M ETHODS IN MOLECULAR BIOLOGY

Transcription

1 M ETHODS IN MOLECULAR BIOLOGY Series editor John M. Walker School of Life and Medical Sciences University of Hertfordshire Hatfield, Herts., United Kingdom For further volumes:

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3 Chikungunya Virus Methods and Protocols Edited by Justin Jang Hann Chu Department of Microbiology and Immunology, National University of Singapore, Singapore Swee Kim Ang Department of Microbiology and Immunology, National University of Singapore, Singapore

4 Editors Justin Jang Hann Chu Department of Microbiology and Immunology National University of Singapore Singapore Swee Kim Ang Department of Microbiology and Immunology National University of Singapore Singapore ISSN ISSN (electronic) Methods in Molecular Biology ISBN ISBN (ebook) DOI / Library of Congress Control Number: Springer Science+Business Media New York 2016 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. Printed on acid-free paper This Humana Press imprint is published by Springer Nature The registered company is Springer Science+Business Media LLC New York

5 Pref ace Chikungunya virus (CHIKV) is a mosquito-borne, single-stranded, positive-sense RNA virus belonging to the alphavirus genus of the family Togaviridae. CHIKV infection in humans has re- emerged as a significant infectious disease which is no longer confined to developing countries in the tropics due to recent outbreaks in various geographical regions worldwide including America and Europe. Chikungunya: Methods and Protocols provides the increasing number of CHIKV researchers a useful handbook covering multidisciplinary approaches on various aspects of CHIKV research brought together by leading laboratories across the globe. Topics covered include techniques in clinical and diagnostic virology, basic protocols in cell and virus culture, and bioinformatics and proteomics approaches in cellular response studies. In addition, methods in immunology and animal model studies, as well as different strategies of antivirals and vaccine development for therapeutics against CHIKV infection are also covered in this comprehensive handbook. Singapore Singapore Justin Jang Hann Chu Swee Kim Ang v

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7 Contents Preface Contributors v xi PART I CLINICAL AND DIAGNOSTIC VIROLOGY 1 Evolution and Epidemiology of Chikungunya Virus Giada Rossini, Maria Paola Landini, and Vittorio Sambri 2 Molecular Epidemiology of Chikungunya Virus by Sequencing Ravindran Thayan, Mohd Apandi Yusof, Zainah Saat, Shamala Devi Sekaran, and Seok Mui Wang 3 Advanced Genetic Methodologies in Tracking Evolution and Spread of Chikungunya Virus Hapuarachchige Chanditha Hapuarachchi and Kim-Sung Lee 4 Synthetic Peptide-Based Antibody Detection for Diagnosis of Chikungunya Infection with and without Neurological Complications Rajpal S. Kashyap, Shradha S. Bhullar, Nitin H. Chandak, and Girdhar M. Taori 5 Expression and Purification of E2 Glycoprotein from Insect Cells (Sf9) for Use in Serology Chong Long Chua, I-Ching Sam, and Yoke Fun Chan 6 Diagnostic Methods for CHIKV Based on Serological Tools Paolo Gaibani, Maria Poala Landini, and Vittorio Sambri 7 Utilization and Assessment of Throat Swab and Urine Specimens for Diagnosis of Chikungunya Virus Infection Chandrashekhar G. Raut, H. Hanumaiah, and Wrunda C. Raut PART II CELL CULTURE, VIRUS REPLICATION, AND CELLULAR RESPONSES 8 Propagation of Chikungunya Virus Using Mosquito Cells Swee Kim Ang, Shirley Lam, and Justin Jang Hann Chu 9 Infectious Viral Quantification of Chikungunya Virus Virus Plaque Assay Parveen Kaur, Regina Ching Hua Lee, and Justin Jang Hann Chu 10 Detection and Quantification of Chikungunya Virus by Real-Time RT-PCR Assay Seok Mui Wang, Ummul Haninah Ali, Shamala Devi Sekaran, and Ravindran Thayan 11 Chikungunya Virus Infection of Aedes Mosquitoes Hui Vern Wong, Yoke Fun Chan, I-Ching Sam, Wan Yusof Wan Sulaiman, and Indra Vythilingam vii

8 viii Contents 12 Analysis of CHIKV in Mosquitoes Infected via Artificial Blood Meal Jeremy P. Ledermann and Ann M. Powers 13 Chikungunya Virus Growth and Fluorescent Labeling: Detection of Chikungunya Virus by Immunofluorescence Assay Meng Ling Moi and Tomohiko Takasaki 14 Virus Isolation and Preparation of Sucrose-Banded Chikungunya Virus Samples for Transmission Electron Microscopy Chang-Kweng Lim 15 Viral Host Protein Interaction Studies Using Yeast Two- Hybrid Screening Method Namrata Dudha and Sanjay Gupta 16 Application of GelC-MS/MS to Proteomic Profiling of Chikungunya Virus Infection: Preparation of Peptides for Analysis Atchara Paemanee, Nitwara Wikan, Sittiruk Roytrakul, and Duncan R. Smith 17 Bioinformatics Based Approaches to Study Virus Host Interactions During Chikungunya Virus Infection Sreejith Rajasekharan and Sanjay Gupta 18 T-Cell Epitope Prediction of Chikungunya Virus Christine Loan Ping Eng, Tin Wee Tan, and Joo Chuan Tong PART III IMMUNOLOGY AND ANIMAL MODEL STUDIES 19 Mouse Models of Chikungunya Virus Lara J. Herrero, Penny A. Rudd, Xiang Liu, Stefan Wolf, and Suresh Mahalingam 20 Generation of Mouse Monoclonal Antibodies Specific to Chikungunya Virus Using ClonaCell-HY Hybridoma Cloning Kit Chow Wenn Yew and Yee Joo Tan 21 Immunohistochemical Detection of Chikungunya Virus Antigens in Formalin-Fixed and Paraffin-Embedded Tissues Chun Wei Chiam, I-Ching Sam, Yoke Fun Chan, Kum Thong Wong, and Kien Chai Ong PART IV ANTIVIRALS AND VACCINES 22 Antiviral Strategies Against Chikungunya Virus Rana Abdelnabi, Johan Neyts, and Leen Delang 23 A Real-Time Cell Analyzing Assay for Identification of Novel Antiviral Compounds against Chikungunya Virus Keivan Zandi 24 Using Bicistronic Baculovirus Expression Vector System to Screen the Compounds That Interfere with the Infection of Chikungunya Virus Szu-Cheng Kuo, Chao-Yi Teng, Yi-Jung Ho, Ying-Ju Chen, and Tzong-Yuan Wu

9 Contents ix 25 Neutralization Assay for Chikungunya Virus Infection: Plaque Reduction Neutralization Test Nor Azila Muhammad Azami, Meng Ling Moi, and Tomohiko Takasaki 26 Reverse Genetics Approaches for Chikungunya Virus Patchara Phuektes and Justin Jang Hann Chu 27 Production of Chikungunya Virus-Like Particles and Subunit Vaccines in Insect Cells Stefan W. Metz and Gorben P. Pijlman 28 Protocols for Developing Novel Chikungunya Virus DNA Vaccines Christopher Chung, Kenneth E. Ugen, Niranjan Y. Sardesai, David B. Weiner, and Kar Muthumani Index

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11 Contributors RANA ABDELNABI Laboratory of Virology and Chemotherapy, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven University of Leuven, Leuven, Belgium UMMUL HANINAH ALI Department of Medical Microbiology, Faculty of Medicine, University of Malaysia, Jalan Universiti, Kuala Lumpur, Malaysia ; Virology Unit, Infectious Diseases Research Center, Institute for Medical Research, Kuala Lumpur, Malaysia SWEE KIM ANG Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore NOR AZILA MUHAMMAD AZAMI Department of Virology I, National Institute of Infectious Diseases, Tokyo, Japan ; Graduate School for Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan SHRADHA S. BHULLAR Biochemistry Research Laboratory, Central India Institute of Medical Sciences, Nagpur, India YOKE FUN CHAN Department of Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia NITIN H. CHANDAK Biochemistry Research Laboratory, Central India Institute of Medical Sciences, Nagpur, India YING-JU CHEN Bioengineering Group, Institute of Biologics, Development Center for Biotechnology, New Taipei, Taiwan CHUN WEI CHIAM Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia JUSTIN JANG HANN CHU Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore CHONG LONG CHUA Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia CHRISTOPHER CHUNG Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA LEEN DELANG Laboratory of Virology and Chemotherapy, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven University of Leuven, Leuven, Belgium NAMRATA DUDHA Center for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India CHRISTINE LOAN PING ENG Department of Biochemistry, Yong Loo School of Medicine, National University of Singapore, Singapore, Singapore PAOLO GAIBANI Regional Reference Centre for Microbiological Emergencies (CRREM), Unit of Microbiology, S. Orsola-Malpighi Hospital, Bologna, Italy SANJAY GUPTA Center for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India H. HANUMAIAH National Institute of Virology, Bangalore Unit, Bangalore, India xi

12 xii Contributors HAPUARACHCHIGE CHANDITHA HAPUARACHCHI Environmental Health Institute, National Environment Agency, Singapore, Singapore LARA J. HERRERO Emerging Viruses and Inflammation Research Group, Institute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, Australia YI-JUNG HO Institute of Prevention Medicine, National Defense Medical Center, Taipei, Taiwan RAJPAL S. KASHYAP Biochemistry Research Laboratory, Central India Institute of Medical Sciences, Nagpur, India PARVEEN KAUR Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore SZU-CHENG KUO Institute of Prevention Medicine, National Defense Medical Center, Taipei, Taiwan SHIRLEY LAM Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore MARIA POALA LANDINI Unit of Microbiology, Regional Reference Centre for Microbiological Emergencies (CRREM), St. Orsola Malpighi Hospital, Bologna, Italy ; DIMES, University of Bologna, Bologna, Italy JEREMY P. LEDERMANN Centers for Disease Control and Prevention, Fort Collins, CO, USA KIM-SUNG LEE School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, Singapore, Singapore REGINA CHING HUA LEE Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore CHANG-KWENG LIM Laboratory of Neurovirology, Department of Virology 1, National Institute of Infectious Diseases, Tokyo, Japan XIANG LIU Emerging Viruses and Inflammation Research Group, Institute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, Australia SURESH MAHALINGAM Emerging Viruses and Inflammation Research Group, Institute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, Australia STEFAN W. METZ Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA ; Laboratory of Virology, Wageningen University, Wageningen, The Netherlands MENG LING MOI Department of Virology 1, National Institute of Infectious Diseases, Tokyo, Japan; Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan KAR MUTHUMANI Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA JOHAN NEYTS Laboratory of Virology and Chemotherapy, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven University of Leuven, Leuven, Belgium KIEN CHAI ONG Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia

13 Contributors xiii ATCHARA PAEMANEE Institute of Molecular Biosciences, Mahidol University, Nakorn Pathom, Thailand ; National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand PATCHARA PHUEKTES Department of Pathobiology, Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen, Thailand GORBEN P. PIJLMAN Laboratory of Virology, Wageningen University, Wageningen, The Netherlands ANN M. POWERS Centers for Disease Control and Prevention, Fort Collins, CO, USA SREEJITH RAJASEKHARAN Center for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India CHANDRASHEKHAR G. RAUT National Institute of Virology, Bangalore Unit, Bangalore, India WRUNDA C. RAUT Dr. D. Y. Patil Medical College, Hospital and Research Center, Pune, India GIADA ROSSINI Unit of Microbiology, Regional Reference Centre for Microbiological Emergencies (CRREM), St. Orsola Malpighi Hospital, Bologna, Italy SITTIRUK ROYTRAKUL National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand PENNY A. RUDD Emerging Viruses and Inflammation Research Group, Institute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, Australia ZAINAH SAAT Virology Unit, Infectious Diseases Research Centre, Institute for Medical Research, Kuala Lumpur, Malaysia I-CHING SAM Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia VITTORIO SAMBRI DIMES, University of Bologna, Bologna, Italy ; Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Pievesestina, Italy NIRANJAN Y. SARDESAI Inovio Pharmaceuticals, Plymouth Meeting, PA, USA SHAMALA DEVI SEKARAN Department of Medical Microbiology, Faculty of Medicine, University of Malaysia, Jalan Universiti, Kuala Lumpur, Malaysia DUNCAN R. SMITH Institute of Molecular Biosciences, Mahidol University, Nakorn Pathom, Thailand ; Center for Emerging and Neglected Infectious Diseases, Mahidol University, Bangkok, Thailand WAN YUSOF WAN SULAIMAN Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia TOMOHIKO TAKASAKI Department of Virology 1, National Institute of Infectious Diseases, Tokyo, Japan YEE JOO TAN Monoclonal Antibody Unit, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research, Singapore, Singapore ; Department of Microbiology, Yong Loo Lin School of Medicine, National University Health System (NUHS), National University of Singapore, Singapore, Singapore TIN WEE TAN Department of Biochemistry, Yong Loo School of Medicine, National University of Singapore, Singapore, Singapore GIRDHAR M. TAORI Biochemistry Research Laboratory, Central India Institute of Medical Sciences, Nagpur, India

14 xiv Contributors CHAO-YI TENG Bioengineering Group, Institute of Biologics, Development Center for Biotechnology, New Taipei, Taiwan RAVINDRAN THAYAN Virology Unit, Infectious Diseases Research Centre, Institute for Medical Research, Kuala Lumpur, Malaysia JOO CHUAN TONG Department of Biochemistry, Yong Loo School of Medicine, National University of Singapore, Singapore, Singapore ; Institute of High Performance Computing, Agency for Science, Technology and Research, Singapore, Singapore KENNETH E. UGEN Department of Molecular Medicine, University of South Florida Morsani College of Medicine, Tampa, FL, USA INDRA VYTHILINGAM Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia SEOK MUI WANG Faculty of Medicine, Jalan Hospital, Universiti Teknologi MARA (UiTM), Selangor, Malaysia DAVID B. WEINER Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA NITWARA WIKAN Institute of Molecular Biosciences, Mahidol University, Nakorn Pathom, Thailand STEFAN WOLF Emerging Viruses and Inflammation Research Group, Institute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, Australia KUM THONG WONG Department of Pathology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia HUI VERN WONG Department of Microbiology Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia TZONG-YUAN WU Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan CHOW WENN YEW Monoclonal Antibody Unit, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research, Singapore, Singapore MOHD APANDI YUSOF Virology Unit, Infectious Diseases Research Centre, Institute of Medical Research, Kuala Lumpur, Malaysia KEIVAN ZANDI Tropical Infectious Disease Research and Education Center (TIDREC), Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia