Des modèles épidémiologiques capables de représenter des situations naturelles peuvent en principe permettre de caractériser et quantifier les risques d'épidémies ainsi que d'optimiser les moyens de les contrôler. On présente d'abord quelques modèles épidémiologiques d'usage courant et évalue leur capacité à représenter correctement une situation biologique. L'emphase est placée sur l'importance des délais ainsi que sur l'impact des conditions environnantes. On montre que des modèles basés sur l'équation de diffusion répondent particulièrement bien à ces critères et mènent à une formulation générale, directe et élégante. Sous certaines hypothèses, ces systèmes peuvent être partiellement solutionnés analytiquement, réduisant substantiellement les traitements numériques et permettant une meilleure compréhension de structures sous-jacentes. On compare ensuite certains de ces modèles dans le contexte particulier du virus du Nil Occidental et élabore une approche spécifique et réaliste afin de fournir des outils supplémentaires au processus décisionnel de prévention de cette maladie. / Epidemiological models capable of representing naturally occurring situations may in principle permit the characterization of the risks of epidemies as well as the optimization of means for controlling them. First, we present some typical epidemiological models currently in use and evaluate their ability to correctly describe a biological situation. Emphasis is placed on the possibility of the treatment of delays and on the inclusion of the effects of environmental conditions. We show that models based on a diffusion-type equation are particularly well suited to satisfy these conditions and lead to a general, direct and elegant formulation. Under not too restrictive hypotheses, the corresponding models can in part be treated analytically, reducing substantially the computational efforts, and allowing for a better understanding of the associated underlying structures. We then compare some of the models for the application to the West Nile virus and develop a specific and realistic approach to provide additional tools for the decision process in matters of prevention and propagation of the disease.

Les maladies émergentes à transmission vectorielle sont une préoccupation croissante et particulièrement lorsqu’elles affectent les chevaux, une population spécifiquement à risque vis-à-vis de la propagation de maladies. En effet, les chevaux voyagent fréquemment et, malgré l’impact sanitaire et économique des maladies équines, les règlementations sanitaires et les principes de biosécurité et de traçabilité censés assurer la sécurité des mouvements d'équidés ne sont pas toujours en place. Notre travail propose d'améliorer la surveillance des maladies à transmission vectorielle chez les chevaux en utilisant différentes méthodes pour estimer la probabilité d'émergence d'une maladie. Tout d'abord, nous avons développé un modèle quantitatif et spatio-temporel combinant différentes probabilités pour estimer les risques d'introduction de la peste équine et de l’encéphalose équine. Ces combinaisons permettent d’obtenir une image plus détaillée du risque posé par ces agents pathogènes. Nous avons ensuite évalué des systèmes de surveillance syndromique par deux approches méthodologiques: l'approche classique avec un seuil d'alarme basé sur un multiple de l'erreur standard de prédiction, et l'approche bayésienne basée sur le rapport de vraisemblance. Nous avons travaillé ici principalement sur la détection précoce du virus West Nile en utilisant les symptômes nerveux des chevaux. Les deux approches ont fourni des résultats prometteurs, mais l’approche bayésienne était particulièrement intéressante pour obtenir un résultat quantitatif et pour combiner différentes informations épidémiologiques. Pour finir, l'approche bayésienne a été utilisée pour combiner quantitativement différentes sources d'estimation du risque : surveillance syndromique multivariée, et combinaison de la surveillance syndromique avec les résultats d’analyses de risques. Ces combinaisons ont données des résultats prometteurs. Ce travail, basé sur des estimations de risque, contribue à améliorer la surveillance des maladies à transmission vectorielle chez les chevaux et facilite la prise de décision. Les principales perspectives de ce travail sont d'améliorer la collecte et le partage de données, de mettre en oeuvre une évaluation complète des performances des systèmes de surveillance multivariés, et de favoriser l'adoption de ce genre d’approche par les décideurs en utilisant une interface conviviale et en mettant en place un transfert de connaissance. / Emerging vector-borne diseases are a growing concern, especially for horse populations, which are at particular risk for disease spread. In general, horses travel widely and frequently and, despite the health and economic impacts of equine diseases, effective health regulations and biosecurity systems to ensure safe equine movements are not always in place. The present work proposes to improve the surveillance of vector-borne diseases in horses through the use of different approaches that assess the probability of occurrence of a newly introduced epidemic. First, we developed a spatiotemporal quantitative model which combined various probabilities in order to estimate the risk of introduction of African horse sickness and equine encephalosis. Such combinations of risk provided more a detailed picture of the true risk posed by these pathogens. Second, we assessed syndromic surveillance systems using two approaches: a classical approach with the alarm threshold based on the standard error of prediction, and a Bayesian approach based on a likelihood ratio. We focused particularly on the early detection of West Nile virus using reports of nervous symptoms in horses. Both approaches provided interesting results but Bayes’ rule was especially useful as it provided a quantitative output and was able to combine different epidemiological information. Finally, a Bayesian approach was also used to quantitatively combine various sources of risk estimation in a multivariate syndromic surveillance system, as well as a combination of quantitative risk assessment with syndromic surveillance (applied to West Nile virus and equine encephalosis, respectively). Combining evidence provided promising results. This work, based on risk estimations, strengthens the surveillance of VBDs in horses and can support public health decision making. It also, however, highlights the need to improve data collection and data sharing, to implement full performance assessments of complex surveillance systems, and to use effective communication and training to promote the adoption of these approaches.

Les Flavivirus transmis par les moustiques comme le virus du Nil occidental, le virus de la dengue, le virus de la fièvre jaune, le virus de l’encéphalite japonaise et le virus Zika constituent des préoccupations croissantes de santé publique. Ils se sont répandus dans le monde au cours des dernières décennies, et les épidémies sont devenues plus fréquentes et plus sévères. Chaque année, des millions de personnes sont infectées et environ 50 000 patients décèdent d’infections à Flavivirus. Malgré les nombreux efforts de recherche, il n’y a actuellement aucun médicament antiviral spécifique disponible, et des nouvelles stratégies antivirales sont indispensables. Comprendre comment les Flavivirus fonctionnent au niveau moléculaire aidera à découvrir des nouvelles cibles pour l'intervention thérapeutique. Les Flavivirus ont un génome d'ARN simple brin de polarité positive qui code pour trois protéines structurales et huit protéines non structurales. Seules deux des huit protéines non structurales ont des activités enzymatiques. NS3 possède un domaine protéase et un domaine hélicase, et NS5 a un domaine méthyl- et guanylyltransférase et un domaine ARN polymérase ARN-dépendante. Ensemble, ils répliquent le génome viral. Ici, nous caractérisons l'interaction entre NS3 et NS5 dans le complexe de réplication du virus du Nil occidental pendant la synthèse d’ARN de polarité positive. Un modèle d'interaction comprenant NS3, NS5 et l’ARN viral a été développé basé sur des structures cristallines connues ainsi que des activités enzymatiques des deux protéines individuelles, et ce modèle a été soumis à des simulations de dynamique moléculaire. Les interactions potentielles entre les protéines NS3 et NS5 ont été identifiées. Les résidus impliqués dans ces interactions ont été mutés dans un réplicon du virus du Nil occidental et les effets de ces mutations sur la réplication virale ont été évalués. Une région particulière à la surface de la protéine NS3 a été identifiée comme étant cruciale pour la réplication virale, très probablement parce qu'elle interagit avec NS5. Cette région pourrait être une cible attrayante pour la recherche de composés qui pourraient interférer avec l'interaction entre NS3 et NS5 et donc posséder un potentiel antiviral intéressant. / Abstract : Mosquito-borne Flaviviruses like West Nile virus, Dengue virus, Yellow Fever virus, Japanese encephalitis virus, and Zika virus are increasing public health concerns. They have spread globally during the past decades, and outbreaks have recently become more frequent and more severe. Every year, millions of people are infected, and approximately 50,000 patients die from Flavivirus infections. Despite extensive research efforts, there are currently no specific antiviral drugs available, and new antiviral strategies are greatly needed. Understanding how Flaviviruses work on a molecular level will help in uncovering new points for therapeutic intervention. Flaviviruses have a single-stranded RNA genome of positive polarity that encodes three structural and eight non-structural proteins. Only two of the eight non-structural proteins have enzymatic activities. NS3 has an N-terminal protease domain and a C-terminal helicase domain, and NS5 has an N-terminal capping enzyme domain and a C-terminal RNA-dependent RNA polymerase domain. Together, they replicate the viral genome. Here we characterize the NS3:NS5 interaction within the West Nile virus RNA replicase complex during positive strand synthesis. An interaction model including NS3, NS5 and viral RNA was developed based on the known crystal structures as well as enzymatic activities of the two individual proteins, and this model was subjected to molecular dynamics simulations. Potential interactions between the NS3 and NS5 proteins were identified. Residues involved in these interactions were mutated in a West Nile virus replicon, and the effects of these mutations on viral replication were evaluated. One particular region on the surface of the NS3 protein was identified to be crucial for viral replication, most likely because it mediates the interaction with NS5. This region might be an attractive target for the search of compounds that could interfere with the NS3:NS5 interaction and therefore possess an interesting antiviral potential.

Master of Science / Department of Biology / Samantha M. Wisely / Nearly 30% of emerging infectious diseases are caused by vector-borne pathogens with wildlife origins, posing a risk for public health, livestock, and wildlife species of conservation concern. Understanding the spatial patterns of exposure to dipteran vectors and their associated pathogens is critical for epidemiological research to target prevention and control of vector-borne infectious diseases. In recent years, Western Equine encephalitis, St. Louis encephalitis, West Nile Virus encephalitis and avian malaria have not only been a public health concern but also a conservation concern, specifically the conservation of grassland nesting birds. Although the central Great Plains is the most specious region for grassland nesting birds, their role in the enzootic (primary) amplification cycle of infectious diseases may lead to further population depressions, and could potentially result in spill-over events to humans and livestock. The goals of my thesis were 1) to identify the underlying causes of spatio-temporal abundance patterns of mosquito vectors within the grasslands of the eastern Smoky Hills, and 2) to create probabilistic distributions of functional disease vectors, to evaluate disease risk in Greater Prairie-chicken (Tympanuchus cupido, surrogate species for other grassland nesting birds). First, I found that temporal dynamics in mosquito abundances were explained by maximum and minimum temperature indices. Spatial dynamics in mosquito abundances were best explained by environmental variables, such as curvature, TWI (Topographic Wetness Index), distance to woodland and distance to road. Second, the overall predictive power of the ecological niche models of important vector species in the grasslands of the Smoky Hills was better than random predictions, indicating that the most important predictor variables in their distribution were: distance to water, TWI, AASHTO (soil particle size distribution), and mean temperature during the coldest quarter. Furthermore, the spatial analysis indicated that Greater Prairie-chicken nest in areas with a higher probability of vector occurrence than other potentially available habitats within the grasslands. However, I failed to detect a significant difference in the probability of vector occurrence at nest of infected versus uninfected females. Understanding the distribution and abundance patterns of vectors of infectious diseases can provide important insights for wildlife conservation as well as public health management.

Mud volcanoes constitute an important component of petroliferous basins and their understanding is essential for successful exploration and development of hydrocarbon fields. They occur in both extensional and compressive tectonic settings, along with passive and active continental margins. Although extensive research exists on the geochemistry, geomorphology and stratigraphic evolution of these localized fluid flow structures, little is known about their geomechanical characteristics. This research investigates the geomechanics of mud volcanoes from the South Caspian Basin and West Nile Delta. This is achieved by establishing a workflow for geomechanical assessment of mud volcanoes using a P-wave velocity dataset from across the mud volcano within the offshore South Caspian Basin. This objective is developed further with the availability of seismic and wellbore data from around the Giza mud volcano, offshore West Nile Delta. Preliminary results of this study from the South Caspian Basin enable confidence in estimating the realistic magnitudes of elastic rock properties, stresses and fluid pressures from empirical and analytical correlations. Moreover, analysis of the variations in fluid pressures allow the fluid flow models around the mud volcano to be constrained and their gradients provide preliminary estimates of the drilling window. Structural and stratigraphic analysis around the Giza mud volcano offers insight into the formation of the mud volcano during the Quaternary and how the fault networks on the hanging wall of the arcuate tectonic fault have acted as conduits for primarily the pre-Pliocene fluids exploiting the areas of weakness along the hanging wall of the fault by entraining the Pliocene sediments. Fluid pressure evaluation reveals small overpressures caused by disequilibrium compaction. Further analysis offers insight into the critical fluid pressures that control fault movement, the stresses responsible for rock deformation around the wellbore and the width of the drilling window constrained by the fracturing of the strata. Analysis presented here provides details on the geomechanical significance of mud volcano environments, with implications for engineering practices. Overall, findings contribute to a systematic understanding of mud volcano settings not only from a field exploration and development point of view, but also at a wider scale for basin analysis and relatively small scale for play analysis.

L'objectif était d'évaluer le risque de circulation enzootique du virus West Nile (WN) chez le cheval en Camargue, région dans laquelle ce virus a déjà causé plusieurs épizooties. L'épidémiologie de la maladie de WN est très complexe, du fait de l'implication potentielle d'un grand nombre d'espèces de vecteurs et d'hôtes. De par sa transmission principalement vectorielle, la circulation du virus WN est fortement influencée par des facteurs environnementaux. L'espèce équine a été choisie comme témoin de la circulation du virus WN, car le cheval est particulièrement sensible à l'infection par ce virus. La méthode appliquée est basée sur l'utilisation du lien direct existant entre l'environnement et la circulation enzootique du virus WN, par l'étude de la séropositivité (IgG) chez le cheval. Dans les deux premières études présentées, certains facteurs de risque environnementaux ont été identifiés, comme des classes d'occupation du sol (zones agricoles hétérogènes, végétation inondée) ou des indices de paysage (Indice d'Imbrication et de Juxtaposition), ayant conduit à l'élaboration d'une carte de risque pour cette circulation dans le bassin méditerranéen français. Des facteurs de risque individuels, comme la race, l'âge et l'activité du cheval, ont également été identifiés. Dans la troisième étude présentée, des hypothèses de transmission du virus en Camargue ont été testées. Dans la région d'étude, le virus serait introduit par les oiseaux migrateurs et amplifié par Culex modestus et plusieurs espèces d'oiseaux compétentes. L'effet de dilution n'aurait pas d'impact sur l'amplification du virus en Camargue. Le virus serait transmis au cheval par C. modestus et C. pipiens.

The flavivirus West Nile virus (WNV) encodes a single polyprotein that is processed into three structural and seven nonstructural proteins. Various WNV bicistronic replicons that direct cap-dependent translation of an N-terminal viral capsid or capsid/Renilla luciferase fusion protein as well as IRES-dependent translation of the nonstructural proteins were constructed. An original replicon consisting of the WNV 5' NCR, the 5' 198 nts of the capsid coding sequence, which included the 5' cyclization sequence (Cyc), and an EMCV IRES followed by the WNV nonstructural genes and 3' NCR was generated. Real time qRT-PCR analysis of intracellular levels of this replicon RNA showed a 4 fold increase by 96 hr after transfection of BHK cells. Increasing the distance between the 5' Cyc and IRES by insertion of a 5' IRES flanking sequence alone or together with a Renilla luciferase reporter did not increase RNA replication. Addition of only a reporter decreased RNA replication. The insertion of an extended capsid coding sequence also did not enhance RNA replication, but did enhance both cap- and IRES-dependent translation of replicon RNA, as indicated by immunofluorescence and Western blot analysis. These results suggest the presence of a translation enhancer in the 3' portion of the capsid coding region. Simian hemorrhagic fever virus (SHFV) is a member of the family Arteriviridae, order Nidovirales. SHFV is unique among Nidoviruses in having three instead of two papain-like cysteine protease (PCP) motifs designated alpha, beta, and gamma, within the N-terminal region of its ORF1a. Mutations of putative PCP cleavage sites showed that the most efficient cleavage was by PCP beta at its downstream cleavage site. A large deletion located between the two catalytic residues of PCP alpha was hypothesized to render this protease inactive. However, processing was observed at the cleavage site following PCP alpha. Mutational analyses confirmed that PCP alpha is an inactive protease, and that the cleavage sites downstream of PCP alpha are cleaved by PCP gamma. When the catalytic residues of PCP gamma were mutated, PCP beta was also able to back cleave at these sites. This "back" cleavage is a previously unreported activity for an arterivirus PCP.

The aim of this study is to improve our understanding of the ecology, spatiotemporal patterns, and risk of infectious pathogens of migratory waterfowl, using the blue-winged teal (Anas discors, BWTE), as a model. From 2007-2010, 1,869 BWTE were sampled in the prairie provinces (Alberta, Saskatchewan and Manitoba, Canada) to examine infection status and/or evidence of previous exposure to avian influenza virus (AIV), West Nile virus (WNV), and avian paramyxovirus-1 (APMV-1), in relation to host demographic variables (age, sex, body condition, exposure to other pathogens), other ecological variables such as local waterfowl breeding population density and local pond density, and year. The probability of AIV infection depended on an interaction between age and AIV antibody status. Hatch year birds with antibodies to AIV were more likely to be infected, suggesting an antibody response to an active infection. After hatch year birds with antibodies to AIV were less likely to be infected, suggesting immunity resulting from previous exposure. AIV infection was positively associated with local BWTE density, supporting the hypothesis of density dependent transmission. Exposure to WNV and APMV-1 were also associated with age and year. Furthermore, the probability of WNV exposure was positively associated with local pond density rather than host population density, likely because ponds provide suitable breeding habitat for mosquitoes, the primary vectors for transmission. We also investigated large-scale spatiotemporal trends in apparent prevalence of AIV across Canada and the United States throughout the year, using data from national avian influenza surveillance programs in Canada and the US in 2007-2010. Our analyses revealed that age, sex, year of sampling, flyway, latitude, and season (categorized by stages of the BWTE annual life cycle) were all important variables in predicting probability of AIV infection. There was an interaction between age and season. During late summer staging (August) and fall migration (September-October), hatch year birds were more likely to be infected than after hatch year birds, however there was no difference between age categories for the remainder of the year (winter, spring migration, and breeding season). Probability of infection increased non-linearly with latitude, and was highest in summer, corresponding to the beginning of fall migration when densities of birds and the proportion of susceptible hatch year birds in the population are highest. Birds in the Pacific, Central and Mississippi flyways were significantly more likely to be infected compared to those in the Atlantic flyway. Observed trends in seasonal, annual, and geographic patterns of AIV infection in BWTE across Canada and the US were primarily driven by the dynamics of AIV infection in hatch year birds. Our results demonstrate demographic as well as seasonal, latitudinal and flyway trends across Canada and the US. This research provided further evidence for the role of wild dabbling ducks, particularly BWTE, in the maintenance and ecology of AIV. This improved understanding of the role of BWTE as natural hosts, and the geographic, demographic and temporal variables that affect infection and transmission parameters, moves us closer to deciphering the overall ecology of the virus and its transmission and transportation pathways at the individual, population and continental levels. This knowledge, in turn, will permit development of better tools to predict and perhaps to prevent possible outbreaks in domestic animals as well as in humans.

The induction of type I interferon (IFN) and subsequent activation of interferon stimulated genes (ISGs) represent a first line of defense against viral infection. Typically type I IFN signaling leads to the phosphorylation of the STAT1 and STAT2 transcription factors (TFs) which then form a trimetric complex with IRF-9 and translocate to the nucleus to induce ISG expression. However, the results of this study showed that IFN-mediated upregulation of the ISG Oas1b, the product of which confers resistance to flavivirus induced disease, can be induced in a STAT1-independent manner. Since numerous ISGs have antiviral functions, many viruses have evolved strategies to disrupt the type I IFN-signaling pathway. In cases when STAT1 activation is blocked by a viral infection, STAT1-independent upregulation of ISGs provides an additional strategy for the cell to mount an effective antiviral response. Infection of mouse embryofibroblasts (MEFs) with West Nile virus (WNV) induced the production of IFN beta and STAT1 and STAT2 phosphorylation but blocked nuclear translocation and binding of these TFs to the promoters of the ISGs, Oas1a, Oas1a, Irf7 and Irf1. However, each of these antiviral ISGs was efficiently upregulated in infected cells and IRF-9 was shown to be crucial for the upregulation of Oas1a, Oas1b and Irf-7. IRF-3 or IRF-7 was needed to maintain the upregulation of these genes at later times of infection. In contrast, the upregulation of Irf1 by WNV infection did not depend on the tested IRFs but was reduced by inhibition of the p38 or NF-kappa B pathways. Although Irf1 mRNA was efficiently upregulated in WNV-infected cells IRF-1 protein synthesis was blocked. The precise mechanism of the IRF-1 translational suppression is not yet known, but the suppression was shown not to be due to increased proteasomal degradation of IRF-1 nor to alternative splicing of Irf1 mRNA. Preliminary results suggest miRNAs may play an indirect role in regulating IRF-1 translation. The results of this study expand knowledge about the strategies evolved by viruses to evade host cell antiviral responses and also provide valuable insights about alternative mechanisms utilized by the host cell to counteract viral infections.

Foreign animal disease outbreaks can cause substantial economic losses. Policy makers need information on both the vulnerability of the food supply to disease epidemics and the impacts of alternative protection actions. This research focused on the assessment of the U.S. agricultural sector and human vulnerability to a Rift Valley Fever (RVF) outbreak and the value of a select set of alternative disease control strategies. RVF is a vector-borne, zoonotic disease that affects both livestock and humans; thus both animal and human consequences of an outbreak were examined. This research was conducted in two parts. Livestock impact assessment used an integrated epidemic/economic model to examine the extent of RVF spread in the animal population and its consequences plus the outcome of implementing two different control strategies: emergency vaccination and larvicide vector control. The number of infected, aborted, and dead animals is best controlled by coupling vaccination along with larvicide, but results in the second highest median national welfare loss. Therefore, careful decisions must be made as to what actions should be taken. Total national producer welfare is reduced with each scenario, and is more severe than the total national welfare loss (producer, consumer, and processor together). Consumer welfare is increased with each scenario due to a drop in prices of some commodities, and in some instances, an increase in supply as well. The majority of the national welfare loss can be attributed to the producers' and processors' loss in welfare. The highest damages are seen in the regions of the outbreak such as the South Central (SC). Other regions such as the Corn Belt, Lake States, and South East regions also see high damages due to price changes. The outbreak did not have substantial price effect on dairy products, but did have noticeable price changes for live cattle such as heifer calves, stocked yearling, and dairy calves. Prices for substitutes such as pork, chicken, and turkey experienced a price reduction, which can also be a factor resulting in consumer welfare gains. Human impact assessment utilized an inferential procedure for estimating the human consequences which comprise of a cost of illness calculation to assess the dollar cost of human illnesses and deaths, as well as a Disability Adjusted Life Year calculation to give an estimate of the burden of disease on public health as a whole. With potential costs above $2 billion for human illness, and with this number not accounting for loss or damages to other sectors of the economy, it can be highly probable that investing in a human vaccination campaign can be cost-effective and possibly cost-reducing. This cost along with the economic loss of the agriculture sector suggests substantial potential losses to the U.S. if this hypothetical situation were to become reality. Combining total loss estimates from the cost of illness and ASM models, potential damage of a RVF outbreak could range from 121 million to 2.3 billion US 2010$. The results of this study show the economic damages of an outbreak in the livestock population being much greater relative to the outbreak in the human population (roughly 16 times greater). It should be pointed out that both cost estimates are most likely under estimated. The animal outbreak is not incorporating all susceptible livestock (e.g. hogs and goats), and the human illness is not incorporating other damages to society (e.g. damages due to loss of tourism). By providing estimates on the potential economic outcomes, policy makers can better choose where, when, and how to invest their resources.