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Impact of Irrigation Expansion on the Inter-Epidemic and Between-Season Transmission of Rift Valley Fever in Bura Sub-County, Tana River County, Kenya

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Impact of Irrigation Expansion on the Inter-Epidemic and Between-Season Transmission of Rift Valley Fever in Bura Sub-County, Tana River County, Kenya Aus dem Institut für Parasitologie und Tropenveterinärmedizin des Fachbereichs Veterinärmedizin der Freien Universität Berlin und dem International Livestock Research Institute Impact of irrigation expansion on the inter-epidemic and between-season transmission of Rift Valley fever in Bura Sub-County, Tana River County, Kenya Inaugural-Dissertation zur Erlangung des Grades eines PhD in Biomedical Sciences an der Freien Universität Berlin vorgelegt von Deborah R. Nyakwea Mbotha aus Nairobi, Kenia Master of Science in Veterinary Epidemiology Bachelor of Veterinary Medicine Berlin 2020 Journal-Nr.:4201 Gedruckt mit Genehmigung des Fachbereichs Veterinärmedizin der Freien Universität Berlin Dekan: Univ.-Prof. Dr. Jürgen Zentek Erster Gutachter: Prof. Dr. Peter-Henning Clausen Zweiter Gutachter: Prof. Dr. Johanna Lindahl Dritter Gutachter: Univ.-Prof. Dr. Ard Nijhof Deskriptoren: rift valley fever, rift valley fever virus, phlebovirus, emerging infectious diseases, irrigation, land use planning, culicidae, species diversity, polymerase chain reaction, kenya Tag der Promotion: 14.08.2020 Dedicated to my beloved little girl, Keanna Nwoke (Kikki) Table of contents Table of Contents List of abbreviations ................................................................................................................ iii Preface ...................................................................................................................................... iv 1.0 CHAPTER 1: Introduction .................................................................................................. 1 1.1 Background of the thesis ............................................................................................... 1 1.2 Scope and objectives of the thesis ............................................................................... 2 1.3 References ...................................................................................................................... 4 2.0 CHAPTER 2: Literature review .......................................................................................... 7 2.1 Rift Valley fever ............................................................................................................... 7 2.1.1 RVF transmission and disease ............................................................................... 8 2.1.2 RVF Epidemiology ................................................................................................... 9 2.1.3 The Virus..................................................................................................................11 2.1.4 The hosts .................................................................................................................12 2.1.5 The vectors ..............................................................................................................14 2.1.6 Risk factors for the emergence and re-emergence of RVF ..................................15 2.1.7 Mosquito surveillance .............................................................................................16 2.2 References .....................................................................................................................22 3.0 CHAPTER 3: Publication 1 ...............................................................................................34 3.1 Inter-epidemic Rift Valley fever virus seroconversions in an irrigation scheme in Bura, south-east Kenya.................................................................................................34 3.1.1 Abstract ...................................................................................................................35 3.1.2 Introduction .............................................................................................................36 3.1.3 Materials and Methods ............................................................................................37 3.1.4 Results .....................................................................................................................42 3.1.5 Discussion ...............................................................................................................47 3.1.6 Acknowledgement ..................................................................................................49 3.2 References .....................................................................................................................50 4.0 CHAPTER 4: Publication 2 ...............................................................................................54 4.1 Relative Distribution, Diversity, and Bloodmeal Sources of Mosquitoes and Known Vectors of Rift Valley Fever Phlebovirus in Three Differing Ecosystems in Bura, Tana River County, Kenya ............................................................................................54 4.1.1 Abstract ...................................................................................................................55 4.1.2 Introduction .............................................................................................................56 4.1.3 Materials and Methods ............................................................................................56 i Table of contents 4.1.4 Results .....................................................................................................................59 4.1.5 Discussion ...............................................................................................................73 4.1.6 Conclusion ..............................................................................................................74 4.1.7 Acknowlegement .....................................................................................................75 4.2 References .....................................................................................................................76 5.0 CHAPTER 5: Overall discussion and recommendations ...............................................79 5.1 Impact of irrigation expansion on mosquito density and diversity in Bura Sub- County, Tana River County...........................................................................................80 5.2 Conclusion and recommendations for future study ...................................................82 5.3 References .....................................................................................................................84 Summary .................................................................................................................................86 Zusammenfassung .................................................................................................................88 List of own publications .........................................................................................................90 Disclosure of contribution to the intellectual content ..........................................................92 Acknowledgments ..................................................................................................................93 Statement of Authorship ........................................................................................................94 ii List of abbreviations List of abbreviations AIC Akaike Information Criterion BLAST Basic Local Alignment Search Tool BP Base Pair CI Confidence interval CO2 Carbon Dioxide cRNA complementary RNA DAAD Deutscher Akademischer Austauschdienst (German Academic Exchange Service) DNA Deoxyribonucleic Acid DVS State Department for Veterinary Services, Kabete, Kenya EIP Extrinsic Incubation Period ELISA Enzyme-Linked Immunosorbent Assay FAO Food and Agriculture Organization IEP Inter-Epidemic Period IFAD International Fund for Agricultural Development of the United Nations ILRI International Livestock Research Institute KNBS Kenya National Bureau of Statistics NCBI National Center for Biotechnology Information OIE World Organization for Animal Health PCR Polymerase Chain Reaction RNA Ribonucleic Acid RT-PCR Reverse-Transcription Polymerase Chain Reaction RVF Rift Valley Fever RVFV Rift Valley Fever Virus VC Vectorial capacity WHO World Health Organization iii Preface Preface The world around us is changing. There are more humans on the planet now than at any other point in human history, with the global population having grown from 1 billion in 1800 to over 7.5 billion in 2018. As the human population continues to grow, urbanization, immigration, trade and travel become inevitable. Modern theorists and philosophers have touted the impressive technological innovations and advances as the panacea to the resource conflicts and tensions brought about by the unprecedented growth, but as these advances continue to shape our human experience and make our lives easier, another type of change, a more surreptitious one is taking place. Environmental changes, which can be local, regional or global, are fast outpacing our ability to innovate and provide sustainable and lasting solutions. Local or regional changes include land degradation, forest depletion, urbanization, stresses on food-producing systems, land-use changes, irrigation establishment or expansion, changes in hydrological systems and supplies of freshwater, changes in ecosystems due to modifications or loss of biodiversity, local energy resource use and depletion, among others. Global environmental changes occur as cumulative effects of local and regional changes, and these include climate change and climate variability,
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