2015 [Methods in Molecular Biology] Coronaviruses Volume 1282 __

Coronaviruses Helena Jane Maier Erica Bickerton Paul Britton Editors Methods and Protocols Methods in Molecular Biology 1282 M E T H O D S I N M O L E C U L A R B I O L O G Y Series Editor John M. Walker School of Life and Medical Sciences University of Hertfordshire Hat fi eld, Hertfordshire, AL10 9AB, UK For further volumes: http://www.springer.com/series/7651 Coronaviruses Methods and Protocols Edited by Helena Jane Maier The Pirbright Institute, Compton, Newbury, Berkshire, UK Erica Bickerton The Pirbright Institute, Compton, Newbury, Berkshire, UK Paul Britton The Pirbright Institute, Compton, Newbury, Berkshire, UK ISSN 1064-3745 ISSN 1940-6029 (electronic) Methods in Molecular Biology ISBN 978-1-4939-2437-0 ISBN 978-1-4939-2438-7 (eBook) DOI 10.1007/978-1-4939-2438-7 Library of Congress Control Number: 2015932490 Springer New York Heidelberg Dordrecht London © Springer Science+Business Media New York 2015 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifi cally the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfi lms 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 specifi c 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 Humana Press is a brand of Springer Springer Science+Business Media LLC New York is part of Springer Science+Business Media (www.springer.com) Editors Helena Jane Maier The Pirbright Institute, Compton Newbury, Berkshire , UK Paul Britton The Pirbright Institute, Compton Newbury, Berkshire , UK Erica Bickerton The Pirbright Institute, Compton Newbury, Berkshire , UK v In this book we aimed to describe a variety of techniques that refl ect the wide range of research currently being performed in the fi eld of coronavirology. However, most of the techniques described are also applicable to a wide variety of other virology fi elds, so we hope that this book will have wider appeal. As such, we have started this book with an over- view chapter of current understanding of coronavirus replication and pathogenesis to intro- duce nonspecialist readers to the fi eld. Since the emergence of SARS-Coronavirus in 2003, numerous new coronaviruses have been identifi ed. The emergence of MERS-Coronavirus in 2012 and the continued occur- rence of human cases highlight the importance of techniques to verify the presence of coronaviruses in a sample as well as identify new coronaviruses that may pose a potential threat to the health of both humans and livestock. As such, chapters have been chosen to describe identifi cation, diagnosis, and study of evolution of coronaviruses. To allow the study of viruses, propagation and quantifi cation of virus is essential. Therefore, we have included chapters describing preparation of cells and organ cultures useful in propagating coronaviruses and titration techniques. In addition, several tech- niques for analyzing virus function require purifi cation of virus, so purifi cation protocols suitable for different downstream techniques have been included. The ability to reverse engineer virus genomes and recover recombinant viruses with defi ned mutations is invaluable in the progression of understanding the mechanisms for virus pathogenicity, viral protein and RNA function and understanding virus-host interac- tions. Therefore, chapters describing two commonly used reverse genetics techniques for coronaviruses are included. A key step in virus replication is attachment to and entry into the host cell. Techniques detailing identifi cation of cellular receptors, binding profi les of viral attachment proteins, and virus-cell fusion are described. Finally, a major area of coronavirus research currently is the interaction between the virus and the host cell to gain insight into requirements of the virus to enable replication but also how the host cell responds to virus infection. Understanding these processes is vital in enabling future control of virus replication with antiviral therapeutics or prevention through vaccination. Therefore, several chapters have been included covering a broad spec- trum of techniques to identify virus-host protein-protein interactions, confi rm the func- tional role of these proteins in virus replication, study host cell responses through genome-wide or pathway-specifi c approaches, and visualise virus replication complexes. We would like to thank the authors who have contributed to this book for the time they have taken to prepare detailed methods as well as provide practical hints and tips that are often essential to get a new working protocol. Compton, UK Helena Jane Maier Erica Bickerton Paul Britton Pref ace vii Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix 1 Coronaviruses: An Overview of Their Replication and Pathogenesis . . . . . . . . 1 Anthony R. Fehr and Stanley Perlman PART I DETECTION, DIAGNOSIS AND EVOLUTION OF CORONAVIRUSES 2 Identification of a Novel Coronavirus from Guinea Fowl Using Metagenomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 Mariette F. Ducatez and Jean-Luc Guérin 3 Serological Diagnosis of Feline Coronavirus Infection by Immunochromatographic Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 Tomomi Takano and Tsutomu Hohdatsu 4 Estimation of Evolutionary Dynamics and Selection Pressure in Coronaviruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 Muhammad Munir and Martí Cortey PART II PROPOGATION, TITRATION, AND PURIFICATION OF CORONAVIRUSES 5 The Preparation of Chicken Tracheal Organ Cultures for Virus Isolation, Propagation, and Titration . . . . . . . . . . . . . . . . . . . . . . . . 51 Ruth M. Hennion 6 The Preparation of Chicken Kidney Cell Cultures for Virus Propagation . . . . . 57 Ruth M. Hennion and Gillian Hill 7 Isolation and Propagation of Coronaviruses in Embryonated Eggs . . . . . . . . . 63 James S. Guy 8 Characterization of Human Coronaviruses on Well- Differentiated Human Airway Epithelial Cell Cultures. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73 Hulda R. Jonsdottir and Ronald Dijkman 9 Quantification of Infectious Bronchitis Coronavirus by Titration In Vitro and In Ovo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89 Joeri Kint , Helena Jane Maier , and Erik Jagt 10 Purification of Coronavirus Virions for Cryo-EM and Proteomic Analysis . . . . 99 Stuart Dent and Benjamin W. Neuman 11 Partial Purification of IBV and Subsequent Isolation of Viral RNA for Next-Generation Sequencing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109 Sarah M. Keep , Erica Bickerton , and Paul Britton Contents viii PART III MANIPULATING THE GENOMES OF CORONAVIRUSES 12 Transient Dominant Selection for the Modification and Generation of Recombinant Infectious Bronchitis Coronaviruses. . . . . . . . . . . . . . . . . . . . 115 Sarah M. Keep , Erica Bickerton , and Paul Britton 13 Engineering Infectious cDNAs of Coronavirus as Bacterial Artificial Chromosomes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135 Fernando Almazán , Silvia Márquez-Jurado , Aitor Nogales , and Luis Enjuanes PART IV CORONAVIRUS ATTACHMENT AND ENTRY 14 Protein Histochemistry Using Coronaviral Spike Proteins: Studying Binding Profiles and Sialic Acid Requirements for Attachment to Tissues. . . . . 155 Iresha N. Ambepitiya Wickramasinghe and M. Hélène Verheije 15 Identification of Protein Receptors for Coronaviruses by Mass Spectrometry. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165 V. Stalin Raj , Mart M. Lamers , Saskia L. Smits , Jeroen A. A. Demmers , Huihui Mou , Berend-Jan Bosch , and Bart L. Haagmans 16 Single Particle Tracking Assay to Study Coronavirus Membrane Fusion. . . . . . 183 Deirdre A. Costello and Susan Daniel PART V STUDYING VIRUS-HOST INTERACTIONS 17 Studying Coronavirus–Host Protein Interactions. . . . . . . . . . . . . . . . . . . . . . . 197 Chee-Hing Yang , Hui-Chun Li , Cheng-Huei Hung , and Shih-Yen Lo 18 A Field-Proven Yeast Two-Hybrid Protocol Used to Identify Coronavirus–Host Protein–Protein Interactions . . . . . . . . . . . . . . . . . . . . . . . 213 Pierre- Olivier Vidalain , Yves Jacob , Marne C. Hagemeijer , Louis M. Jones , Grégory Neveu , Jean-Pierre Roussarie , Peter J. M. Rottier , Frédéric Tangy , and Cornelis A. M. de Haan 19 Investigation of the Functional Roles of Host Cell Proteins Involved in Coronavirus Infection Using Highly Specific and Scalable RNA Interference (RNAi) Approach . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 231 Jean Kaoru Millet and Béatrice Nal 20 Transcriptome Analysis of Feline Infectious Peritonitis Virus Infection. . . . . . . 241 Parvaneh Mehrbod , Mohammad Syamsul Reza Harun , Ahmad Naqib Shuid , and Abdul Rahman Omar 21 Quantification of Interferon Signaling in Avian Cells. . . . . . . . . . . . . . . . . . . . 251 Joeri Kint and Maria Forlenza 22 Studying the Dynamics of Coronavirus Replicative Structures . . . . . . . . . . . . . 261 Marne C. Hagemeijer and Cornelis A. M. de Haan 23 Preparation of Cultured Cells Using High-Pressure Freezing and Freeze Substitution for Subsequent 2D or 3D Visualization in the Transmission Electron Microscope . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271 Philippa C. Hawes Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283 Contents ix FERNANDO ALMAZÁN • Department of Molecular and Cell Biology , Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid , Cantoblanco, Madrid , Spain IRESHA N. AMBEPITIYA WICKRAMASINGHE • Department of Pathobiology, Faculty of Veterinary Medicine , Utrecht University , Utrecht , The Netherlands ERICA BICKERTON • The Pirbright Institute , Compton, Newbury, Berkshire , UK BEREND-JAN BOSCH • Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine , Utrecht University , Utrecht , The Netherlands PAUL BRITTON • The Pirbright Institute , Compton, Newbury, Berkshire , UK MARTÍ CORTEY • The Pirbright Institute , Pirbright, Woking, Surrey , UK DEIRDRE A. COSTELLO • School of Chemical and Biomolecular Engineering , Cornell University , Ithaca , NY , USA SUSAN DANIEL • School of Chemical and Biomolecular Engineering , Cornell University , Ithaca , NY , USA CORNELIS A. M. DE HAAN • Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine , Utrecht University , Utrecht , The Netherlands JEROEN A. A. DEMMERS • Proteomics Department , Erasmus Medical Center , Rotterdam , The Netherlands STUART DENT • School of Biological Sciences , University of Reading , Reading , UK RONALD DIJKMAN • Federal Department of Home Affairs , Institute of Virology and Immunology , Berne and Mittelhäusern , Switzerland MARIETTE F. DUCATEZ • INRA, UMR1225, IHAP , Toulouse , France ; Université de Toulouse, INP, ENVT, IHAP , Toulouse , France LUIS ENJUANES • Department of Molecular and Cell Biology , Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid , Cantoblanco, Madrid , Spain ANTHONY R. FEHR • Department of Microbiology , University of Iowa Carver College of Medicine , Iowa City , IA , USA MARIA FORLENZA • Cell Biology and Immunology Group, Wageningen Institute of Animal Sciences , Wageningen University , Wageningen , The Netherlands JEAN-LUC GUÉRIN • INRA, UMR1225, IHAP , Toulouse , France ; Université de Toulouse, INP, ENVT, UMR1225, IHAP , Toulouse , France JAMES S. GUY • Department of Population Health and Pathobiology, College of Veterinary Medicine , North Carolina State University , Raleigh , NC , USA BART L. HAAGMANS • Department of Viroscience , Erasmus Medical Center , Rotterdam , The Netherlands MARNE C. HAGEMEIJER • Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine , Utrecht University , Utrecht , The Netherlands ; Laboratory of Host-Pathogen Dynamics, Cell Biology and Physiology Center (CBPC) , National Heart Lung and Blood Institute (NHLBI), National Institutes of Health , Bethesda , MD , USA Contributors