Rift Valley fever (RVF) is a mosquito-borne zoonotic disease caused by a virus of the family Bunyaviridae, genus Phlebovirus. It is responsible for extensive outbreaks of disease in livestock in Africa with significant mortality and economic impact. Virus neutralization is considered the gold standard for confirming Rift Valley fever virus (RVFV) infection but the procedure is time consuming and expensive. Real-time reverse transcription-polymerase chain reaction (rRT-PCR), histopathology, and immunohistochemistry (IHC) are the diagnostic methods most often used in South Africa to confirm or exclude a diagnosis of RVF in necropsied animals. Validated estimates of diagnostic accuracy of these tests, in naturally infected livestock, however, have not been published. The objective of this study was to estimate the diagnostic sensitivity and specificity of rRT-PCR, histopathology, and IHC using Bayesian latent class methods in the absence of a gold standard. A secondary objective was to estimate stratum-specific values based on species, age, degree of specimen autolysis, and the presence/absence of tissue pigments. The Sensitivity (Se) and Specificity (Sp) of qRT-PCR were 97.4% (95% credibility interval (CI): 95.2% - 98.8%) and 71.7% (95% CI: 65% - 77.9%) respectively. The extraordinary analytical sensitivity of PCR makes this test very susceptible to false positive reactions, and thus reduced specificity. This is more likely during large-scale epidemics due to crosscontamination of specimens at necropsy facilities or testing laboratories. The Se and Sp of histopathology were 94.6% (95% CI: 91% - 97.2%) and 92.3% (95% CI: 87.6% - 95.8%) respectively. Single cases of RVF could be confused with acute poisoning with plants, bacterial septicaemias, and viral diseases such as infectious bovine rhinotracheitis and Wesselsbron disease. Most of these conditions, however, can be excluded using histological examination of the liver, special stains, bacterial culture, and toxicological or serological investigations. The Se and Sp of IHC were 97.6% (95% CI: 93.9% - 99.8%) and 99.4% (95% CI: 96.9% - 100%) respectively. Immunohistochemistry is highly specific because characteristic positive immunolabelling of the cytoplasm of hepatocytes can be correlated with the presence of hepatocellular injury typical for RVFV infection. False negative results are sometimes obtained with IHC because of reader error or loss of the antigenic epitopes due to advanced autolysis. Scant positive immunolabelling might be missed or viral proteins might be absent from sections of liver with advanced hepatocellular damage. The stratified analysis suggested differences in test accuracy in foetuses and severely autolysed specimens. The Sp of histopathology in foetuses (83.0%) was 9.3% lower than the value obtained for the sample population (92.3%). Lesions in some foetuses are more subtle and the typical eosinophilic intranuclear inclusions are often difficult to detect. In severely autolysed specimens, the Se of IHC decreased by 16.1% and the Sp of rRT-PCR by 17.4%. There is no plausible biological explanation for this decrease in the Sp of rRTPCR since the RNA of RVFV is resistant to degradation in autolysed tissues. Conversely, the antibody used to detect RVFV using IHC detects epitopes raised against nucleoproteins of the virus and it is possible that viral proteins become too widely dispersed and/or degraded in autolysed tissues to detect by light microscopy. It is possible that the marked decrease in Se of histopathology and IHC in severely autolysed specimens caused an apparent decrease in Sp of rRT-PCR, due to the latent class method. In conclusion, the high estimated Sp (99.4%) of IHC and the low Sp of rRT-PCR (71.3%) suggests that the definitive diagnosis or exclusion of RVF should not rely on a single PCR test and that IHC would be an effective confirmatory test for rRT-PCR positive field cases necropsied during an epidemic. Immunohistochemistry results from severely autolysed specimens, however, should be interpreted with caution and aborted foetuses in areas endemic for RVF should be screened using a variety of tests. The diagnostic Se and Sp of histopathology was much higher than expected confirming the value of routine post mortem examinations and histopathology of liver specimens. The most feasible RVF testing option in areas that do not have suitably equipped PCR laboratories, and where disease is often not detected in livestock until after human cases have been diagnosed, would be routine histopathology screening with IHC confirmation. Key Words: Rift Valley fever; Rift Valley fever virus; Bayesian; latent-class model; real-time reverse transcription-polymerase chain reaction; immunohistochemistry; histopathology; diagnosis; sensitivity; specificity. / Dissertation (MSc)--University of Pretoria, 2014. / gm2014 / Paraclinical Sciences / unrestricted

From 1930 to 2000 Rift Valley Fever (RVF) was limited to the African continent. It is vector borne disease caused by a virus of the genus Phlebovirus, member of the Bunyaviridae family. The main vectors for transmission are Aedes and Culex. In September 2000 it was reported for the first time out of Africa, affecting Yemen and Saudi Arabia. This epidemic opened a new era in the history of RVF. It proved that the virus had the capaciity to affect new zones, different eco-systems and to spread to any area in the world. The outbreak lifted many hypothesis related to its introduction and to the factors associated with the outbreak. Although difficult to evaluate precisely its socio-economic impact was considered to be the heaviest in the modern history of Yemen animal diseases even when compared to the rinderpest outbreak that the country encountered in the seventies because of its zoonotic characteristic. To answer to these hypotheses it was of great importance to study and investigate all the factors associated with the outbreak. Thus after estimating the socio-economic impact of the disease in the world and more specifically in Yemen we studied the descriptive epidemiology of RVF in the first and most affected zone of the outbreak of 2000-2001 (Tihama Wadi Mawr) and then we analysed the socio-economic and environmental factors associated to the outbreak, to finish with the risk assessment of the re-introduction of RVFV from the Horn of Africa through legal animals trade. The descriptive study showed that at the national level 90% of the RVF cases were in the plain of Tihama coast, Hodiedah, Hajjah and Sadah governorates, the majority of the villages being located around the main canals of Wadi Mawr at an altitude < 300 m. Environmental as well as socio-economic factors likely to play a role in RVF transmission in Yemen were highlighted with the study of the period 1997-2007 in the country. As in previous RVF outbreaks in neighbouring countries in the Horn of Africa, the year 2000 presented above-normal vegetation index values, which reflected important precipitations, for both rainy seasons (the first occurring between March and May; the second between July and October). These environmental conditions favourable to the vectors populations were found concomitant with a late starting date of Eid-al Kabeer celebration (March) in 2000, related to high hosts (cattle, sheep and goats) densities. According to these criteria, 2000 was considered as an atypical year. Yemeni Veterinary Services did not declare any RVF outbreak since 2000. Thus, we assumed Yemen free of the disease when assessing the risk of introduction of RVF into Yemen via the legal trade of small ruminants from the Horn of Africa (Kenya, Somalia, Djibouti, and Ethiopia). After precisely describing the routes and volume of trade from the Horn of Africa to Yemen, the pathway and different scenarios for introduction were developed following the OIE risk assessment method. A matrix of likelihood combinations including four possible levels (very low, low, medium, high) was built and used to combine likelihood of events. The overall probability of introduction was assessed very low to medium depending on the period of the year and most likely to occur via ovine males exported during festival periods that change depending of the year considered. The uncertainty was considered to be low. The socio-economic impact although difficult to estimate was shown to be dramatic as RVF affects all the chain of life in particular of those associated to livestock and animal products trade. Despite the dramatic impact of the outbreak of RVF in 2000 but it had the advantage to draw the attention of decision makers, of international organizations and of local veterinary services on the importance of livestock diseases and their possible effects on human health and national economies. Veterinary education also improved significantly in Yemen. It enhanced the epidemiologists skills, disease surveillance in general and the cooperation between human health care people and veterinary services. A national P3 laboratory should also soon open with the help of the IAEA and the FAO and Al-Mukkah quarantine could be modernized and extended in the near future. Regional collaboration and improvement of knowledge on animal trade but also field studies related to the disease and its entomological features are seen as compulsory to hope improving the prevention and control of RVF.But the best way and strategy for prevention of Rift Valley Fever in Yemen as well as in the world is to develop more efficient surveillance and control tools to implement coordinated regional monitoring and control programmes. - Résumé - De 1930 à 2000, la Fièvre de la Vallée du Rift (RVF) était une maladie essentiellement africaine. Cest une maladie vectorielle causée par un virus du genre Phlebovirus de la famille des Bunyaviridae. Les principaux vecteurs sont les Aedes et les Culex. En Septembre 2000, des cas furent rapportés pour la première fois hors du continent africain touchant le Yémen et lArabie Saoudite. Cette épidémie ouvrit une nouvelle ére dans lhistoire de la RVF. Elle prouva la capacité du virus à infecter des zones nouvelles, des écosystèmes différents et sa capacité à se propager à nimporte quelle région du monde. Plusieurs hypothèses furent avancées concernant son introduction et les facteurs socio-économiques associés aux foyers. Sil est difficile dévaluer précisement son impact socio-economique, il fut considéré comme le plus lourd de lhistoire moderne des maladies animales au Yémen même comparé à celui de la peste bovine dans les années 70 à cause de son caractère zoonotique. Pour répondre à ses hypothèses, il était important détudier et de rechercher tous les facteurs associés aux foyers. Ainsi après avoir estimé limpact soci-èconomique de la maladie dans le monde et plus particulièrement au Yemen, lon sintéréssa à lépidémiologie descriptive de la RVF dans les premières zones touchées mais aussi les plus affectées lors des foyers de 2000-2001 (Tihama Wadi Mawr) Puis lon analysa les facteurs socio-économiques et environmentaux associés aux foyers pour finir avec lévaluation de risque de la réintroduction du RVFV à partir du commerce légal danimaux de la Corne dAfrique. Létude descriptive montre quau niveau national, en 2000-2001 environ 90 % des cas étaient dans la plaine de la côte de Tihama, Hodiedah, Hajjah et Sadah, la plupart des villages étant localisées autour des canaux principaux de Wadi Mawar à une altitude infereure à 300 Mètres (m). Les facteurs environmentaux et socioèconomiques susceptibles davoir un rôle dans la transmission de la RVF au Yémen furent soulignés avec létude de la période 1997-2007 dans le pays. Comme dans les foyers précédents de RVF dans les pays voisins de la Corne de lAfrique, lannée 2000 présentait des valeurs anormalement élevées dindex normal de végétation refletant dimportantes précipitations lors des deux saisons des pluies (la première entre mars et mai, la seconde entre juillet et octobre). Ces conditions environmentales favorables aux populations de vecteurs apparurent concommitantes avec une date tardive de début des festivités de lEid-al Kabeer en (mars) 2000 entraînant à une densité importante de populations hôtes (bovins, moutons, chèvres). Considérant ces facteurs lannée 2000 fut considérée comme une année atypique. Les services vétérinaires yéménites ne déclarèrent pas de foyers de RVF depuis 2000. Ainsi on fit lhypothèse que le Yémen nétait plus infecté pusqon lon sintéressa au risque de ré-introduction de la RVF au Yémen via le commerce légal de petits ruminants depuis la Corne de lAfrique (Kenya, Somalie, Djibouti et Ethiopie). Après avoir précisemment décrit les routes et volumes déchanges depuis la Corne de lAfrique jusquau Yémen, les chemins événementiels et différents scénarios dintroduction furent développé en suivant la méthode de lOIE. Une matrice de combinaison des probabilités incluant quatre niveaux (très bas, bas, modéré, élevé) fut construite et utilisée pour combiner les probabilité de réalisation des évènements. La probabilité globale dintroduction fut trouvée très basse à modérée en fonction de la période de survenue dans lannée et plus probablement via lintroduction dovins males exportés pendant les périodes de fêtes dont loccurrence change en fonction de lannée considérée. Lincertitude fut considérée basse. Si l'impact socio-économique de la RVF est difficile à évaluer, il est pourtant dramatique en atteignant tous les maillons du réseau de ceux dont la vie sorganise autour du bétail et de son commerce ou du commerce de ses produits. Malgré limpact dramatique des foyers de RVF en 2000, ceci a eu lavantage de dattirer l'attention de décideurs, dorganisations internationales et des services vétérinaires locaux sur l'importance des maladies de bétail et leurs effets possibles sur la santé humaine et les économies nationales. L'éducation vétérinaire s'est aussi améliorée de façon significative au Yémen. La qualification des épidémiologistes et la surveillance des maladies en général sen sont trouvées meilleures, ainsi que la coopération entre les services médicaux humains et les services vétérinaires. Un laboratoire national P3 devrait voir le jour prochainement avec laide de lIAEA (International Atomic Energy Agency) et de la FAO (Food and Agriculture Organization). La modernisation et l'extension de la quarantaine Al-Mukkah, est aussi prévue dans un avenir proche. La collaboration régionale, lamélioration de la connaissance du commerce du bétail mais aussi des études de terrain relatives à la maladie et à ses caractéristiques épidémiologiques sont indispensables pour espérer améloirer la prévention et le contrôle de la RVF. Mais la meilleures stragtègie pour la prevèntion de la fièvre de la vallée de Rift au Yemen comme dans le monde est de developper une surveillance plus efficace et controler des outils pour mettre en place un suivi regional coordonnée et des programmes de contrôle.

Rift Valley Fever virus (RVFV) causes an infection with severe impact on animal and human health. The disease is endemic throughout almost the entire African continent and large regions of the Arabian Peninsula. During epidemics, high mortality is observed in animals, especially among cattle, goats, and sheep. In humans, the symptoms vary from a benign influenza-like disease to a life-threatening hemorrhagic fever. Due to the devastating effect on communities in endemic regions and the possibility of further spread of this virus, there is an imperative need to improve and develop control measurements against this emerging disease. Therefore, this thesis focuses on diagnostics and vaccines against RVFV. RVFV infection kinetics was studied in a mouse model system by detection and quantification of viral genomes, using a developed quantitative real-time PCR (QRT-PCR) method. This novel QRT-PCR method proved to be reliable and serves as a supplement to standard diagnostics, direct virus isolation and serological methods. High levels of viral RNA were found in blood and liver samples from experimentally infected mice during the first days post infection. Thereafter the levels declined rapidly and dropped below detection limit approximately seven days post infection. The QRT-PCR technique was also used in a study aimed to improve diagnosis of RVFV from field samples collected on filter strips. Today, the available RVFV vaccines are only approved for animal use and these vaccines have several shortcomings. Since RVFV is a highly pathogenic organism requiring bio-safety level 3 laboratories, two different none-replicating vaccine approaches have been applied and evaluated using a mouse model. A DNA based vaccine, administered via gene-gun, and the use of virus-like particles (VLP), by the intra-peritoneal route. RVFV specific and neutralising antibodies were raised with both vaccine approaches. However, VLP vaccination against Rift valley Fever proved to be more promising as a future vaccine, since higher titres of neutralising antibodies and improved survival rate were found upon a lethal RVFV challenge in mice. In conclusion, a sensitive and specific method for quantifying RVFV infection and a promising vaccine candidate against RVFV were developed.

Rift Valley Fever Virus is a plebovirus that causes epidemics and epizootics in sub-Saharan African countries but has expanded to Egypt and the Arabian Peninsula. The laboratory rat (Rattus norvegicus) is susceptible to RVFV and has been shown to manifest the characteristic responses of humans and livestock. The rat has frequently been used as a model to study RVFV pathogenesis. Several strains have been infected and some found to be resistant to hepatic disease while others were not. This resistance was found to be associated with a dominant gene inherited in Mendelian fashion. The congenic rat strain WF.LEW and several substrains of the parental strains were used to try and locate the resistance gene. Microsatellites and single nucleotide polymorphisms were used to characterize the genomes of various rat substrains in an attempt to map the gene. Breeding and viral challenge experiments were used to further characterize the strains and assign a location to the resistance gene. The LEW/SsNHsd rats showed approximately 37% genomic difference as compared with LEW/MolTac rats, and 8% difference as compared with LEW/Crl rats. WF/NHsd rats demonstrated a difference of approximately 8% as compared with WF/CrCrl rats. Genotyping of the congenic WF.LEW revealed Lewis markers on RNO3 and RNO9. Subsequent backcross experiments and viral challenge experiments assigned the resistance gene to the distal end of RNO3.

Coccidioidomycosis (Valley Fever) is an environmentally-mediated respiratory disease caused by the inhalation of airborne spores from the fungi Coccidioides spp. The fungi reside in arid and semi-arid soils of the Americas. The disease has increased epidemically in Arizona and other areas within the last two decades. Despite this increase, the ecology of the fungi remains obscure, and environmental antecedents of the disease are largely unstudied. Two sources of soil disturbance, hypothesized to affect soil ecology and initiate spore dissemination, are investigated. Nocturnal desert rodents interact substantially with the soil substrate. Rodents are hypothesized to act as a reservoir of coccidioidomycosis, a mediator of soil properties, and a disseminator of fungal spores. Rodent distributions are poorly mapped for the study area. We build automated multi-linear regression models and decision tree models for ten rodent species using rodent trapping data from the Organ Pipe Cactus National Monument (ORPI) in southwest Arizona with a combination of surface temperature, a vegetation index and its texture, and a suite of topographic rasters. Surface temperature, derived from Landsat TM thermal images, is the most widely selected predictive variable in both automated methods. Construction-related soil disturbance (e.g. road construction, trenching, land stripping, and earthmoving) is a significant source of fugitive dust, which decreases air quality and may carry soil pathogens. Annual differencing of Landsat Thematic Mapper (TM) mid-infrared images is used to create change images, and thresholded change areas are associated with coordinates of local dust inspections. The output metric identifies source areas of soil disturbance, and it estimates the annual amount of dust-producing surface area for eastern Pima County spanning 1994 through 2009. Spatially explicit construction-related soil disturbance and rodent abundance data are compared with coccidioidomycosis incidence data using rank order correlation and regression methods. Construction-related soil disturbance correlates strongly with annual county-wide incidence. It also correlates with Tucson periphery incidence aggregated to zip codes. Abundance values for the desert pocket mouse (Chaetodipus penicillatus), derived from a soil-adjusted vegetation index, aspect (northing) and thermal radiance, correlate with total study period incidence aggregated to zip code.

The goal of this dissertation is to characterize the distribution and determinants of coccidioidomycosis in greater Tucson, Arizona, using landscape ecology and complex survey methods to control for environmental factors that affect <italic>Coccidioides</italic> exposure. Notifiable coccidioidomycosis cases reported to the health department in Arizona have dramatically increased since 1997 and indicate a potential epidemic of unknown causes. Epidemic determination is confounded by concurrent changes in notifiable disease reporting-compliance, misdiagnosis, and changing demographics of susceptible populations. A stratified, two-stage, address-based telephone survey of greater Tucson, Arizona, was conducted in 2002 and 2003. Subjects were recruited from direct marketing data by census block groups and landscape strata as determined using a geographic information system (GIS). Subjects were interviewed about potential risk factors. Address-level state health department notifiable-disease surveillance data were compared with self-reported survey data to estimate the true disease frequency.Comparing state surveillance data with the survey data, no coccidioidomycosis epidemic was detectable from 1992 to 2006 after adjusting surveillance data for reporting compliance. State health department surveillance reported only 20% of the probable reportable cases in 2001.Utilizing survey data and geographic coding, it was observed that spatial and temporal disease frequency was highly variable at the census block-group scale and indicates that localized soil disturbance events are a major group-level risk factor. Poststratification by 2000 census demographic data adjusted for selection bias into the survey and response rate. Being Hispanic showed similar odds ratio of self-reporting coccidioidomycosis diagnosis as of being non-Hispanic White race-ethnicity when controlled by other risk factors. Cigarette smoking in the home and having a home located in the low Hispanic foothills and low Hispanic riparian strata were associated with elevated risk of odds ratios for coccidioidomycosis. Sample stratification by landscape and demographics controlled for differential classification of susceptibility and exposures between strata.Clustered, address-based telephone surveys provide a feasible and valid method to recruit populations from address-based lists by using a GIS to design a survey and population survey statistical methods for the analysis. Notifiable coccidioidomycosis case surveillance can be improved by including reporting compliance in the analysis. Pathogen exposures and host susceptibility are important predictable group-level determinants of coccidioidomycosis that were controlled by stratified sampling using a landscape ecology approach.

Impulsive differential equations are useful for modelling certain biological events. We present three biological applications showing the use of impulsive differential equations in real-world problems. We also look at the effects of stability on a reduced two-dimensional impulsive HIV system. The first application is a system describing HIV induction-maintenance therapy, which shows how the solution to an impulsive system is used in order to find biological results (adherence, etc). A second application is an HIV system describing the interaction between T-cells, virus and drugs. Stability of the system is determined for a fixed drug level in three specific regions: low, intermediate and high drug levels. Numerical simulations show the effects of varying drug levels on the stability of a system by including an impulse. We reduce these two models to a two-dimensional impulsive model. We show analytically the existence and uniqueness of T-periodic solutions, and show how stability changes when varying the immune response rate, the impulses and a certain nonlinear infection term. The third application shows how seasonal changes can be incorporated into an impulsive differential system of Rift Valley Fever, and looks at how stability may differ when impulses are included. The analysis of impulsive differential systems is crucial in developing more realistic mathematical models for infectious diseases.

Master of Science / Department of Diagnostic Medicine/Pathobiology / A. Sally Davis / Rift Valley fever virus (RVFV) is a mosquito-borne, zoonotic Phlebovirus that is a significant threat to ruminants and humans. RVFV is categorized as an overlap Select Agent by the Department of Health and Human Services and US Department of Agriculture. Therefore, the study of RVFV’s pathogenesis and the development of novel diagnostic tools for the prevention and control of outbreaks and virus spread is crucial. RVF is endemic to sub-Saharan Africa but has spread beyond the continent to the Arabian Peninsula indicating the competence of the virus to emerge in new areas. Thus, the high likelihood of RVF’s spread to other non- endemic countries also spurs the need for development and implementation of rapid diagnostic tests and surveillance programs. In the US, RVFV is a Select Agent, requiring BSL-3 enhanced containment practices for research work. First, we developed a method for the detection of RVFV RNA by reverse transcriptase real-time PCR (RT-qPCR) using non-infectious, formalin- fixed, paraffin-embedded tissues (FFPET). The results from FFPET RT-qPCR were compared to prior results for fresh-frozen tissues (FFT) RT-qPCR, as well as immunohistochemistry and histopathology completed on the same FFPET blocks. We developed a novel technique using a rapid and low cost magnetic bead extraction method for recovery of amplifiable RVFV RNA from FFPET. FFPET RT-qPCR can serve as an alternative tissue-based diagnostic test, which does not require a BSL-3 research facility. Second, we assessed the diagnostic accuracy and precision of a recombinant RVFV nucleoprotein based competitive ELISA (cELISA) assay to detect RVFV antibodies. The cELISA results were compared to the virus neutralization test, the gold standard serological assay for RVFV. This prototype cELISA is easy to implement, sensitive, specific, and safe test for the detection of antibodies to RVFV in diagnostic and surveillance applications. RVF is an important transboundary disease that should be monitored on a regular basis. The diagnostic tests developed and validated in this thesis could be used in endemic or non-endemic countries for the early detection of RVF and assist with the implementation of countermeasures against RVFV.

Doctor of Philosophy / Department of Diagnostic Medicine/Pathobiology / A. Sally Davis / William Wilson / Rift Valley fever virus (RVFV) is a zoonotic arbovirus that is a significant threat to livestock and humans. It is listed as #3 for most dangerous animal threats and is in the top 10 pathogens needing urgent research in preventative and control measures. Although RVFV has never been reported in the US or Europe, outbreaks outside the African continent have sparked renewed interest in developing diagnostics and vaccines to protect both agriculture and public health. Having specific and versatile diagnostics is critical for vaccine development and application. For example, diagnostic tools that aid in identifying key immunogens and understanding the virus-host interaction directly contribute to developing protective vaccines. Additionally, vaccines that are used prophylactically or in response to an outbreak require diagnostic tests to differentiate infected from vaccinated animals (DIVA). This is critical for assessing the return to ‘disease free’ status after an outbreak. Unfortunately, there are limited RVFV diagnostic tests that are versatile and DIVA compatible with the newest RVFV vaccines. We describe the development of several diagnostic tools that are DIVA compatible for detecting RVFV nucleic acid, antibodies, and antigens. First, we evaluate a fluorescence microsphere immunoassay (FMIA) for the detection of antibodies against a RVFV surface glycoprotein and the nucleocapsid protein. The targets developed in this assay provide the basis for a DIVA-compatible serological assay with a candidate RVFV Gn/Gc subunit vaccine, as well as, offer a multiplexing platform that can simultaneously screen for several ruminant diseases. Second, we describe a novel chromogenic in situ hybridization (ISH) assay to detect RVFV in formalin-fixed, paraffin-embedded (FFPE) tissues. This molecular assay offers a highly sensitive, multiplexing platform that detects RVFV RNA on the cellular level of diagnostic tissue samples. Moreover, we demonstrate the first application of ISH as a DIVA-compatible assay for candidate RVFV gene-deletion vaccines. Third, we provide working protocols for western blot (WB), immunohistochemistry (IHC), and immunofluorescence (IF) that use monoclonal or polyclonal antibodies against key RVFV antigens. These tools can be applied to pathogenesis research and used in the development of vaccine and therapeutic countermeasures against RVFV. The RVFV diagnostic methods developed and evaluated in this dissertation can serve as a model for developing diagnostic strategies for other transboundary animal diseases.

La fièvre de la Vallée du Rift (FVR) est une zoonose émergente provoquée par un virus. La FVR affecte principalement le bétail. Chez l'Homme, la maladie peut évoluer sous deux formes mortelles: une fièvre hémorragique et une encéphalite. Malgré l'importance du fonds génétique dans l'issue de la FVR, l'identité des gènes responsables reste inconnue. Nous avons étudié les facteurs génétiques qui déterminent la sensibilité de la lignée de souris MBT/Pas et la résistance de la lignée BALB/c à la FVR. Nous avons identifié trois QTLs sur les chromosomes 2, 5 et 11, nommés, respectivement, Rvfs1, Rvfs3 et Rvfs2. Une infection des lignées congéniques correspondantes, C.MBT Rvfs1, -2 et -3, a confirmé le rôle de la région Rvfs2 dans la sensibilité à la FVR. Une analyse pathophysiologique a montré que les souris C.MBT Rvfs2 et BALB/c développent précocement une hépatite. Les souris C.MBT Rvfs2 meurent de cette hépatite aiguë. En revanche, les souris BALB/c régénèrent leur foie, ce qui leur permet de mieux tolérer l'atteinte du foie. La majorité des souris BALB/c sont décédées plus tard d'une encéphalite. Ces observations montrent que les modèles étudiés reproduisent chacune des deux formes de la maladie observées chez l'Homme. Nous avons produit des lignées sous-congéniques pour la région Rvfs2 et avons testé leur sensibilité à la FVR. Les résultats ont été croisés avec une analyse des variants de structure et de régulation présents dans l'intervalle. Cette stratégie a permis d'identifier 3 gènes candidats : Rnf213, Cd7 et Fasn. La fonction du gène Fasn suggère qu'il puisse jouer un rôle lors de la régénération du foie et ainsi être le facteur génétique que nous recherchons. / Rift Valley fever (RVF) is an emerging zoonosis caused by an arbovirus. The disease affects mainly livestock, but it can have a severe impact on human health. In humans, RVF may progress into fatal outcomes due to acute hepatitis or encephalitis. Despite the influence of the host genetic background on the outcome of the disease, the identity of causative genes remains unknown. We studied the genetic factors determining the susceptibility of MBT/Pas and the resistance of BALB/c mouse strains to RVF. We identified 3 QTLs linked to survival on chromosomes 2, 5 and 11 and named them, respectively, Rvfs1, Rvfs3 and Rvfs2. The infection of the corresponding congenic strains, C.MBT Rvfs1, 2 and 3, confirmed the role of Rvfs2 on the susceptibility to RVF. A pathophysiological investigation showed that both C.MBT Rvfs2 and BALB/c mice exhibit early onset severe hepatitis. However, while C.MBT Rvfs2 died rapidly from liver failure, BALB/c mice tolerated the liver disease and regenerated the hepatic tissue. These mice eventually died at a later stage from encephalitis. These observations indicate that each of the studied mouse models recapitulates one form of the human disease. We generated subcongenic strains harboring the Rvfs2 region and tested their susceptibility to RVF. The results were combined with high-throughput analyses of the structural and regulatory variants found in the region. Our combined approach allowed the identification of three candidate genes: Rnf213, Cd7 and Fasn. The function of the Fasn gene suggests that it could play a role in the mechanism of liver regeneration and, thus, Fasn is our best candidate gene to account for the susceptibility phenotype.