Submitted by Marcos Anselmo (marcos.anselmo@unipampa.edu.br) on 2017-06-09T17:31:45Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) ALESSANDRA ARANDA GAVIAO.pdf: 1650079 bytes, checksum: 0968c238fcfd9ba854ff63559a71860c (MD5) / Approved for entry into archive by Marcos Anselmo (marcos.anselmo@unipampa.edu.br) on 2017-06-09T17:31:59Z (GMT) No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) ALESSANDRA ARANDA GAVIAO.pdf: 1650079 bytes, checksum: 0968c238fcfd9ba854ff63559a71860c (MD5) / Made available in DSpace on 2017-06-09T17:31:59Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) ALESSANDRA ARANDA GAVIAO.pdf: 1650079 bytes, checksum: 0968c238fcfd9ba854ff63559a71860c (MD5) Previous issue date: 2017-03-01 / A febre aftosa (FMD) é economicamente a doença mais importante de biungulados e a ocorrência de um surto produz repercussões nacionais e internacionais. O vírus da febre aftosa (FMDV), agente causal, é extremamente infeccioso e contagioso. A infecção afeta principalmente bovinos, bubalinos, suínos, ovinos, caprinos entre outras espécies domésticas e silvestres. O controle da enfermidade é realizado pelo rápido diagnóstico, vacinação preventiva e restrição da movimentação de animal. Assim sendo, as medidas de controle são direcionadas em medidas de prevenção, que incluem vigilância ativa e passiva. O último surto de FMDV no Rio Grande do Sul ocorreu em 2001 e atualmente o estado é reconhecido como zona livre com vacinação. Para que o Estado mantenha este status, faz-se necessário um sistema de vigilância eficaz capaz de integrar o Serviço Veterinário Oficial (SVO) e a cadeia produtiva (diferentes agentes envolvidos). O objetivo deste estudo foi avaliar a percepção de risco dos produtores, médicos veterinários e transportadores de bovinos da cadeia produtiva na Fronteira Oeste do Rio Grande do Sul. Todos os atores entrevistados reconhecem a importância da febre aftosa. No entanto, uma parcela dos produtores (15%), transportadores (17%) e veterinários (17%) acredita que a doença ocorra no Estado. Também uma quantia considerável de produtores e transportadores acredita que o risco de o vírus ser introduzido na região seja baixo, desprezível e alguns ainda não souberam responder. Observou-se que os entrevistados reconhecem os principais sinais clínicos, porém possuem pouco conhecimento quanto a ovinos, suínos, cervos e porcos selvagens serem suscetíveis a febre aftosa. Grande parte dos entrevistados acredita ser importante comunicar um caso suspeito, porém uma parcela tentaria resolver de outra maneira, caso suspeitasse da doença. Quase a totalidade dos produtores afirmou vacinar seus rebanhos, no entanto alguns possuem conhecimento de produtores que não realizam a vacinação. Além disso, alguns entrevistados não sabem a idade inicial para realizar a vacinação. Dessa forma, é de extrema importância o Serviço Veterinário Oficial atuar com mais intensidade em atividades de educação sanitária, no que diz respeito a idade correta para vacinação, as espécies afetadas e a notificação, tornando os atores mais sensíveis a qualquer suspeita da doença. / Foot-and-mouth disease (FMD) is the most important animal disease and the occurrence of an outbreak has national and international repercussions. Foot-and-mouth disease virus (FMDV), the causative agent, is extremely infectious and contagious. The infection mainly affects cattle, buffaloes, swine, sheep, goats among other domestic and wild species. Disease control is performed by a fast diagnosis, preventive vaccination and restriction of animal movement. Therefore, control measures are directed at prevention measures, which include active and passive surveillance. The last FMDV outbreak in Rio Grande do Sul occurred in 2001 and the State is recognized as a free zone with vaccination. In order for the State to maintain this status, an effective surveillance system capable of integrating the Official Veterinary Service and the production chain (producers and handlers) is necessary. The objective of this study was to evaluate the risk perception of producers, veterinarians and cattle transporters in the production chain in the West Frontier of Rio Grande do Sul, Brazil. All interviewed actors recognize the importance of foot-and-mouth disease. However, a proportion of the producers (15%), transporters (17%) and veterinarians (17%) believe that the disease occurs in the State. Also, a considerable number of producers and transporters believe that the risk of the virus being introduced in the region is low, negligible and some have not yet been able to respond. It was observed that the interviewees recognize the main clinical signs, but they have little knowledge about sheep, pigs, deer and wild pigs being susceptible to foot-and-mouth disease. Most interviewees believe it is important to report a suspected case, but a portion would try to solve it differently if they suspected the disease. Almost all producers claimed to vaccinate their herds, however some are aware of producers who do not carry out the vaccination. In addition, some interviewees do not know the starting age to carry out the vaccination. Therefore, it is extremely important for the Official Veterinary Service to work with more intensity in health education activities, regarding the correct age for vaccination, affected species and notification, making the actors more sensitive to any suspicion of the disease.

Background / Hand, foot, and mouth disease (HFMD), in particular those associated with enterovirus 71 (EV71), has caused large outbreaks in the Western Pacific and Southeast Asian countries in the past three decades. There is currently no effective chemoprophylaxis or vaccination for HFMD or EV71 infection. Public health strategies rest on good understanding of the epidemiological features of HFMD. The present series of studies examined the epidemiological characteristics of HFMD in Hong Kong, with a view to better understand the disease epidemiology so as to guide public health actions. / Methods and results of individual studies / Study (1)--characterizing the changing epidemiological features identified from various surveillance systems for HFMD / The trend of HFMD activities from 2001-2009 was analyzed using the sentinel surveillance statistics and HFMD outbreaks. The type of institutions reporting HFMD over time, incidences of outbreaks in 18 districts, and age and sex distribution of affected persons of HFMD outbreaks were analyzed. The clinical presentation, hospitalization rate, complication rate and case fatality of outbreaks were examined. The circulating enterovirues each year were determined by laboratory surveillance findings from 2001-2009 and test for morbidity caused by EV71. Seasonal peak was detected from warmer months of May through July but a smaller winter peak was found from October to December since 2006. An increasing trend of more older children aged above 5 years were infected, from 25.4% in 2001 to 33.0% in 2009 (p=0.01, Mantel-Haenszel Chi-square test). Laboratory surveillance detected a cyclical high activity of EV71 in every 3 to 4 years, which was associated with a higher average hospitalization rate among patients of the HFMD outbreaks reported in corresponding year, although it was only marginally significant (p=0.09, linear regression test). / Study (2)--analyzing the characteristics of EV71 epidemic in 2008 / All EV71 cases diagnosed by PHLC from 1998-2008 were analyzed. The complication and case fatality rates, percentage requiring hospitalization, median duration of hospital care, and the likelihood of being associated with an HMFD outbreak in institution in 2008 were compared with the corresponding rates calculated from cases reported from 1998-2007. Phylogenetic tree was constructed by using the neighbour-joining method and the molecular epidemiology of EV71 detected in 2008 was compared with the past years’ trends. Ninety-eight EV71 cases were reported in 2008, highest in the past decade. The annual incidence was 1.4/100 000 in general population, with highest incidence reported in children aged 0-4 years old (27.9/100 000). 11.2% had complications including meningitis or encephalitis (6.1%), pneumonia (3.1%), acute flaccid paralysis (1.0%), and shock (1.0%). There was only one fatal case (CFR: 1.0%) attributed to interstitial pneumonitis. 45.9% had concurrent HFMD outbreaks in their schools or institutions, and six schools required temporarily class suspension for 14 days. Both the complication rate and CFR werenot significantly different from the corresponding rates of the past 10 years (p=0.12 and 1.00 respectively). Phylogenetic analysis found that most cases reported in 2008 were C4 strains, which were the predominant circulating strains in the past ten years. / Study (3)--examining the association between meteorological parameters and HFMD activity / The sentinel consultation rate of HFMD was tested for any association with the meteorological parameters obtained from the Hong Kong Observatory from 2000-2004. Different regression models were examined to find the best model for predicting HFMD consultation rates from 2005-2009. In multivariate regression analysis, model M2 (in which mean temperature, diurnal difference in temperature, relative humidity and wind speed were positively associated with HFMD) was found to have a higher R2 (0.119) than M0 and M1 models with an R2 of 0.079 and 0.062 respectively, indicating that HFMD consultation rates were better explained using meteorological parameters measured 2 weeks earlier. The predicted trend of HFMD consultation rates for 2005 to 2009 matched well with the observed one (Spearman’s rank correlation coefficient=0.276, P=0.000). Sensitivity analysis showed that the estimated HFMD consultation rates were mostly affected by varying the relative humidity and least affected by wind speed. / Study (4)--determining the basic reproduction number of coxsackievirus A16 and enterovirus 71 using mathematical model / The basic reproduction numbers (R0) of EV71 and CoxA16 from laboratory confirmed HFMD outbreaks reported to DH from 2004-2009 were determined using mathematical model. Thirty four outbreaks were analyzed, 27 due to CoxA16 and seven due to EV71. The median R0 of EV71 was 5.48 with an inter-quartile range of 4.206.51 while median R0 of CoxA16 was 2.50 with an inter-quartile range of 1.963.67. In the sensitivity analysis, R0 of EV71 was significantly higher than that of CoxA16 in whole range of incubation periods, p≦0.025. R0was not associated with outbreak setting, size of the institution or number of persons affected. / Study (5)--assessing the impact of SARS and pandemic influenza H1N1 on transmission of HFMD in Hong Kong / I compared the observed HFMD consultation rates and the projected rates, which were constructed using mathematical model, in defined periods of 2003 and 2009 during which territory-wide public health interventions (including school closure) against Severe Acute Respiratory Syndrome (SARS) and pandemic influenza H1N1 were implemented. There was a reduction of 57.2% (95% C.I.:53.0-60.7%) in observed HFMD consultation rates during SARS period in 2003 and a reduction of 26.7% (95% C.I.:19.5-32.7%) during pandemic influenza H1N1 period in 2009. In 2003, the projected rates were still lower than the observed rates beyond week 31 until almost the end of the year. On the contrary, in 2009, the observed HFMD consultation rates became comparable to that of the projected rates in August, before the end of the defined intervention period. / Conclusions / This thesis bridges the knowledge gaps regarding epidemiological characteristics of HFMD. The changing epidemiology of HFMD, including the cyclical high activity of EV71 warrants vigilant surveillance of its activity in order to guide preventive measures. I have demonstrated that climate parameters may help predict HFMD activity, which could assist in explaining the winter peak detected in recent years and issuing early warning in the future. The R0 of EV71 and CoxA16 were first determined in the literature and I found that R0 of EV71 was higher than R0 of CoxA16. The reduction of transmission of HFMD during the SARS and H1N1 periods suggested that public health measures are effective in reducing the transmission of enteroviruses. / Ma, Siu Keung. / Thesis (M.D.)--Chinese University of Hong Kong, 2013. / Includes bibliographical references (leaves 121-149). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Table of content --- p.ii / Acknowledgements --- p.iv / Abbreviations --- p.v / Caption for Tables --- p.vi / Caption for Figures --- p.viii / Précis --- p.1 / Chapter PART I: --- LITERATURE REVIEW ON HFMD --- p.5 / Chapter Chapter 1. --- Current Understanding of Epidemiology of HFMD --- p.6 / Chapter 1.1 --- Causative agents and virology --- p.6 / Chapter 1.2 --- Clinical presentation and management --- p.8 / Chapter 1.3 --- Geographical distribution and past epidemics --- p.14 / Chapter 1.4 --- Host susceptibility and molecular determinants of neruovirulence --- p.26 / Chapter 1.5 --- Routes of transmission and transmission dynamics --- p.27 / Chapter 1.6 --- Knowledge gap identified from literature review --- p.29 / Chapter PART II: --- STUDIES ON EPIDEMIOLOGY OF HFMD IN HONG KONG --- p.33 / Chapter Chapter 2. --- Study Objectives and Main data source for analysis --- p.34 / Chapter 2.1 --- Aim and objectives of this thesis --- p.34 / Chapter 2.2 --- Sentinel surveillance system for monitoring HFMD activity --- p.35 / Chapter 2.3 --- Institutional outbreaks of HFMD reported to DH . --- p.37 / Chapter 2.4 --- EV 71 infection reported to Department of Health --- p.37 / Chapter 2.5 --- Laboratory surveillance for monitoring enteroviruses --- p.37 / Chapter Chapter 3. --- Study (1)--Characterizing the changing epidemiological features identified from various surveillance systems for HFMD --- p.38 / Chapter Chapter 4. --- Study (2)--Analyzing the epidemic of enterovirus 71 in 2008 and its public health implication to Hong Kong --- p.52 / Chapter Chapter 5. --- Study (3)--Examining the association between meteorological parameters and HFMD activity --- p.67 / Chapter Chapter 6. --- Study (4)--Determining the basic reproduction number of coxsackievirus A16 and enterovirus 71 using mathematical model --- p.85 / Chapter Chapter 7. --- Study (5)--Impact of SARS and Pandemic Influenza H1N1 on transmission of HFMD in Hong Kong --- p.100 / Chapter Chapter 8. --- Conclusion --- p.111 / List of publications related to this thesis --- p.119 / References --- p.121

Merino sheep are the most numerous domestic livestock in Australia and feral goats are wide-spread and locally abundant in many of the regions where sheep are grazed. Foot and mouth disease (FMD) is a disease of ungulates that causes severe economic hardship to countries where outbreaks occur or where it has become endemic. In India, Africa, Greece and recently the United Kingdom and Eire, sheep and goats have been implicated in the spread and maintenance of FMD. In Australia, there are contingency plans (AUSVETPLANS) for dealing with an outbreak of FMD. Included in those plans are strategies for control of the disease in feral ungulates including feral pigs and feral goats. Modelling has provided assistance in developing strategies to combat outbreaks in feral pigs and for controlling outbreaks in domestic livestock. No models have been constructed to aid decisions about controlling FMD in feral goats where they co-occur with merino sheep. In Australia, the greatest densities of free-ranging feral goats and domestic livestock occur in the high rainfall zone (> 500 mm mean annual rainfall) along the eastern tablelands and adjacent slopes of the Great Dividing Range. Previous studies of feral goat biology, population dynamics and behaviour in Australia have concentrated on arid and semi-arid zones or on islands. Interactions between free ranging feral goats and merino sheep have not previously been studied in the high rainfall zone. My study investigated the ecological and behavioural characteristics of feral goats and their interactions with sympatric merino sheep at a high rainfall site in central eastern New South Wales. The population dynamics, biological and behavioural parameters of feral goats and sheep were then used to model FMD in such an environment. Deterministic temporal models and a new spatial stochastic model were used. Of particular interest were the rates of contact within and between subgroups of feral goats (termed herds and mobs), within and between subgroups of merino sheep (termed flocks and mobs), and between subgroups of the two species. Feral goats at the study site were found to be numerous (mean density = 34.94 goats km-2, from aerial surveys), in good condition, fecund and had high adult survival and low annual adult mortality (survival= 0.81�1.00) in the absence of harvesting and hunting. They had an observed instantaneous rate of increase of 0.112 per year. Annual rate of increase was similar to other sites in Australia without sustained harvesting pressure. Home ranges were small for both males (3.754 km², s.e. = 0.232, n = 116 goats) and females (2.369 km², s.e. = 0.088, n = 241 goats). From this and other Australasian studies, an inverse power function was found to be an excellent descriptor of the relationship between mean annual rainfall and female home range size. A resource selection function was fitted in a geographic information system to observational data of feral goats. The habitat selection of feral goats included a preference for wooded vegetation on eastern and north eastern aspects at higher elevations. The resource selection function was also used to set the probabilities of occurrence of feral goats in 1 ha areas of the landscape and these probabilities were used to generate heterogeneity in a spatial model of foot and mouth disease virus (FMDV) transmission. Daily per capita contact rates were estimated from observed contacts in the field where a contact between individuals was recognised when one approached within 1 body length ([approx] 1m) of another. The contacts between feral goats within herds were frequent and occurred at a rate of 6.96 (s.e. = 1.27) goat�goat contacts day-1. Sheep to sheep contacts were slightly less frequent (4.22 sheep�sheep contacts day-1, s.e. = 0.65) but both estimates were most likely negatively biased because of observer errors in estimating the number of individual animals coming in contact with observation subject (focal) animals. Contacts between herds of feral goats were not common and those between adjacent populations were fewer than 1 per year. In sheep, flock to flock contact was largely governed by husbandry practices and occurred at a mean daily rate of 0.0014 flock�flock contacts. Contacts between sheep and feral goats were less frequent but nonetheless common (2.82 goat�sheep contacts day-1, s.e. = 0.40). In feral goats the size of the mob in which focal goats were observed was found to be the most important factor in determining contact rates between individuals and a counter-intuitive inverse relationship was identified. Contacts were heterogeneous and density was not an important determinant of contact rates implying that, because of the uniformly high densities at the site, saturation had occurred. The temporal models of FMDV transmission showed that the rate of contact within and between species was such that FMD was predicted to spread rapidly throughout an infected herd or flock. Control strategies of intense culling of feral goats at the population level were predicted to allow the disease to persist at low prevalence, with a small peak corresponding to the annual lambing pulse in sheep. However, the same level of control (>90% reduction) at the herd level was predicted to eliminate FMD and allow the safe reintroduction of sheep. Extreme control that left very small groups (<3 individuals) may be counter productive because such small groups are likely to join the reintroduced sheep in an effort by the goats to meet gregarious urges. The spatial model was more reassuring. It predicted that FMD would die out in a mixed sheep and feral goat population in less than 90 days because of the low rate of herd to herd contact and herd to flock contact. For similar environments, the contingency planning consequences are that an outbreak of FMD introduced into feral goats from sympatric sheep is likely to be containable by removing all the sheep, determining the extent and likely range of the feral goats, then removing a substantial proportion of or eradicating each herd. Feral goats, being relatively sedentary, are unlikely to spread to adjacent populations and the disease will die out through lack of contact between herds and populations. Because feral goat home ranges overlap and are centred on one or two small catchments, a containment ring of feral goat control, set to encompass the home range of a target herd and that of adjacent herds, should be adequate to limit spread of FMD.

This thesis is concerned with studying aspects of the ecology of feral pigs in the wet-dry tropics of the Northern Territory. The data are needed for use in the management of feral pigs to reduce their agricultural and potential epidemiological impact. Particular emphasis is placed on collecting data needed for modelling foot-and-mouth disease in feral pigs, estimating agricultural damage caused by pigs and evaluating control techniques. All fieldwork was conducted in the Douglas Daly district of the Northern Territory.

Foreign animal disease can cause serious damage to the United States (US) agricultural sector and foot-and-mouth disease (FMD), in particular, poses a serious threat. FMD causes death and reduced fecundity in infected animals, as well as significant economic consequences. FMD damages can likely be reduced through implementing pre-planned response strategies. Empirical studies have evaluated the economic consequences of alternative strategies, but typically employ simplified models. This dissertation seeks to improve US preparedness for avoiding and/or responding to an animal disease outbreak by addressing three issues related to strategy assessment in the context of FMD: integrated multi region economic and epidemic evaluation, inclusion of risk, and information uncertainty. An integrated economic/epidemic evaluation is done to examine the impact of various control strategies. This is done by combining a stochastic, spatial FMD simulation model with a national level, regionally disaggregated agricultural sector mathematical programming economic model. In the analysis, strategies are examined in the context of California's dairy industry. Alternative vaccination, disease detection and movement restriction strategies are considered as are trade restrictions. The results reported include epidemic impacts, national economic impacts, prices, regional producer impacts, and disease control costs under the alternative strategies. Results suggest that, including trade restrictions, the median national loss from the disease outbreak is as much as $17 billion when feed can enter the movement restriction zone. Early detection reduces the median loss and the standard deviation of losses. Vaccination does not reduce the median disease loss, but does have a smaller standard deviation of loss which would indicate it is a risk reducing strategy. Risk in foreign animal disease outbreaks is present from several sources; however, studies comparing alternative control strategies assume risk neutrality. In reality, there will be a desire to minimize the national loss as well as minimize the chance of an extreme outcome from the disease (i.e. risk aversion). We perform analysis on FMD control strategies using breakeven risk aversion coefficients in the context of an outbreak in the Texas High Plains. Results suggest that vaccination while not reducing average losses is a risk reducing strategy. Another issue related to risk and uncertainty is the response of consumers and domestic markets to the presence of FMD. Using a highly publicized possible FMD outbreak in Kansas that did not turn out to be true, we examine the role of information uncertainty in futures market response. Results suggest that livestock futures markets respond to adverse information even when that information is untrue. Furthermore, the existence of herding behavior and potential for momentum trading exaggerate the impact of information uncertainty related to animal disease.

Thesis (M.A. in Security Studies (Homeland Security and Defense))--Naval Postgraduate School, March 2005. / Thesis Advisor(s): Christopher Bellavita. Includes bibliographical references (p. 133-139). Also available online.

The foot-and-mouth disease (FMD) virus poses a considerable threat both to farmers and to the wider economy should there be a future incursion into the UK. The most recent large-scale FMD epidemic in the UK was in 2001. Mathematical models were developed and used during this epidemic to aid decision-making about how to most effectively control and eliminate it. While the epidemic was eventually brought to a halt, it resulted in a huge loss of livestock and is estimated to have cost the UK economy around ¿6 billion. The mathematical models predicted the overall spatial spread of FMD well, but had low predictive ability for identifying precisely which farm premises became infected over the course of the epidemic. This will in part have been due to the stochastic nature of the models. However, the transmission probability between two farm premises was represented as the Euclidean distance between their point locations, which is a crude representation of FMD transmission. Additionally, the premises' point location data contain inaccuracies, sometimes identifying the farmer's residential address rather than the farm itself which may be a long way away. Local FMD transmission occurs via contaminated fomites carried by people or vehicles between premises, or by infected particles being blown by wind between proximal fields. Given that these transmission mechanisms are thought to be related to having close field boundaries, it is possible that some of the inaccuracy in model predictions is also due to imprecisely representing such transmission. In this thesis I use fine-scale geographical data of farm premises' field locations to study the contiguity of premises (where contiguous premises (CPs) are defined as having field boundaries < 15m apart). I demonstrate that the distance between two premises' point locations does not accurately represent when they are CPs. Using an area of southern Scotland containing 4767 livestock premises, I compare the predictions of model simulations using two different model formulations. The first is one of the original models based on the 2001 outbreak, and the second is a new model in which transmission probability is related to whether or not premises were contiguous. The comparison suggests that the premises that became infected during the course of the simulations were more predictable using the new model. While it cannot be concluded that this will translate into more accurate predictions until this can be validated during a future outbreak, it does suggest that the new model is more predictable in its route through the landscape, and therefore that it may better reflect local transmission routes than the original model. Networks based on contiguity of premises were constructed for the same area of southern Scotland, and showed that 90.6% (n=4318) of the premises in the area were indirectly connected to one another as part of the Giant Component (GC). The network metric of 'betweenness' was used to identify premises acting as bridges between otherwise disconnected sub-populations of premises. It was found that removing 100 premises with highest betweenness served to fragment the GC. Model simulations indicated that, even with some longer-range transmission possible, removing these premises from the network resulted in a large decrease in mean number of infected premises and outbreak duration. In real terms, premises removal from the network would mean ensuring these premises did not become infected by enhanced biosecurity and/or vaccination depending on policy. In this thesis I also considered the role of biosecurity practices in shaping FMD spread. A sample of 200 Scottish farmers were interviewed on their biosecurity practices, and their biosecurity risk quantified using a biosecurity 'risk score' developed during the 2007 FMD outbreak in Surrey. Using Moran's I and network assortativity measures it was found that there did not appear to be any clustering of biosecurity risk scores on premises. Statistical analysis found no association between biosecurity risk and the mathematical model's premises' susceptibility term (which describes the increase in a premises' susceptibility with increasing numbers of livestock). This suggests that the model's susceptibility term is not indirectly capturing a general pattern in biosecurity on different sized farm premises. Thus, this body of work shows that incorporating a more realistic representation of premises location into mathematical models, in terms of area (i.e. as fields) rather than a point, alters predictions of spatial spread. It also demonstrates that targeted control at a relatively small number of farms could effectively fragment the farming landscape, and has the potential to considerably reduce the size of an FMD outbreak. It also demonstrates that variations in premises' FMD biosecurity risks are unlikely to be indirectly affecting the spatial or demographic components of the model. This increase in understanding of how geographic, social and demographic factors relate to FMD spread through the landscape may enable more effective control of an outbreak, should there be an incursion in the UK in future.

Doctor of Philosophy / Department of Agricultural Economics / Ted C. Schroeder / Concerns regarding management of animal disease and related perceptions about food safety have escalated substantially in recent years. Terrorist attacks of September 2001, discovery of bovine spongiform encephalopathy in a dairy cow in December 2003 in Washington state and subsequent discoveries of BSE infected animals in Texas in 2005 and Alabama in 2006, and recent worldwide outbreaks of highly contagious animal diseases (i.e., Foot-and-Mouth Disease and Avian Influenza A (H5N1)) have made apparent the need for animal traceability in U.S. livestock production and marketing. In addition, animal identification and trace-back systems are rapidly developing throughout the world increasing international trading standards. In recent years, increasing numbers of economic analyses of animal diseases have integrated epidemiological models into economic frameworks. However, there are only a few studies that have used this integrated framework to analyze the effects of animal traceability on highly contagious animal diseases. This study’s goal is to quantify and evaluate the economic impacts of different depths of animal identification/trace-back systems in the event of a hypothetical highly contagious foot-and-mouth disease outbreak that poses a threat to U.S. livestock competitiveness. Specifically, an epidemiological disease spread model is used to evaluate the impact of a foot-and-mouth disease outbreak in southwest Kansas. The information obtained from the disease spread model is then used in conjunction with an economic model to determine the changes in welfare of producers and consumers. Results obtained from the epidemiological model indicate that as the depth of animal identification in cattle is increased, the number of animals destroyed is reduced as are the associated costs. Also, the length of the outbreak is reduced by approximately two weeks. The economic results suggest that as surveillance is increased, decreases in producer and consumer welfare are smaller. Furthermore, as surveillance is increased, decreases in producer and consumer surplus measures can be reduced by approximately 60 percent.

The Picornaviridae family contains a number of pathogens which are economically important including Poliovirus, Coxsakievirus, Hepatitis A Virus, and Foot-and-Mouth-Disease-Virus. Recently the emergence of novel picornaviruses associated with gastrointestinal, neurological and respiratory diseases in humans has been reported. Although effective vaccines for viruses such as FMDV, PV and HAV have been developed there are currently no antivirals available for the treatment of picornavirus infections. Picornaviruses proteins are classified as: the structural proteins VP1, VP2, VP3 and VP4 which form the subunits of the viral capsid and the replication proteins which function as proteases, RNA-polymerases, primers and membrane binding proteins. Although the host specificity and viral pathogenicity varies across members of the family, the icosahedral capsid is highly conserved. The capsid consists of 60 protomers, each containing a single copy of VP1, VP2 and VP3. A fourth capsid protein, VP4, resides on the internal side of the capsid. Capsid assembly is integral to life-cycle of picornaviruses; however the process is complex and not fully-understood. The overall aim of the study was to broaden the understanding of the evolution and function of the structural proteins across the Picornaviridae family. Firstly a comprehensive analysis of the phylogenetic relationships amongst the individual structural proteins was performed. The functions of the structural proteins were further investigated by an exhaustive motif analysis. A subsequent structural analysis of highly conserved motifs was performed with respect to representative enteroviruses, Foot-and-Mouth-Disease-Virus and Theiler’s Virus. This was supplemented by the in silico prediction of interacting residues within the crystal structures of these protomers. Findings in this study suggest that the capsid proteins may be evolving independently from the replication proteins through possible inter-typic recombination of functional protein regions. Moreover the study predicts that protomer assembly may be facilitated through a network of multiple subunit-subunit interactions. Multiple conserved motifs and principle residues predicted to facilitate capsid subunit-subunit interactions were identified. It was also concluded that motif conservation may support the theory of inter-typic recombination between closely related virus sub-types. As capsid assembly is critical to the viral life-cycle, the principle interacting motifs may serve as novel drug targets for the antiviral treatment of picornavirus infections. Thus the findings in the study may be fundamental to the development of treatments which are more economically feasible or clinically effective than current vaccinations.

The suitability of a plant-based transient expression system using the agro-infiltration technique was compared to an Escherichia coli (E. coli)-based expression system to produce the VP1 protein from Serotype O, South Korean strain, of the foot-and mouth disease virus (FMDV). The full-length VP1 coding sequence was expressed in Escherichia coli as a fusion protein and purified as a His-tagged VP1 fusion protein with a yield of 14 mg L-1 bacterial culture. For transient expression in tobacco, the VP1 coding sequence was cloned into binary vector pMYV497, containing a CTB (cholera toxin B subunit) signal peptide and SEKDEL ER retention signal, and transiently agro-infiltrated into non-transgenic N. benthamiana and transgenic N. tabacum plants constitutively expressing the rice cysteine protease inhibitor OC-I. A protein resembling VP1 was detected using immuno-blotting analysis in both N. benthamiana and OC-I N. tabacum plants seven days post agro-infiltration. Although a possible stabilizing effect on VP1 was found due to OC-I expression, protein yields were not significantly different between transformed OC-I and non-OC-I control plants. Also, simultaneous co-infiltration with a plasmid allowing additional transient OC-I expression did not significantly improve VP1 production. The average VP1 amount achieved in OC-I expressing plants was 0.75% of total soluble protein. Overall, this study has shown that transient VP1 expression in tobacco is possible, but requiring further optimization, and that OC-I might have a stabilizing effect against proteolytic degradation of VP1 during advanced stages of senescence in agro-infiltrated plants coinciding with peaks in protein expression. Copyright / Dissertation (MSc)--University of Pretoria, 2012. / Plant Science / unrestricted