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This Thesis Has Been Submitted in Fulfilment of the Requirements for a Postgraduate Degree (E.G This thesis has been submitted in fulfilment of the requirements for a postgraduate degree (e.g. PhD, MPhil, DClinPsychol) at the University of Edinburgh. Please note the following terms and conditions of use: • This work is protected by copyright and other intellectual property rights, which are retained by the thesis author, unless otherwise stated. • A copy can be downloaded for personal non-commercial research or study, without prior permission or charge. • This thesis cannot be reproduced or quoted extensively from without first obtaining permission in writing from the author. • The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the author. • When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given. Antigenic diversity in Theileria parva in vaccine stabilate and African buffalo Johanneke Dinie Hemmink PhD University of Edinburgh 2014 I declare that the work presented in this thesis is my own original work, except where specified, and it does not include work forming part of a thesis presented successfully for a degree in this or another university. Johanneke Dinie Hemmink Edinburgh 2014 Abstract Theileria parva is a tick-borne intracellular protozoan parasite which infects cattle and African buffalo in Eastern and Southern Africa. Cattle may be immunised against T. parva by the infection and treatment method (ITM), which involves inoculation with live sporozoites and simultaneous treatment with oxytetracycline. One such ITM vaccine is the Muguga Cocktail, which is composed of a mixture of three parasite stocks: Muguga, Serengeti-transformed and Kiambu 5. Although the vaccine has been used with success in the field in several areas in Eastern Africa, there is evidence that vaccination using cattle-derived parasites does not always provide adequate protection against buffalo-derived T. parva. A number of T. parva antigens recognised by CD8+ T cells from cattle immunised by ITM have been identified in previous studies. A proportion of these antigens show a high degree of sequence polymorphism and allelic diversity is believed to be much greater in buffalo-derived T. parva than in cattle-derived parasites. The present study focussed on the development and application of a deep sequencing technique for characterising genotypically heterogeneous T. parva DNA samples. A panel of genes encoding CD8+ T cell antigens was used as the basis of a multi-locus sequence typing system (MLST) built upon Roche 454 amplicon sequencing technology. This system was validated using parasite stocks of known composition and then utilised to investigate genetic and antigenic diversity in vaccine stabilates and samples derived from African buffalo. The MLST profile obtained for the Muguga Cocktail stocks was compared to those of African buffalo in two geographically separated sites and was also compared with micro/mini-satellite DNA profiles of Muguga Cocktail stocks. The three components of the T. parva Muguga Cocktail vaccine were found to have limited genotypic and antigenic diversity using both methods. The composition of vaccine batches produced in a single production run (ILRI0801-ILRI0804) was shown to be relatively consistent. In contrast, the composition of the component stocks was shown to alter following passage through cattle and ticks. The deep multi- locus sequence profile and satellite DNA profile established in this study may be used as a reference for comparison with future vaccine batches. It is suggested that i formulation of a new cocktail vaccine containing three parasite clones selected on the basis of genotypic and antigenic divergence may well provide protection comparable to that obtained with the Muguga Cocktail. The components of such a vaccine could readily be distinguished and the composition of vaccine batches monitored, thus allowing improved quality control and greater consistency of the vaccine. Genetic and antigenic diversity was found to be very high in parasite populations from African buffalo from the Kruger National Park, South Africa and the Ol Pejeta conservancy, Kenya. The estimated average genetic ‘distance’ between any two alleles in the Kruger National Park and within the Ol Pejeta conservancy was very similar for all six genes investigated. Many of the identified alleles were ‘private’ to either the buffalo from Ol Pejeta or the Kruger National Park and many of these alleles were present in several individuals in one location. Principal co-ordinate analysis and phylogenetic investigation of several antigen-encoding loci indicated that extant buffalo parasite populations are geographically sub-structured although some of the underlying diversity may reflect ‘ancient’ polymorphism in an ancestral population. A subset of the CD8+ T cell antigens examined exhibited extensive antigenic polymorphism while others were highly conserved at the amino acid level. These conserved genes may represent good candidates for the development of next generation vaccines, as strain specificity may be overcome if protective CD8+ T cell responses could be generated against these conserved antigens. This would enable the use of sub-unit vaccines in areas where cattle co-graze with buffalo. Theileria sp (buffalo) was identified in cell lines isolated from cattle, indicating that this parasite can transform bovine lymphocytes and may therefore be implicated in pathology in cattle. Phylogenetic analysis of T. parva and T. sp (buffalo) clones using the 5S subunit ribosomal RNA gene, Tp6, Tp7 and Tp8 showed a clear distinction between the two parasite species. These genes could thus be considered as candidates for an improved diagnostic test for T. parva in South Africa. ii Acknowledgements0B Firstly, I would like to thank my supervisor Ivan Morrison, for all the advice, help and discussions about my work. I also would like to thank all the other members of the group. Especially the coffee breaks in the morning gave me the feeling to be part of a group. The discussions about science, life and random subjects often revived me. I would also like everyone at the University of Glasgow for welcoming me on several occasion and Willie Weir for his great input into my PhD work. The days scheduled of tryps to help me with bioinformatics and population genetics are greatly appreciated. Your helpful and positive encouragement is much appreciated. I am also grateful I had the opportunity to spend time at ILRI to work on several aspects of my work. It is great to feel so welcome in another country. Thanks everyone on campus and all others I interacted with outside the campus. I especially like to thank the people that helped me in the lab or with the animal work: Elias, Rosemary, Thomas and Stephen. Not to forget Nick for hosting me during one of my visits. Thanks to all the people I have lived with over the years. It was a pleasure sharing a house with you and to be able to share the ups and downs of life with you. I also would like to thank my family for all their support and beliefs in me. Especially, my dad had an unbelievable faith I would succeed (RIP). I also would like to thank all my friends in the UK, the Netherlands and elsewhere in the world for their friendship and support in sometimes difficult times. Lastly, I would like to thank Dennis for all his support and love for the time we have known each other. iii Table of Contents Abstract .........................................................................................................................i Acknowledgement ......................................................................................................iii Table of contents.........................................................................................................iv List of figures ............................................................................................................... x List of tables.............................................................................................................. xiv Abbreviations………………………………………………………………………xvii Chapter 1: General introduction................................................................................... 1 1.1 Theileria parva................................................................................................... 1 1.1.1 Life-cycle .................................................................................................... 1 1.1.2 Clinical signs and nomenclature ................................................................. 4 1.1.3 Diagnosis..................................................................................................... 5 1.1.4 Control of T. parva...................................................................................... 6 1.2 The Muguga cocktail ......................................................................................... 8 1.2.1 Introduction................................................................................................. 8 1.2.2 Vaccine stabilate production – Muguga Cocktail....................................... 9 1.2.3 Challenges in the vaccine production process .......................................... 12 1.3 Characterisation of vaccine stabilates.............................................................. 13 1.4 Characterisation of Theileria parva in the field ............................................... 15 1.4.1 DNA probes and Restriction Fragment length polymorphism (RFLP)
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