University of Veterinary Medicine Hannover Diagnostic approaches for zoonotic hemorrhagic fever viruses of the order Bunyavirales in livestock Inaugural-Dissertation in fulfillment of the requirements of the degree of Doctor of Veterinary Medicine -Doctor medicinae veterinariae- (Dr. med. vet.) submitted by Nicole Cichon Krefeld Hannover 2020 Academic supervision: Prof. Dr. Martin H. Groschup Institute of Novel and Emerging Infectious Diseases Friedrich-Loeffler-Institut Greifswald-Insel Riems 1. Referee: Prof. Dr. Martin H. Groschup Institute of Novel and Emerging Infectious Diseases Friedrich-Loeffler-Institut Greifswald-Insel Riems 2. Referee: Prof. Dr. Paul Becher Department of Virology University of Veterinary Medicine Hannover Day of the oral examination: 12.11.2020 Sponsorship: This work was supported by the Federal Foreign Office within the German Biosecurity Programme. Table of contents 1 Introduction ........................................................................................................ 1 2 Literature review ................................................................................................ 3 2.1 Classification ................................................................................................. 3 2.2 Morphology and genome characterization ..................................................... 4 2.3 Epidemiology ................................................................................................. 7 2.4 Transmission ............................................................................................... 10 2.5 Clinical signs and pathology ........................................................................ 13 2.6 Diagnostics .................................................................................................. 15 2.7 Vaccination and treatment ........................................................................... 17 3 Materials and Methods .................................................................................... 19 3.1 Serological assays....................................................................................... 19 3.2 PCR ............................................................................................................. 19 3.3 Extraction and purification kits ..................................................................... 20 3.4 Sequencing ................................................................................................. 20 3.5 Protein expression ....................................................................................... 20 4 Manuscript I Cocirculation of Orthobunyaviruses and Rift Valley fever virus in Mauritania, 2015 ....................................................................................................... 21 4.1 Abstract ....................................................................................................... 21 4.2 Introduction .................................................................................................. 22 4.3 Materials and methods ................................................................................ 24 4.4 Results ........................................................................................................ 28 4.5 Discussion ................................................................................................... 30 4.6 Tables and Figures ...................................................................................... 33 4.7 Acknowledgments ....................................................................................... 40 5 Manuscript II Prevalence of Rift Valley Fever virus and Crimean-Congo hemorrhagic fever virus in livestock in Egypt ............................................................ 41 5.1 Abstract ....................................................................................................... 41 5.2 Introduction .................................................................................................. 42 5.3 Materials and Methods ................................................................................ 44 5.4 Results ........................................................................................................ 47 5.5 Discussion ................................................................................................... 48 5.6 Tables and Figures ...................................................................................... 53 5.7 Acknowledgments ....................................................................................... 57 6 Manuscript III Serological and molecular investigation of Batai virus infection in ruminants from the State of Saxony-Anhalt, Germany, 2018 ................................... 58 6.1 Abstract ....................................................................................................... 58 6.2 Introduction .................................................................................................. 58 6.3 Materials and Methods ................................................................................ 60 6.4 Results ........................................................................................................ 62 6.5 Discussion ................................................................................................... 62 6.6 Tables and Figures ...................................................................................... 64 7 General discussion .......................................................................................... 69 8 Summary ........................................................................................................... 77 9 Zusammenfassung .......................................................................................... 79 10 Bibliography ..................................................................................................... 79 11 Supplements .................................................................................................. 105 11.1 Manuscript I ............................................................................................... 105 12 Authors ‘contribution .................................................................................... 116 13 Acknowledgments ......................................................................................... 117 Manuscripts extracted from the doctorate project: 1. N. Cichon, B. Yayha, F. Stoek, U. Ziegler, J. Schulz, D. Höper, M. H. Groschup, M. Eiden; Cocirculation of Orthobunyaviruses and Rift Valley fever virus in Mauritania, 2015 (to be submitted) 2. N. Cichon, H. El-Adawy, M. Rissmann, J. Schulz, S. Abdel Ghafar Elsayed El- soally, M. Eiden and M. H. Groschup; Prevalence of Rift Valley Fever virus and Crimean-Congo hemorrhagic fever virus in livestock in Egypt (to be submitted) 3. N. Cichon, M. Eiden, J. Schulz, A. Günther, P. Wysocki, J. Borgwardt, W. Gaede, M. H. Groschup, U. Ziegler; Serological and molecular investigation of Batai virus infection in ruminants from the State of Saxony-Anhalt, Germany, 2018 (to be submitted) Parts of the results have been presented in conference: Junior Scientist Zoonoses Meeting, Hamburg, Germany, 2018: “Ngari virus, a natural Bunyamwera and Batai virus reassortant” (Poster and oral presentation) FLI Junior Scientists Symposium, Greifswald, Germany, 2018: “Ngari virus, a natural Bunyamwera and Batai virus reassortant” (Poster presentation) Conference “Strengthening the co-operation with Egypt on biosecurity and biosafety”, Kafr El Sheikh, Egypt, 2018:” RVFV infections in livestock in Egypt” (Oral presentation) Medical Biodefense Conference, München, Germany, 2018:” CCHFV and RVF virus infections in animals in Egypt” (Poster presentation) FLI Junior Scientists Symposium, Jena, Germany, 2019:” Ngari virus, natural reassortment of the Bunyamwera serogroup” (Poster presentation) International Symposium on Zoonoses Research, Berlin, Germany, 2019:” Ngari virus, a natural Bunyamwera and Batai virus reassortant” (Poster presentation) List of abbreviations µg Microgram µl Microliter ABTS 2. 2′-azino di-ethylbenzothiazoline sulphonic acid Arbovirus Arthropod-borne virus BATV Batai virus BUNV Bunyamwera virus CCHFV Crimean-Congo hemorrhagic fever virus CO2 Carbon dioxide CT Cycle thresholds CVV Cache Valley virus Cy3 Cyanine 3 DIC Disseminated intravascular coagulation E. coli Escherichia coli ELISA Enzyme linked immunosorbent assay FITC Fluorescein isothiocyanate FMDV Foot-and-Mouth Disease virus FLI Friedrich-Loeffler-Institut Gc Glycoprotein c (-terminal) Gn Glycoprotein n (-terminal) HRPO Horseradish peroxidase ICTV International Committee on Taxonomy of Viruses IgG Immunoglobulin G IgM Immunoglobulin M (I)IFA (Indirect) immunofluorescence assay kDa Kilo Dalton L segment Large segment M Molar mg Milligramm min Minute ml Milliliter mRNA Messenger Ribonucleic acid M segment Medium segment ND50 50% neutralization dose nm Nanometre Np Nucleoprotein NSm Nonstructural protein, encoded on the medium segment NSs Nonstructural protein, encoded on the small segment NRIV Ngari virus OD405 Optical density at 405nm OIE World Organization for Animal Health ORF Open reading frame PBS Phosphate buffered saline PBST PBS containing 0.1% Tween PCR Polymerase chain reaction PFA Paraformaldehyde pH Potential of hydrogen RdRp RNA-dependent RNA polymerase RNA Ribonucleic acid RNP Ribonucleoprotein RT-qPCR Quantitative real-time reverse transcriptase polymerase chain reaction RVFV Rift Valley fever