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Molecular Screening of Potential Bat-Borne

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Molecular Screening of Potential Bat-Borne MOLECULAR SCREENING OF POTENTIAL BAT-BORNE HANTAVIRUSES AND DETERMINATION OF SPECIES RICHNESS AND COMPOSITION OF BATS IN SELECTED HABITATS WITHIN THE WOODLAND AND SAVANNA BIOMES IN NAMIBIA A THESIS SUBMITTED IN FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE IN BIOLOGY AT THE UNIVERSITY OF NAMIBIA BY Augustinus Tumbo Mbangu (Student number: 9999078) April 2020 Supervisors: Prof. J.K.E. Mfune (University of Namibia) Dr S. Weiss (Charite University) ii ABSTRACT Bats are present and they play unique ecological roles in various habitats in Namibia. Yet the patterns of species richness and composition of bats associated with these habitats within different biomes in Namibia still remain unknown. Bats are also important carrier hosts and transmitters of zoonotic viruses of public health significance including old and emerging hantaviruses. The burden of hantavirus disease is globally well-documented but this remains unknown and unrecognised in many African countries including in Namibia. This study investigated the patterns of species richness and composition of bats as well as the potential prevalence of bat-borne hantaviruses at selected habitats in the broad-leaved tree and shrub savanna, and the Acacia tree and shrub savanna biomes in Namibia. Live bats were sampled using Dinier mist nets, biometrically processed and the species identifications were morphologically and molecularly determined. Blood and organ tissue samples were collected from live and sacrificed bats respectively, and they were molecularly screened for hantavirus using the two-step Pan-Hanta RT- PCR technique. A total of 219 bat captures were recorded from 17 selected habitats in both the broad-leaved tree (n = 7) and Acacia tree (n = 10) savanna biomes. Only 103 bat lung and blood samples were collected and screened for hantavirus. No hantavirus however was detected. A combined total of 11 species of bats were recorded from selected habitats in both biomes, and these included the following four families of the order Chiroptera: 1) Pteropodidae (1 species); 2) Molossidae (3 species); 3) Vespertilionidae (5 species); and 4) Rhinolophidae (2 species). Seven bat species were observed in selected habitats in the broad-leaved and eight in the Acacia tree savanna biomes, while 9 and 12 species, iii respectively, were predicted. Species richness of bats did not differ significantly across the biomes. In addition, there was no significant difference in species composition between selected habitats in the two biomes. Thus the influence of the biomes on the species richness and composition of bats appears to be minimal at a broad spatial scale. The results indicate a compositional overlap in species of bats in selected habitats across biomes which suggest that the two biomes broadly harbour similar species. Habitats characterised by riparian vegetation, non- perennial riverine vegetation, and semi-urban environments were up to four times more species rich than other habitats. These habitats may represent important areas that support high species richness of bats characterised by variable patterns of species composition, based on species habitat requirements. In addition, four highway bridges at selected habitats in the Acacia tree and shrub savanna biomes showed high abundance of Robert’s flat-headed bat (Sauromys petrophilus), indicating the importance of bridges to the roosting ecology and hence conservation of the species. Since no hantavirus could be detected, future detection of hantavirus and to gain more insights into our understanding of in situ patterns of bat species richness and composition may require more intensive sampling efforts and screening of bats in various habitats, and using a range of active (e.g., mist nets and harp traps) and passive (e.g., acoustic recording devices such as an Anabat) efforts. Key words: hantavirus, bats, species richness and composition, molecular techniques, cytochrome b, Namibia iv DEDICATION This thesis is dedicated to the honour and memory of my late parents Kefas and Lahja who encouraged, insisted and sacrificed all the little they had to get me educated. May they both continue to Rest in Eternal Peace! v ACKNOWLEDGEMENTS I would like to extend many thanks and gratitude to the following; without whom the completion of this work would not have been possible: I give Glory to God for the gift of life, good health and for protecting us from all the long distance drives and late night work on bats, at times in strange and isolated places, without a single incident. I appreciate my main supervisor, Prof John K. Mfune for his mentorship, guidance, supervision and companionship during the difficult nights of trapping bats. His guidance and comments during the write up of the thesis is highly appreciated. I am grateful to my co-supervisors, Dr Peter Witkowski and Dr Sabrina Weiss for their guidance and advice on matters relating to molecular techniques in the laboratory as well as sequence analysis. I would also like to thank Dr Ndapewa Iithete for Pan-Hanta RT- PCR training and guidance, Dr E. Kwembeya, for advice on data analysis, my comrades, Kaveire Kaitjizemine and Dr Uzabakiriho for unquestioned support, and Prof P. Chimwamurombe and Ms F. Kangombe for their advice during the proposal drafting stage of my study. I also thank the hantavirus research project (DFG) for funding the research project. Moreover, my gratitude is also extended to colleagues in the Department of Biological Sciences, my friends, and family for their support and encouragement. vi DECLARATION I, Augustinus T. Mbangu, hereby declare that this study is my own work and is a true reflection of my research, and that this work, or any part thereof has not been submitted for a degree at any other institution. No part of this thesis/dissertation may be reproduced, stored in any retrieval system, or transmitted in any form, or by any means (e.g., electronic, mechanical, photocopying, recording or otherwise) without the prior permission of the author, or The University of Namibia in that behalf. I, Augustinus T. Mbangu, grant The University of Namibia the right to reproduce this thesis in whole or in part, in any manner or format, which The University of Namibia may deem fit. ……………………… ……………... ……………….. Name of Student Signature Date vii LIST OFACRONYMS ANDV Andes virus ANOSIM Analysis of Similarity ATSS Acacia tree and shrub savanna (biome) BLAST Basic Local Alignment Search Tool BLTSS Broad leaved tree and shrub savanna (biome) BOWV Bowie virus DNA Deoxyribonucleic acid DOBV Dobrava-Belgrade Virus EHF Epidemic hemorrhagic fever ELISA Enzyme linked immunosorbent assay GPS Global Positioning System HCA Hierarchical cluster analysis HCPS Hantavirus cardiopulmonary syndrome HFRS Hemorrhagic fever with renal syndrome HPS Hantavirus pulmonary syndrome HTNV Haantan virus IFA Indirect fluorescent assay IFAT Immunofluorescent antibody test IgM Immunoglobulin M KHF Korean hemorrhagic fever M Medium MGBV Magboi Virus N Nucleocapsid protein NCBI National center for Biotechnology information NE Nephropathia Epidemica viii NSs Non structural proteins OKH Okahandja OPW Opuwo PCR Polymerase chain reaction PUUV Pumaala Virus PRNT Plague reduction neutralization test RNA Ribonucleic acid RT-PCR Reverse transcriptase polymerase chain reaction SARS-CoV Severe Acute Respiratory Syndrome-Coronavirus SEOV Seoul virus SNV Sin Nombre virus TANGV Tanganya virus TULV Tula virus UNAM University of Namibia USA United States of America WHK Windhoek WHO World health organisation ix TABLE OF CONTENTS ABSTRACT ................................................................................................................................... II DEDICATION ............................................................................................................................. IV ACKNOWLEDGEMENTS .......................................................................................................... V DECLARATION ......................................................................................................................... VI LIST OFACRONYMS ............................................................................................................... VII TABLE OF CONTENTS ............................................................................................................ IX LIST OF TABLES .................................................................................................................... XIII LIST OF FIGURES ...................................................................................................................XIV LIST OF APPENDICES ......................................................................................................... XVII CHAPTER 1 ................................................................................................................................... 1 INTRODUCTION .......................................................................................................................... 1 1.1 General introduction ............................................................................................................... 1 1.2 Statement of the problem ........................................................................................................ 5 1.3 Aims and objectives ................................................................................................................ 7 x 1.4 Research questions .................................................................................................................
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