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    Probability of freedom from foot-and-mouth disease virus serotype Asia 1 in Southeast Asia, China and Mongolia
    (Elsevier B V, 2025-11-01) Wada M; Han J-H; Purevsuren B; Rinzin K; Sutar A; Abila R; Subharat S
    Foot-and-mouth disease virus (FMDV) serotype Asia 1 has not been reported in Southeast Asia, China and Mongolia between 2018 and 2024, despite the endemicity of FMD in this region and the continued circulation of serotype Asia 1 in South Asia. While vaccines against Asia 1 are still occasionally used in this region, it is unknown whether the absence of reports indicates true disease freedom or surveillance gaps. This study aimed to estimate the sensitivity of existing passive surveillance systems, and the probability of regional freedom from serotype Asia 1 across eight countries using the scenario tree approach. Two stochastic scenario tree models were developed to estimate surveillance sensitivity for FMD (any serotypes) and serotype Asia 1 specifically. Country-specific input parameters were derived from a questionnaire survey of in-country experts on FMD vaccination practices, smallholders’ behaviour, sampling protocols and diagnostic laboratory capacity. Additionally, 2010 – 2022 data on FMD clinical samples submitted and confirmed Asia 1 cases were obtained from the World Reference Laboratory for FMD. Under a design annual incidence rate of 10 % at the village level and 20 % at the animal level, estimated surveillance sensitivity for FMD ranged from 100.0 % in Mongolia and 95.9 % in China to 1.7 % in Cambodia and < 0.1 % in Myanmar. Using the effective design incidence rate with a median of 0.02 – 0.07 % at the village level and 20 % at the animal level, the probability of detecting Asia 1 was estimated to be 0.0 – 6.7 % per country and 14.5 % for the region. The estimated probability of regional freedom from Asia 1 was 53.9 % after the first year without reporting. Over years of no reporting, this probability would increase, only if an annual risk of introduction remained below 6 %. The results were most sensitive to parameters related to sampling intensity and smallholders’ behaviour, particularly in countries with high surveillance sensitivity, such as Mongolia and China. Our findings highlight the low sensitivity of passive surveillance in the region, suggesting that serotype Asia 1 may have remained undetected under the current surveillance efforts. Strengthening data collection and continued efforts in increasing surveillance intensity are essential to improving confidence in the regional freedom from serotype Asia 1.
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    Development and validation of a field deployable test for the diagnosis of high-priority infectious animal diseases in New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science at Massey University, Manawatu, Palmerston North, New Zealand
    (Massey University, 2024-03-15) Bueno, Rudolfo
    In the event of infectious disease incursions, rapid and accurate diagnosis is essential for ensuring appropriate and prompt control measures are put in place to minimise further transmission. Foot and mouth disease (FMD) is one example of an exotic disease that could severely affect New Zealand’s livestock industries if introduced to this country. Pen-side testing can help by providing a rapid confirmation of a provisional diagnosis without the delays and risks associated with sending samples to a diagnostic laboratory. The aim of the work presented in this thesis was to develop and validate a field deployable diagnostic test system for prompt and accurate detection of FMD virus (FMDV). In addition, the test can be used to simultaneously detect two other viruses that would be expected to be on the differential diagnosis list: bovine viral diarrhoea type 1 (BVDV-1) and type 2 (BVDV-2). Chapter 1 comprises a brief literature review of FMDV infections in susceptible species, followed by a review of the current and emerging trends in field deployable diagnostics as applicable to animal diseases. In Chapter 2, a multi-criteria scoring and ranking model for identifying the best test platform for development of the deployable field test is presented. The general flow of the method consisted of defining the requirements for the ideal test platform, identifying, and shortlisting potential candidate systems, describing the criteria for evaluation, and scoring the candidate platforms against the criteria by a panel of recruited experts. This participatory and collective opinion provided a basis for selecting T-COR 8™ (Tetracore®) as the best overall fit-for-purpose. In Chapter 3, several easy techniques for processing clinical samples compatible with the selected test platform were examined. These protocols were applied to test panels comprising serial dilutions of BVDV-1 or equine rhinitis A virus (ERAV) in serum or oral swab samples. The latter was used as a proxy for FMDV. The protocols were compared to a reference extraction method based on the observed detection limit, as judged by quantification cycle (Cq) values generated in virus-specific reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays. The complexity of sample manipulation and time required were also considered. Dilution of the sample with phosphate-buffered saline (PBS), with or without a pre-heating step, was chosen as the most suitable method for integration in the pen-side PCR testing. Development of the field assay’s controls is described in Chapter 4. These included a synthetic positive control transcript (R3+) that could be safely used with assays aimed at the detection of several pathogens associated with development of vesicular disease in cattle. The universal control transcript also incorporated an exogenous internal control (IC) target, which was designed to be used with a phage based (Qβ) internal control (IC) system. Optimization of a Qβ IC assay for use in the pen-side multiplex RT-qPCR (mRT-qPCR) is also included in this Chapter. In Chapter 5, development, and optimisation of mRT-qPCR for the differential detection of FMDV, BVDV-1 and BVDV-2, including detection of a Qβ as exogenous IC, is presented. The optimised mRT-qPCR showed linearity over five 10-fold dilutions of R3+ transcript, good efficiency, and low intra-and inter-assay variability. The mRT-qPCR was highly specific for the detection of representative FMDV serotypes and was also able to simultaneously detect BVDV-1 and BVDV-2 isolates. The assay did not react with other viruses that can produce vesicular lesions, nor did it react with unrelated bovine pathogens endemic in New Zealand. Multiplexing the four primer- and probe sets did not affect the performance and analytical sensitivity of the assay for the detection of individual components when compared to the respective singleplex assays. The diagnostic performance of the optimised mRT-qPCR for detecting FMDV, BVDV-1 and BVDV-2 is presented in Chapters 6 and 7. Diagnostic specificity was evaluated using sera and oral swabs from New Zealand cattle. Diagnostic sensitivity for FMDV detection was assessed using mock oral swabs from outbreak samples in two endemic countries (Lao PDR and Myanmar). The robustness of the field PCR was evaluated at three field locations with varied environmental conditions (New Zealand, Lao PDR, and Myanmar). Overall, the diagnostic specificity (DSp) of the field mRT-qPCR for three target viruses (FMDV, BVDV-1 and BVDV-2) was close to 100%, which was similar to the performance of respective reference PCRs. Although the diagnostic sensitivity (DSe) of the FMDV component was comparable to that obtained with the reference method, care must be taken in interpreting the result since FMD positive samples used for evaluation of the sensitivity of the mRT-qPCR were not sourced from New Zealand cattle. The mRT-qPCR also had high DSe for detecting BVDV-1 infected cattle when the BVDV RNA levels expected to be present in clinical samples from either persistently infected (PI) or transiently infected animals were considered. Pre-heating of samples increased the sensitivity of the BVDV-1 component of the assay. Further validation using additional FMDV-positive and negative clinical specimens should be attempted in the future. Overall, the work presented in this thesis resulted in the development of a simple, extraction-free pen-side PCR test that can be deployed around New Zealand for rapid and reliable detection of FMDV in the event of a suspected incursion. Future work to enhance its use would involve exploration of other methods of preparing samples so that the test can be utilised in screening sub-clinical FMDV infections during post-outbreak surveillance.
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    Enhancing an evidence-based decision making system for foot-and-mouth disease : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy at Massey University, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
    (Massey University, 2016) Wada, Masako
    Foot-and-mouth disease (FMD) is a highly contagious disease with significant economic consequences, for which urgent and rational decisions are essential. It is a great concern for countries worldwide where livestock industries are important, regardless of the current FMD status. This thesis addressed the problems in the existing decision support systems used by the current FMD-free countries, with a particular focus on New Zealand. Because the exact source of infection is uncertain in the spatially and temporally concentrated focus of an FMD epidemic, it is challenging to predict the behaviour of FMD and determine the best control alternatives within a given susceptible population. The studies proposed a new approach for descriptive spatio-temporal analyses of local spread patterns, which was applied to the data from the FMD outbreaks in Cumbria (UK, 2001), Miyazaki (Japan, 2010), and Andong (Republic of Korea, 2010). The analyses identified herd-specific risk factors of local spread: size of a susceptible premises, infectious premises with pigs and susceptible premises with cattle were positively associated with hazard of local spread in all the three epidemics. In addition, the adjusted hazard of local spread varied markedly by outbreak. The UK FMD epidemic in 2001 had the highest hazard of local spread. The findings highlight the needs of care in interpolating the local spread probabilities from one epidemic for use of disease modelling for a different susceptible population. Detailed investigation of the FMD epidemic in Japan in 2010 illustrated a dynamic change in the patterns of local spread during the epidemic prior to emergency vaccination, suggesting contribution of human activities in addition to purely environmental factors to local spread. A stochastic spatial simulation model, using the local spread parameters derived from the analyses showed a high predictive accuracy, in terms of demographical, temporal and spatial patterns of infection. The model indicated that emergency vaccination played an important role in mitigating potentially unwanted outcomes of an epidemic, such as disease spread outside the prefecture. In addition, the model predicted that both epidemiological and economic consequences of the epidemic could have been reduced by earlier application of vaccination with a smaller vaccination ring for the epidemic in Japan in 2010. To enhance contingency planning for FMD, a disease simulation modelling system was developed, by adding an economic module to the existing FMD simulation model for New Zealand. The modelling system allowed estimation of the direct and macroeconomic costs of a simulated FMD epidemic. Analyses of data generated by the disease simulation modelling system indicated that vaccinate-to-die was economically preferred to stamping-out alone or vaccinate-to-live, for a simulated FMD epidemic in the Auckland Region with local spread potential similar to that of the Cumbria outbreak in 2001, which had a high potential of developing into a large epidemic, indicated by a high density of premises, a high cumulative number of IPs, or a high estimated dissemination rate, and local spread patterns similar to Cumbria outbreak (2001). Vaccinate-to-live was economically suboptimal under the current OIE standard regarding recovery of FMD-free status. The results were robust to the uncertainty in the resource capacity, vaccination effectiveness, and the early scale of an epidemic, but sensitive to the choice of vaccination radius. VTL was always economically suboptimal under the current OIE code, but would be advantageous if the OIE’s waiting period was shortened by 3 months. Using more refined parameters, future work is required to investigate other potentially more advantageous options, such as vaccination applied to specific species or in alternative prioritisation. The studies presented in this thesis demonstrated that simulation models that incorporated the current best epidemiological and economic knowledge might enhance contingency planning and decision making for the management of FMD. Simulation models could also be used as the quantitative basis of communication with decision makers and stakeholders, which would then encourage informed discussion around disease control measures.
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    Multi-criteria decision analysis (MCDA) for control of transboundary livestock diseases using the example of the 2010/11 foot-and-mouth disease (FMD) outbreak in the Republic of Korea : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science at Massey University, Manawatū
    (Massey University, 2015) Kim, EuTteum
    Decisions regarding transboundary livestock disease control strategies differ from personal decisions, such as buying groceries, in important ways: the stakes are high and the outcome of a decision will affect people in different fields. Decision making for transboundary livestock disease control strategies requires consideration of a number of factors including the epidemiology of the disease, economic cost of control, and environmental and social impact. For example, when applying pre-emptive slaughtering as a control measure for FMD, decision makers need to consider the epidemiologic effectiveness of the control measure, financial loss to farmers, the operational cost of slaughtering, negative impacts on the environment due to burning or burial of culled animals, and the public’s concerns for the welfare of slaughtered animals. Therefore, it can be challenging for decision makers to choose the best control strategy among alternative strategies. The study presented in the thesis describes the application of multi-criteria decision analysis (MCDA) process as a decision support tool for decision making about transboundary livestock disease control strategies using an example of a simulated FMD outbreak. The first research chapter (Chapter 3) investigates the preferences of chief veterinary officers (CVOs) for the criteria of FMD-control strategies in the Asia-Oceania region, which comprises countries free from or having experienced FMD. Criteria were grouped into epidemiologic, economic, and social-environmental. The CVOs in the Asia-Oceania region considered the epidemiologic criterion more important than the economic or the social-environmental criterion. The importance of the economic criterion differed with FMD status of a country: specifically, those countries considered free of FMD ranked the economic criterion as more important than those without. Among the criteria comprising the epidemiologic criterion, the most important was the size of the FMD-infected area, defined as the geographical size of FMD outbreak area. Within the economic criterion, the operational cost of the FMD-control strategy was considered the most important, and within the social-environmental criterion, the mental health of FMD-affected farmers was the most important criterion. Chapter 4 describes the construction of an epidemiologic model of the spread of the 2010/11 FMD outbreak in the city of Andong, Republic of Korea, to measure the epidemiologic effectiveness of FMD-control strategies. According to the simulation results, the model accurately represented the FMD outbreak in two ways: 1) the median number of simulated FMD-detected farms was the same as the number of detected farms during the actual FMD epidemic, and 2) the simulated epidemic curve was similar to the actual epidemic curve for the 2010/11 FMD epidemic. Thus, the constructed model could be used as a reference for evaluating the effectiveness of alternative FMD-control strategies. The control strategy applied during the 2010/11 FMD epidemic consisted of a pre-emptive slaughter area with a radius of three kilometres, 100 day movement restriction, and vaccination of all FMD-susceptible animals in the country. This was used as a baseline strategy in the study. Alternative levels of these control measures for the FMD-control strategy were simulated to evaluate the effect of alternative strategies. Changes in control measures were: 1) pre-emptive slaughtering within a radius of 0.5, one, and five kilometres of FMD-infected farms; 2) movement restriction of 30 days and 60 days; 3) ring vaccination in a band three to five kilometres from FMD-infected farms. According to the simulation results, the five kilometres slaughtering strategy resulted in the fewest FMD-infected farms. Cost-effectiveness (CE) analysis was applied to evaluate the economic effectiveness of FMD-control strategies using the results of epidemiologic simulation model (Chapter 5). This showed that ring vaccination in a band three to five kilometres from FMD-infected farms was the most cost efficient among alternative FMD-control strategies. The other FMD-control strategies, in decreasing order of economic efficiency, were five kilometre slaughtering, 30 day stop movement, and 60 day stop movement. The 0.5 kilometre and one kilometre slaughtering strategy were excluded in the analysis because these strategies did not control FMD spread during the simulations. Chapter 6 describes the MCDA process for choosing the optimal FMD-control strategy based on the results from Chapters 3, 4 and 5. The measurements of the criteria were merged with the weight of criteria to calculate the overall score of each FMD-control strategy. In the Asia-Oceania region, CVOs preferred ring vaccination over alternative FMD-control strategies, with 30 day stop movement being the least preferred of the FMD-control strategies. The findings presented in each of these chapters have broadened our knowledge of the decision making process regarding FMD-control strategies. The processes were reliable, transparent, and reproducible and can be applied not only to FMD but also to other transboundary livestock diseases such as classical swine fever or highly pathogenic avian influenza.
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    Application of a global sensitivity analysis technique to the New Zealand standard model of foot-and-mouth disease : a dissertation presented in partial fulfilment of the requirements for the degree of Master of Veterinary Studies at Massey University
    (Massey University, 2012) Owen, L. Katharine A.
    “All models are wrong, but some are useful” George Edward Pelham Box (Box, 1987) Unfortunately, often people don’t realise that models are wrong, or alternatively do not appreciate that they are not supposed to be ‘right’. A model, whether a map, a regression model or a stochastic model that creates data, is merely a representation of reality. It is a tool and is bound by assumptions, the quality of the data used to create it as well as the code itself. This dissertation attempts to provide a simple guide to help non-modellers to understand what a model is and the uncertainties that exist in the modelling process, the methods available for sensitivity analysis and describes the role of this analysis in corroborating a model. In New Zealand we are fortunate not to have had an outbreak of foot-and-mouth disease (FMD), but recognise the devastating consequences of an outbreak and the need to develop appropriate controls for eradication of the virus. Given the complexity of the interactions over time and space between the virus, the unique environment of New Zealand, its livestock industries and the controls available, it is unlikely that these issues could be explored adequately and with sufficient rigour without the use of modelling. This thesis is divided into three main sections. In the first section a review of the literature related to simulation modelling and sensitivity analysis is provided. In New Zealand we are fortunate to have a well corroborated platform for disease modelling – InterSpread Plus. This has allowed development of a model scenario for exploring FMD spread within a set of InterSpread Plus parameters termed the New Zealand Standard model (NZSM). The NZSM is a complex epidemiological model and has been, at the time of writing, under-utilised. An element of the under-utility is due to the complexity and computational demands that are inherent to an epidemiological model. The second section of this thesis provides a description of the New Zealand standard model in an attempt to explain its logical framework. In the third section a sensitivity analysis of the NZSM is carried out in an effort to identify those settings in the model that had the greatest influence on the predicted number of infected premises in a simulated outbreak of FMD in New Zealand. The outcomes of the sensitivity analysis have increased the understanding of the NZSM model itself and have provided initial insight into ways the model may be improved and refined. If heeded, this can result in an increased ability to interpret and communicate model outputs. This, in turn, will increase confidence that the NZSM parameter set provides an appropriate indication of the way FMD might spread if it were introduced into the farm animal population in New Zealand, and therefore better preparation for any future FMD outbreak.
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    The development of a decision support system for an animal disease emergency : a thesis presented in partial fulfilment of the requirement for the degree of Doctor of Philosophy at Massey University
    (Massey University, 1993) Sanson, Robert Lawrence
    An epidemiological information management system (EpiMAN) has been developed to aid the Ministry of Agriculture & Fisheries (MAF) contain and eradicate a foot-and-mouth disease (FMD) epidemic, should one ever occur. Design objectives for the information management elements of the system included the need to manage the vast quantities of data that eradication procedures for an epidemic would be expected to generate within a very short time; the ability to apply current epidemiological understanding of disease spread to the data processing tasks; to reduce some of the foreseen processing bottlenecks; and to provide decision support to the data entry personnel. Design objectives for the veterinary management elements of the system included the presentation of up-todate status reports in formats that facilitate national decision-making; the ability to optimize manpower resource allocation; and the capacity to evaluate the relative merits of alternative technical decisions, each of which carried different implicit risks. The system combines a database management system (DBMS), a geographic information system (GIS), expert system elements, various models of specific aspects of FMD epidemiology, and a statistical analysis capability. EpiMAN comprises tightly coupled spatial and textual databases. Farm locations and other geographical information are managed by the GIS, while the textual component incorporating farm profile information and epidemic data is manipulated by the DBMS. The models of spread of FMD and the expert systems jointly provide the epidemiological knowledge components. The models are linked to the databases to help quantify the risks of FMD spread and allow the evaluation of management options, based on the current situation. The expert systems advise various operational sections of the emergency headquarters (EHQ) on priorities for control activities. The analytical system (termed the epidemiologist's workbench) is an integrated suite of tools which allows the state of the epidemic to be examined and control options to be evaluated. The system has been designed as a transportable system to operate wherever the EHQ is set up. It is implemented as a multi-user system, with the database server and the GIS each residing on a UNIX workstation, with IBM-compatible PCs used as terminals. Communications links to MAF's computer network are provided for. It is hoped the system will never need to be used for a FMD emergency in New Zealand. However the system can be easily adapted for use in other countries, and the methodology is also being extended to other disease syndromes. A number of studies were conducted to assess the risk of FMD entry into New Zealand, and examine the potential for disease spread through normal farm movement patterns. The best current estimate of the risk of an FMD outbreak is about once in 50 years (0.0199). The mean expected number of FMD infected secondary properties under MAF's exotic diseases and pests responses programme is 61 (median 33, range 1 to 1103). In order to contain 95% of the movements that might occur off an index farm prior to diagnosis, an infected area would have to have a radius of 100 km around the property. A cost benefit analysis supported the development of EpiMAN.
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    Decision-making for foot-and-mouth disease control: Objectives matter.
    (2016-06) Probert WJM; Shea K; Fonnesbeck CJ; Runge MC; Carpenter TE; Dürr S; Garner MG; Harvey N; Stevenson MA; Webb CT; Werkman M; Tildesley MJ; Ferrari MJ
    Formal decision-analytic methods can be used to frame disease control problems, the first step of which is to define a clear and specific objective. We demonstrate the imperative of framing clearly-defined management objectives in finding optimal control actions for control of disease outbreaks. We illustrate an analysis that can be applied rapidly at the start of an outbreak when there are multiple stakeholders involved with potentially multiple objectives, and when there are also multiple disease models upon which to compare control actions. The output of our analysis frames subsequent discourse between policy-makers, modellers and other stakeholders, by highlighting areas of discord among different management objectives and also among different models used in the analysis. We illustrate this approach in the context of a hypothetical foot-and-mouth disease (FMD) outbreak in Cumbria, UK using outputs from five rigorously-studied simulation models of FMD spread. We present both relative rankings and relative performance of controls within each model and across a range of objectives. Results illustrate how control actions change across both the base metric used to measure management success and across the statistic used to rank control actions according to said metric. This work represents a first step towards reconciling the extensive modelling work on disease control problems with frameworks for structured decision making.