A Thesis submitted to the Faculty of Science in ful lment of the requirements for the degree of Doctor of Philosophy, School of Computer Science and Applied Mathematics. Johannesburg, 2016. / In this thesis in order to study the complex dynamics of Rift Valley fever (RVF) we combine two modelling approaches: equation-based and simulation-based modelling. In the first approach we first formulate a deterministic model that includes two vector populations, Aedes and Culex mosquitoes with one host population (livestock), while considering both horizontal and vertical transmissions. An easy applicable expression of the basic reproduction number, R0 is derived for both periodic and non-periodic environment. Both time invariant and time varying uncertainty and sensitivity analysis of the model is carried out for quantifying the attribution of model output variations to input parameters over time and novel relationships between R0 and vertical transmission are determined providing important information useful for improving disease management. Then, we analytically derive conditions for stability of both disease-free and endemic equilibria. Using techniques of numerical simulations we perform bifurcation and chaos analysis of the model under periodic environment for evaluating the effects of climatic conditions on the characteristic pattern of disease outbreaks. Moreover, extending this model including vectors other than mosquitoes (such as ticks) we evaluate the possible role of ticks in the spread and persistence of the disease pointing out relevant model parameters that require further attention from experimental ecologists to further determine the actual role of ticks and other biting insects on the dynamics of RVF. Additionally, a novel host-vector stochastic model with vertical transmission is used to analytically determine the dominant period of disease outbreaks with respect to vertical transmission efficiency. Then, novel relationships among vertical transmission, invasion and extinction probabilities and R0 are determined. In the second approach a novel individual-based model (IBM) of complete mosquito life cycle built under daily temperature and rainfall data sets is designed and simulated. The model is applied for determining correlation between abundance of mosquito populations and rainfall regimes and is then used for studying disease inter-epidemic activities. We find that indeed rainfall is responsible for creating intra- and inter-annual variations observed in the abundance of adult mosquitoes and the length of gonotrophic cycle, number of eggs laid per blood meal, adults age-dependent survival and fight behaviour are among the most important features of the mosquito life cycle with great epidemiological impacts in the dynamics of RVF transmission. These indicators could be of great epidemiological significance by allowing disease control program managers to focus their e orts on specific features of vector life cycle including vertical transmission ability and diapause. We argue that our IBM model is an ideal extendible framework useful for further investigations of other relevant host-vector ecological and epidemiological questions for providing additional knowledge important for improving the length and quality of life of humans and domestic animals. / LG2017

Thesis (Ph. D.)--University of Wisconsin--Madison, 1961. / Typescript. Vita. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references (leaves 183-189).

Veterinarians in Tucson and Phoenix were surveyed by mail, requesting information about their patients recently diagnosed or treated for Valley Fever. Information obtained included risk factors and outcome.

Four to six month old healthy puppies were enrolled in a longitudinal study of their serostatus against the Coccidioides spp. Dog were tested every six months for one year. At the request of investigators, some dogs continued to be tested every six months for two years. Dogs that became ill with clinical signs consistent with coccidioidomycosis received additional testing. Owners were asked to complete a questionnaire regarding exposure risk factors at each routine testing visit.

381 dogs between 4 and 18 months of age were tested for the presence of antibodies to Coccidioides one time. Dogs were reported as either healthy or sick by the referring veterinarian. Owners were asked to complete a questionnaire regarding their dog's risk factors associated with exposure to Coccidioides at the time of sample collection.

Diss. (sammanfattning) Umeå : Umeå universitet, 2010. / Härtill 4 uppsatser.

Rift Valley fever virus (RVFV) is a Phlebovirus member of the Bunyaviridae family and it is the causative agent of Rift Valley fever (RVF), a mosquito-borne viral zoonotic disease that poses a significant threat to domestic ruminants and human health in Africa. The RVFV is an encapsulated, negative-sense, single-stranded RNA virus with a tripartite segmented genome, containing L (large), M (medium) and S (small) segments. The S segment codes for two proteins, namely the nucleocapsid (N) protein and non-structural protein (NSs). There is evidence that the NSs protein is involved in virulence by blocking the expression of the interferon beta (IFN-β) promoter. It has been recently demonstrated that the SAP30-NSs-YY1 multiprotein complex represses the IFN-β promoter. Consequently, the interferon expression is blocked, allowing virus to replicate. A total of 45 isolates of RVFV recovered over a period of 53 years in 14 African countries, Madagascar and Saudi Arabia were characterized by full sequencing of the S segment of the virus. This data was added to another 27 strains of RVFV available on GenBank for phylogenetic analysis using MEGA4, giving a total of 72 strains analyzed. Alignments were made of the entire S segment, the NSs gene, the N gene, and their deduced amino acid sequences. The laboratory strains, clone 13, MP12 and Smithburn, were also included in the alignments. Two isolates were passaged ten times through two different amplification systems to asses the potential for sequence variation to occur in the original material through routine laboratory manipulations. Sequencing data was generated from the virus RNA present in the original clinical specimens and from the extracted RNA from the tenth passage of virus in each amplification system. The results showed 100% homology for each respective isolate, demonstrating that the RVFV S segment remained stable during ten serial passages in different propagation systems. Phylogenetic analysis was conducted on the naturally occurring RVFV strains (n = 72) and the findings indicate that circulating strains are compartmentalized and belong to one of three major lineages, namely Egyptian, western African, and central, eastern and southern African. The strains clustered in the Egyptian lineage had an average p-distance of 1.0%, the western African strains 0.9%, and the central, southern and eastern African strains 2.0%. The overall average p-distance was 2.5%, with a range from 0 to 4.1%. For the N gene, the range was from 0 to 4.2%, with an average of 2.2%. For the N protein, the range was from 0 to 2%, with an average of 0.2%. The NSs gene had a range of 0 to 4.6%, with an average of 2.4%. The NSs protein had a range of 0 to 3.8%, with an average of 1.7%. The intergenic region (IGR) had a range of 0 to 9.2%, with an average of 4.8%. Results of the study suggest that RVF outbreaks can result from either the rapid spread of a single strain over vast distances or from an increased activity of a strain circulating at an endemic level within an area/region during prolonged dry periods. Sequencing alignment showed that the length of the S segment ranged from 1690 to 1692 nucleotides. This difference in length was due to insertions and deletions found in the IGR, which is also the region with the most sequence divergence (4.8%). Both the NSs and N genes had neither insertions nor deletions, and were both found to be stable, though the NSs gene was slightly more variable than the N gene (2.5% versus 2.2%) The deduced amino acid sequences of the NSs protein were considerably more variable than that of the N protein (1.7% versus 0.2%). Alignment of the NSs protein demonstrated that the 5 cysteine residues at positions 39, 40, 150, 179 and 195, are highly conserved among the isolates analyzed. These residues are important for conservation of the three-dimensional structure of the protein and the formation of filamentous structures observed in cells infected with natural strains of RVFV. The NSs protein is now implicated as the major factor of virulence and that its pathogenicity is associated with the blocking of interferon production. Therefore, any amino acid changes that result in changes to the filamentous structure of the NSs protein might impact on the binding kinetics between the NSs protein, SAP30 (Sin3A Associated Protein 30) and YY1 (Yin Yang-1). There were 6 amino acid changes in the NSs-SAP30 binding domain, with one being unique to the live-attenuated Smithburn vaccine strain. Generated sequencing data contributes to global phylogenetic characterization of RVFV isolates and and molecular epidemiology of the virus. In addition, findings of this study will further aid investigation on reassortment events occurring between strains of RVFV and genetically related viruses, the role of the NSs protein in the replicative cycle of the virus, the pathogenic effects of the NSs protein within the RVFV-infected host cells, and might help to identify molecular basis of RVFV virulence.

Doctor of Philosophy / Department of Diagnostic Medicine/Pathobiology / Wenjun Ma / Rift Valley fever virus (RVFV) is an enveloped, negative-sense, ssRNA virus with a tripartite genome that causes morbidity and mortality in both livestock and humans. Although RVFV is mainly circulating in mainland Africa, this arthropod-borne virus is a potential threat to the other parts of the world. No fully licensed vaccines for human or animal use in the U.S., and effective antiviral drugs have not been identified. As virulent RVFV strains are only handled in biosafety level (BSL) 3 or higher level facilities in the U.S., few laboratories have access to RVFV which limits antiviral development. However, it is crucial to develop effective antivirals to protect public and animal health. Animal models that reproduce Rift Valley fever are vital to identifying and developing antiviral compounds. The currently available attenuated RVFV strain, MP12, provides a BSL-2 challenge model virus for preliminary investigations of RVFV prior to using the virulent RVFV strains. All strains of RVFV have a highly conserved genome, indicating that antivirals or vaccines effective against any RVFV strain will most likely be effective for all RVFV strains. Therefore, we hypothesize that the MP12 is a suitable model virus that can be used for identification and evaluation of effective RVF antivirals. The first objective of this project was to establish a mouse model susceptible to MP12 infection. Based on the literature, we selected and screened six different strains of mice to test their susceptibilities to MP12. We found the STAT-1 knockout mice are the most susceptible to MP12 infection based on clinical symptoms, mortality, viremia, virus replication, histopathological, and immunochemical analyses. Importantly, these mice displayed acute-onset hepatitis and delayed-onset encephalitis similar to severe cases of human RVFV infection. Our second objective was to identify potential antiviral drugs in vitro. We developed and employed a cell-based assay using the recombinant MP12 virus expressing Renilla luciferase to screen a library of 727 small compounds purchased from National Institutes of Health. Of the compounds, 23 were identified and further tested for their inhibitory activities on the recombinant MP12 virus expressing green fluorescent protein. Further plaque reduction assays confirmed that two compounds inhibited replication of parental RVFV MP12 strain with limited cytotoxic effects. The 50% inhibitory concentrations using an MP12 multiplicity of infection (MOI) of 2 were 211.4 µM and 139.5 µM, respectively. Our third objective was to evaluate these two candidates, 6-azauridine and mitoxantrone, in vivo using our mouse model. After one-hour post MP12 infection via an intranasal route, treatment was given intranasally twice daily. Mice treated with placebo and 6-azauridine displayed severe weight loss and reached the threshold for euthanasia with obvious neurological signs, while mice treated with ribavirin (a known antiviral drug) or mitoxantrone showed delayed onset of disease. This result indicates that the mitoxantrone can improve the outcome of RVFV infection in our mouse model. The underlying mechanism of mitoxantrone to inhibit RVFV replication remains to be investigated. Our studies build the foundation for identification and development of antivirals against RVFV in a BSL-2 environment.

Coccidioidomycosis, or Valley Fever, is an infectious disease caused by inhalation of soil-dwelling fungus Coccidioides posadasii spores in the Lower Sonoran Life Zone (LSLZ) in Arizona. In the context of climate change, the habitat of environmentally-mediated infectious diseases, such as Valley Fever, are expected to change. Connections have been drawn between climate and Valley Fever infection. The operational scale of the organism is still unknown. Here, we use climatic variables, including precipitation, soil moisture, and temperature. We use PRISM precipitation and temperature data, and Moderate Resolution Imaging Spectroradiometer (MODIS) Normalized Difference Vegetation Index (NDVI) as a measure of soil moisture for the entire state of Arizona, divided into 126 primary care areas (PCA). These data are analyzed and regressed with Valley Fever incidence to determine the effects of climatic variability on disease distribution and timing. This study confirms that Valley Fever occurrence is clustered in the LSLZ. Seasonal Valley Fever outbreak was found to be variable year-to-year based on climatic variability. The inconclusive regression analyses indicate that the operational scale of Coccidioides is smaller than the PCA region. All variables are related to Valley Fever infection, but one variable was not found to hold more predictive power than others.

An epidemiological survey of Valley Fever (coccidioidomycosis) was conducted in dogs in Tucson and Phoenix. Dogs were tested for delayed type hypersensitivity (DTH) using coccidioidin, a reagent that is not commercially available and results of the skin tests were compared with corresponding serologic test results.