M. Tech. Veterinary Technology. / Aims of this study were to: determine the suitable buffers and optimal concentrations of these buffers, to be used in the ISA 206 B oil-based vaccine formulations that will ensure pH levels of &#x2265%x; 7.0; consistent emulsion type and particle sizes following a storage period of at least 24 months at 4 C ; determine the effects of temperature on the stability of the vaccine formulation during storage ; determine the optimal buffer antigen ratio in the water phase of the ISA 206 B oil-adjuvanted FMD vaccine containing SAT serotypes ; determine the effects of saponin (Q-Vac trade mark) on the buffering capacity during storage, in the ISA 206 B oil-adjuvanted FMD vaccine containing the SAT serotypes; and determine the shelf life of this improved (stabilised) oil vaccine. Previous research by the ARC scientists has shown that the immunity elicited by the ISA 206 oil adjuvanted vaccines could persist up to 50 weeks post vaccination in cattle (Cloete et al., 2008; Hunter, 1996). However, they did not show if this immunity was protective or not. Although it is known within the FMD field that sometimes immunity levels do not always translate into protection against an infection, if protection can be shown - even after vaccination using a stored vaccines - achievement of the above mentioned objectives could enable a once-a-year vaccination regimen in the control zone of RSA. Moreover, this once-a-year vaccination regimen could also substantially reduce the logistical costs involved during vaccination campaigns, compared to the current biannual vaccination regimen. Once the shelf life of the vaccine has been established, the vaccine could also be registered as a stock remedy under the Fertilisers, Farm Feed, Agricultural Remedies and Stock Remedies Act, 36 of 1947, administered by DAFF. The registration of this vaccine could in turn enable the RSA to supply the vaccine to neighbouring South African Development Community (SADC) countries and the rest of African countries where the SAT serotypes occur.

The introduction of FMD into the US would have serious economic and societal effects on the livelihoods and sustainability of affected livestock producers. Livestock producers serve as an important line of defense in both detecting an introduction of FMD as well, helping to prevent disease spread. However, due to the complexity of moral, social, and economic issues surrounding the control of highly contagious diseases, producer cooperation during an outbreak may not be assured. This study was conducted using a mixed-methods approach, including qualitative analysis of interviews and quantitative analysis of a postal survey, in order to explore the factors likely to influence producer cooperation in FMD detection and control in Texas. Reporting of cattle with clinical signs of FMD in the absence of an outbreak was related to producers´ beliefs about the consequences of reporting, beliefs about what other producers would do, trust in agricultural agencies, and their perception of the risk posed by FMD. During a hypothetical outbreak, intentions to report were determined by beliefs about the consequences of reporting, and perception of the risk posed by FMD. Intentions to gather and hold cattle when requested during an outbreak were determined by beliefs about the consequences of gathering and holding, beliefs about barriers to gathering and holding, trust in other producers, and perception of the risk posed by FMD. Compliance with animal movement restrictions was determined by experiential attitudes, beliefs about the availability of feed, space, and disinfection procedures, beliefs about what other producers would do, and perception of the risk posed by FMD. Recommendations for improving producer cooperation include targeting specific beliefs in both planning and communication, increasing transparency in the post-reporting process, planning for and communicating plans for maintaining business continuity in order to better inform risk perception, and partnering with organizations to ensure sustained and meaningful communication that supports trust between producers within the affected agricultural community.

A Leucose Enzoótica dos Bovinos (LEB) é uma enfermidade neoplásica, infectocontagiosa, pluri-sintomática, de evolução crônica, que compromete os órgãos linfopoiéticos e está associada ao desenvolvimento de linfocitose persistente (LP) e linfossarcoma. Acarreta diminuição na produção, quer por seus efeitos danosos diretos, quer pelos indiretos. No entanto, seu efeito na função e na quantidade das diferentes subpopulações de linfócitos, assim como seu papel no estabelecimento de outras doenças oportunistas, ainda não está claro. O presente estudo avaliou a resposta imunitária de bovinos da raça Holandês Preto e Branco naturalmente infectados pelo vírus da LEB (VLB), após desafio antigênico fornecido por vacinação contra o vírus da febre aftosa. Para tal, foram coletadas amostras sanguíneas antes do desafio e, após o desafio, semanalmente, por sete semanas, de dez vacas soropositivas, sem LP; de dez vacas soropositivas, manifestando LP; e de dez vacas soronegativas. Foram avaliadas as alterações quantitativas das diferentes subpopulações de leucócitos circulantes; a função dos linfócitos B, por meio da quantificação de diferentes isotipos de imunoglobulinas (Ig) séricas; os índices de proliferação linfocitária; os índices de morte celular por apoptose ou por necrose; e as concentrações séricas de interleucina-10 (IL-10), IL-12, inteferon- (IFN-&gamma;) e fator de necrose tumoral-&alpha; (TNF-&alpha;). Foi verificada a normalidade da distribuição dos resultados obtidos, utilizando-se do teste de Anderson-Darling, e sua homoscedasticidade, utilizando-se do teste F (para dados que apresentaram distribuição normal) ou do teste de Lavene (para dados que não apresentaram distribuição normal). Para a avaliação das diferenças entre as médias dos resultados obtidos, de acordo, respectivamente, com a ocorrência ou não de homoscedasticidade, foram feitos, para dados com distribuição normal, os testes de análise de variância (One-way ANOVA), seguida do teste de Tukey-Kramer ou o teste t; e, para dados que não apresentaram distribuição normal, o teste de Mann-Whitney ou o teste de Kruskal-Wallis. Para todos os resultados, foram consideradas significantes as análises que apresentaram p&le;0,05. Verificou-se que não houve diferença nas concentrações séricas de IgG1, de IgM e de IgA, tanto entre os tempos de coleta, quanto, a cada tempo, entre animais pertencentes aos diferentes grupos. As concentrações séricas de IgG2 aumentaram, após a vacinação, em todos os animais (p<0,05). Todavia, 17 dias após o desafio antigênico, as concentrações séricas de IgG2, em animais manifestando LP foram, a cada tempo de coleta, menores (p<0,01) que aquelas verificadas nos animais pertencentes aos demais grupos, indicando que animais com LP apresentam resposta humoral menos intensa e menos duradoura. Observou-se que ocorreu um aumento no índice de proliferação de linfócitos sanguíneos (p<0,01), 24 dias após a vacinação contra o vírus da febre aftosa, independente da presença de infecção pelo VLB. A partir deste momento, ocorre um aumento na porcentagem de linfócitos &gamma;&sigma; circulantes (p<0,05) e posterior diminuição nas concentrações séricas de IgG2 (p<0,05), indicando regulação desta resposta humoral por linfócitos &gamma;&sigma;. Em bovinos com LP, o aumento na porcentagem de linfócitos circulantes foi maior (p<0,05), ocasionando diminuição mais intensa e mais precoce nas concentrações séricas de IgG2. Constatou-se que a LP ocorre em decorrência de menor índice de apoptose, posto que as porcentagens de leucócitos sofrendo processo de apoptose foram menores (p&le;0,001) entre as células obtidas de animais manifestando LP, do naquelas coletadas dos animais pertencentes aos demais grupos. Verificou-se que as concentrações séricas das citocinas de perfil Th1, IL-12 e IFN-&gamma;, são maiores em amostras sangüíneas de animais infectados pelo VLB, alinfocitóticos (p<0,01), ao passo que as concentrações séricas das citocinas de perfil Th2, IL-10 e TNF-&alpha;, são maiores em amostras sangüíneas de animais infectados manifestando LP (p<0,01), indicando que alterações no perfil sérico de citocinas podem ser causa ou consequência da LP. Em resposta ao desafio vacinal, ocorre uma elevação nas concentrações séricas de IL-10 (p<0,01), de TNF-&alpha; (p=0,005) e de IFN-&gamma; (p<0,01), três dias após o desafio, e de IL-12 (p<0,001), dez dias após o desafio. A elevação na concentração sérica de IL-10 perdura até 31 dias após o desafio e pode ser responsável pelo maior índice de proliferação de linfócitos &gamma;&sigma; verificado a partir de 31 dias após a vacinação. Foi observado que a maioria dos linfócitos B circulantes, em bovinos, consiste de linfócitos B1 e, em animais infectados pelo VLB, a LP ocorre em decorrência de um aumento na porcentagem de linfócitos B1a (p<0,05). Além disso, em animais infectados pelo VLB, apresentando LP, as relações entre linfócitos T auxiliares e citotóxicos são menores (p<0,01) e a porcentagem de linfócitos &gamma;&sigma; é maior (p<0,01), indicando atividade viral nas células infectadas. Assim, os resultados permitem-nos concluir que animais infectados pelo VLB, manifestando LP, apresentam alterações na resposta imunitária frente vacinação contra o vírus da febre aftosa. / Enzootic Bovine Leukosis (EBL) is an infectious, multi-symptomatic, chronic, neoplastic disease, which undermines the lymphopoietic organs and is associated with the development of persistent lymphocytosis (PL) and lymphosarcoma. Infected animals present a decrease of production, either by its direct or its indirect harmful effects. However, its effect on the function and quantity of different lymphocyte subpopulations, as well as its role in the establishment of other opportunistic diseases, are unclear. This study evaluated the immune response of Holstein dairy cattle naturally infected with Bovine Leukosis Virus BLV, after antigen challenge provided by vaccination against foot and mouth disease (FMD) virus. To this end, blood samples were collected before challenge and after challenge, weekly, for seven weeks, from ten seropositive cows without PL, from ten seropositive cows expressing PL, and from ten seronegative cows. We evaluated the quantitative changes of different subpopulations of leukocytes; the function of B lymphocytes, through the quantification of different isotypes of immunoglobulins (Ig) serum concentration; the rate of lymphocyte proliferation; the rate of cell death by apoptosis or necrosis; and the serum concentrations of interleukin-10 (IL-10), IL-12, inteferon-&gamma; (IFN-&gamma;), and tumor necrosis factor-&alpha; (TNF-&alpha;). It was verified the normality of distribution of the results using the Anderson-Darling test, and their homoscedasticity, using the F test (for data with normal distribution) or the Levene test (for data without normal distribution). For the evaluation of differences between the average results, according respectively to the presence or absence of homoscedasticity, we used, for data with normal distribution, One-way ANOVA test, followed by the Tukey-Kramer test or the t test, and, for data without normal distribution, the Mann-Whitney test or the Kruskal-Wallis test. Results with p&le;0.05 were considered statistically significant. There were no differences related to serum IgG1, IgM, and IgA concentrations, both among sampling time and, every time, among animals belonging to different groups. IgG2 serum concentrations increased after vaccination in all animals (p<0.05). However, in animals expressing PL, each collection time, 17 days after antigen challenge, IgG2 serum concentration was lower (p<0.01) than those observed in animals belonging to other groups, indicating that animals with PL present less intense and less enduring humoral response. It was observed that there was an increase in the rate of lymphocyte proliferation (p<0.01) 24 days after vaccination against FMD virus, irrespective of the presence of infection by BLV. From this moment, there was an increase in the percentage of &gamma;&sigma;-lymphocytes (p<0.05) and a subsequent decrease in serum IgG2 (p<0.05), indicating regulation of this humoral response by &gamma;&sigma;-lymphocytes. In cattle with PL, the increase in the percentage of &gamma;&sigma;-lymphocytes was higher (p<0.05), leading to more intense and earlier decrease in IgG2 serum concentration. It was found that PL is due to a lower rate of apoptosis, since the percentage of leukocytes undergoing apoptosis was lower (p&le;0.001) among cells obtained from animals expressing PL, when compared to those collected from animals from the other groups. It was found that serum concentrations of Th1 cytokines, specifically IL-12 and IFN-&gamma;, were higher in blood samples from nonlymphocytotic infected animals (p<0.01), whereas serum concentrations of Th2 cytokines, particularly IL-10 and TNF-&alpha;, were higher in blood samples from infected animals expressing LP (p<0.01), indicating that changes in serum cytokines profile may be a cause or a consequence of PL. IL-10 (p<0.01), TNF-&alpha; (p=0.005), and IFN-&gamma; (p<0.01) serum concentrations increased three days after the challenge, and IL-12 serum concentration increased (p<0.001), ten days after the challenge. The increase in IL-10 serum concentration lasts until 31 days after the challenge and may account for the higher rate of &gamma;&sigma;-lymphocyte proliferation found from 31 days after vaccination. It was observed that the majority of circulating B lymphocytes in cattle consists of B1 lymphocytes and that, in BLV-infected animals, PL occurs due to an increase in the percentage of B1a lymphocytes (p<0.05). Moreover, in lymphocytotic BLV-infected animals, the rate between helper and cytotoxic Tlymphocytes are smaller (p<0.01) and the percentage of &gamma;&sigma;-lymphocytes is greater (p<0.01), indicating viral activity in infected cells. Thus, results allow us to conclude that lymphocytotic BLV-infected animals show changes in the immune response after vaccination against FMD virus.

Ce travail a analysé tous les cas de HFMD déclarés à Hai Phong pendant l’épidémie de 2011 et 2012 qui a été la plus importante au Vietnam et la première enregistrée dans le nord du pays. Hai Phong a connu la plus forte incidence au Nord Vietnam. C’était donc un bon modèle pour étudier la dynamique de cette maladie sans interférence et reliquats de précédentes épidémies ou de patients immunoadaptés.La première section est consacrée à une revue de la littérature sur EV-A71 et les entérovirus. La seconde section est divisée en trois chapitres, chacun abordant un aspect spécifique du projet.Le premier chapitre aborde la dynamique de la maladie et le rôle des directives officielles pour la gestion de l’épidémie de 2011-2012. Outre les éléments de base, cette étude apporte des résultats sur l’influence des directives HFMD durant l’épidémie, ce qui n’avait pas encore été fait. La publication des directives a conduit à un accroissement du score de sévérité et d’une réduction du délai entre le premier pic de fièvre et l’admission. Cet effet est associé à un accroissement de la sensibilisation qui a conduit à déclarer la plupart des patients avec des symptômes sévères pour assurer de meilleurs traitements et suivis. Le travail décrit dans ce chapitre a aussi démontré que trois vagues avec des caractéristiques différentes et causées par trois virus différents s’étaient succédées. La vague 1 et la vague 3 ont été causées respectivement par EV-A71 et par une combinaison de CV-A6 et CV-A16 alors que la vague 2 a été causée par un virus inconnu. Ce travail est aussi une analyse intégrative incluant une analyse spatiotemporelle. La maladie semble s’être étendue vers l’est en suivant les rivières pour atteindre les des zones plus peuplées à partir desquelles elle s’est répandue par les routes secondaires locales. Etant donné l’âge moyen des patients, environ 2 ans, la source de contamination doit être cherchée chez les adultes asymptomatiques contaminés lors de leurs activités professionnelles et des mobilités locales.Le deuxième chapitre aborde la phylogénie et la distribution spatiotemporelle de EV-A71 dans le nord du Vietnam et apporte un éclairage sur l’évolution et la dynamique de cet entérovirus. La protéine de capside VP1 a été ciblée. La première conclusion de ce chapitre est que l’épidémie de 2011 et 2012 n’a pas été causée par une souche exogène mais par des souches d’EV-A71 déjà présentes au Nord Vietnam. Ceci indique qu’elles peuvent se maintenir à faible niveau, asymptomatique, en stase génomique et avec une structuration géographique. La cause de l’épidémie devrait donc être recherchée dans le tissu socio-économique plutôt que dans une émergence extérieure. Une autre conclusion de ce chapitre est la corrélation observée ente les groupes de variants I/V et phylogénie, pathogénicité et groupe ethnique. Les profils des mutations I/V aux positions 249, 262 et 284 sur la protéine VP1 pourraient jouer un rôle dans la pathogénicité, ce qui est appuyé par la corrélation entre variants I/V et sévérité/ethnicité.Le dernier chapitre aborde la modélisation mathématique d’une maladie multiphases telle que HFMD. Il est essentiel de détecter aussi tôt que possible une nouvelle vague associée à un nouvel agent. Grace à la grande taille de la cohorte disponible pour ce travail (environ 9000 patients), nous avons pu développer un système d’équations différentielles apportant une forte correspondance avec les données observées. Le modèle a confirmé l’existence de trois vagues en 2011-2012, ayant des niveaux de virulence différents. Il permet aussi de caractériser chaque vague, de détecter l’apparition d’une nouvelle vague et d’associer des groupes patients à un tableau clinique.En conclusion, ce travail de thèse a permis de souligner plusieurs éléments clés à aborder de façon coordonnée afin de faciliter une surveillance efficace de l’HFMD au Vietnam. / This work analyzed all HFMD cases reported in Hai Phong in 2011 and 2012 outbreak which was the largest to have ever occurred in Vietnam and the first recorded in the northern part of the country. Hai Phong city experienced the highest HFMD incidence in North Vietnam. It was thus a good model for investigating the dynamic of the disease without interference and potential remains from previous outbreaks or patient immunological adaptation.The first section is dedicated to a review of the literature on EV-A71 and enteroviruses. The second section is divided in three chapters, each one addressing a specific issue of the project.The first chapter addresses the dynamic of the disease and the role of official guidelines in the handling of the 2011-2012 epidemic. Beside basic epidemiological features, the study also provides findings relating to the influence of HFMD guidelines during the outbreak period that has never been described before. The guideline release led to a significant increase of the severity score and reduced delay between onset and admission. This effect is linked to an increased awareness leading to patients being mostly declared with severe symptoms in order to ensure a better treatment and surveillance. The work presented in this chapter also demonstrated that three waves occurred with different characteristics and caused by three different viruses. Wave 1 and wave 3 were caused by EV-A71 and a combination of CV-A6 and CV-A16, respectively while Wave 2 was caused by an unknown virus. This work is also an integrative analysis including a spatiotemporal analysis. The disease seems to have expanded following the eastbound river system to reach densely populated settlements from where it secondarily expanded through local roads. Owing to the average age of the patients, around 2, the source of contamination must be sought for within asymptomatic adults being contaminated during their occupational activities and in local movements.The second chapter addresses the phylogeny and spatiotemporal distribution of EV-A71 in North Vietnam and provides an insight on the evolution and dynamic of the EV-A71 enterovirus. The VP1 capsid protein was used as target. The first conclusion of this chapter is that the 2011-2012 outbreak was not caused by an incoming strain but by EV-A71 strains which were already present in North Vietnam. This indicates that they can remain in a low level, asymptomatic state, in genomic stasis and with a geographic structuration. The cause for outbreaks should thus be sought for in the socio-economic patterns rather than in exogenous emergence. Another outcome of this chapter is the observed correlation between I/V variant groups and phylogeny, pathogenicity and ethnicity. The I/V pattern at positions 249, 262 and 284 on the VP1 protein might play a role in pathogenicity. The observed correlation of the I/V variant populations with severity and ethnicity strengthen this hypothesis.The last chapter addresses the mathematical modelling of a multiphase disease such as HFMD. It is essential to detect as soon as possible the emergence of new wave, associated to a novel agent. Owing to the large size of the cohort available for this work (ca. 9000 patients), we have been able to develop a differential equation model providing a very high fit with the observed data. The model confirmed that three waves were present in 2011-2012 with differing virulence. It also allows to characterize each wave, detect the start of a new one and associate groups of patients with specific patterns of symptoms.As a conclusion, this PhD work as underlined some key issues to be addressed in a coordinated way in order help developing an efficient surveillance and monitoring system for HFMD in Vietnam.

La fièvre aphteuse (FMD pour Foot-and-mouth disease en anglais) est une maladie très contagieuse touchant les animaux biongulés. Elle provoque des dégâts économiques considérables sur toute la surface du globe. La fièvre aphteuse est provoquée par un virus, le FMDV. Il s'agit d'un virus à ARN simple brin, de polarité positive appartenant au genre Aphtovirus dans la famille Picornaviridae. Ce virus se réplique et se propage dans l'hôte très rapidement. Dans les zones infectées, les deux principales stratégies de contrôle utilisées sont l'abattage systématique des animaux infectés et la vaccination. A l'inverse, les vaccins ne sont pas utilisés dans les zones sans FMDV, mais l'apparition d'une épidémie nécessite des stratégies pour arrêter ou au moins limiter la diffusion du virus. Actuellement, les vaccins inactivés sont les vaccins les plus utilisés pour prévenir la maladie. Cependant, ils requièrent une production à grande échelle du virus, et malgré les mesures mises en place (laboratoire sécurisé, etc), des épidémies ont été provoquées par le passé du fait de la fuite de virus FMDV. De plus, il est difficile de distinguer les animaux infectés des vaccinés (DIVA). Il est donc nécessaire de développer de nouveaux vaccins. Au cours de l'infection, la polyprotéine du virus est clivée par des protéases virales en précurseurs structural (P1) et non structuraux (P2 et P3). La protéase 3C est responsable de la majorité des clivages ; ainsi, le précurseur P1 est clivé par la 3C en trois protéines structurales, VP1, VP3 et VP0, formant le protomère de FMDV, l'unité de base de la capside virale. La protéine VP1 joue des rôles importants dans l'attachement, la protection et le sérotypage. Du fait de la présence d'un site antigénique linéaire suffisant à la protection par production d'anticorps neutralisants, VP1 est considérée comme la protéine la plus immunogénique du virus. Dans cette étude, nous avons développé un nouveau vaccin contre la FMD, basé sur l'adénovirus canin de type 2 (Cav2). L'évaluation du transfert de gène médié par Cav2 chez le porc et le bétail in vitro montre des résultats prometteurs pour le développement de vaccins pour ces espèces, notamment l'expression des antigènes de FMDV par les candidats vaccins Cav2-FMDV. L'immunogénicité de ces candidats vaccins a été montrée chez les modèles murins et cobayes. De plus, des résultats encourageants ont été observés chez le cobaye, suggérant que la réponse immunitaire élicitée par les vecteurs recombinants pouvait conduire à une protection partielle des animaux après épreuve. Cependant, une optimisation de l'immunisation doit être faite dans le but de confirmer ces résultats. Ce type de vaccin peut de plus être utilisé comme vaccin marqueur, car il ne contient aucune protéine non structurale. / Foot-and-mouth disease (FMD) is a highly contagious and economically devastating disease affecting cloven-hoofed livestock worldwide. Foot-and-mouth disease virus (FMDV) is the causative agent of FMD and one of the most infectious known animal viruses. FMDV is a positive-sense, single-stranded RNA virus belonging to the Aphthovirus genus in the Picornaviridae family. FMDV replicates and spreads in the host extremely rapidly. Slaughter and vaccination are the two major strategies used to control FMD in infected countries. In FMDV-free countries, vaccines are not used, and once the disease breaks out in these areas, strategies are required to stop or at least slow the spread of the virus. Currently, inactivated vaccines are by far the most commonly used vaccines to prevent FMD. Such vaccines, however, require large-scale production of virus, and despite the use of bio-safety facilities, vaccine production has led to inadvertent virus release and FMDV outbreak. Another limitation of inactivated vaccines is the difficulty in distinguishing between infected and vaccinated animals (DIVA). Therefore, improved vaccines need to be developed.During infection, the FMDV polyprotein is cleaved into structural (P1) and non-structural (P2 and P3) precursors by a viral protease. The non-structural 3C protein is the protease that is responsible for most of the maturation events. The P1 precursor is processed by 3C protease into three structural proteins, VP1, VP3 and VP0, forming the FMDV protomer. The VP1 protein plays important roles in attachment, protective immunity and serotype specificity. VP1 is considered to be the major immunogenic protein, as it contains a linear antigenic site that is able to induce neutralizing antibodies that suffice to protect animals against the disease.In this project, we developed a novel vaccine against FMD, based on canine adenovirus type 2 (Cav2). In vitro evaluation of Cav2 mediated gene transfer in pigs and cattle showed that the Cav2 vector holds promise for the development of vaccines for pigs and cattle. Study of these recombinant viruses indicated that Cav2-FMDV supported expression of FMDV capsid proteins in vitro. The immunogenicity of these recombinant viruses was evidenced in mouse and guinea pig models, and encouraging results in guinea pigs suggested that the immune response elicited against FMD by recombinant virus could afford partial protection against FMDV challenge. In the future, immunization with Cav2-derived vector should be optimized to confirm these preliminary results. This type of vaccine, when designed to express capsid but not non-structural proteins of FMDV, can serve as a marker vaccine against FMD.

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

Development of transfrontier conservation areas (TFCAs) in southern Africa depends, among other, on the ability of stakeholders to find practical and sustainable solutions for wildlife‐livestock integration in the conservation landscape. Due to the presence of buffalo Syncerus caffer in most of the TFCAs in southern Africa, foot‐and‐mouth disease (FMD) has to be controlled in susceptible livestock species sharing the rangelands with wildlife. Conventional FMD control measures act as an additional burden on communal livestock producers and may hamper rural development and wildlife‐livestock integration even further. However, commodity‐based trade in the form of an integrated approach to the control of both food safety and disease risk along the entire beef value chain has been proposed as a more favourable alternative for ensuring market access for beef produced at the wildlife‐livestock interface. Such a non‐geographic based approach could allow for trade to continue despite high risk of FMD if appropriate disease risk and food safety measures are implemented by farmers and subsequent role players along the value chain and hence, could promote greater wildlife‐livestock compatibility. / The objective of the present study was to analyse beef production, health and trade systems of farmers at the wildlife‐livestock interface within foot‐and‐mouth disease (FMD) protection zones in order to identify challenges, risks and limitations that may limit compliance with proposed commodity‐based trade prerequisites as well as value chain participation. Based on the findings of this study a holistic, integrated approach is proposed at the village level that could be implemented to serve as an incentive for equitable participation by farmers whilst 1) addressing the risks and limitations of a farming system, 2) ensuring greater wildlife‐livestock compatibility, and 3) promote consistent market access by fulfilling the requirements of an integrated value chain approach based on commodity‐based trade standards. / A farming systems approach was used to investigate beef production, health and trade systems in FMD protection zones mainly within the Zambezi Region (ZR) of Namibia, which is situated within the KAZA TFCA (Kavango‐Zambezi Transfrontier Conservation Area), but also the Mnisi study area (MSA) in South Africa adjacent to the Great Limpopo Transfrontier Conservation Area (GLTFCA). A combined qualitative and quantitative approach was used to assess and describe farmers’ perceptions in selected study areas about beef production, trade, and wildlife conservation. Secondary data obtained from state veterinary services, the Meatco abattoir in Katima Mulilo, as well as previous studies were analysed and modelled to describe spatial‐temporal trends in trade as well as cattle distribution in relation to resource availability. / The results indicate that beef production systems in some of the most remote areas of the ZR as well as in the MSA resemble a typical low‐input low‐output production system, mainly due to the high level of risk farmers had to cope with and the limited opportunity to offset losses. The major challenges within livestock farming in all the areas studied were animal diseases, grazing competition, predation, stock theft and contact with wildlife, although the importance of each varied between study areas. Herd size effect in the MSA significantly explained the variation in attitude towards trade, production and management of cattle between farmers with below average and farmers with above average herd sizes. In the MSA, home slaughter contributed significantly more to direct household food security in households with larger herd sizes than in households with smaller herd sizes, and in the ZR farmers with smaller herd sizes were discouraged from participation in formal trade. / The attitudes and perceptions of farmers In the ZR towards wildlife and conservation often varied between survey areas as a consequence of the variation in the geophysical properties of the landscape, proximity to conservation areas, as well as the form of the interface with conservation areas. The perceived spatial‐temporal movement of buffalo varied between survey areas in the ZR. However, the frequency and nature of buffalo‐cattle interaction was generally high and intimate. Most farmers associated buffalo with risk of disease, especially FMD, but some were more concerned about grazing competition and the negative effect on husbandry practises. Farmers readily deployed traditional risk mitigation tactics in the form of kraaling at night and herding at day to control the movement of their animals and to reduce risks. Herding was found to be a potential strategy to specifically mitigate cattlebuffalo contact despite the lack of evidence that an overall strategic approach to herding exist. Although the majority of farmers in the ZR were in favour of conservation and its benefits, the negative impact of increasing wildlife numbers on farmers’ attitudes was an indication that the generally positive sentiment was changing and may in future deter conservation efforts. / Indications are that the cattle population in the ZR at its estimated density and distribution had reached the ecological capacity of the natural resource base in the ZR and animal performance and survival was therefore subjected to increased variability in resource availability linked to climate change. The cattle population’s existence at ecological capacity and the inability of farmers to offset the loss of condition in the dry season with supplementary feed were reflected in the changes in carcass quality and grades across seasons. However, there was sufficient forage produced in the ZR to sustain animal performance to some extent throughout the year, but those areas with surplus forage existed beyond the assumed grazing range around villages and perennial rivers where most cattle and wildlife concentrate. The future ability of farmers to access such underutilised grazing resources in order to strategically counter the negative consequences of climate change and growing wildlife numbers could be an important coping and risk management mechanism linked to commodity‐based trade and sustained animal quality. / Regular FMD outbreaks had a significant impact on the consistency with which the Meatco abattoir in the ZR operated between the years 2007‐2011, with negative consequences to both farmers and the abattoir itself. It was found that the formal trade system in the ZR discriminated against farmers with below average herd sizes, and that the disposition held by farmers with smaller herd sizes are most significant in areas further than approximately 55km away from quarantine camps. Vegetation type and possible contact with buffalo or previous FMD outbreaks in the area did not significantly affect market participation nor off‐take rates at a crush‐pen level in the ZR. The negative effect that distance from a quarantine station had on formal off‐take rate and the level of sales to Meatco at crush‐pen level, was the most significant in the winter months and crush‐pens situated beyond 55km from a quarantine station. The results indicate that the trade range of the Meatco abattoir was less than its trade threshold which contributed to its struggle to sustain throughput and profitability. / Finally the loss of income farmers experienced in both the ZR and the MSA during simultaneous FMD outbreaks in the year 2012 was quantified, as well as the impact it had on livelihoods in the ZR. A commodity‐based trade approach may have reduced the impact on farmers’ income significantly. However, we farmers are unable to comply with the proposed requirements for mitigating risk and ensuring food safety and quality in such communal systems in the absence of interventions to build the necessary capacity and awareness. It is recommended that at the wildlife‐livestock interface such as those investigated in this study, an integrated value chain approach to trade could serve as a catalyst to incentivise and enable farmer participation in holistic, integrated rangeland and livestock management practises that will promote conservation and rural development. / Thesis (PhD)--University of Pretoria, 2016. / The Institute for Tropical Medicine, Antwerp, Belgium / University of Pretoria / National Research Foundation of South Africa / Veterinary Tropical Diseases / PhD / Unrestricted

This dissertation reports on the technology of cell-free protein synthesis (CFPS) including 1) stabilized lyophilized cell-free systems and 2) enhanced heterogeneous cell extracts. This work further considers applications of CFPS systems in 1) rapid vaccine development, 2) functional virus-based nanoparticles, 3) site-specific protein immobilization, and 4) expanding the language of biology using unnatural amino acids. CFPS technology is a versatile protein production platform that has many features unavailable in in vivo expression systems. The primary benefit cell-free systems provide is the direct access to the reaction environment, which is no longer hindered by the presence of a cell-wall. The “openness" of the system makes it a compelling candidate for many technologies. One limitation of CFPS is the necessity of freezing for long-term viable storage. We demonstrate that a lyophilized CFPS system is more stable against nonideal storage than traditional CFPS reagents. The Escherichia coli-based CFPS system in this work is limited by the biocatalytic machinery found natively in E. coli. To combat these limitations, exogenous biocatalysts can be expressed during fermentation of cells prepared into extract. We demonstrate that simple adjustments in the fermentation conditions can significantly increase the activity of the heterogeneous extract. Towards virus-based particles and vaccines, we demonstrate that the open nature of CFPS can be utilized for coexpression of virus proteins and self-assembly of virus particles. This technique allows for the rapid production of potential vaccines and novel functional virus-based nanoparticles. Unnatural amino acids expand the effective language of protein biology. Utilizing CFPS as an expression system, we demonstrated that the incorporation of a single specific unnatural amino acid allows for site-specific immobilization, thus stabilizing the protein against elevated temperatures and chemical denaturants. Current unnatural amino acid incorporation technologies are limited to one or few simultaneous incorporations and suffer from low efficiency. This work proposes a system that could potentially allow for upwards of 40 unnatural amino acids to be simultaneously incorporated, effectively tripling the protein code. These projects demonstrate the power and versatility of CFPS technologies while laying the foundation for promising technologies in the field of biotechnology.

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Foot-and-mouth disease (FMD) is a highly contagious and economically important disease that affects even-toed hoofed mammals. The FMD virus (FMDV) is the causative agent of FMD, of which there are seven clinically indistinguishable serotypes. Three serotypes, namely, South African Territories (SAT)1, SAT2 and SAT3 are endemic to southern Africa and are the most antigenically diverse among the FMDV serotypes. A negative consequence of this antigenic variation is that infection or vaccination with one virus may not provide immune protection from other strains or it may only confer partial protection. The identification of B-cell epitopes is therefore key to rationally designing cross-reactive vaccines that recognize the immunologically distinct serotypes present within the population. Computational epitope prediction methods that exploit the inherent physicochemical properties of epitopes in their algorithms have been proposed as a cost and time-effective alternative to the classical experimental methods. The aim of this project is to employ in silico epitope prediction programmes to predict B-cell epitopes on the capsids of the SAT serotypes. Sequence data for 18 immunologically distinct SAT1, SAT2 and SAT3 strains from across southern Africa were collated. Since, only one SAT1 virus has had its structure elucidated by X-ray crystallography (PDB ID: 2WZR), homology models of the 18 virus capsids were built computationally using Modeller v9.12. They were then subjected to energy minimizations using the AMBER force field. The quality of the models was evaluated and validated stereochemically and energetically using the PROMOTIF and ANOLEA servers respectively. The homology models were subsequently used as input to two different epitope prediction servers, namely Discotope1.0 and Ellipro. Only those epitopes predicted by both programmes were defined as epitopes. Both previously characterised and novel epitopes were predicted on the SAT strains. Some of the novel epitopes are located on the same loops as experimentally derived epitopes, while others are located on a putative novel antigenic site, which is located close to the five-fold axis of symmetry. A consensus set of 11 epitopes that are common on at least 15 out of 18 SAT strains was collated. In future work, the epitopes predicted in this study will be experimentally validated using mutagenesis studies. Those found to be true epitopes may be used in the rational design of broadly reactive SAT vaccines / Life and Consumer Sciences / M. Sc. (Life Sciences)