| Mark Hutchinson (Chair) | University of Adelaide and SABRE Alliance |
| Edward Holmes | University of Sydney |
| Michelle Wille | University of Melbourne |
| Jess Morgan | QLD Department of Agriculture and Fisheries |
| God’spower Okoh | NT DITT – Berrimah Veterinary Laboratory |
| Guy Weerasinghe | DAFF |
| Stacey Lynch | Australian Centre for Disease Preparedness |
| Sarah Richmond | Bioplatforms Australia |
KEY INFORMATION
ACKNOWLEDGEMENT INFORMATION
Bioplatforms Initiative DOI: https://doi.org/10.25953/qzxv-md52
Umbrella Bioproject ID: PRJNA1217493
Please use this ID when submitting any derived data to a database that is a member of the International Nucleotide Sequence Database Collaboration (INSDC), such as GenBank/NCBI, ENA or DDBJ.
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Citation Guidelines
To cite the general initiative:
Australian Animal Disease Genomics Initiative, 2025, https://doi.org/10.25953/qzxv-md52
To cite a specific dataset:
The Australian Animal Disease Genomics Initiative, 2025, https://doi.org/10.25953/qzxv-md52, [year-of-data-download], [full dataset title], [dataset-access-URL], accessed [date-of-access].
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Acknowledgement Statement
We would like to acknowledge the contribution of the Australian Animal Disease Genomics Initiative Consortium in the generation of data used in this publication. The Initiative is supported by funding from Bioplatforms Australia, enabled by the Commonwealth Government National Collaborative Research Infrastructure Strategy (NCRIS).
If relevant, also credit other organisations involved in the collection of the particular dataset you are using, as listed in the ‘project_lead’ and ‘project_collaborators’ in the metadata record.
CONTACT US
Project Manager
Mabel Lum – Bioplatforms Australia
mlum@bioplatforms.com
General Manager
Sarah Richmond – Bioplatforms Australia
srichmond@bioplatforms.com
DATA AND COLLABORATION POLICY
Data generated through this initiative is subject to the Data and Collaboration policy. Please review it here.