Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
1 Coronaviruses: An Overview of Their Replication and Pathogenesis . . . . . . . . 1
Anthony R. Fehrand Stanley Perlman
PART I DETECTION, DIAGNOSIS AND EVOLUTION OF CORONAVIRUSES
2 Identification of a Novel Coronavirus from Guinea Fowl
Using Metagenomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Mariette F. Ducatezand Jean-Luc Guérin
3 Serological Diagnosis of Feline Coronavirus Infection
by Immunochromatographic Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Tomomi Takanoand Tsutomu Hohdatsu
4 Estimation of Evolutionary Dynamics and Selection Pressure
in Coronaviruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Muhammad Munirand 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. Hennionand 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. Jonsdottirand 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 Dentand 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
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 Wickramasingheand 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. Costelloand 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 Milletand 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 Kintand Maria Forlenza
22 Studying the Dynamics of Coronavirus Replicative Structures . . . . . . . . . . . . . 261
Marne C. Hagemeijerand 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
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