Rift Valley fever (RVF), is a mosquito-borne viral disease affecting humans and some species of ruminants including sheep, cattle, goats, buffalos and to a lesser extent wild animals. It is a re-emerging disease responsible for major losses in livestock production, with negative impacts on livelihoods of both commercial and resource- poor farmers in sub-Saharan African and some countries in the Middle East. It remains a threat to both endemic and non-endemic countries where competent mosquito vectors exist. The RVF virus (RVFV) causes the disease and though only a single serotype exists, differences in virulence and pathogenicity of the virus have been observed in a wide range of affected mammalian host species. This necessitates the need for a detailed genetic characterization of various isolates of the virus and whether the causal factors for host tissue tropism can be explained. Therefore, the aims of this study were to obtain comprehensive information on the genetic composition of the RVFVs circulating in South Africa between 2008 and 2010 and to differentiate these isolates based on cell infectivity and genomic parameters. In the first chapter the status of some published literature on the disease as well as the virus are reviewed. Viral characteristics, replication, assembly and release of the viral particle from the cell as well as virus-host receptors documented are also mentioned in this chapter. Chapter two focused on the genetic composition of RVFVs that caused outbreaks during 2008- 2010 in South Africa. Complete genome sequence analysis of isolates from different hosts and tissues collected at discrete foci of outbreaks were analysed and compared with virus sequences from earlier outbreaks in South Africa and from other countries. Phylogenetic analysis indicated that viruses that caused outbreaks during 2008-2010 were most probably reassortants, resulting from exchange of portions of the genome of different isolates, particularly of Segment M. In addition, the analysis indicated that the viruses were not introduced from outside the country but mutated in time and caused the outbreaks when the environmental conditions became favourable. Although no clear association between the virus genotype and phenotype has been established, various amino acid substitutions have been implicated for changes in the phenotype. The third chapter describes the characterization of isolates derived from different hosts (bovine and ovine), but from the same tissue (liver). The isolates from bovine liver presented a different growth phenotype in a cell culture-based system as well as some amino acid substitutions when compared with isolates from ovine livers. Although the codon usage patterns of the six isolates were the same, they differed with those of their hosts. Further investigation of the coding regions of the genome, molecular modelling of glycoproteins and codon usage bias failed to explain the phenotypic changes. The fourth chapter focused on an attempt to identify RVFV glycoprotein receptors using the yeast two-hybrid (Y2H) system. Baby hamster kidney cells were chosen as host cells in the laboratory because hamsters are known to be highly susceptible to RVFV. The complexity of the cDNA library constructed from BHK cells were assessed by random sequencing of 100 clones and revealed that 51 clones were genes from mRNA from the Syrian/Golden hamster using BLAST. The constructed library can also be used to study other animal pathogens such as bluetongue virus and African horse sickness virus. The constructed bait plasmids did not show any autoactivation or toxicity in yeast, thus making them suitable to be used in the Y2H system. Twelve unique clones (4 clones using transformants of the glycoprotein Gn and 8 clones using transformants of glycoprotein Gc) were screened from the cDNA library. Identification and further characterization of the clones is necessary. Sampling of the isolates that caused the 2008-2010 outbreaks in South Africa and full genome sequencing indicated that the isolates were genetically distinct, grouping in different clades, namely C and H. Reassortment have been identified in some of these isolates, particularly in their M segments. The majority of isolates that emerged in the outbreaks accumulated mutations over time while circulating in South Africa. The impact of these mutations on the pathogenicity of RVFV should be further investigated. Sequencing should be done on clinical samples directly to have a better idea of the phenotype and the effect of amino acid substitutions. Different phenotypes observed between cattle and sheep in tissue culture systems should be further investigated including investigation of different phenotypes in vivo using small experimental animals. The study has laid a foundation in understanding the pathogenicity of RVFV and necessitates the importance of understanding molecular mechanisms of the virus. / Thesis (PhD)--University of Pretoria, 2019. / Veterinary Tropical Diseases / PhD / Unrestricted

Foetal loss can be devastating to a cattle farmer. In the Free State province many commercial cattle farms contend with foetal loss due to abortion. The causes of most of these abortions are never diagnosed because of inappropriate samples submitted; diagnostics being too expensive or non-submission of samples due to ignorance. The aim of this study was to investigate the apparent seroprevalence of Brucella species and Coxiella burnetii in commercial cattle of five epidemiological units. The overall apparent seroprevalence in this study was 22% and 11% respectively for Brucella species and Coxiella burnetii antibodies. Although the presence of antibodies does not lead to a definitive diagnosis, it is now known that there are bacterial challenges in these commercial cattle, and this could form the basis of future studies. Improved education of the public as well as communication with the human health sector is necessary to effectively control brucellosis and Q-fever. / Dissertation (MSc)--University of Pretoria, 2019. / Veterinary Tropical Diseases / MSc / Unrestricted

African swine fever (ASF) has been reported and confirmed in South Africa since the early 20th century, which lead to the inception of the Swine Fever control zone in 1935. In the South African context, the sylvatic cycle is the main maintenance and transmission cycle that leads to sporadic outbreaks in the domestic pig population, particularly reported in the designated ASF control area. ASF is endemic in sub-Saharan Africa and maintains itself through three different epidemiological cycles in different regions of the continent. The current outbreaks in the Caucasus and Russia have shown the ability of African swine fever virus (ASFV) to establish itself where low biosecurity conditions exist. In South Africa, the spread of ASF has been successfully controlled in the domestic pig populations with control based on the Animal Disease Act 35 of 1984. The act prohibits the movement of all suid species and their products from the ASF control area in the north, except where special permission has been granted by the Provincial Veterinary Services. One of the key uncertainties related to climate change is potential variations in the weather patterns and fluctuations in climatic conditions that could lead to alterations in production systems and land use patterns. These in turn raise the possibility of redistribution of both the arthropod vectors and wild suids to environmentally suitable areas. It is therefore critical for the zoning of ASF that patterns of distribution of the reservoir hosts are monitored in line with the possible variations in the weather patterns around and along the ASF control line. Nonetheless, there are no known records of the reassessment of the swine fever control line, which was instituted based on the distribution of previous outbreaks and the presence of warthogs and tampans, since its inception in 1935. The objective of this study was to evaluate the distribution of the ASF disease determinants; warthogs and warthog burrows, Ornithodoros moubata and ASFV; along the ASF control line with the view of determining whether there was a need to re-align the trajectory of the line or not. A total of 304 farms were randomly selected 20 km north and 20 km south of the ASF control line from the North West, Gauteng, Limpopo and Mpumalanga Provinces through proportional weighting. A total of 73 farms from the initial sample, distributed along the ASF control line, were sampled for the presence of warthogs, warthog burrows and soft ticks of the Ornithodoros spp. (tampans). One hundred and fifty seven warthog burrows were found, of which 92% were recently used by warthogs. Tampans were recovered from 22.2% of the 63 farms where warthog burrows were found and 12.74% of the total (157) warthog burrows. Of the infested warthog burrows, only 5% (one of the twenty burrows) constituting 7.14% (one out of 14 farms) found south but in close proximity to the ASF control line, was positive for ASFV DNA. There were no warthog burrows found with PCR positive tampans north of the ASF control line. The spread of tampans beyond the ASF control line poses a question on whether the control line needs to be moved further south in the affected parts of the country. The study confirmed that the reservoirs are found beyond the current ASF control line. Although the causes for this apparent re-distribution are unclear, changes in land use and the increase in wildlife farming may contribute to this finding. Examination of weather data along the control line between 1993 and 2012 found the maximum temperatures was increasing and humidity is decreasing. In the absence of previous data on warthog and tampan distribution along the control line, the present study cannot evaluate if these changes have had an impact on the distribution of warthogs and tampans in the vicinity of the control line. This study provides baseline data for future monitoring of the control line and concluded that there was currently no need to realign the trajectory of the ASF disease control line but to conduct scheduled monitoring of the O. moubata status in the future. / Dissertation (MSc)--University of Pretoria, 2015. / tm2015 / Production Animal Studies / MSc / Unrestricted

In rural areas of developing countries like South Africa, people typically depend on goat farming for both meat and milk production due to the shortage of grazing and the higher maintenance cost of cattle. An understanding of the functionality of the mammary gland and subsequent drug transport into milk are important factors in determining milk withdrawal periods and drug residues in milk intended for human consumption. Tight cellular monolayers, cultured to resemble the in vivo blood-milk-barrier, are used to evaluate the transepithelial transport of drugs into milk in vitro. The aim of this study was to culture and maintain tight monolayers of primary Boer goat mammary epithelial cells that would be a barrier to paracellular drug movement. Cells were cultured and maintained similarly to the method described by Pantschenko and colleagues (2000), with some adaptations and with MCF10a as growth medium. The formation of tight barriers was evaluated by measuring transepithelial electrical resistance (TEER) and the paracellular movement of dextran-FITC. An aggregated monolayer was established which had the characteristic cobblestone appearance, typical of epithelial cells, with no fibroblasts seen microscopically. On day 11 the monolayers appeared to be confluent under microscopic examination, they presented a significant barrier to the movement of FD70 dextran (Papp = 0.001), and the transepithelial electrical resistance (TEER) was greater than 200 ?.cm2. At day 18 of culture, macroscopically the cells started to stack and cell debris formed, presumably due to overgrowing and cell differentiation, and the monolayers were no longer appropriate for use. Furthermore, cryopreservation techniques were performed on the cells and these cells were frozen, stored, and regrown as viable epithelial cells. Primary Boer goat mammary epithelial cells, cultured and maintained using the methods described in this dissertation, form tight monolayers that are a significant barrier to the paracellular movement of relatively large molecules like dextran70, with TEER values appropriate for xenobiotic transcellular flux studies between day 11 and 18 of culture. This timeframe corresponds with the time in which drug transfer studies are typically done in cell cultures from other species. Viable cryopreservation of Boer goat mammary epithelial cells is a useful tool that can be used to enhance these studies. / Dissertation (MSc)--University of Pretoria, 2015. / tm2016 / Paraclinical Sciences / MSc

Emerging small-scale pig farmers in Limpopo province perceive pig production and management as an important means of improving their livelihood and alternative investment option for the future. Their performance has not been optimal due to the lack of practical understanding of the basics of animal production, biosecurity and efficient production system. Thus, an attempt was made to evaluate the challenges and constrains of pig farm production systems identified and reported by emerging small scale pig farmers (ESSPF) in the province. In addition, the risk factors associated with pig movement by ESSPF by means of spatio-temporal analysis was evaluated. The study revealed that the average number of sows/farm was 7.4, while the number of boars/farm was 1.7. On average, the number of days that the sows take to return to oestrus from weaning was 42.9 days while the number of piglet s weaned/sow/year was 4.85 pigs. Also the study showed that 98.77% of ESSPF don t vaccinate their breeding stock against major pig diseases and only 2.47% ESSPF farmers had previously benefited from the infrastructure programme of the department referred to as Comprehensive Agricultural Support Programme (CASP). The majority of the respondents (82.61%) will prefer to sell their pigs at local points and within communities and only 9.32% and 14.09% will sell at the auctions or formal abattoir/supermarkets respectively. It is therefore recommended CASP be evaluated to reach and impact more pig farmers positively. Good animal husbandry and transfer of knowledge by the veterinary officials is central to the growth of farmers and their productivity. The provision of regional slaughter facilities will reduce the travelling costs to Bronkhorstspruit and Belfast, but also reduce the likelihood of the disease spread within or outside the province. The involvement of different stakeholders should be encouraged to ensure ESSPF are trained, mentored, coached, with the aim of improving their livelihood, food security and safety. / Limpopo provinsie is n belangrike vark produseerende gebied met n groot populasie van huishoudelike en wilde diere. Om die rede dien dit as n interfase tussen huishoudelike diere, mense en wilde diere.Alhoewel opkomende varkboere in die provinsie die produksie en bestuur as n belangrike verbetering in hul lewensbestaan asook alternatiewe finansiële beleggingsopsies vir die toekoms beskou, is hul prestasie nie optimaal nie as gevolg van die gebrek aan praktiese begrip van die basiese beginsels van diereproduksie, biosekuriteit en doeltreffende produksie stelsels. Dus, is 'n poging aangewend om die uitdagings en beperkings van varkplaas produksiestelsels te ïdentifiseer en die opkomende kleinskaalse varkboere (ESSPF) in die provinsie te evalueer. Bykomend is die risikofaktore wat verband hou met vark beweging deur ESSPF deur middel van tydruimtelike analise ontleed. Die studie het getoon dat die gemiddelde aantal sôe per plaas was 7,4 terwyl die aantal bere per plaas 1,7 was. Die sôe neem gemiddeld 42,9 dae om terug te keer na estrus vanaf speen, terwyl die aantal varkies gespeen / sog / jaar is 4,85 varkies. Die studie het ook getoon dat 98,77% van ESSPF nie hul teeldiere ent teen die hoof vark siektes en slegs 2,47% ESSPF boere het voorheen voordeel getrek uit die program infrastruktuur van die departement verwys na as omvattende landbou?ondersteuningsprogram (CASP). Die meerderheid van die respondente (82,61%) verkies om hul varke by plaaslike punte binne gemeenskappe te verkoop en slegs 9,32% en 14,09% onderskeidelik verkoop by veilings of formele slagpale/ supermarkte. Dit word dus aanbeveel dat CASP herevalueer om n positiewe impak te bereik by meer varkboere. Goeie veeteelt en die oordrag van kennis deur die veeartseny?amptenare is sentraal tot die groei van die boere en hul produktiwiteit. Die voorsiening van plaaslike slaggeriewe sal die reiskoste na Bronkhorstspruit en Belfast (beide buite die provinsie en tans gekiesde slagpale van die ESSPF) verminder, maar ook die waarskynlikheid van die verspreiding van siektes binne of buite die provinsie verminder. Die betrokkenheid van die verskillende belanghebbendes moet aangemoedig word om te verseker ESSPF opgelei word, gementor, afgerig, met die doel om van die verbetering van hul lewensbestaan, voedselsekuriteit en veiligheid. / Dissertation (MMedVet)--University of Pretoria, 2015. / tm2016 / Production Animal Studies / MMedVet

Small stock farming and production accounted for approximately 8.4% of total animal product based agricultural output in the 2011 / 2012 season in South Africa. Large scale commercial farming aside, small stock farming also takes on an important role in poorer and developing rural areas of South Africa, where small stock are kept for a combination of economic and non-economic reasons including financial investment or security, food and resource production, as well as religious or traditional reasons. Blowflies are Dipterids with complex life cycles and complete metamorphoses, causing damage to hides and frequent death in their ovine hosts, as a result of cutaneous myiasis caused by the larval stages. All economically important blowfly species causing veterinary myiasis belong to the superfamily Oestroidea, which contains the three major families Oestridae, Calliphoridae and Sarcophidae. The two most significant blowfly genera in South Africa, Lucillia and Chrysomya, both belong to the family Calliphoridae. Chemical means of preventing and treating blowfly strike by topical application remains the most widely used method and appears to be indispensable at this stage. New molecules or formulations effective against blowfly strike are constantly being sought and form part of an active field of research. Bayer currently manufactures and markets Drastic Deadline Extreme ®, a pour-on formulation containing flumethrin and fluazuron for the control of blue ticks (Rhipicephalus decoloratus) in cattle; its possible action against blowflies in sheep was investigated in an in-vitro model, subsequent to a pilot pharmacokinetic study evaluating the kinetics of fluazuron when applied topically to sheep in this particular combination. The first objective of the project was to determine whether fluazuron has any effect at all on the development of blowfly larvae. An active ingredient from the same family of compounds, namely triflumeron, has been successfully used for several years to control blowfly strike in sheep in South Africa (Zapp ® Pour on - Bayer), but it was uncertain whether or not fluazuron would be effective. Raw fluazuron was applied to six pieces of beef according to a dose calculation based on the registered dose of the test product in cattle, while another six pieces were treated with saline in a similar fashion (n=6). Each piece of beef was placed in its own container along with six late instar larvae and placed in the incubator at 35°C for a further nine days. In this instance, the treated group demonstrated significant development defects with regard to pupation (uneclosed pupae) when analysed using the Mann-Whitney non-parametric t-test (p = 0.002). / Dissertation (MSc)--University of Pretoria, 2016. / Paraclinical Sciences / MSc / Unrestricted

Shiga toxin-producing E. coli (STEC) is a food pathogen causing infections characterised by mild watery to severe bloody diarrhea and complications such as the hemolytic uremic syndrome (HUS). Humans acquire STEC through consumption of contaminated foods of animal origin, vegetables and water. Cattle are the main reservoir of STEC. The severity of STEC infections in humans depends on a number of virulence factors encoded in the bacterium’s genome. The seven major STEC serogroups most frequently incriminated in severe human disease outbreaks and HUS worldwide include O157, O45, O103, O111, O121, O145 and, O26, commonly referred to as the "top/big seven". Although STEC has been incriminated in human disease in South Africa, data on the role of played by cattle in human disease and virulence characteristics of cattle STEC are lacking. Therefore, the objectives of this study were to (i) investigate the presence of the seven major STEC serotypes in healthy beef cattle (cow-calf operations) and (ii) characterise isolates by serotype, virulence genes and markers, and antimicrobial resistance profiles. Polymerase chain reaction (PCR) was carried out to identify STEC serotypes (O and H antigens) and characterize the isolates by virulence factors and markers. The disk diffusion technique (Kirby Bauer test) was used to determine the antimicrobial resistance profiles of STEC isolates against a panel of 15 antimicrobials. Five hundred and seventy-eight STEC isolates (N=578), which had been previously recovered from 559 cattle from five beef farms were screened for STEC O26, O45, O103, O111, O121, O145 and O157. Confirmed STEC belonging to serogroups O26, O45, O103, O111, O121, O145 and O157 to isolates were characterised for major virulence genes including stx1, stx2, eaeA and ehxA. Furthermore, 140 isolates were characterised for xiii Shiga toxins (stx) subtypes, plasmid and pathogenicity island-encoded genes, and antimicrobials resistance profiles. / Dissertation (MSc)--University of Pretoria, 2017. / Paraclinical Sciences / MSc / Unrestricted

Brucellosis is an economically important bacterial disease of both animals and humans. In sub-Saharan Africa, the diagnosis of the disease remains a challenge. Brucellosis is underreported in South Africa, due to inconsistency in reports of bacteriological and serological tests, which lack adequate sensitivity and specificity in the diagnosis of the disease. They also are ineffective in confirming brucellosis during early stages of the disease. The aim of this study was to develop a 16S-23S ribosomal deoxyribonucleic acid (rDNA) internal transcribed spacer (ITS) quantitative polymerase chain reaction (qPCR) assay for early diagnosis of brucellosis and as a rapid screening tool. To achieve this, blood, milk and tissue samples were spiked with B. abortus biovar (bv.) 1 (B01988-18 strain) to determine the analytical sensitivity and specificity of the assay. The efficiency was 105% in tissue, 99% in blood, and 93% in milk. The 95% limit of detection (LOD) of the ITS qPCR assay was highest in tissue, followed by blood, then milk; thus (1.45, 13.30 and 45.54 bacterial genome copies/PCR reaction). Furthermore, the diagnostic performance of the assay was compared to the Brucella cell surface protein real time polymerase chain reaction (BCSP31 qPCR) assay. Out of 56 aborted foetal tissue samples from bovine, ovine and caprine, 33% (19/56) were positive for Brucella spp. The sensitivity and specificity of the ITS qPCR assay were 87% and 95% respectively, compared to the 92% and 89% for the BCSP31 qPCR assay and 47% and 55% for bacterial culture, respectively. The ITS qPCR gave earlier CT’s with a difference in CT (ΔCT) between ITS and BCSP31 ranging between 7.1 and 3.24. The assay was efficient, sensitive and specific. It detected as little as 1.45 bacterial genome copies/PCR reaction in tissue, making this assay a valuable tool in early detection of the presence of the Brucella pathogen. It is sensitive and specific in the diagnosis of brucellosis. / Dissertation (MSc)--University of Pretoria, 2019. / Veterinary Tropical Diseases / MSc / Unrestricted