The Molecular Characterization and the Generation of a Reverse Genetics System for Kyasanur Forest Disease Virus by Bradley William Michael Cook A Thesis submitted to the Faculty of Graduate Studies of The University of Manitoba in partial fulfilment of the requirements of the degree of Master of Science Department of Microbiology University of Manitoba Winnipeg, Manitoba, Canada Copyright © 2010 by Bradley William Michael Cook 1 List of Abbreviations: AHFV - Alkhurma Hemorrhagic Fever Virus Amp – ampicillin APOIV - Apoi Virus ATP – adenosine tri-phosphate BAC – bacterial artificial chromosome BHK – Baby Hamster Kidney BSA – bovine serum albumin C1 – C-terminus fragment 1 C2 – C-terminus fragment 2 C - Capsid protein cDNA – comlementary Deoxyribonucleic acid CL – Containment Level CO2 – carbon dioxide cHP - capsid hairpin CNS - Central Nervous System CPE – cytopathic effect CS - complementary sequences DENV1-4 - Dengue Virus DIC - Disseminated Intravascular Coagulation (DIC) DNA – Deoxyribonucleic acid DTV - Deer Tick Virus 2 E - Envelope protein EDTA - ethylenediaminetetraacetic acid EM - Electron Microscopy EMCV – Encephalomyocarditis Virus ER - endoplasmic reticulum FBS – fetal bovine serum FP - fusion peptide GGEV - Greek Goat Encephalitis Virus GGYV - Gadgets Gully Virus GMP - Guanosine mono-phosphate GTP - Guanosine tri-phosphate HBV- Hepatitis B Virus HDV – Hepatitis Delta Virus HIV - Human Immunodeficiency Virus IFN – interferon IRES – internal ribosome entry sequence JEV - Japanese Encephalitis Virus KADV - Kadam Virus kDa - kilo Dalton KFDV - Kyasanur Forest Disease Virus KSIV - Karshi Virus KUNV - Kunjin Virus kV – kilo volts 3 LB – Luria-Bertani LD - Lipid Droplets LGTV - Langat Virus LIV - Louping Ill Virus M - Membrane protein M-TB - Mammalian-Tick Borne MAC - Membrane Attack Complex (MAC) MB - Mosquito-Borne MCS – multiple cloning site MEAV - Meaban Virus MgCl2 – magnesium chloride MMLV - Montana Myotis Leukoencephalitis Virus MODV - Modoc Virus mRNA - messenger RNA MTPase - methyl-transferase MVEV - Murray Valley Encephalitis Virus N1 – N-terminus fragment 1 NaCl – sodium chloride NKV - No Known Vector NML – National Microbiology Laboratory NS - Non-Structural proteins NTP - nucleoside triphosphate NTPase - nucleoside tri-phosphatase 4 OHFVUVE/Li/Lin - Omsk Hemorrhagic Fever Virus PFU – plaque forming units PHAC – Public Health Agency of Canada POWV - Powassan Virus prM - pre-Membrane protein RBV - Rio Bravo Virus RC - replication complex RdRp - RNA-dependent RNA polymerase RFV - Royal Farm Virus RGS – reverse genetics system RNA - Ribonucleic Acid RNP – ribonucleoprotein complex RPM – revolutions per minute RT-PCR – reverse transcription polymerase chain reaction RTPase - RNA tri-phosphatase S-TB - Seabird-Tick Borne SDS – sodium dodecyl sulfate SDS-PAGE – sodium dodecyl sulfate-polyacrylamide gel electrophoresis SL - stem-loop SLEV - St. Louis Encephalitis Virus SREV - Saumarez Reef Virus ss - single-stranded SSEV - Spanish Sheep Encephalomyelitis Virus 5 TAP – tobacco acid pyrophosphatase TB - Tick-Borne TBE – tris-borate ethylenediaminetetraacetic acid TBE serocomplex - Tick-Borne Encephalitis serocomplex TBEVFE/Sib/EU - Tick-Borne Encephalitis Virus TSEV - Turkish Sheep Encephailitis Virus TYUV - Tyuleniy Virus UAR - Upstream AUG Region UTR - Untranslated Region WNV - West Nile Virus YFV/YFV17D - Yellow Fever Virus YOKV - Yokose Virus 6 Abstract: Kyasanur Forest Disease Virus (KFDV) is a tick-borne, hemorrhagic fever- causing member of the Flaviviridae. With infections annually ranging from 50 to 1000 people in south-west India and the lack of effective treatments, a better understanding of this virus is needed. The development of a Reverse Genetics System for KFDV would provide the opportunity to address these issues in future studies. Using molecular techniques, the KFDV genome sequence was elucidated and the reverse genetics system was created. Utilizing this system live, infectious KFDV particles were produced from mammalian cell culture, thereby validating the success of the reverse genetics system. The implementation of this system will enable researchers to better study pathogenesis and disease progression, virus-host interplay, virion structure, genome replication and the emergence of effective therapeutics and vaccines. 7 Acknowledgements: I would first like to acknowledge Dr. Steven Theriault and Dr. Deborah Court, for allowing me the opportunity to do the research that I enjoy and for being extremely patient and supportive. Thank you to my remaining committee members Dr. Teresa de Kievit and Dr. David Levin for their interest, knowledge and support. Mr. Jay Krishnan and Mr. Todd Cutts, thank you both for your endless knowledge, expertise and guidance. Diane Gordon, Bree-Ann Carruthers and the past members of the Applied Biosafety Research Program (ABRP) thanks for your continued encouragement. The National Microbiology Laboratory for the use of their facilities, especially the DNAcore department. The University of Manitoba and the department of Microbiology, with a special thank you to: Dr. Georg Hausner, for sequence analyses and Dr. Ivan Oresnik, for convincing me to pursue graduate work. Also thank you to Dr. Michael Holbrook for his advice. I could not have done this without all of you! 8 Dedication: My work is dedicated to my savior Jesus Christ and to the loving memories of my grandmother, mother and sister. I would also like to dedicate this work to: My Kim Tran, for her endless support and to the rest of my close friends for their assistance. 9 LIST OF ABBREVIATIONS: ........................................................................................ II ABSTRACT: ................................................................................................................. VII ACKNOWLEDGEMENTS: ....................................................................................... VIII DEDICATION: ............................................................................................................... IX LIST OF TABLES .......................................................................................................... 12 LIST OF FIGURES ........................................................................................................ 12 CHAPTER 1: INTRODUCTION .................................................................................. 14 1.1 Introduction to the Flaviviridae .............................................................................. 14 1.2 KFDV Virus Epidemiology ...................................................................................... 24 1.3 KFDV Virus Transmission....................................................................................... 28 1.3.1 Arthropods as Vectors for Virus Transmission ................................................... 28 1.3.2 Tick Feeding Anatomy and Patterns in Virus Transmission ............................... 29 1.3.3 Ticks and Transmission of KFDV, OHFV and AHFV........................................ 34 1.4 Flavivirus Structure .................................................................................................. 36 1.5 Flavivirus Life Cycle ................................................................................................. 41 1.5.1 Viral entry ............................................................................................................ 42 1.5.2 Viral translation and replication........................................................................... 46 1.5.3 Virus assembly and release .................................................................................. 54 1.6 Reverse Genetic Systems (RGS) .............................................................................. 55 1.6.1. Infectious Clone Systems for Analyzing Viral Replication ................................ 55 1.6.2. Reverse Genetic Systems for analyzing infectious disease ................................ 61 1.6.3. Generation of a RGS for KFDV ......................................................................... 63 1.7. Research goals .......................................................................................................... 70 CHAPTER 2: MATERIALS AND METHODS .......................................................... 71 2.1. KFD infection, RNA harvest and reverse transcription....................................... 71 10 2.2. PCR reactions for all four fragments for sequencing and RGS construction, 3’ UTR-adapter cDNA, 5’ UTR-ligated cDNA product and all 10 KFDV rescue proteins from the cDNA template ................................................................................. 73 2.3. Colony-PCR screening reactions for all four fragments for sequencing and RGS construction, 3’ UTR-adapter, 5’ UTR-ligated product and all 10 KFDV rescue proteins from cDNA template ........................................................................................ 74 2.4. Restriction digestion of DNA for cloning and clone confirmation ...................... 75 2.5. Ligation reaction for sequencing and RGS cloning .............................................. 75 2.6. Transformation of Escherichia coli ........................................................................ 76 2.7. Plasmid DNA harvesting and purification via alkaline lysis procedure ............. 78 2.8. Media and antibiotic preparations ......................................................................... 78 2.9. KFDV rescue ...........................................................................................................