School of BioSciences - Research Publications
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ItemNo Preview AvailableDevelopment of a transboundary model of livestock disease in Europe(Cold Spring Harbor Laboratory, 2021)Epidemiological models of notifiable livestock disease are typically framed at a national level and targeted for specific diseases. There are inherent difficulties in extending models beyond national borders as details of the livestock population, production systems and marketing systems of neighbouring countries are not always readily available. It can also be a challenge to capture heterogeneities in production systems, control policies, and response resourcing across multiple countries, in a single transboundary model. In this paper we describe EuFMDiS, a continental-scale modelling framework for transboundary animal disease, specifically designed to support emergency animal disease planning in Europe. EuFMDiS simulates the spread of livestock disease within and between countries and allows control policies to be enacted and resourced on per-country basis. It provides a sophisticated decision support tool that can be used to look at the risk of disease introduction, establishment and spread; control approaches in terms of effectiveness and costs; resource management; and post-outbreak management issues.
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ItemModelling the spread and control of African swine fever in domestic and feral pigs(University of Melbourne, 2021)
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ItemNo Preview AvailableComparing surveillance approaches to support regaining free status after a foot-and-mouth disease outbreak(ELSEVIER, 2021-09)Following an FMD eradication program, surveillance will be required to demonstrate that the program has been successful. The World Organization for Animal Health (OIE) provides guidelines including waiting periods and appropriate surveillance to support regaining FMD-free status. Serological surveillance is the recommended method for demonstrating freedom but is time consuming and expensive. New technologies such as real-time reverse transcription polymerase chain reaction (RT-qPCR) tests and sampling techniques such as bulk milk testing (BMT) of dairy cattle, oral swabs, and saliva collection with rope tethers in piggeries could enable surveillance to be done more efficiently. Epidemiological modelling was used to simulate FMD outbreaks, with and without emergency vaccination as part of the response, in Australia. Baseline post-outbreak surveillance approaches for unvaccinated and vaccinated animals based on the European FMD directive were compared with alternative approaches in which the sampling regime, sampling approaches and/or the diagnostic tests used were varied. The approaches were compared in terms of the resources required, time taken, cost, and effectiveness i.e., ability of the surveillance regime to correctly identify the infection status of herds. In the non-vaccination scenarios, the alternative approach took less time to complete and cost less, with the greatest benefits seen with larger outbreaks. In vaccinated populations, the alternative surveillance approaches significantly reduced the number of herds sampled, the total number of tests done and costs of the post-outbreak surveillance. There was no reduction in effectiveness using the alternative approaches, with one of the benefits being a reduction in the number of false positive herds. Alternative approaches to FMD surveillance based on non-invasive sampling methods and RT-qPCR tests have the potential to enable post outbreak surveillance substantiating FMD freedom to be done more quickly and less expensively than traditional approaches based on serological surveys.
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ItemNo Preview AvailablePost-outbreak surveillance strategies to support proof of freedom from foot-and-mouth disease( 2021-04-28)Abstract Whilst emergency vaccination may help contain foot-and-mouth disease in a previously FMD-free country, its use complicates post-outbreak surveillance and the recovery of FMD-free status. A structured surveillance program is required that can distinguish between vaccinated and residually infected animals, and provide statistical confidence that the virus is no longer circulating in previously infected areas. Epidemiological models have been well-used to investigate the potential benefits of emergency vaccination during a control progam and when/where/whom to vaccinate in the face of finite supplies of vaccine and personnel. Less well studied are post-outbreak issues such as the management of vaccinated animals and the implications of having used vaccination during surveillance regimes to support proof-of-freedom. This paper presents enhancements to the Australian Animal Disease Model (AADIS) that allow comparisons of different post-outbreak surveillance sampling regimes for establishing proof-of-freedom from FMD. A case study is provided that compares a baseline surveillance sampling regime (derived from current OIE guidelines), with an alternative less intensive sampling regime. It was found that when vaccination was not part of the control program, a reduced sampling intensity significantly reduced the number of samples collected and the cost of the post-outbreak surveillance program, without increasing the risk of missing residual infected herds.
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ItemA Simulation Study of the Use of Vaccination to Control Foot-and-Mouth Disease Outbreaks Across Australia(FRONTIERS MEDIA SA, 2021-08-11)This study examines the potential for foot-and-mouth disease (FMD) control strategies that incorporate vaccination to manage FMD spread for a range of incursion scenarios across Australia. Stakeholder consultation was used to formulate control strategies and incursion scenarios to ensure relevance to the diverse range of Australian livestock production regions and management systems. The Australian Animal Disease Spread model (AADIS) was used to compare nine control strategies for 13 incursion scenarios, including seven control strategies incorporating vaccination. The control strategies with vaccination differed in terms of their approaches for targeting areas and species. These strategies are compared with two benchmark strategies based on stamping out only. Outbreak size and duration were compared in terms of the total number of infected premises, the duration of the control stage of an FMD outbreak, and the number of vaccinated animals. The three key findings from this analysis are as follows: (1) smaller outbreaks can be effectively managed by stamping out without vaccination, (2) the size and duration of larger outbreaks can be significantly reduced when vaccination is used, and (3) different vaccination strategies produced similar reductions in the size and duration of an outbreak, but the number of animals vaccinated varied. Under current international standards for regaining FMD-free status, vaccinated animals need to be removed from the population at the end of the outbreak to minimize trade impacts. We have shown that selective, targeted vaccination strategies could achieve effective FMD control while significantly reducing the number of animals vaccinated.
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ItemA generalised and scalable framework for modelling incursions, surveillance and control of plant and environmental pests(Elsevier BV, 2021-05)Invasive plant and environmental pests can seriously impact environment, economy, health and amenity. It is challenging to form response policies given the diversity of pest species; complex spatiotemporal interplay between arrival, spread, surveillance, and control; and limited field data when pests are rare/absent. Models can provide useful decision support through the exploration of incursion pathways and comparison of surveillance and control strategies. However, increased use of quantitative models to inform pest management requires adaptable modelling frameworks. The new Australian Priority Pest and Disease modelling framework (APPDIS) allows pest models to be constructed through user configuration choices for a broad range of different pest types. Pest populations may be defined as point incursions, established populations, or estimated mechanistically from environmental criteria. Spread occurs at multiple scales, through either simple mathematical kernels, or more complex spatial pathways, depending on data availability and pest type. Useful experiments can be conducted on general surveillance, specific surveillance, and treatment regimes. Control activities are dynamically resource-constrained and costed for relative comparisons in terms of benefit and cost. A case study on a tramp ant incursion is provided for illustrative purposes.
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ItemModelling the spread of transboundary animal disease in and between domestic and wild swine populations(EuFMD, 2020)The challenge of planning for transboundary animal disease outbreaks can be compounded by the complex epidemiological interplay between livestock, wild animals, and the environment. Wild boar populations can form direct and indirect spread pathways for contagious livestock diseases such as FMD, ASF and CSF, both within and between countries. In this poster we describe the enhancement of the EuFMDiS decision support tool to assist disease managers explore the sometimes unpredictable interface between domestic pigs and wild boar. A key modelling outcome was the fusion of an existing agent-based model of livestock disease transmission with a new geographic automata model of wildlife disease transmission.
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ItemTransmission network reconstruction for foot-and-mouth disease outbreaks incorporating farm-level covariates(PUBLIC LIBRARY SCIENCE, 2020-07-15)Transmission network modelling to infer ‘who infected whom’ in infectious disease outbreaks is a highly active area of research. Outbreaks of foot-and-mouth disease have been a key focus of transmission network models that integrate genomic and epidemiological data. The aim of this study was to extend Lau’s systematic Bayesian inference framework to incorporate additional parameters representing predominant species and numbers of animals held on a farm. Lau’s Bayesian Markov chain Monte Carlo algorithm was reformulated, verified and pseudo-validated on 100 simulated outbreaks populated with demographic data Japan and Australia. The modified model was then implemented on genomic and epidemiological data from the 2010 outbreak of foot-and-mouth disease in Japan, and outputs compared to those from the SCOTTI model implemented in BEAST2. The modified model achieved improvements in overall accuracy when tested on the simulated outbreaks. When implemented on the actual outbreak data from Japan, infected farms that held predominantly pigs were estimated to have five times the transmissibility of infected cattle farms and be 49% less susceptible. The farm-level incubation period was 1 day shorter than the latent period, the timing of the seeding of the outbreak in Japan was inferred, as were key linkages between clusters and features of farms involved in widespread dissemination of this outbreak. To improve accessibility the modified model has been implemented as the R package ‘BORIS’ for use in future outbreaks.