Infectious diseases pose a significant threat to animal and human health across the globe, with much of the burden falling on low-income countries. Despite efforts to control many of these diseases, very few have ever been eradicated. Their dynamics are often embedded in complex, heterogeneous landscapes defined by interacting population and landscape level processes. As such, landscape heterogeneity plays a key role in driving disease transmission and persistence. Incorporating landscape heterogeneity in studies of pathogen dynamics is challenging but the accessibility of data, particularly next generation sequencing data, has opened new avenues of research. Landscape epidemiology involves using an integrated approach to understand spatial patterns of disease, using methods that combine landscape genetics, ecology and epidemiology. in this thesis I use these integrative methods to determine the underlying mechanisms facilitating the spread and persistence of canine rabies virus in Tanzania. Whole genome level characterisation of rabies virus samples was achieved and used in combination with cutting-edge inference techniques to explore spatial patterns of rabies at different spatial scales. Phylogeographic patterns were able to characterise spatial scales of endemic rabies transmission in Tanzania, uncovering strong viral population structure at sub-continental levels with evidence of a more fluid dispersal dynamic at local ( less than 100km2 area) spatial scales . Within-country phylogeographic patterns revealed large regional movements within Tanzania that could be attributed to human-mediated movements and revealed the presence of multiple co-circulating lineages within a single administrative district. Finely resolved incidence data from the Serengeti District complemented with whole genome sequences enabled the exploration of local scales of transmission in more detail. By extending phylogeographic diffusion models to incorporate landscape heterogeneity I was able to uncover evidence supporting landscape predictors of rabies diffusion. While much of the spatial structure was attributable to the effects of isolation by distance, landscape predictors had discernible effects on diffusion. In particular, rivers appeared to act as a barrier to dispersal and road networks facilitated diffusion and I found evidence to support vaccination as an effective control measure for canine rabies in the Serengeti District. Importantly, I also found evidence to support vaccination as resistance to diffusion and therefore an effective control measure for dog rabies. As a complementary approach a space-time-genetic algorithm was used to determine who-infected-whom in the Serengeti District. The model explicitly accounted for the possibility of exogenous sources of infection and how to incorporate genetic data available for only a proportion of samples. Direct transmission events were estimated between 42% of observed cases and highlighted the co-circulation of two major lineages in both time and space. Direct transmission events predominantly occurred over very small distances, less than 1km, but a large proportion of cases had unobserved sources that could represent transmission from dogs in neighbouring regions or larger indirect transmission events. A future development of the model is to delineate between these possibilities to assess the true contribution of exogenous sources to the system dynamic. Ultimately these integrative models are at an early stage of development but highlight the power of genetic data to delineate fine-scale transmission patterns. The results from this thesis suggest that landscape features such as rivers could be exploited as barriers in step-wise vaccination campaigns and highlight the utility of genetic surveillance to monitor control and elimination as rabies management progresses.

Emerging infectious diseases continue to represent serious threats to global human health. Novel zoonotic pathogens are continually being recognised, and some ultimately cause significant disease burdens and extensive epidemics. Research and public health initiatives often face emerging pathogens with limited knowledge and resources. Inferences from empirical modelling have begun to uncover the factors determining cross-species transmission and emergence in humans, and subsequently guide risk assessments. However, the dynamics of virulence and transmissibility during the process of emergence are not well understood. Here, I focus on RNA viruses, a priority pathogen type because of their potential for rapid evolution. I use comparative trait-based analyses to investigate how aspects of both host and virus ecology contribute to the risk of virulence and transmissibility within human RNA viruses. To explore these questions, data were collected via systematic literature search protocols. In the first half of this thesis, I focus on viral determinants of virulence and transmissibility. I ask whether virulence can be predicted by viral traits of tissue tropism, transmission route, transmissibility and taxonomic classification. Using a machine learning approach, the most prominent predictors of severe virulence were breadth of tissue tropism, and nonvector-borne transmission routes. When applied to newly reported viruses as test set, the final model predicted disease severity with 87% accuracy. Next, I assess support for hypothesised routes of adaptation during emergence using phylogenetic state-switching models. Propensity for adaptation in small ‘stepwise’ movements versus large ‘off-the-shelf’ jumps differed between virus taxa, though no single route dominated, suggesting multiple independent trajectories of adaptation to human hosts. In addition, phylogenetic regressions showed vector and respiratory-transmitted viruses to be more likely to progress through early stages of emergence. In the second half of this thesis, I focus on how dynamics of virulence and transmissibility differ with respect to nonhuman host diversity, identity, and ecology. Using a regression framework, I observe that viruses with a broader mammalian host range exhibited higher risk of severe virulence, but lower risk of transmissibility, which may reflect potential trade-offs of host specificity. Furthermore, viruses with artiodactyl hosts exhibited lower risk of severe virulence and viruses with bat or nonhuman primate hosts exhibited higher risk of transmissibility. Next, I test hypotheses that mammal species with faster-paced life history may be predisposed to host viruses with greater virulence and transmissibility. Mammal body mass was used as an established proxy for pace of life history. In regression analyses, mammals with faster-paced life history hosted more viruses with severe virulence, though evidence for a relationship with transmissibility was limited. The broad-scale associations presented in this thesis suggest the evolution of virulence and human-to-human transmissibility during zoonotic emergence is a multifactorial, highly dynamic process influenced by both virus and host ecology. Despite this, general characteristics of high-risk emerging viruses are evident. For example, severe virulence was associated with broad niche diversity of both tissue tropisms at the within-host scale, and host species at the macroecological scale. However, risk factors for virulence and human-to-human transmissibility often did not coincide, which may imply an overarching trade-off between these traits. These analyses can contribute to preparedness and direction within public health strategies by identifying likely candidates for high-impact emergence events among previously known and newly discovered human viruses. The inherent connectivity between RNA viruses, their nonhuman hosts and the resulting implications for human health emphasise the holistic nature of emerging diseases and supports the One Health perspective for infectious disease research.

Parmi les nouvelles stratégies thérapeutiques, la thérapie génique contre le VIH connaît actuellement un regain d'intérêt. La description du premier cas de guérison avéré après greffe de cellules souches mutantes pour le corécepteur majeur du VIH (CCR5) a relancé l'intérêt de la communauté pour développer des stratégies de thérapies géniques ciblant CCR5. Durant ma thèse, j'ai développé une stratégie basée sur l'inhibition de l'entrée du virus dans les lymphocytes T CD4 humains. Nos gènes thérapeutiques comprennent un inhibiteur de fusion membranaire (peptide C46) et un inhibiteur d'expression de CCR5. L'expertise de l'équipe dans les modèles de souris humanisées m'a permis de valider l'intérêt pré-clinique de cette stratégie dans un modèle de transfert de lymphocytes T modifiés. J'ai pu montrer que les lymphocytes T modifiés possédaient un avantage sélectif massif in vivo comparé à des cellules non protégées, ainsi qu’une protection totale contre la délétion induite par le VIH. De plus, dans une autre étude, j'ai montré que la dynamique virale dans les modèles de souris humanisées par transfert de CSH est plus proche des patients. Cette étude nous montre qu'il n'est pas nécessaire d'invoquer la réponse immune, pour expliquer les profils de réplication virale observés dans la phase primaire de l'infection. Ce résultat suggère donc qu'une partie de la dynamique virale est dépendante du nombre de cellules à infecter et du nombre de virions disponibles. L'ensemble des résultats de ma thèse a permis (i) de faire progresser notre compréhension de la dynamique virale, et (ii) de valider la combinaison d'inhibiteurs d'entrée dans un vecteur lentiviral. / Among new therapeutic strategies to fight the infection, gene therapy targeting CCR5 will be an asset. Indeed, the first patient to be cured from the infection received hematopoietic progenitors deprived of CCR5. This finding has ignited a flurry of research on genetic means to decrease CCR5 from the cell surface.During my PhD, I developed a gene therapy strategy based on entry inhibition of HIV in CD4 T cells. Our therapeutic genes are a membrane fusion inhibitor (the C46 peptide) and a CCR5 expression inhibitor, based on a super-agonist ligand. The experience of the team in humanized mice models allowed the validation of the strategy in vivo in a model of gene-modified T cell transfer. I first showed that the combination of the transgenes was able to prevent HIV infection in vitro in a dose dependent manner. Most importantly, I then showed that this protection conferred modified T cells with a huge selective advantage in vivo. This advantage was associated with a complete protection of CD4 T cells from HIV-induced deletion. Moreover, in another study, I showed that the viral dynamics in mouse models humanized by transferring HSC is closer to patients. This study also teaches us that it is not necessary to invoke the immune response to HIV, to explain the profiles of viral replication observed early after infection. This result suggests that part of the viral dynamic is dependent on the target/virus ratio. Together, results collected during my PhD thesis provides new information on viral dynamic and establish the interest of combining two viral entry inhibitors for gene therapy of HIV infection.