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European Bats As Carriers of Zoonotic Viruses? European Bats as Carriers of Zoonotic Viruses? Claudia Kohl | Prüm There is a theory which states that if ever anyone discovers exactly what the Universe is for and why it is here, it will instantly disappear and be replaced by something even more bizarre and inexplicable. There is another theory which states that this has already happened. “ Douglas Adams “The Restaurant at the End of the Universe” European Bats as Carriers of Zoonotic Viruses? Dissertation zur Erlangung des akademischen Grades des Doktors der Naturwissenschaften (Dr. rer. nat.) eingereicht im Fachbereich Biologie, Chemie, Pharmazie der Freien Universität Berlin vorgelegt von Dipl.-Ing (FH) Claudia Maria Kohl 2013 Die vorliegende Arbeit wurde zwischen April 2010 und Oktober 2013 am Zentrum für Biologische Gefahren und Spezielle Pathogene (ZBS1 und ZBS5) des Robert Koch-Instituts in Berlin unter Betreuung von PD Dr. Andreas Nitsche und Dr. Andreas Kurth angefertigt. Prof. Dr. Rupert Mutzel übernahm die Begutachtung seitens des Fachbereichs Biologie, Chemie, Pharmazie der Freien Universität Berlin. 1. Gutachter: PD Dr. Andreas Nitsche 2. Gutachter: Prof. Dr. Rupert Mutzel Disputation am _____29.11.2013____ DECLARATION Gemäß § 7 Abs. 4 der Promotionsordnung vom 04.09.2007 des Fachbereichs Biologie, Chemie, Pharmazie der Freien Universität Berlin versichere ich hiermit, dass ich die vorliegende Dissertationsschrift mit dem Titel „European Bats as Carriers of Zoonotic Viruses?“ selbstständig und ohne unerlaubte Hilfe angefertigt habe. _________________________________ Ort, Datum _________________________________ Unterschrift Acknowledgement ACKNOWLEDGEMENT I Table of Content TABLE OF CONTENT ACKNOWLEDGEMENT ...................................................................................................................... I TABLE OF CONTENT ....................................................................................................................... III 1 INTRODUCTION .................................................................................................................... 1 1.1 BATS ........................................................................................................................................ 1 1.1.1 Unique Features of Bats ................................................................................................ 1 1.1.2 European Bats ............................................................................................................... 4 1.1.3 Evolution and Diversity of Bats ...................................................................................... 4 1.2 BATS AS VIRUS RESERVOIR HOSTS .................................................................................................. 8 1.2.1 Zoonoses and Disease Emergence ................................................................................. 8 1.2.2 Key Examples: Bats Worldwide as Potential Reservoir Hosts ........................................ 9 1.2.3 Viruses in European Bats ............................................................................................. 14 1.3 VIRUS DETECTION AND CHARACTERIZATION METHODS .................................................................... 19 1.3.1 Virus Detection ............................................................................................................ 19 1.3.2 Next Generation Sequencing ....................................................................................... 21 1.3.3 Sequence Analysis in silico ........................................................................................... 24 2 STUDY DESIGN .................................................................................................................... 28 2.1 EXAMINATION OF EUROPEAN BATS FOR THE PRESENCE OF SPECIFIC PATHOGENS................................... 28 2.1.1 Description of the Comprehensive Study ..................................................................... 28 2.1.2 Virological Examination at the RKI .............................................................................. 29 2.1.3 Aims of this Thesis within the Comprehensive Study .................................................. 31 3 SUMMARY OF RESULTS ...................................................................................................... 33 3.1 PUBLISHED RESULTS OF THIS THESIS.............................................................................................. 33 3.2 PARTICULAR CONTRIBUTION TO THE MANUSCRIPTS ......................................................................... 34 3.3 ABSTRACT MANUSCRIPT I: .......................................................................................................... 35 3.4 ABSTRACT MANUSCRIPT II: ......................................................................................................... 35 3.5 ABSTRACT MANUSCRIPT III: ........................................................................................................ 36 3.6 ABSTRACT MANUSCRIPT IV: ........................................................................................................ 37 3.7 ABSTRACT MANUSCRIPT V: ......................................................................................................... 38 4 DISCUSSION ........................................................................................................................ 39 4.1 VIRUS SCREENING AT THE RKI ..................................................................................................... 39 4.1.1 PCR Screening for Zoonotic Viruses Strongly Associated with Bats ............................. 40 4.1.2 PCR Screening for Other Highly Pathogenic Viruses and Relatives ............................. 44 4.1.3 Conclusive Statement to PCR Screening ...................................................................... 50 4.1.4 Virus Isolation .............................................................................................................. 52 4.1.5 Conclusive Statement to Virus Isolation ...................................................................... 55 4.2 VIRAL METAGENOMICS .............................................................................................................. 55 4.2.1 Development of the TUViD-VM Protocol ..................................................................... 56 4.2.2 Preliminary Results: Bat Viral Metagenomics ............................................................. 58 4.3 RELEVANCE AND RISK ASSESSMENT FOR EUROPEAN BATS ................................................................. 59 4.3.1 Principle of Cause-and-effect: The Henle–Koch Postulates ......................................... 59 4.3.2 Bats as Reservoir Hosts ............................................................................................... 60 4.3.3 Zoonotic Bat Viruses in Europe? .................................................................................. 63 5 CONCLUSIONS AND FUTURE PROSPECTS ............................................................................ 69 5.1 CONCLUSIONS .......................................................................................................................... 69 5.2 FUTURE PROSPECTS ................................................................................................................... 70 6 ABSTRACT ........................................................................................................................... 71 7 ZUSAMMENFASSUNG ......................................................................................................... 72 II Table of Content 8 TABLES AND FIGURES ......................................................................................................... 73 8.1 TABLES ................................................................................................................................... 73 8.2 FIGURES .................................................................................................................................. 73 9 LITERATURE ........................................................................................................................ 74 10 LIST OF PUBLICATIONS ........................................................................................................ 85 11 CONTRIBUTIONS TO CONFERENCES .................................................................................... 86 12 CURRICULUM VITAE............................................................................................................ 87 13 APPENDIX ........................................................................................................................... 88 13.1 TABLE A1: CHARACTERISTICS OF EUROPEAN BAT SPECIES ............................................................. 88 13.2 TABLE A2: VIRUSES FOUND IN EUROPEAN BATS ......................................................................... 93 13.3 MANUSCRIPTS ..................................................................................................................... 96 13.3.1 Manuscript 1 ............................................................................................................... 96 13.3.2 Manuscript 2 ............................................................................................................. 102 13.3.3 Manuscript 3 ............................................................................................................. 110 13.3.4 Manuscript 4 ............................................................................................................
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