School of BioSciences - Research Publications
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ItemModelling post-border spread and control of African swine fever on a national scale (Biosecurity Innovation Program Project 182021). Technical report prepared for the Department of Agriculture, Fisheries & Forestry(University of Melbourne, 2022)African swine fever (ASF) represents a significant threat to the Australian pork sector and the economy in general. Estimates of the economic damages from a large multistate outbreak of ASF in Australia exceed $A2 billion. ASF outbreaks are widespread and increasing in number in Asia and Europe. Although ASF is not present in Australia, detections of ASF viral fragments in undeclared pork products intercepted at the Australian border and the recent spread of the disease to neighbouring Papua New Guinea demonstrate the significance of the threat. The AADIS-ASF model (Bradhurst et al., 2021c), simulates the spread and control of ASF in domestic and feral pigs. It was developed through Biosecurity Innovation Project 192027 and CEBRA project 20121501, with Queensland as the test case. This project expanded the AADIS-ASF model up to national scale. The upgraded model will help evaluate different outbreak scenarios in time and space, and trial various control measures. This will assist in the development of animal health policy and preparedness and planning for ASF outbreaks.
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ItemNo Preview AvailableAnalysis of livestock movements and the benefits and costs of livestock standstills in Australia as part of the response to foot and-mouth disease(CSIRO, 2022)This project involved analysis of livestock movements and used epidemiological modelling and cost analysis to estimate the benefits and costs of implementing livestock standstills in response to a foot-and-mouth disease (FMD) outbreak in Australia. This was done in four steps: 1) assessing the extent of livestock movement, 2) conducting a cross sectional analysis of the impact (reduction of outbreak size and economic cost) of implementing a national standstill/movement control, 3) use of case specific studies to estimate impact of state/territory level implementation of standstill, and 4) cost analysis and comparison of national standstill with the state/jurisdictional level and risk-based approach strategies. Estimation of the extent of livestock movement within and between jurisdictions was done using the 2019 (calendar year) Australian National Livestock Identification System (NLIS) data, i.e., prior to the COVID 19 pandemic, for cattle, sheep and goats and pigs. Estimation of the epidemiological and economic impact of implementing standstill to control FMD at the national and state levels was done using the Australian Animal Disease Spread (AADIS). To test the hypothesis that a national livestock standstill is effective in reducing spread of infection, a wide range of potential FMD incursions (n=10,000) was used and the actual numbers of infected herds in the population were compared after 7 days of control, with and without a 3-day national livestock standstill. Additionally, five detailed outbreak incursion scenarios, developed in consultation with jurisdictions or based on previous national modelling scenarios, were also simulated. These were biased to larger multi-jurisdictional outbreaks aimed at showing any potential benefits of livestock standstills in reducing the size and duration of the ensuing outbreaks. National 3- and 10-day livestock standstills were compared with other standstills involving the infected jurisdiction(s) only, or regional standstills (infected and adjacent jurisdictions). Cost analysis involved identifying components associated with implementing and managing livestock standstills. This included analysis of three approaches to managing livestock in transit: (a) livestock in transit continuing the movement to their initially intended destination (Proceed to Destination); (b) a risk assessed option (Mixed option) which considered type of property of origin and destination, whether involving single/multiple consignments on transport vehicles and distances travelled; and (c) a third option of redirecting all livestock in transit to abattoir (Redirect to Slaughter). The key finding of this study include: • The average number of animals (all referenced species) moved per day was 237,000 (range 1,000 – 533,000) of which 76.9% were intrastate and 23.1% were interstate movements (Table 1) with majority destined for processing. • Although interstate movement of livestock was relatively low compared to intrastate movements, it was still an important component of livestock production systems in Australia. • In simulated FMD outbreaks it was not uncommon for interstate spread of infection to occur, given three to four weeks until disease is detected, particularly for outbreaks starting in south-eastern Australia. • No consistent benefit of 3- or 10-day national standstills over state/territory wide based standstill/movement controls, in terms of reducing the size of a potential FMD outbreak in Australia was demonstrated. • Implementation of 3-day national livestock standstill was estimated to cost up to $75.6 million when animals not initially intended for processing abattoir were primarily directed to abattoirs (i.e., Redirect to Slaughter). • The cost of implementation of a risk assessed option (Mixed option), was approximately to be $50 million on the upper range value. • The option for livestock in transit to Proceed to Destination provided the minimum cost of implementing a standstill, ranging between $0.4 million and $3.6 million. Factors contributing to national livestock standstill disease control benefits not being demonstrated include that a significant proportion of inter-jurisdictional movements involve movements to a terminal destination. In simulated outbreaks, spread of infection by livestock movements accounted for a relatively small proportion of all infections. Most new infections result from ‘local’ spread i.e. short-range transmission of disease from an infected herd to neighbouring susceptible herds. Local spread is recognised as an important pathway for FMD, particular in high-density farming areas. Once disease has been detected and state/territory wide control measures implemented in infected jurisdictions, livestock movements are further reduced. Another important factor is the behaviour of livestock producers/industry in non-infected jurisdictions in response to the changed market conditions subsequent to a detection of FMD. The suspension of access to export markets for susceptible livestock and livestock products and concerns about biosecurity means it is not ‘business as usual’. This was modelled by a 50% reduction in the number of ‘normal’ movements expected to occur. There may be ancillary benefits to a national livestock standstill in terms of information for trading partners and international organizations regarding the comprehensiveness of Analysis of livestock movements and the benefits and costs of livestock standstills in Australia as part of the response to foot-and-mouth disease. Australia’s approach to managing the outbreak, perhaps translating into increased confidence and willingness to negotiate the re-establishment of market access more rapidly. Assumptions were necessarily included in this study, which included: • The NLIS data was an accurate representation of livestock movements. It is important to note that AADIS cannot model/account for movement of livestock between properties under the same property identification code, given these do not need to be recorded within NLIS. Whilst these movements may be local/regional, the actual level of movement will be greater than that analysed as part of this project. • Vaccination was not used and ‘stamping out’ occurred for each of the modelled outbreaks. • Reporting of suspect cases, surveillance and tracing were highly effective. • No disease spread resulted from in-transit animals returning to their origin (multi-consignment/property transport was not modelled to return to property of origin). • The 3-day national livestock standstill did not cause significant loss of livestock or product quality or involve additional capital investment for implementing the standstill. • Reduced value of livestock and product was not attributed to the standstill but instead considered to result from the immediate suspension of export market access following the detection of FMD. • The modelling assumed that disease reporting, tracing and surveillance were all conducted in a highly effective manner, based on previous experience and estimated performance of tracing systems. National livestock standstills may provide more benefit in situations where response measures are not as effective as assumed. In conclusion, this study did not demonstrate that a national standstill on livestock movements, for 3 days or 10 days, was effective in reducing the size or duration of an FMD outbreak in Australia compared to state-based restrictions. The estimated high cost of a national standstill if implemented in accordance with the current National Agreed Standard Operating Procedure for livestock in transit at the time of declaration of a national livestock standstill is a further consideration. Although this study did not show a clear benefit, it is possible that a national livestock standstill may be effective under very specific circumstances i.e., in multi-state outbreaks where there have been large numbers of animal movements. Risk-based implementation of state/territory wide livestock standstills by jurisdictions upon detection or strong suspicion of FMD may be a viable alternative policy rather than a mandatory national livestock standstill implemented automatically on strong suspicion or detection of FMD in any state/territory. This risk management should take into account location of the outbreak, industry sectors involved, time of year and any information on extent and destination of livestock movements. Further, where standstills are applied, management of livestock in transit, could be on a risk assessed basis taking into account type of property of origin and destination, single/multiple transport and distances travelled.
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ItemModel-based estimation of the impact on rotavirus disease of RV3-BB vaccine administered in a neonatal or infant schedule(TAYLOR & FRANCIS INC, 2022-11-30)Rotavirus infection is a common cause of severe diarrheal disease and a major cause of deaths and hospitalizations among young children. Incidence of rotavirus has declined globally with increasing vaccine coverage. However, it remains a significant cause of morbidity and mortality in low-income countries where vaccine access is limited and efficacy is lower. The oral human neonatal vaccine RV3-BB can be safely administered earlier than other vaccines, and recent trials in Indonesia have demonstrated high efficacy. In this study, we use a stochastic individual-based model of rotavirus transmission and disease to estimate the anticipated population-level impact of RV3-BB following delivery according to either an infant (2, 4, 6 months) and neonatal (0, 2, 4 months) schedule. Using our model, which incorporated an age- and household-structured population and estimates of vaccine efficacy derived from trial data, we found both delivery schedules to be effective at reducing infection and disease. We estimated 95-96% reductions in infection and disease in children under 12 months of age when vaccine coverage is 85%. We also estimate high levels of indirect protection from vaccination, including 78% reductions in infection in adults over 17 years of age. Even for lower vaccine coverage of 55%, we estimate reductions of 84% in infection and disease in children under 12 months of age. While open questions remain about the drivers of observed lower efficacy in low-income settings, our model suggests RV3-BB could be effective at reducing infection and preventing disease in young infants at the population level.
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ItemFMD vaccine allocation and surveillance resourcing options for a potential Australian incursion(WILEY, 2022-11)Australian Animal Disease Spread (AADIS) epidemiological simulation modelling of potential foot-and-mouth disease outbreaks in the state of Victoria, Australia examined the targeted use of limited vaccine supplies in combination with varying surveillance resources. Updated, detailed estimates of government response costs were prepared based on state level data inputs of required and available resources. Measures of outbreak spread such as duration and numbers of animals removed through depopulation of infected and vaccinated herds from the epidemiological modelling were compared to summed government response costs. This comparison illustrated the trade-offs between targeted control strategies combining vaccination-to-remove and varying surveillance capacities and their corresponding costs. For this intensive cattle and sheep producing region: (1) Targeting vaccination toward intensive production areas or toward specialized cattle operations had outbreak control and response cost advantages similar to vaccination of all species. The median duration was reduced by 27% and response costs by 11%. (2) Adding to the pool of outbreak surveillance resources available further decreased outbreak duration and outbreak response costs. The median duration was reduced by an additional 13% and response costs declined by an additional 8%. (3) Pooling of vaccine resources overcame the very early binding constraints under proportional allocation of vaccines to individual states with similar reductions in outbreak duration to those with additional surveillance resources. However, government costs rose substantially by over 40% and introduced additional risk of a negative consumer response. Increased knowledge of the outbreak situation obtained from more surveillance led to better-informed vaccination deployment decisions in the short timeframe they needed to be made.
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ItemThe economic benefits of targeted response strategies against foot-and-mouth disease in Australia.(Elsevier BV, 2022-07)Recent developments in control of highly infectious diseases attempt to improve emergency response efforts by more clearly focusing or targeting response tools according to risk. For example, advances in surveillance testing and sampling deliver their results by more accurately and precisely targeting the population of interest. In this work, targeted implementation of trading zones and vaccination were examined for simulated outbreaks of foot-and-mouth disease (FMD) in Australia. Trading zones allowing unaffected Australian states to resume exports following an outbreak of FMD were assessed using multiple tools. A Victorian incursion scenario with traditional stamping out and vaccination as control options, was simulated using the AADIS model Version 2.47, to characterise the geographic extent of potential outbreaks, the number of animals infected, and the date of last cull indicating duration of the outbreak. Information on disease spread from the AADIS simulations was then used to identify the boundaries of trading zones for the incursion scenario, in which vaccination with trading zones was found to further reduce disease impacts relative to stamping out alone with trading zones. The number of animals culled due to disease provided supply shocks for stamping out alone and vaccinate-to-retain, while the number of vaccinated animals was added to the number of animals culled due to disease for the supply shock of vaccinate-to-remove. The day of last cull was combined with historical FMD trade recovery and Australian export data to estimate the share of Australian exports that would be embargoed under trading zones. The market impacts - changes in equilibrium quantities and prices - of the supply shock, trading zones, and consumer reactions - were simulated within ABARES' AgEmissions partial equilibrium model of Australian agriculture. For this simulated large outbreak, where vaccinate-to-remove was utilised along with trading zones, producer losses were reduced by AUD 4 billion in present value terms over 10 years estimated at a 7% discount rate (PV10,7%) compared to an outbreak where stamping out alone is applied with trading zones. Introducing FMD virus risk mitigation measures for wool to further target trading zones reduced the economic impacts by an additional AUD 3.6 billion (PV10,7%). Outbreak response cost savings and additional potential costs under vaccinate-to-retain with trading zones were also compared to the vaccinate-to-remove control with trading zones. Results emphasised the importance of outbreak characteristics in determining trading zones and targeting of vaccination. Economic analyses identified how additional investments in targeting outbreak response is of value to producers.
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ItemEconomic benefits of implementing trading zones for Australian livestock disease outbreaks of limited duration(Wiley, 2022-01-20)OBJECTIVE: The objective is to estimate the economic benefits of trading zones as part of foot-and-mouth disease (FMD) control measures for limited duration outbreaks. DESIGN: The proposed trading zones for FMD at the state level are determined using multiple tools. Eleven individual incursion scenarios in six Australian states are simulated within the Australian Animal Disease Spread epidemiological model to identify the potential geographic extent of outbreaks, as well as the number of animals infected and the duration of outbreaks. The disease spread information is used to identify the boundaries of trading zones. The outbreak duration data are combined with historical export data to estimate the share of Australian exports that could be embargoed. The market impacts of the potential export embargoes including changes in equilibrium quantities, prices and revenue are simulated within the Australian Bureau of Agricultural and Resource Economics and Sciences' AgEmissions partial equilibrium model of Australian agriculture. RESULTS: Results emphasize the importance of jurisdictional and outbreak characteristics in determining trading zones. Should Australia effectively implement trading zones at the state level in response to small FMD outbreaks, the potential reductions of embargoed exports lead to a reduction in estimated producer revenue losses compared with losses under a national embargo. Producer revenue losses are reduced between $3 billion and $9 billion estimated in present value terms over 10 years at a 7% discount rate. CONCLUSION: Economic analysis of the implications of trading zones identifies additional investments that would be of value to livestock industries.
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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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ItemDevelopment of a transboundary model of livestock disease in Europe(WILEY-HINDAWI, 2022-07)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 a 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.