[Truncated abstract] A functional ecosystem is increasingly being recognised as a requirement for health and well being of resident human populations. Clearing of native vegetation for agriculture has left 1.047 million hectares of south-west Western Australia affected by a severe form of environmental degradation, dryland salinity, characterised by secondary soil salinisation and waterlogging. This area may expand by a further 1.7-3.4 million hectares if current trends continue. Ecosystems in saline affected regions display many of the classic characteristics of Ecosystem Distress Syndrome (EDS). One outcome of EDS that has not yet been investigated in relation to dryland salinity is adverse human health implications. This thesis focuses on one such potential adverse health outcome: increased incidence of Ross River virus (RRV), the most common mosquito-borne disease in Australia. Spatial analysis of RRV notifications did not reveal a significant association with dryland salinity. To overcome inherent limitations with notification data, serological RRV antibody prevalence was also investigated, and again no significant association with dryland salinity was detected. However, the spatial scale imposed limited the sensitivity of both studies. ... This thesis represents the first attempt to prospectively investigate the influence of secondary soil salinity on mosquito-borne disease by combining entomological, environmental and epidemiological data. The evidence collected indicates that RRV disease incidence is not currently a significant population health priority in areas affected by dryland salinity despite the dominant presence of Ae. camptorhynchus. Potential limiting factors include; local climatic impact on the seasonal mosquito population dynamics; vertebrate host distribution and feeding behaviour of Ae. camptorhynchus; and the scarce and uneven human population distribution across the region. However, the potential for increased disease risk in dryland salinity affected areas to become apparent in the future cannot be discounted, particularly in light of the increasing extent predicted to develop over coming decades before any benefits of amelioration strategies are observed. Finally, it is important to note that both dryland salinity and salinity induced by irrigation are important forms of environmental degradation in arid and semi-arid worldwide, with a total population of over 400 million people. Potential health risks will of course vary widely across different regions depending on a range of factors specific to the local region and the complex interactions between them. It is therefore not possible to make broad generalisations. The need is highlighted for similar research in other regions and it is contended that an ecosystem health framework provides the necessary basis for such investigations.

Introdução: Conhecer e monitorar fatores associados a transmissão de arboviroses são um grande desafio para os gestores de saúde pública e também uma necessidade para regiões onde há registro da circulação de arbovírus e a presença de vetores. Objetivos: Identificar os principais grupos de recipientes que podem se tornar ou são criadouros de mosquitos vetores no Município de São Paulo e verificar se os mesmos sofrem influências de fatores sazonais e socioeconômicos em sua distribuição. Método: Foram levantados dados das inspeções realizadas nas atividades de vigilância e controle de Aedes aegypti no período de 2012-2016, por Supervisão Técnica de Saúde e para o município. Em seguida foram construídos grupos de recipientes para avaliar predominância nas diferentes condições de encontro (existente, com água, com larva). Os indicadores gerados foram utilizados para testar diferenças significativas das frequências entre as estações do ano e analisar correspondência entre incidência de casos dengue e predominância de grupos de criadouros. Posteriormente, foi realizada análise de agrupamento por fatores socioeconômicos para identificar diferenças na distribuição dos grupos de recipientes. Para as análises de variância foi utilizado o teste não paramétrico de Kruskal-Wallis. Resultados: O grupo de recipientes móveis foi o potencial criadouro mais frequente em todos os anos, seguido dos grupos planta e pneus. Móvel e planta foram os criadouros mais frequentes para o município. O grupo móveis, apesar de numeroso, não foi o mais colonizado. Por outro lado, os depósitos para armazenamento de água tiveram baixa frequência, porém alta proporção de colonização. A sazonalidade influenciou na distribuição de recipientes com água e com larva, sendo que as maiores frequências ocorreram no verão e outono. A proporção de imóveis tendo recipientes com água aumentou de acordo com o tempo, principalmente em 2015. O grupo que teve maior incremento do índice nesse período foi o de depósito não ligado à rede. Foram gerados cinco grupos de STS por condições socioeconômicas, nos quais houve diferenças no padrão de distribuição de potenciais criadouros e criadouros. Regiões com melhor condição socioeconômica apresentaram menor frequência dos indicadores, mas não necessariamente menor risco de transmissão de dengue no período avaliado. Conclusões: Os principais grupos de criadouros mais frequentes no Município de São Paulo dentro do período analisado foram os de menor tamanho, principalmente os do tipo móvel. Reservatórios de maior tamanho e destinados ao armazenamento de água demonstraram importância na proporção de colonização e tiveram sua frequência aumentada no período da crise hídrica do abastecimento. Fatores sazonais e condições socioeconômicas influenciaram a distribuição de criadouros em São Paulo. Para melhor direcionamento das ações de prevenção e controle de vetores, analises sistemáticas e continuas por regiões devem ser realizadas. / Introduction: Knowing and controlling factors associated with arbovirus transmission is a major challenge for public health managers, but it is necessary for regions where arbovirus circulation and the presence of vectors are present. Objectives: To identify the main groups of containers that can become or are breeding sites of mosquito vectors in the São Paulo Municipality and verify if their distribution are influenced by seasonal and socioeconomic factors. Method: Data were collected from the inspections carried out in the surveillance and control activities of Ae. aegypti in the period 2012-2016, by Health Technical Supervision and county. Groups of containers were then created to evaluate predominance in the different checked conditions (existing, with water, with larvae). The generated indicators were used to test significant differences of the frequencies between the seasons of the year and to analyze correspondence between incidence of dengue cases and predominance of breeding sites groups. After, a socioeconomic grouping analysis was performed to identify differences in the distribution of groups of recipients. The Kruskal-Wallis non-parametric test was used for the variance analysis. Results: The group of mobile containers was the most frequent potential breeding site in all the years, followed by container plants and tires groups. Mobile and plant were the most frequent breeding sites for the county. The mobile group, although numerous, was not the most colonized. On the other hand, deposits for water storage had a low frequency, but a high proportion of colonization. Seasonality influenced the distribution of water and larvae containers, with the highest frequencies occurring in summer and fall. The proportion of buildings having containers with water increased over time, especially in 2015. The group that had the largest increase in the index in this period was the deposit not connected to the water supply network. Five Health Technical Supervision groups were generated by socioeconomic conditions, in which there were differences in the pattern of distribution of potential breeding sites and breeding sites for mosquitoes. Regions with better socioeconomic status had lower frequency of indicators, but not necessarily a lower risk of dengue transmission in the period evaluated. Conclusions: The main breeding sites groups most frequent in the city of São Paulo during the analyzed period were the smaller groups, mainly those of the mobile type. Larger reservoirs destined to water storage showed importance in the proportion of colonization and had their frequency increased in the period of the water supply crisis. Seasonal factors and socioeconomic conditions influenced the distribution of breeding sites in. To better target vector prevention and control actions, systematic and continuous analyzes by regions should be performed.

Le virus du Nil occidental (VNO) est un flavivirus présent au Canada depuis 2001, affectant principalement les oiseaux, les chevaux et les humains. En 2003, l’Agence canadienne d’inspection des aliments (ACIA) a inscrit le VNO sur la liste des maladies à notification immédiate (MANI) et depuis, les cas chez les animaux domestiques sont rapportés dès l’obtention d’un résultat positif à l’autorité fédérale. Aucune étude au Canada n’a encore colligé tous les cas de VNO chez une espèce animale afin d’améliorer la compréhension de la distribution du VNO au pays et de formuler des recommandations pour la prévention de futures infections. Dans le cadre de cette étude, tous les cas de VNO rapportés à l’ACIA chez les chevaux ont été analysés afin de décrire, dans un premier temps, l’incidence des cas rapportés de VNO au Canada (2003 à 2019) et les caractéristiques principales des cas récents (2015 à 2019). Dans un second temps, une analyse géospatiale a été effectuée afin de décrire les patrons spatiotemporels de la distribution des cas de VNO rapportés de 2003 à 2020 chez les chevaux. Au cours de la période d’étude, 848 cas de VNO chez les chevaux ont été rapportés à l’ACIA. Ces cas étaient répartis dans toutes les provinces, à l’exception des quatre provinces de l’Atlantique (Nouveau-Brunswick, Nouvelle-Écosse, Île-du-Prince-Édouard, Terre-Neuve-et-Labrador). La région de l’Ouest (Colombie-Britannique, Alberta, Saskatchewan, Manitoba) a déclaré un plus haut taux d’incidence (15,4 cas/100 000 chevaux-année) que la région de l’Est (8,3 cas/100 000 chevaux-année) (Ontario, Québec, Atlantique). Les taux d’incidence étaient particulièrement élevés en Saskatchewan avec en moyenne 33,2 cas/100 000 chevaux-année entre 2003 et 2019. L’analyse descriptive des caractéristiques des cas a démontré que 96 % de ceux-ci n’étaient pas vaccinés et que le taux de létalité était de 31,9 %. La distribution spatiotemporelle des cas a été décrite par région en analysant d’abord la récurrence annuelle des cas dans les divisions de recensement et ensuite la présence d’agrégats spatiotemporels pour investiguer les excès de risque. L’analyse des patrons spatiotemporels a révélé une dispersion vaste et rapide ainsi qu’une récurrence élevée du VNO dans la région de l’Ouest. En revanche, pour la région de l’Est, la dispersion du VNO a été plus lente et graduelle. Les agrégats spatiotemporels identifiés ont permis de démontrer que, malgré la présence répétée des cas dans certaines divisions de recensement, des excès de risque spatiotemporels peuvent être observés. Ces patrons indiquent que les cas de fièvre du VNO peuvent être anticipés dans les endroits où la récurrence annuelle est plus élevée et, parfois, conduire à des éclosions de la maladie. En somme, cette étude a mis en évidence l’importance de la surveillance du VNO chez les chevaux en décrivant notamment la saisonnalité du VNO et en délimitant des zones avec une forte récurrence de cas. Ces caractéristiques illustrent l’apport considérable de la surveillance chez les chevaux à un système de surveillance intégrée. Les résultats pourront aussi aider les autorités sanitaires et les médecins vétérinaires praticiens à cibler leurs efforts de prévention et de contrôle dans les zones les plus touchées. / West Nile virus (WNV) is a flavivirus which has been present in Canada since 2001, affecting mostly birds, horses and humans. In 2003, the Canadian Food Inspection Agency (CFIA) included WNV on its list of immediately notifiable diseases (INDs), and since then, cases in domestic animals are reported to the federal authority as soon as positive samples are obtained from diagnostic laboratories. To date, no study in Canada has compiled all reported WNV cases in an animal species to describe the distribution of this virus in the country and formulate recommendations for future prevention strategies. In this study, all WNV cases reported to the CFIA in horses were analyzed to describe their incidence in Canada (2003 to 2019) and the main characteristics of the recent ones (2015 to 2019). A geospatial analysis was also conducted to describe the spatiotemporal patterns of reported WNV cases in horses from 2003 to 2020. Over the study period, 848 cases of WNV in horses were reported to the CFIA. These cases were distributed in all provinces, except for the Atlantic provinces (New Brunswick, Nova Scotia, Prince Edward Island, Newfoundland and Labrador). The western region of Canada (British Columbia, Alberta, Saskatchewan, Manitoba) reported a higher incidence rate (15.4 cases/100,000 horse-year) than the eastern region (8.3 cases/100,000 horse-year) (Ontario, Quebec, Atlantic). The reported incidence rates were particularly high in Saskatchewan, with an average of 33.2 cases/100,000 horse-year between 2003 and 2019. The descriptive analysis of case characteristics showed that 96% of cases were not vaccinated, and the case fatality rate was 31.9%. The regional spatiotemporal distribution of cases was described by first analyzing the annual recurrence of cases in census divisions and then the presence of spatiotemporal high-risk clusters. The analysis of spatiotemporal patterns revealed a swift spread and a high recurrence of WNV cases in the western region. In contrast, in the eastern region, the dispersion was slower and more gradual. The identified clusters showed that, despite the repeated presence of cases in some census divisions, excess in spatiotemporal risk can be observed. These patterns indicate that cases of WNV fever can be anticipated in areas with higher annual recurrence, and in some instances, can result in disease outbreaks. This study highlights the importance of WNV surveillance in horses, enabling a better understanding of the seasonality of WNV in horses and the identification of areas with a high recurrence of cases. The findings are a considerable contribution in an integrated surveillance system. The results can also assist health authorities and veterinary practitioners in targeting prevention and control efforts to the most affected areas.

Viruses are entities which are made of a few genes and are reliant on obligate parasitism to propagate. Due to the obligate connection to their hosts, virus evolution is constrained to the type of host. Viruses however do transmit to evolutionary distinct hosts; in these cases, the phylogenetic relationship of the hosts usually are close. In some instances, RNA-viruses have made host jumps between evolutionary distant hosts, such as the host jump from invertebrates to vertebrates, and fungi to arthropod. Partitiviruses are double stranded RNA viruses which mainly infect fungi and plants. The defining characteristic of these double stranded RNA viruses are the double layered capsids which are formed by a single open reading frame (ORF). The capsid proteins form icosahedral virus particles which are in the magnitude of 30-40 nm. Metagenomic studies have discovered partitiviruses originating from an insect in the Odanata family, a finding which contradicts the fungal host specificity of partitiviruses. The finding of the Hubei.PLV 11 thus implies the existence of a partitiviruses containing structural elements in their capsids which could be involved in the infection of arthropods. Thus, this virus could be used as a model for a structural comparison with its fungi infecting relatives with hopes to identify common viral structural factors necessary for the infection of arthropods. For this purpose, the Hubei.PLV ORF was cloned and then transfected into insect Spodoptera frugiperda (Sf-9) cells using a baculovirus expression system, “bac-to-bac” expression system. The FLAG-tagged capsid proteins were expressed by the Sf-9 cells to be approximately 60 kDa. After ultra-centrifugation in a sucrose gradient, some spontaneous assembly into the expected ~40 nm icosahedral virus-like particles were observed using low resolution scanning electron microscopy. The observed particles were also confirmed by a dynamic light scattering experiment (DLS) and a higher resolution cryo-EM microscope. Thus, the bac-to-bac expression system can be used to produce VLPs from this genus of viruses, and this metagenomically derived virus genome. However, for future success in defining a high-resolution model of this virus, it is recommended that the Sf-9 culture volume is sufficiently high for enough particle production which is necessary for a high-resolution map. The other virus, the Southern pygmy squid Flavilike virus (SpSFV) has been suggested to be the oldest relative of the land based flaviviruses. The SpSFV was found to be the most divergent of the flaviviruses, and to infect invertebrates. Solving for the structure of the SpSFV and comparing it to vertebrate infecting flaviviruses could therefore lead to the identification of factors necessary for the adaptation to vertebrates and thus the humoral immunity by flaviviruses. The soluble E-protein was expressed using the bac-to-bac expression system. The protein was indicated to be multiglycosylated and approximately 50 kDa which is in line with other strains in the genus. Affinity chromatography did not elute this protein, likely due to the His-tag not being spatially available. Cation exchange could elute some protein, but not much from the small ~30 mL culture. To conclude, VLP assembly was confirmed by the Hubei.PLV, thus, solving for the structure is a distinct possibility when a larger Sf-9 culture is used to produce the VLPs. For the SpSFV soluble E-protein, the protein is secreted into the supernatant of the Sf-9 cultures, making purification a possibility. For this, a large Sf-9 culture can be used to produce this protein and then purify it with a cat-ion exchange chromatography.

La dengue circule en Polynésie française sur un mode épidémique depuis plus de 35 ans. Néanmoins, en dépit de la taille relativement faible de la population de Polynésie française, la circulation de la dengue peut persister à de faibles niveaux pendant de nombreuses années. L’objectif de ce travail de thèse est de déterminer si l'épidémiologie de la dengue dans le système insulaire de la Polynésie française répond aux critères d’un contexte de métapopulation. Après avoir constitué une base de données regroupant les cas de dengue répertoriés sur les 35 dernières années, nous avons réalisé des analyses épidémiologiques descriptives et statistiques. Celles-ci ont révélé des disparités spatio-temporelles distinctes pour l’incidence de la dengue des archipels et des îles, mais la structure de l'épidémie globale à l’échelle de la Polynésie française pour un même sérotype ne semble pas être affectée. Les analyses de la métapopulation ont révélé l'incidence asynchrone de la dengue dans un grand nombre d’îles. Celle-ci s’observe plus particulièrement par la différence de dynamique de l’incidence entre les îles plus peuplées et celles ayant une population plus faible. La taille critique de la communauté nécessaire à la persistance de la dengue n’est même pas atteinte par la plus grande île de Polynésie Française, Tahiti. Ce résultat suggère que la dengue peut uniquement persister grâce à sa propagation d’île en île. L'incorporation de la connectivité des îles à travers des modèles de migration humaine dans un modèle mathématique a produit une dynamique de la dengue davantage en adéquation avec les données observées, que les tentatives de modélisation traitant la population dans son ensemble. Le modèle de la métapopulation a été capable de simuler la même dynamique que les cas de dengue observés pour l'épidémie et la transmission endémique qui a suivi pour la période de 2001 à 2008. Des analyses complémentaires sur la différenciation de l'incidence de la maladie et de l'infection seront probablement instructives pour affiner le modèle de métapopulation de l'épidémiologie de la dengue en Polynésie française. / Dengue has been epidemic in French Polynesia for the past 35 years. Despite the relatively small population size in French Polynesia, dengue does not disappear and can persist at low levels for many years. In light of the large number of islands comprising French Polynesia, this thesis addresses the extent to which a metapopulation context may be the most appropriate to describe the epidemiology and persistence of dengue in this case. After compiling a database of dengue cases over the last 35 years, we used a number of descriptive and statistical epidemiological analyses that revealed distinct spatio-temporal disparity in dengue incidence for archipelago and islands. But the global structure of the epidemics of the same serotype were not affected. Metapopulation analyses revealed asynchronous dengue incidence among many of the islands and most notably larger islands lagged behind the smaller islands. The critical community size, which determines dengue persistence, was found to exceed even the largest island of Tahiti, suggesting that dengue can only exist by island-hopping. Incorporation of island connectedness through patterns of human migration into a mathematical model enabled a much better fit to the observed data than treating the population as a whole. The metapopulation model was able to capture to some extent the epidemic and low level transmission dynamics observed for the period of 2001-2008. Further analyses on differentiating incidence of disease and infection will likely prove informative for the metapopulation model of dengue epidemiology in French Polynesia.