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Molecular Epidemiological Study of Canine Rabies in the Free State Province (South Africa) and Lesotho

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Molecular Epidemiological Study of Canine Rabies in the Free State Province (South Africa) and Lesotho Molecular epidemiological study of canine rabies in the Free State province (South Africa) and Lesotho by Chuene Ernest Ngoepe Submitted in partial fulfilment of the requirements for the degree MASTERS OF SCIENCE (Microbiology) in the Department of Microbiology and Plant Pathology Faculty of Natural and Agricultural Science University of Pretoria Pretoria, South Africa Supervisor: Prof L H Nel Co-supervisor: Dr C T Sabeta July 2008 © University of Pretoria I declare that the dissertation which I hereby submit for the degree MSc at the University of Pretoria, South Africa is my own work and has not been submitted for a degree at another university Chuene Ernest Ngoepe i ACKNOWLEDGEMENTS I would like to thank the following people for their contribution towards the completion of this project: Dr. C. T. Sabeta (Onderstepoort Veterinary Research Institute) Prof. L. H. Nel (University of Pretoria) Prof. T. Musoke (Onderstepoort Veterinary Research Institute) Ms. Debrah Mohale (Onderstepoort Veterinary Research Institute) Dr. Mojapelo [Free State province, Department of Agriculture (veterinary services)]. Students and colleagues at Onderstepoort Veterinary Research Institute and University of Pretoria My family for their support they showed throughout this project. Funding for this project Department of Science and Technology (DST) Agricultural Research Council-Onderstepoort Veterinary Institute (ARC-OVI) Poliomyelitis Research Foundation (PRF) Department of Agriculture (DoA) Give thanks to Almighty God for the wisdom and strength He gave me that kept me going during the project. ii SUMMARY Molecular epidemiological study of canine rabies in the Free State province (South Africa) and Lesotho by Chuene Ernest Ngoepe Supervisor: Prof. L. H. Nel Department of Microbiology and Plant pathology University of Pretoria Co-supervisor: Dr. C. T. Sabeta Virology, Rabies Unit Onderstepoort Veterinary Research Council Department of Microbiology and Plant pathology For the MSc degree (Microbiology) There are two rabies virus biotypes recognized in southern Africa namely; the canid and mongoose rabies virus biotypes. The host vectors of canid rabies biotype in South Africa are domestic dogs, black-backed jackals and bat-eared foxes, whereas the mongoose rabies biotype is maintained by the yellow mongoose. The canid rabies virus was introduced into southern Africa from Angola (1940s) and spread within the sub- continent, firmly establishing itself in the domestic dog population in Zimbabwe (1950s) and South Africa (1960s). Canine rabies became established in the coastal regions of South Africa (KwaZulu Natal) in 1976 where it has been problematic ever since. Historical data demonstrate that canine rabies has spread from KwaZulu Natal into the north-eastern corner of Lesotho in 1982, spreading throughout the country and reaching the western border of Lesotho and South Africa (FS province) in the mid-1980s without penetrating into this region of South Africa. iii In contrast, the historical evidence suggests that mongoose rabies virus existed in southern Africa in the early 1800s. Mongoose rabies was confirmed in 1928 in South Africa and since then was consistently diagnosed in the yellow mongoose with apparent spill over into domestic animals on the central plateau of South Africa. The FS province was mainly associated with mongoose rabies; however, recent studies utilizing antigenic characterization have suggested an increase of the canid rabies biotype of RABV since the late 1990s, peaking in 2002. The aim of this investigation was to better understand the molecular epidemiology of canine rabies in the FS province by establishing genetic relationships between rabies viruses obtained from FS province and Lesotho, with the purpose of determining the origin of canine rabies into the province and the radiation of mongoose rabies biotype of RABV into dog host. The coding region of cytoplasmic domain of glycoprotein gene and G-L intergenic region of 113 rabies viruses from FS province and Lesotho was amplified and sequenced. It was found that canid rabies virus isolates from the FS province and those from Lesotho were very closely related demonstrating a mean nucleotide sequence homology of 99%. This result indicated a single overlapping epidemiological rabies cycle between the two regions. The results also confirmed that the spill over of mongoose rabies virus into dog host does not establish dog to dog transmission and therefore leads to dead end infection. Therefore parenteral vaccination of domestic dogs and cats remains an important priority in any effort to control rabies in these regions. iv TABLE OF CONTENTS Acknowledgements ………………………………………………………………. i Summary …………………………………………………………………………. iii-iv List of abbreviations……………………………………………………………… vii-ix List of figures and tables ………………………………………………………… x Chapter 1: General Introduction 1.1 Historical perspectives of rabies ………………………………………………. 2 1.2 Classification of lyssaviruses ………………………………………………….. 2-4 1.3 The rabies virus ………………………………………………………………... 4 1.3.1 Morphology ………………………………………………………………….. 4-5 1.3.2 Biochemical properties of the virus …………………………………………. 5 1.3.3 Pathogenicity and symptoms ………………………………………………... 6-8 1.3.3 Organization of the rabies virus genome ……………………………………. 8 1.3.3.1 The nucleoprotein (N) ……………………………………………………... 8-9 1.3.3.2 The phosphoprotein (P) ……………………………………………………. 9-10 1.3.3.3 The matrix protein (M) ……………………………………………………..10 1.3.3.4 The glycoprotein (G) ……………………………………………………….10-11 1.3.3.5 The RNA polymerase (L) …………………………………………………..11-12 1.3.3.6 Non-coding regions of the viral genome …………………………………...12 4. Transcription and replication …………………………………………………….12-14 5. The quasispecies theory ………………………………………………………….14-15 6. Rabies control ……………………………………………………………………15 6.1 Techniques for rabies diagnosis ………………………………………………..16 6.2 Vaccines ………………………………………………………………………..17-18 6.3 Pre and post exposure prophylaxis ……………………………………………..18-19 7. The epidemiology of rabies …………………………………………………….19-20 7.1 Europe and North America ……………………………………………………. 20-22 7.2 Asia and Africa …………………………………………………………………22-23 7.3 Southern Africa …………………………………………………………………23-24 Chapter 2: Literature review 2.1 The host species ………………………………………………………………...26-28 2.2 Differentiation of lyssaviruses ………………………………………………….28-29 2.3 The intergenic regions of rabies virus genome …………………………………29-31 2.4 Phylogenetic methods …………………………………………………………..31-33 2.5 Free State province ……………………………………………………………..33-38 2.6 The kingdom of Lesotho ………………………………………………………..39-42 2.7 Aims of the project ……………………………………………………………...42 v Chapter 3: Materials and Methods 3.1 Viruses ………………………………………………………………………….44 3.2 Viral RNA extraction …………………………………………………………..44 3.3 cDNA synthesis ………………………………………………………………...45 3.4 Polymerase Chain Reaction (PCR) …………………………………………….45 3.5 DNA purification and nucleotide sequencing ………………………………….46-47 3.6 Phylogenetic analysis …………………………………………………………..47 Chapter 4: Results ………………………………………………………………..51-73 Chapter 5: Discussion …………………………………………………………….74-80 Chapter 6: Conclusion ……………………………………………………………81-84 REFERENCES ……………………………………………………………………..85-106 APPENDIX 1 ………………………………………………………………………108 APPENDIX 2 ………………………………………………………………………110 APPENDIX 3 ………………………………………………………………………111 APPENDIX 4 ………………………………………………………………………131 APPENDIX 5 ………………………………………………………………………150 COMMUNICATIONS …………………………………………………………….161 PUBLICATIONS ………………………………………………………………….161 vi LIST OF ABBREVATIONS A Adenosine aa Amino acid ABLV Australian Bat Lyssavirus A.D. Anno Domino ATP Adenosine triphosphate B.C. Before Christ BHK Baby Hamster Kidney cells bp Base pairs cDNA Complementary DNA oC Degrees Celsius CNS Central Nervous System CVS Challenge virus strain Da Daltons DNA Deoxyribonucleic acid dNTPs Deoxyribonucleotide triphosphate EBLV 1 European Bat Lyssavirus type 1 EBLV2 European Bat Lyssavirus type 2 EC Eastern Cape EDTA Ethylene-Diamino-Tetra-Acetate ERA Evelyn Rokitniki Abelseth et al and others FAT Fluorescent antibody test FS Free State g Grams GABA Gamma Amino Butyric Acid G Glycoprotein GGP Gross geographic product gt Genotype HDCV Human diploid cell vaccine vii HEP High egg passage i.e. In other words kb Kilobase Km Kilometer KZN Kwazulu Natal L Polymerase protein MEGA Molecular Evolutionary Genetic Analysis mRNA Messenger ribonucleic acid M-MLV Moloney Murine Leukemia Virus mABs Monoclonal antibodies MgCL2 Magnesium Chloride MIT Mouse inoculation test mm Millimetre mg Milligrams mM milliMolar M Matrix protein N Nucleoprotein nAChR Acetylcholine receptor NCAM Neuronal cell adhesion molecule NICD National Institute for Communicable Diseases NJ Neighbour joining method nm Nanometer OIE Office International des Epizooties OVI Onderstepoort Veterinary Institute P75NTR p75 neurotrophin receptor P Phosphoprotein PCEC Purified chick embryo cell PCR Polymerase chain reaction pmol Picomolar PV Pasteur virus RNP Ribonucleoprotein viii RNA Ribonucleic acid rNTPs Ribonucleoside triphosphates RABV Rabies virus RTCIT Rabies tissue culture infection test RT-PCR Reverse transcriptase polymerase chain reaction RNAsin Ribonucleic acid enzymes inhibitor SAD Street-Alabama-Dufferin SAG 1 Avirulent-Gif Street Alabama Dufferin type 1 SAG 2 Avirulent-Gif Street Alabama Dufferin type 2 UV Ultraviolet µl Microlitre USA United States of America VNAs Virus neutralizing antibodies VRG Vaccinia rabies glycoprotein recombinant virus WHO World Health Organization VSV Vesicular Stomatitis Virus WCBV Western Caucasian Bat Virus Ψ Pseudo gene ix List of figures and
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