School of BioSciences - Research Publications
Permanent URI for this collection
Search Results
1 - 10 of 12
-
ItemUsing decision support tools in emergency animal disease planning and response: Foot and mouth disease (CEBRA Project 1404D), Technical Report prepared for the Department of Agriculture and Water Resources(University of Melbourne, 2016)Modelling studies both in Australia and overseas have shown that vaccination can be very effective in reducing the size and duration of an FMD outbreak. Vaccination is most effective in reducing the duration and size of an outbreak when used early and is less effective the longer you delay. However, a decision to vaccinate early in the outbreak may result in using vaccination in situations where it is not actually required, with consequent implications for post-outbreak surveillance, the management of vaccinated animals and the ability to regain FMD-free status and access to markets. Overall, the choice of control measure to adopt in an FMD outbreak will thus depend on the variable and potentially conflicting objectives of the control program. As an important component of disease planning and preparedness for the department, the project will report on key information that could be used in an FMD outbreak to infer the potential scale of an outbreak and information to support disease management decision-making.
-
ItemIncorporating economic components in Australia's FMD modelling capability and evaluating post-outbreak management to support return to trade (CEBRA project 1608D), Technical Report for the Department of Agriculture, Water and Environment(University of Melbourne, 2017)Following an outbreak of FMD, surveillance will be required to demonstrate that infection has been eradicated from the population and enable any remaining movement restrictions to be lifted within the country. Proof of freedom will also be needed to satisfy trading partners and regain access to international markets. Although vaccination is increasingly being recognised as an important tool to assist in containing and eradicating FMD outbreaks, it will make achieving recognition of free status more difficult—keeping vaccinated animals in the population will delay the period until FMD-free status is regained under the World Organisation for Animal Health (OIE) guidelines and add additional complications to the postoutbreak surveillance program. There is no agreed approach to post-outbreak management of vaccinated animals in AUSVETPLAN with the options being to: (1) allow vaccinated animals to remain in the population to live out their normal commercial lives (vaccinate-to-live); (2) remove all vaccinated animals from the population (vaccinateand- remove). Under option 2, vaccinated animals could be subject to (a) slaughter to waste i.e. remove and dispose of vaccinated animals; or (b) slaughter and salvage i.e. attempt to sell either raw or processed product from vaccinated animals. For (b) there may be some residual value of products that could offset some of the costs. The project will bring together epidemiological and economic expertise from the Department, the Australian National University, and CEBRA to formally explore and establish a science-based and cost effective approach to regaining free-status after an FMD outbreak as expeditiously as possible. The project will expand the Department’s modelling capability as well as providing insights into postoutbreak FMD management and contribute to Australia’s FMD preparedness.
-
ItemNational-level farm demographic data for preparedness of highly-infectious livestock disease epidemics. Review of data sources in New Zealand, approach to modelling populations and the effect of population uncertainty on disease modelling.(University of Melbourne, 2016)Isolation and strict biosecurity measures implemented by Australia and New Zealand have prevented the incursion of many organisms of biosecurity concern. The agricultural industry is a key part of the economy for both countries, and preventing the arrival of diseases of concern, including foot-and-mouth (FMD) disease, is crucial to maintaining access to international markets, reputation, and protecting the economy and industry. Early detection of, and a rapid, effective response to such diseases have a large impact on limiting the economic damage caused by epidemics. An acknowledged weakness of biosecurity preparedness and response to agricultural diseases in both countries is the lack of a single source of accurate, up-to-date farm livestock demographics information. This report reviews the use of animal counts for investigation of, preparedness for and response to exotic animal disease outbreaks, and analyses the available New Zealand datasets in depth. Gaps and weaknesses in the current data landscape are documented. The project objectives then focus on developing methodologies to estimate national-level farm demographic data and assess the use of modelled and inaccurate data in disease simulation models. There are nine key deliverables outlined in the report which were carried out over the two year duration of the project.
-
ItemCost-benefit analysis of the yellow crazy ant eradication program. Technical Report prepared for the Wet Tropics Management Authority(Centre of Excellence for Biosecurity Risk Analysis, 2019)Yellow crazy ants (Anoplolepis gracilipes) (YCA) are one of the world’s 100 worst invasive species (Lowe et al. 2000). Previous assessments of YCA invasions have demonstrated that YCA can dramatically reduce native species richness in invaded areas, including in the Seychelles (Bos et al. 2008), Christmas Island (O'Dowd et al. 2003), and Hawaii (Plentovich et al. 2011). Native species losses include direct losses of competing invertebrate species and indirect losses resulting from ecological interdependencies, which can result in “ecological meltdown” in extreme cases such as Christmas Island (O'Dowd et al. 2003). YCA can also cause large losses to people living in infested areas through nuisance and health effects (Lach and Hoskin 2015) and can also adversely affect agricultural producers (Young et al. 2001) through reducing yields and/or increasing pesticide costs. YCA was first detected in Cairns and its southern suburbs in 2001, and an eradication program was initiated by the Department of Natural Resources and Mines (DNRM) and Biosecurity Queensland as part of a larger state-wide program. Later discoveries of YCA across the state, including in and around the WTWHA led to the state-wide eradication program being discontinued. An application was then made by WTMA to continue eradication efforts in and around the WTWHA. The program has been funded by the Australian Government and the Queensland Government in two overlapping projects, as described in the Executive Summary.
-
ItemA hybrid modeling approach to simulating foot-and-mouth disease outbreaks in Australian livestock(Frontiers Media, 2015)Foot-and-mouth disease (FMD) is a highly contagious and economically important viral disease of cloven-hoofed animals. Australia's freedom from FMD underpins a valuable trade in live animals and animal products. An outbreak of FMD would result in the loss of export markets and cause severe disruption to domestic markets. The prevention of, and contingency planning for, FMD are of key importance to government, industry, producers and the community. The spread and control of FMD is complex and dynamic due to a highly contagious multi-host pathogen operating in a heterogeneous environment across multiple jurisdictions. Epidemiological modeling is increasingly being recognized as a valuable tool for investigating the spread of disease under different conditions and the effectiveness of control strategies. Models of infectious disease can be broadly classified as: population-based models that are formulated from the top-down and employ population-level relationships to describe individual-level behavior; individual-based models that are formulated from the bottom-up and aggregate individual-level behavior to reveal population-level relationships; and hybrid models which combine the two approaches into a single model. The Australian Animal Disease Spread (AADIS) hybrid model employs a deterministic equation-based model (EBM) to model within-herd spread of FMD, and a stochastic, spatially-explicit agent-based model (ABM) to model between-herd spread and control. The EBM provides concise and computationally efficient predictions of herd prevalence and clinical signs over time. The ABM captures the complex, stochastic and heterogeneous environment in which an FMD epidemic operates. The AADIS event-driven hybrid EBM/ABM architecture is a flexible, efficient and extensible framework for modeling the spread and control of disease in livestock on a national scale. We present an overview of the AADIS hybrid approach, a description of the model's epidemiological capabilities, and a sample case study comparing two strategies for the control of FMD that illustrates some of AADIS's functionality.
-
ItemNo Preview AvailableImproving the computational efficiency of an agent-based spatiotemporal model of livestock disease spread and control(ELSEVIER SCI LTD, 2016-03)Agent-based models (ABMs) are well suited to representing the spatiotemporal spread and control of disease in a population. The explicit modelling of individuals in a large population, however, can be computationally intensive, especially when models are stochastic and/or spatially-explicit. Large-scale ABMs often require a highly parallel platform such as a high-performance computing cluster, which tends to confine their utility to university, defence and scientific research environments. This poses a challenge for those interested in modelling the spread of disease on a large scale with access only to modest hardware platforms.The Australian Animal DISease (AADIS) model is a spatiotemporal ABM of livestock disease spread and control. The AADIS ABM is able to complete complex national-scale simulations of disease spread and control on a personal computer. Computational efficiency is achieved through a hybrid model architecture that embeds equation-based models inside herd agents, an asynchronous software architecture, and a grid-based spatial indexing scheme.
-
ItemEarly Decision Indicators for Foot-and-Mouth Disease Outbreaks in Non-Endemic Countries(Frontiers Media, 2016)This Research Topic presents valuable studies presenting different aspects and implementations of mathematical modeling for disease spread and control in the veterinary field.
-
Item
-
ItemReconstructing foot-and-mouth disease outbreaks: a methods comparison of transmission network models(NATURE PORTFOLIO, 2019-03-18)A number of transmission network models are available that combine genomic and epidemiological data to reconstruct networks of who infected whom during infectious disease outbreaks. For such models to reliably inform decision-making they must be transparently validated, robust, and capable of producing accurate predictions within the short data collection and inference timeframes typical of outbreak responses. A lack of transparent multi-model comparisons reduces confidence in the accuracy of transmission network model outputs, negatively impacting on their more widespread use as decision-support tools. We undertook a formal comparison of the performance of nine published transmission network models based on a set of foot-and-mouth disease outbreaks simulated in a previously free country, with corresponding simulated phylogenies and genomic samples from animals on infected premises. Of the transmission network models tested, Lau's systematic Bayesian integration framework was found to be the most accurate for inferring the transmission network and timing of exposures, correctly identifying the source of 73% of the infected premises (with 91% accuracy for sources with model support >0.80). The Structured COalescent Transmission Tree Inference provided the most accurate inference of molecular clock rates. This validation study points to which models might be reliably used to reconstruct similar future outbreaks and how to interpret the outputs to inform control. Further research could involve extending the best-performing models to explicitly represent within-host diversity so they can handle next-generation sequencing data, incorporating additional animal and farm-level covariates and combining predictions using Ensemble methods and other approaches.
-
ItemDoes Size Matter to Models? Exploring the Effect of Herd Size on Outputs of a Herd-Level Disease Spread Simulator(FRONTIERS MEDIA SA, 2018-05-04)Disease spread modeling is widely used by veterinary authorities to predict the impact of emergency animal disease outbreaks in livestock and to evaluate the cost-effectiveness of different management interventions. Such models require knowledge of basic disease epidemiology as well as information about the population of animals at risk. Essential demographic information includes the production system, animal numbers, and their spatial locations yet many countries with significant livestock industries do not have publically available and accurate animal population information at the farm level that can be used in these models. The impact of inaccuracies in data on model outputs and the decisions based on these outputs is seldom discussed. In this analysis, we used the Australian Animal Disease model to simulate the spread of foot-and-mouth disease seeded into high-risk herds in six different farming regions in New Zealand. We used three different susceptible animal population datasets: (1) a gold standard dataset comprising known herd sizes, (2) a dataset where herd size was simulated from a beta-pert distribution for each herd production type, and (3) a dataset where herd size was simplified to the median herd size for each herd production type. We analyzed the model outputs to compare (i) the extent of disease spread, (ii) the length of the outbreaks, and (iii) the possible impacts on decisions made for simulated outbreaks in different regions. Model outputs using the different datasets showed statistically significant differences, which could have serious implications for decision making by a competent authority. Outbreak duration, number of infected properties, and vaccine doses used during the outbreak were all significantly smaller for the gold standard dataset when compared with the median herd size dataset. Initial outbreak location and disease control strategy also significantly influenced the duration of the outbreak and number of infected premises. The study findings demonstrate the importance of having accurate national-level population datasets to ensure effective decisions are made before and during disease outbreaks, reducing the damage and cost.