This study examines, from a modelling point of view, the dynamics of infectious diseases in wildlife caused by macroparasites and by tick-borne infections. The overall aim was to investigate the important role played by parasite aggregation in the dynamics of both systems. For macroparasites we first developed some deterministic models that incorporate explicit mechanisms for generating aggregation in parasite distribution, specifically multiple infections and host heterogeneity. We explored the role of aggregation in host regulation and in determining a threshold value for parasite establishment. A large aggregation makes it more difficult for parasites both to regulate hosts, and to get established in a population at carrying capacity. Furthermore, the stabilization yielded by aggregation strongly depends on the mechanism that produces the aggregation. We then introduced some uncertainties into the host-macroparasite system, presenting an individual-based stochastic model that incorporated the same assumptions as the deterministic model. Stochastic simulations, using parameter values based on some real case studies, preserved many features of the deterministic model, like the average value of the variables and the approximate length of the cycles. An important difference is that, even when deterministic models yield damped oscillations, stochastic simulations yield apparently sustained oscillations. The amplitude of such oscillations may be so large as to threaten the parasites’ persistence. With respect to tick-borne diseases we presented a general model framework that incorporated both viraemic and non-viraemic routes of infections. We compute the threshold for disease persistence and study its dependence on the parameters and on host densities. The effects of tick aggregation and correlation between different tick stages on the host have both an important effect on infection persistence, if non-viraemic transmission occurred. In the case of Lyme Disease and Tick-borne Encephalitis (TBE) in Trentino (northern Italy) we showed some numerical results, using parameter estimates based on a detailed field study, and explored the effects of uncertainty on the endemic equilibrium of both diseases assuming only viraemic transmission for Lyme Disease while for TBE we permitted only non-viraemic transmission through co-feeding ticks. In conclusion we have examined the patterns and changes of aggregation in a number of contrasting systems and believe that these studies highlight both the importance of considering heterogeneities in modelling host-parasite interactions and, more specifically, modelling the biological mechanisms that produce aggregation in parasite distributions.

Kyasanur Forest disease virus (KFDV) of the Flaviviridae virus family has caused seasonal infections and periodic outbreaks in Karnataka, India. First identified in 1957, KFDV annually infects 400-500 people and has a fatality rate of 3-5%; there are no approved antivirals and the existing licensed vaccine’s effectiveness appears to be questionable. Many tools for KFDV research are limited and this work sought to develop methods for analysing antivirals, including interferon (IFN)-α/β species. The BHK-21 (ATCC) cell line allowed for high virus propagation and distinguishable cytopathic effects (CPE) for determining antiviral effectiveness. The additional tool of a reverse genetics system expressing a full-length cDNA KFDV genome with a GFP reporter failed to propagate, despite numerous GFP genome-insertion strategies. The clinically approved IFN-α2a or IFN-α2b has had variable success at combatting flavivirus diseases in people, especially in the immuno-compromised. The continued passaging of KFDV-infected cells with repeated IFN-α2a treatment did not eliminate KFDV and had little effect on infectious particle production. IFN-αspecies, αWA and α were more effective than IFN-α2a and α2b at reducing KFDV; however dose ranges indicated that while low concentrations could limit CPE, higher concentrations were needed to inhibit virion release. Avoidance of IFN-α/β through Jak/STAT signalling repression was attributed to the NS5 protein, specifically the RdRp domain based on data obtained with luciferase and vesicular stomatitis virus (VSV) recovery assays. However, the mechanism appears to act subsequently to STAT1/2 activation without NS5 binding to any Jak/STAT components. A non-infectious, replicative system serving as a platform for antiviral drug testing against KFDV in a high throughput manner could only provide luciferase signals when the NS proteins capable of driving replication, were supplied in cis (subgenomic) but not in trans (antigenome). To conclude, IFN-α species such as IFN-αWA may be better suited than the licensed IFN-α2a for treatment of KFDV infections; however, IFN effects appear to be subdued in vitro due to the actions of the NS5 protein. While IFN may not be a successful antiviral against KFDV, the work in this thesis provides a foundation for evaluating other potential anti-KFDV therapeutics. / February 2016

No description available.

We develop and evaluate a novel host-vector model of West Nile virus (WNV) transmission that incorporates multiple avian host species and host stage-structure (juvenile and adult stages), with both species-specific and stage-specific biting rates of vectors on hosts. We use this model to explore WNV transmission dynamics that occur between vectors and multiple structured host populations as a result of heterogeneous biting rates. Our analysis shows that increased exposure of juvenile hosts results in earlier, more intense WNV transmission when compared to the effects of differential host species exposure, regardless of other parameter values. We also find that, in addition to competence, increased juvenile exposure is an important mechanism for determining the effect of species diversity on the disease risk of a community.

All wildlife populations harbour parasites. However, seabirds are likely to play a particularly important role in the maintenance and dispersal of infectious agents as a result of their colonial breeding habits. Seabird colonies are also known to be highly spatially structured, but little is known about the effects of this spatial structuring on seabird parasite dynamics. In this thesis, I use a tick-borne virus, Great Island virus (GIV), found in a large common guillemot (Uria aalge) colony bordering the North Sea as a model system to explore this relationship. I use a multidisciplinary approach, framed by a simple epidemiological model of the guillemot-tick-virus system. In Chapter 2, I describe a novel epidemiological model and parameterise it using the existing literature. The model suggests the importance of spatial structure within the guillemot colony, but also identifies a key missing parameter, the rate of virus transmission between pre-breeding and breeding areas. In Chapter 3, I go on to test the potential role of independent tick movement in driving transmission between these two areas, by quantifying the mobility of host-seeking seabird ticks, Ixodes uriae. I show the potential for ticks to walk ranges described anecdotally in the literature, in just a few minutes, but stress the importance of further experiments in the field. Chapter 4, I test the potential role of guillemot-mediated tick movement between pre-breeding and breeding areas. I show that pre-breeding guillemots spend a limited proportion of time ashore during daylight hours, which increases significantly as the season progresses and varies between individuals. A similar pattern is observed when considering how often they enter breeding areas when ashore; generally infrequently but varying spatiotemporally and between individuals. In Chapter 5, I apply finite mixture modelling techniques to improve existing estimates of age- and strain-specific GIV seroprevalence and force of infection in the guillemot colony. I also provide the first estimates of these parameters for eight strains, and highlight the importance of understanding strain-specific differences in GIV dynamics in future studies. Finally, I bring all four data chapters together in Chapter 6, by inputting my new parameter estimates (Chapters 3-5) into my existing model (Chapter 2). Taken together, my results suggest that GIV transmission within the guillemot colony may increase in the future as a result of declining breeding abundance and success, with more frequent or extreme disruption leading to a higher risk of infection within the colony. More generally, my results suggest that seabird colonies can be highly sensitive to changes in their spatial structure, and that endemic parasites have the potential to substantially impact, and hence to be an added threat to, their seabird hosts.

Doctor of Philosophy / Department of Electrical and Computer Engineering / Caterina Scoglio / Vector-borne diseases not only cause devastating economic losses, they also significantly impact human health in terms of morbidity and mortality. From an economical and humane point of view, mitigation and control of vector-borne diseases are essential. Studying dynamics of vector-borne disease transmission is a challenging task because vector-borne diseases show complex dynamics impacted by a wide range of ecological factors. Understanding these factors is important for the development of mitigation and control strategies. Mathematical models have been commonly used to translate assumptions concerning biological (medical, demographical, behavioral, immunological) aspects into mathematics, linking biological processes of transmission and dynamics of infection at population level. Mathematical analysis translates results back into biology. Classical deterministic epidemic models do not consider spatial variation, assuming space is homogeneous. Spatial spread of vector-borne diseases observed many times highlights the necessity of incorporating spatial dynamics into mathematical models. Heterogeneous demography, geography, and ecology in various regions may result in different epidemiological characteristics. Network approach is commonly used to study spatial evolution of communicable diseases transmitted among connected populations. In this dissertation, the spread of vector-borne diseases in time and space, is studied to understand factors that contribute to disease evolution. Network-based models have been developed to capture different features of disease transmission in various environments. Network nodes represent geographical locations, and the weights represent the level of contact between regional pairings. Two competent vector populations, Aedes mosquitoes and Culex mosquitoes, and two host populations, cattle and humans were considered. The deterministic model was applied to the 2010 Rift Valley fever outbreak in three provinces of South Africa. Trends and timing of the outbreak in animals and humans were reproduced. The deterministic model with stochastic parameters was applied to hypothetical Rift Valley fever outbreak on a large network in Texas, the United States. The role of starting location and size of initial infection in Rift Valley fever virus spread were studied under various scenarios on a large-scale network. The reproduction number, defined as the number of secondary infections produced by one infected individual in a completely susceptible population, is typically considered an epidemic threshold of determining whether a disease can persist in a population. Extinction thresholds for corresponding Continuous-time Markov chain model is used to predict whether a disease can perish in a stochastic setting. The network level reproduction number for diseases vertically and horizontally transmitted among multiple species on heterogeneous networks was derived to predict whether a disease can invade the whole system in a deterministic setting. The complexity of computing the reproduction number is reduced because the expression of the reproduction number is the spectral radius of a matrix whose size is smaller than the original next generation matrix. The expression of the reproduction number may have a wide range of applications to many vector-borne diseases. Reproduction numbers can vary from below one to above one or from above one to below one by changing movement rates in different scenarios. The observations provide guidelines on executing movement bans in case of an epidemic. To compute the extinction threshold, corresponding Markov chain process is approximated near disease free equilibrium. The extinction threshold for Continuous-time Markov chain model was analytically connected to the reproduction number under some assumptions. Numerical simulation results agree with analytical results without assumptions, proposing a mathematical problem of proving the existence of the relationships in general. The distance of the extinction threshold were shown to be closer to one than the reproduction number. Consistent trends of probability of extinction varying with disease parameters observed through numerical simulations provide novel insights into disease mitigation, control, and elimination.

Les méthodes de trajectographie conventionnelles par mesures d’angle supposent que la source est en mouvement rectiligne uniforme tandis que l’observateur est manœuvrant. Dans cette thèse, nous remettons en cause cette hypothèse en proposant un autre modèle de cinématique de la source : le mouvement circulaire uniforme. Nous prouvons qu’une telle trajectoire est observable à partir d’un observateur en mouvement rectiligne uniforme. Puis, nous étudions l’apport de mesures additionnelles de fréquence ou la faisabilité de la trajectographie par mesures de distances. Le cas d’une source en mouvement rectiligne uniforme et d’un observateur manœuvrant est étudié pour ce dernier type de mesures. Chaque cas donne lieu à une analyse de l’observabilité de la trajectoire de la source et à la mise au point de l’estimateur du maximum de vraisemblance. Nous montrons que ce dernier s’avère le plus souvent efficace. / The conventional bearings-only target motion analysis methods assume that the source is in constant velocity motion (constant speed and heading) while the observer maneuvers. In this thesis, we reassess this hypothesis and propose another model of the kinematics of the source: the constant turn motion (an arc of circle followed at constant speed). We prove that this kind of trajectory is observable by an observer in constant velocity motion. Then, we study the contribution of the addition of frequency measurements or the feasibility of target motion analysis methods that use range only measurements. The case of a source in constant velocity motion with a maneuvering observer is examined for this last type of measurements. Each case leads to an analysis of the observability of the trajectory of the source and to the development of the associated maximum likelihood estimator. We show that this estimator often appears to be efficient.

Houve um crescimento no consumo de alimentos fora do domicílio nas últimas décadas, impulsionado pela urbanização, economia, fatores demográficos e participação das mulheres no mercado de trabalho. O consumo em restaurantes de hotéis passou de 1,4 kg para 7,2 kg per capita entre 2005 e 2014 e apesar de seguir as orientações sanitárias, pode ser risco à saúde humana, devido ao tipo de prato, matéria prima ou cozimento. Assim, foram avaliados os cardápios de hotéis através de um índice de risco sanitário para os usuários, e comparou-se este índice médio do cardápio com características organizacionais e demográficas dos hotéis, seu sucesso midiático e a percepção do pessoal de problemas sanitários. Foi possível mostrar que há um conhecimento de risco pelo maior preço de pratos com risco mais alto. Os hotéis com mais risco têm cardápios mais variados e taxa de ocupação mais alta, sem diferença nos demais critérios demográficos. O pessoal de atendimento tem mais consciência de riscos que a gerência e avaliações midiáticas são menores nos hotéis de maior risco. Quanto à gestão do restaurante pelo hotel, este se mostrou mais segura para os hóspedes na gestão, sendo os restaurantes independentes mais ativos em número de pratos e turismo gastronômico, o que leva a uma melhor avaliação midiática, independente do maior risco. A avaliação do risco médio do cardápio pode levar uma melhor segurança sanitária do hóspede, mas existem outros fatores mercadológicos que podem interferir no cardápio do restaurante. Este conhecimento de risco sanitário pode orientar a escolha mercadológica do restaurante do hotel, provendo um elemento de julgamento da oferta de alimentos que podendo aumentar a fidelização e a segurança sanitária dos hóspedes. A alimentação segura de hóspedes é um processo extremamente importante para o sucesso da hotelaria, já que estes são associados a problemas pelos clientes, o que implica em maior cuidado sanitário na atual expansão do turismo de negócio e lazer no Brasil. / There has been an increase in consumption of food outside the home in the last decades, driven by urbanization, economy, demographic factors and women\'s participation in the labor market. The consumption in hotel restaurants went from 1.4 kg to 7.2 kg per capita between 2005 and 2014 and despite following the sanitary guidelines, can be risk to human health, by type of dish, raw food or cooking. Thus, we evaluated the hotel menus through a sanitary risk index for the users, and compared this average menu index with organizational and demographic characteristics of the hotels, their media success and the staff\'s perception of health problems. It was possible to show that there is a knowledge of risk by the higher price of dishes with higher risk. The hotels with more risk have more varied menus and higher occupancy rate, with no difference in the other demographic criteria. Service staff are more aware of risks that management and media reviews are lower in hotels at higher risk. As for the management of the restaurant by the hotel, this is safer for guests in hotel management, with independent restaurants more active in number of dishes and gastronomic tourism, which leads to a better media assessment, regardless of the greater risk. The evaluation of the average risk of the menu may lead to a better sanitary security of the guest, but there are other marketing factors that can interfere with the menu of the restaurant. This knowledge of sanitary risk can guide the market choice of the hotel restaurant, providing an element of judgment of the food supply that can increase the loyalty and sanitary security of the guests. The safe feeding of guests is an extremely important process for the success of the hotel industry, since these are associated with problems by the clients, which implies in greater health care in the current expansion of business and leisure tourism in Brazil.

Resumo: Dos vírus que infectam o maracujazeiro no Brasil, atualmente o Cowpea aphid borne mosaic virus (CABMV), é considerado fator limitante à cultura. Dependendo da velocidade de disseminação e idade com que as plantas são infectadas no campo, a cultura torna-se comercialmente improdutiva. O presente estudo teve como objetivo, avaliar a diversidade e a dinâmica populacional dos afídeos na região da Alta Paulista, SP e a possibilidade de transmissão do vírus pela semente. Assim, quatro locais (Leste e Oeste da cidade de Marília e Municípios de Ocauçú e Guaimbê) foram monitorados durante 24 meses com armadilhas amarelas de água do tipo Moericke. Constatou-se nas quatro regiões a predominância do gênero Aphis. Outras espécies coletadas foram Myzus persicae, Geopenphigus flocculosus, Brevicoryne brassicae, Rhopalosiphum spp, Dysaphis spp e Lipaphis erysimi. A flutuação populacional de formas aladas do gênero Aphis, caracterizou-se por apresentar maiores revoadas em maio, junho, agosto e setembro. As espécies de Aphis (A. fabae, A. gossypii, A. spiraecola) devem ser os principais vetores do CABMV na região. Plantios novos, ao lado de plantações infectadas, tornam-se infectadas em três meses. Nos testes de transmissão através de sementes, do total de 13056 semeadas oriundas de plantas doentes, germinaram 10592, e em avaliações visuais dois meses após a germinação, não foram observadas plantas sintomáticas, indicando a não transmissão pela semente. / Abstract: From the viruses were described infecting passionfruit plants in Brasil, and the Cowpea aphid borne mosaic virus (CABMV), is considered the most hazardous. Depending on the spread velocity of aphids and the age that the plants are infected, the crops doesn’t produce commercial fruits. The present study was designed to evaluate the diversity and dynamic population of aphids in the Alta Paulista, SP region and aspects of seed transmission. For this, four regions (East and West of Marília city, Guaimbê and Ocauçú) were monitored for 24 months using yellow water Moerick trap. The predominance of the genus Aphis was observed in the four evaluated areas. Other species founded in the area were: Myzus persicae, Geopenphigus flocculosus, Brevicoryne brassicae, Rhopalosiphum spp, Dysaphis spp and Lipaphis erysimi. The population curve of alate Aphis spp showed the highest frequency of flights during May, June, August and September. The Aphis spp (A. fabae, A. gossypii, A. spiraecola) probably is the most important vector of the CABMV in the region. New crops near old infected plants, were infected in three months. To evaluate properties of seed transmission, from 13056 collected from infected plants, 10592 were germinated and evaluated during two months for the presence of visual symptoms. No plants with simptoms were observed indicating no seed transmission. / Orientador: Marcelo Agenor Pavan / Coorientador: Valdir Atsushi Yuki / Banca: Renate Krause Sakate / Banca: Aloisio Costa Sampaio / Banca: Alexandre Levi R. Chaves / Banca: Hugo Kuniyuki / Doutor

Thesis (M. Sc. (Soil Science)) --University of Limpopo, 2019 / Many conventional laboratory methods are used to characterise spatial and temporal variation of soil properties in order to understand soil quality for different purposes. Currently there is a high demand for accurate soil information by land users. Therefore there is a need to develop a rapid, inexpensive, non-destructive and accurate technique that could compensate or replace conventional laboratory methodologies. Remote sensing has the potential to serve as an alternative approach to characterise soil properties due to its advantages over conventional laboratory methods such as it is rapid, non-destructive and it has low cost. The objectives of this study were to: (i) evaluate the ability of proximal soil sensing to characterise soil properties namely organic matter, soil moisture content, macronutrients, soil texture, cation exchange capacity (CEC), and pH. (ii) Identify bands of relevance from proximal soil sensing (300-2400 nm) that can provide acceptable reflectance variation for different levels of selected soil properties. (iii) Evaluate the performance of models developed from multispectral space-borne image in characterising selected soil properties. In this study spectroradiometer (proximal sensor) and worldview 2 satellite images (space-borne) were the two remote sensing techniques used to collect information about soil at Syferkuil experimental farm of the University of Limpopo. Visible and near infrared spectral data of 98 soil samples were collected at the study site using Analytical spectral device (ASD) field spectroradiometer. Spectral reflectance from spectroradiometer and those extracted from worldview 2 satellite image were used to develop prediction models of selected soil properties using Partial least square regression (PLSR). Bands of relevance were also identified from PLSR models developed from spectral data acquired by spectroradiometer. The results showed that estimation accuracy of PLSR models developed using spectral data from proximal soil sensing were excellent (Category A) for clay, sand, soil organic matter (SOM), and soil moisture content, while good prediction accuracy (Category B) was observed for other soil properties such as silt, ammonium, nitrate, active acidity (pHw), calcium, magnesium, phosphorus, potassium, sulphur, CEC, and reserve acidity (pHKCl). Then, relevant bands which contributed greatly in the prediction of these soil attributes were selected from the electromagnetic spectrum, the range was from 451 nm to 2400 nm. These bands fall within visible, shortwave infrared and near-infrared x regions of electromagnetic spectrum. In addition all selected soil properties were approximately quantitatively estimated using spectral data from satellite image. Based on the results obtained it can be concluded that proximal soil sensing has the ability to predict selected soil properties with various accuracies and it can be used as an alternative technique to characterise soil properties of South African soils. Soil predicting models developed from proximal soil sensing data also showed that there are bands of relevance within spectral range of 451 nm to 2400 nm. However more work is required for space-borne sensing before it can be used as one of the soil characterisation methods since its prediction accuracy was low as compared to that of hyperspectral proximal soil sensing. Keywords: Space-borne sensing; proximal soil sensing; soil characterisation.