Please read the abstract in the 00front part of this document / Dissertation (MSc Agric (Production Physiology))--University of Pretoria, 2006. / Animal and Wildlife Sciences / unrestricted

Foot-and-mouth disease (FMD) is an economically devastating picornaviral disease affecting over 40 species of cloven-hoofed animals. The virus occurs as seven immunologically distinct serotypes which are characterized by high levels of intra- and intertypic variation. The three South African Territories (SAT) serotypes 1-3 are endemic to sub-Saharan Africa, a region where the epidemiology of the disease is particularly complex due to the presence of six of the seven serotypes, the role of wildlife in virus maintenance and the apparently higher levels of variation in the endemic serotypes. These factors make it imperative to establish methods suited to elucidating the regional epidemiology. One of the integral parts of this process is the genetic characterization of regionally representative viruses in order to assess the variation in the field and to clarify the role of wildlife. Nucleotide sequence data and methods suited to studying the SAT-types are however limited. A first priority was therefore to establish a PCR-based nucleotide sequencing technique targeting the highly immunogenic and phylogenetically informative 1D genome region encoding the VP1 protein. The screening of multiple serotypes and subtypes prevalent on the African continent confirmed that this method was robust and well-suited to molecular epidemiological studies in the southern Africa region. The method was first applied in the characterization of FMD virus recovered from the reproductive tract of free-living African buffalo in the Kruger National Park. Nucleotide sequencing assisted in authentication of the results and indicated that carrier status was likely, but it was not possible to unequivocally demonstrate persistent infection of FMDV. In a separate study, the role of impala antelope (Aepyceros melampus) in the epidemiology of the disease in South Africa was assessed. Genetic characterization of impala and African buffalo (Syncerus caffer) viruses collected over an eleven year period confirmed that inter-species transmission occurred on several occasions and that virus can persist in impala populations for more than 12 months. Inter-species transmission and investigation of the possible mechanisms facilitating virus transmission from persistently infected buffalo focussed on the Kruger National Park in South Africa. In order to ensure regional relevance the study was broadened to incorporate buffalo populations throughout southern Africa. Viruses of the three SAT-types recovered from diverse African buffalo populations were therefore characterized. The results reveal that independently evolving viral lineages occur in distinct geographical regions for each of the SAT-types examined and that the levels of intratypic variation are in the order of 52 - 55 % on nucleotide level across the genome region characterized. Given the strict locality-specific grouping of buffalo viruses the likely usefulness of this database for tracing the origin and course of contemporary and historical SAT-type outbreaks was investigated. Molecular epidemiological studies conclusively show that buffalo are indeed the ultimate source of infection for susceptible cloven-hoofed animals occurring in close proximity, that interspecies transmission occurs between cattle and antelope and that trans-boundary transmission of virus remains a threat to disease security in southern African countries. / Thesis (PhD (Microbiology))--University of Pretoria, 2007. / Microbiology and Plant Pathology / unrestricted

The interface between protected and communal lands presents certain challenges for wildlife conservation and the sustainability of local livelihoods. This is a particular case in South Africa, where foot-and-mouth disease (FMD), mainly carried by African buffalo (Syncerus caffer) is transmitted to cattle despite a fence surrounding the protected areas.The ultimate objective of this thesis was to improve knowledge of FMD transmission risk by analyzing behavioral patterns of African buffalo and cattle near the Kruger National Park, and by modelling at fine spatial scale the seasonal risk of contact between them. Since vegetation is considered as a primary bottom-up regulator of grazers distribution, I developed fine-scale seasonal mapping of vegetation. With that purpose, I explored the utility of WorldView-2 (WV-2) sensor, comparing object- (OBIA) and pixel-based image classification methods, and various traditional and advanced classification algorithms. All tested methods produced relatively high accuracy results (>77%), however OBIA with random forest and support vector machines performed significantly better, particularly for wet season imagery (93%).In order to investigate the buffalo and cattle seasonal home ranges and resource utilization distributions I combined the telemetry data with fine-scale maps on forage (vegetation components, and forage quality and quantity). I found that buffalo behaved more like bulk feeders at the scale of home ranges but were more selective within their home range, preferring quality forage over quantity. In contrast, cattle selected forage with higher quantity and quality during the dry season but behaved like bulk grazers in the wet season.Based on the resource utilization models, I generated seasonal cost (resistance) surfaces of buffalo and cattle movement through the landscape considering various scenarios. These surfaces were used to predict buffalo and cattle dispersal routes by applying a cumulative resistant kernels method. The final seasonal contact risks maps were developed by intersecting the cumulative resistant kernels layers of both species and by averaging all scenarios. The maps revealed important seasonal differences in the contact risk, with higher risk in the dry season and hotspots along a main river and the weakest parts of the fence. Results of this study can guide local decision makers in the allocation of resources for FMD mitigation efforts and provide guidelines to minimize overgrazing. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

The African buffalo (Syncerus caffer) is a member of one of Africa’s most well known tourist attractions and unique grouping of mammals – the ‘big five’. Historical records indicate that during the 19th century approximately 3 million African buffaloes inhabited almost the whole of sub-Saharan Africa. Several factors such as disease, habitat fragmentation, over-hunting and drought reduced the buffalo population to approximately 400 000 by 1990. The African buffalo is host to a variety of sub-acute diseases, such as bovine tuberculosis (BTB), foot-and-mouth disease (FMD) and corridor disease (CD). Disease is an important factor which influenced African buffalo populations throughout the continent and more specifically the Kruger National Park (KNP) and is largely responsible for the fact that buffaloes are restricted to enclosed areas with strict regulations imposed on their movement. The social organization of animals influences the distribution and spread of a disease - especially in the case of the African buffalo in the KNP. The emergence of BTB in the largest conservation area in South Africa (the KNP), threatens wild and domestic animals and humans who are in close proximity to the Park. The potential economic losses associated with this disease are excessive. The results presented in this thesis provide baseline information into the genetic status of sampled African buffaloes in the KNP, genetic relatedness between sampled individuals as well as BTB associations between sampled African buffaloes in the KNP, based on a limited dataset of 181 animals. Twelve microsatellite markers were used to evaluate 181 samples which were collected from 39 locations dispersed throughout the KNP. Specific population genetic parameters revealed information based on the intra and inter - relationships at the ‘per population’ level as well as at the ‘per prevalence group’ level. Evidence indicates a medium to high level of genetic diversity, a low to medium level of inbreeding (inbreeding coefficient (Fis) for each group ranges between 0.143 and 0.147) and a relatively high level of migration for buffaloes associated with each prevalence group. Pairwise relatedness estimates were determined between individuals, to reveal their level of relatedness (unrelated, full siblings, parent-offspring or half siblings), based on Queller and Goodnight’s (1989) coefficient of relatedness. Relatedness was determined on different levels, intra and interpopulation level, BTB infected and BTB uninfected group level as well as prevalence group levels. Evaluation of data based on these different levels and between different groups, painted an overall picture of the disease condition and genetic relatedness within and between sampled BTB infected and BTB uninfected buffaloes. Evidence indicated that the greater majority of our sampled African buffaloes (BTB infected or uninfected), were genetically unrelated (in terms of sibling and parent-offspring relationships), irrespective of their disease status. M. bovis infected buffaloes sampled and used in our study are not more closely related to each other than to uninfected buffaloes in the same population or prevalence group. / Dissertation (MSc)--University of Pretoria, 2010. / Production Animal Studies / unrestricted

Thesis (MScMedSc (Biomedical Sciences. Medical Biochemistry))--University of Stellenbosch, 2010. / ENGLISH ABSTRACT: Mycobacterium bovis has a wide host range and infects many wild and domestic animal species as well as humans. African buffalo (Syncerus caffer) is considered to be a wildlife reservoir of M. bovis in certain environments in South Africa, such as in the Kruger National Park (KNP) and Hluhluwe-iMfolozi Park (HiP). A detailed pathological study was conducted on 19 African buffalos (Syncerus caffer) from a herd in the HiP in South Africa. The animals tested positive to the intradermal bovine tuberculin test and were euthanazed during a test-and-cull operation to decrease the prevalence of bovine tuberculosis (bTB) in the park. The superficial, head, thoraxic and abdominal lymph nodes and the lungs were examined grossly for presence of tuberculous lesions and were scored on a 1-5 scale for macroscopic changes. The gross lesions were examined histologically and scored I-IV according to a grading system used for bTB lesions in domestic cattle. Macroscopical lesions were limited to the retropharyngeal, bronchial, and mediastinal lymph nodes and the lungs. The most frequently affected lymph nodes were the bronchial (16/19) and mediastinal (11/19). All four grades of microscopic lesions were observed, although grade II lesions were the most frequent. Acid-fast bacilli were observed only rarely. Bovine tuberculosis was confirmed by PCR analyses. All animals were in good body condition and most of the lesions were in an early stage of development, indicating an early stage of the disease. The absence of lesions in the mesenteric lymph nodes and the high frequency of lesions in respiratory tract associated lymph nodes suggest that the main route of M. bovis infection in African buffalo is inhalatory rather than alimentary. This study presents a systematic evaluation and semiquantification of the severity and stages of development of tuberculous lesions in buffalo. The results may contribute to i) the understanding of the pathogenesis of the disease, ii) the evaluation of experimental models of M. bovis infection in Syncerus caffer, and iii) the interpretation of pathological data from vaccination trials. / AFRIKAANSE OPSOMMING: Mycobacterium bovis het ‘n wye reeks van gashere en dit infekteer verskeie wilde en mak dierespesies, sowel as mense. Die buffel (Syncerus caffer) word beskou as die wild reservoir van M. bovis in sekere dele van Suid Afrika, soos in die Kruger Nasionale Park (KNP) en Hluhluwe-iMfolozi Park (HiP). ‘n Breedvoerige patologiese studie is uitgevoer op 19 buffels afkomstig vanaf ‘n trop in die HiP in Suid Afrika. Die diere het almal positief getoets vir die intradermale beestuberkulin toets en is uitgesit tydens ‘n toets-en-slag operasie met die doel om die voorkoms van beestuberkulose (bTB) in die park te bekamp. Die oppervlakkige, kop, toraks en abdominale limfknope en longe is oorsigtelik ondersoek vir die teenwoordigheid van tuberkulose letsels en was ‘n punt toegeken op ‘n skaal van 1-5 vir die teenwoordigheid van makroskopiese veranderinge. Die opsigtelike letsels is histologies ondersoek en ‘n I-IV punt toegeken volgens die gradering wat gebruik word vir bTB letsels in beeste. Makroskopiese letsels was beperk tot die retrofaringeale, brongiale, en mediastinale limfknope en in die longe. Die brongiale (16/19) en mediastinale (11/19) limfknope was meestal geaffekteerd. Al vier grade van mikroskopiese letsels is gevind, alhoewel graad II letsels die volopste was. Suur-vaste basille is slegs selde waargeneem. Beestuberkulose is bevestig deur PKR analises. Al die diere was in ‘n goeie kondisie en meeste van die letsels was in ‘n vroeë stadium van ontwikkeling, wat aandui op ‘n vroeë fase van die siekte. Die afwesigheid van letsels in die mesenteriese limfknope en die hoë frekwensie van letsels in die lugweg geassosieerde limfkliere dui daarop dat the belangrikste roete van M. bovis infeksie in die buffel deur inaseming geskied eerder as deur opname in die spysverteringskanaal. Hierdie studie bied ‘n stelselmatige evaluering en semi-kwantifisering van die graad van erns en die stadia van ontwikkeling van tuberkulose letsels in buffels. Die resultate kan bydra tot i) die begrip van die patogenese van die siekte, ii) die evaluering van eksperimentele modelle van M. bovis infeksie in Syncerus caffer, en iii) die interpretasie van patologiese data van inentingsproewe.