2016 [Springer Protocols Handbooks] Animal Coronaviruses __

221 Pages·2016·5.97 MB·English

Animal
Coronaviruses

Leyi Wang Editors

S P R I N G E R P R O T O C O L S H A N D B O O K S

For further volumes:
http://www.springer.com/series/8623

Animal Coronaviruses

Edited by

Leyi Wang

Animal Disease Diagnostic Laboratory, Ohio Department of Agriculture, Reynoldsburg, OH, USA

ISSN 1949-2448
ISSN 1949-2456 (electronic)

Springer Protocols Handbooks
ISBN 978-1-4939-3412-6 ISBN 978-1-4939-3414-0 (eBook)
DOI 10.1007/978-1-4939-3414-0

Library of Congress Control Number: 2016933865

Springer New York Heidelberg Dordrecht London
© 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, 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)

Editor
Leyi Wang
Animal Disease Diagnostic Laboratory
Ohio Department of Agriculture
Reynoldsburg , OH , USA

v

The fi rst coronavirus, avian infectious bronchitis virus, was isolated from chicken eggs in
1937. Porcine transmissible gastroenteritis virus and mouse hepatitis virus were subsequently
identifi ed from pigs and mice, respectively, in the 1940s. In the following decades, while the
human coronaviruses were identifi ed in the 1960s, other animal coronaviruses including
porcine hemagglutinating encephalomyelitis virus (1962), feline coronavirus (1970), canine
coronavirus (1971), bovine coronavirus (1973), turkey coronavirus (1973), porcine epidemic
diarrhea virus (1978), and porcine respiratory coronavirus (1984) were also discovered.
In order to study coronaviruses, various systems of reverse genetics have been established
since 1992 for understanding viral replication, elucidating virus-host interaction and patho-
genesis, and developing novel coronavirus vaccines. Because a high- throughput next-generation
sequencing technology was unveiled in 2005, its application in virology has advanced a new
era of coronavirus discovery. Several emerging animal coronaviruses, such as porcine
deltacoronaviruses, therefore, have been identifi ed and characterized. Although there are
diverse animal coronavirus species, this handbook is primarily focused on coronaviruses of
domestic animals and poultry. This handbook is intended to summarize the currently avail-
able technologies that have been developed and utilized to make the progress of coronavirus
virology possible. The purpose is to provide the diagnosticians and researchers with practical
methodologies and approaches to tackle animal coronaviruses, which cover the conventional
immunohistochemistry, virus neutralization, enzyme-linked immunosorbent assays, expres-
sion and purifi cation of recombinant viral proteins, and various molecular assays, including
conventional and real-time reverse transcription- PCR, reverse genetics methodology, and
next-generation sequencing and sequence analyses. Furthermore, it is reasonable to expect
that the methodologies and approaches highlighted in this handbook are applicable to other
coronavirus species in the Coronaviridae.

Reynoldsburg, OH, USA
Leyi Wang

Pref ace

vii

Contents

Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
v

Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
ix

PART I INTRODUCTION

1 Animal Coronaviruses: A Brief Introduction . . . . . . . . . . . . . . . . . . . . . . . . . .
3

Leyi Wang and Yan Zhang

PART II CONVENTIONAL TECHNOLOGIES

2 Immunohistochemical Staining for Detection of Porcine Epidemic

Diarrhea Virus in Tissues. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
15

Kwonil Jung

3 Virus Neutralization Assay for Turkey Coronavirus Infection. . . . . . . . . . . . . .
25

Yi-Ning Chen , Ching Ching Wu , and Tsang Long Lin

4 Recombinant Turkey Coronavirus Nucleocapsid Protein Expressed

in Escherichia coli . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
33

Chien Chang Loa , Ching Ching Wu , and Tsang Long Lin

5 Antibody-Capture Enzyme-Linked Immunosorbent Assay for Detection

of Antibody to Turkey Coronavirus Using Infectious Bronchitis Virus
or Recombinant Nucleocapsid Protein as Coating Antigen . . . . . . . . . . . . . . .
43

Chien Chang Loa , Mohamed Abdelwahab , Yi-Ning Chen ,
Ming-Kun Hsieh , Ching Ching Wu , and Tsang Long Lin

PART III REVERSE GENETICS

6 Reverse Genetics of Avian Coronavirus Infectious Bronchitis Virus . . . . . . . . .
53

Sarah M. Keep , Erica Bickerton , and Paul Britton

7 Vaccinia Virus-Based Reverse Genetics for Feline Coronaviruses . . . . . . . . . . .
73

Gergely Tekes

PART IV MOLECULAR DIAGNOSTICS

8 Real-Time RT-PCR Detection of Equine Coronavirus. . . . . . . . . . . . . . . . . . .
93

Fabien Miszczak , Nathalie Kin , Vincent Tesson , and Astrid Vabret

9 Detection of Bovine Coronavirus by Conventional Reverse Transcription

Polymerase Chain Reaction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Amauri Alcindo Alfieri , Alice Fernandes Alfieri , and Elisabete Takiuchi

10 Real-Time Reverse Transcription Polymerase Chain Reaction

for Rapid Detection of Transmissible Gastroenteritis Virus . . . . . . . . . . . . . . . 115
Ramesh Vemulapalli

viii

11 An RT-PCR Assay for Detection of Infectious Bronchitis Coronavirus

Serotypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Junfeng Sun and Shengwang Liu

12 A Multiplex Polymerase Chain Reaction for Differential Detection

of Turkey Coronavirus from Chicken Infectious Bronchitis Virus
and Bovine Coronavirus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
Chien Chang Loa , Ching Ching Wu , and Tsang Long Lin

13 Real-Time Reverse Transcription-Polymerase Chain Reaction

for Detection and Quantitation of Turkey Coronavirus RNA in Feces
and Intestine Tissues. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
Yi-Ning Chen , Ching Ching Wu , and Tsang Long Lin

14 PCR Amplification and Sequencing Analysis of Full-Length Turkey

Coronavirus Spike Gene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
Yi-Ning Chen , Aydemir Akin , Chien Chang Loa , Mustafa Ababneh ,
Jianzhong Cao , Wan- Jung Chen , Ching Ching Wu , and Tsang Long Lin

15 Feline Coronavirus RT-PCR Assays for Feline Infectious

Peritonitis Diagnosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
Takehisa Soma

16 Genotype-Specific Detection of Ferret Coronavirus by Conventional

and Real-Time Reverse Transcription Polymerase Chain Reaction . . . . . . . . . . 171
Annabel G. Wise , Matti Kiupel , and Roger K. Maes

17 Molecular Characterization of Canine Coronavirus . . . . . . . . . . . . . . . . . . . . . 189

Rita de Cássia Nasser Cubel Garcia

PART V NEXT GENERATION SEQUENCING

18 Whole-Genome Sequencing of Porcine Epidemic Diarrhea Virus

by Illumina MiSeq Platform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
Leyi Wang , Tod Stuber , Patrick Camp , Suelee Robbe-Austerman ,
and Yan Zhang

19 Next-Generation Sequencing for Porcine Coronaviruses . . . . . . . . . . . . . . . . . 209

Douglas Marthaler , Ann Bohac , Aaron Becker , and Nichole Peterson

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 217

Contents

ix

MUSTAFA ABABNEH • Department of Comparative Pathobiology and Animal Disease

Diagnostic Laboratory , Purdue University , West Lafayette , IN , USA ; Department of Basic
Veterinary Medical Sciences , Jordan University of Science and Technology , Irbid , Jordan

MOHAMED ABDELWAHAB • Department of Comparative Pathobiology and Animal Disease

Diagnostic Laboratory , Purdue University , West Lafayette , IN , USA

AYDEMIR AKIN • Department of Comparative Pathobiology and Animal Disease Diagnostic

Laboratory , Purdue University , West Lafayette , IN , USA

AMAURI ALCINDO ALFIERI • Laboratory of Animal Virology, Department of Veterinary

Preventive Medicine , Universidade Estadual de Londrina , Londrina , PR , Brazil

ALICE FERNANDES ALFIERI • Laboratory of Animal Virology, Department of Veterinary

Preventive Medicine , Universidade Estadual de Londrina (UEL) , Londrina , PR , Brazil

AARON BECKER • University of Minnesota Genomics Center , University of Minnesota ,

Saint Paul , MN , USA

ERICA BICKERTON • The Pirbright Institute , Compton, Newbury , Berkshire , UK
ANN BOHAC • University of Minnesota Genomics Center , University of Minnesota ,

Saint Paul , MN , USA

PAUL BRITTON • The Pirbright Institute , Compton, Newbury , Berkshire , UK
PATRICK CAMP • National Veterinary Services Laboratories, Animal and Plant Health

Inspection Service , United States Department of Agriculture , Ames , IA , USA

JIANZHONG CAO • Department of Comparative Pathobiology and Animal Disease

Diagnostic Laboratory , Purdue University , West Lafayette , IN , USA

WAN-JUNG CHEN • Department of Comparative Pathobiology and Animal Disease

Diagnostic Laboratory , Purdue University , West Lafayette , IN , USA

YI-NING CHEN • Department of Comparative Pathobiology and Animal Disease Diagnostic

Laboratory , Purdue University , West Lafayette , IN , USA ; Department of Bioscience
Technology , Chung Yuan Christian University , Chung Li , Taiwan, ROC

RITA DE CÁSSIA NASSER CUBEL GARCIA • Departamento de Microbiologia e Parasitologia,

Instituto Biomédico, Universidade Federal Fluminense , Niterói , RJ , Brazil

MING-KUN HSIEH • Department of Comparative Pathobiology and Animal Disease Diagnostic

Laboratory , Purdue University , West Lafayette , IN , USA ; Graduate Institute of Microbiology
and Public Health , National Chung Hsing University , Taichung , Taiwan, ROC

KWONIL JUNG • Food Animal Health Research Program, Ohio Agricultural Research and

Development Center, Department of Veterinary Preventive Medicine , The Ohio State
University , Wooster , OH , USA

SARAH M. KEEP • The Pirbright Institute , Compton, Newbury , Berkshire , UK
NATHALIE KIN • Normandie University , Caen , France ; EA4655, U2RM , UNICAEN ,

Caen , France ; Department of Virology , University Hospital , Caen , France; Laboratoire
de Virologie, Centre Hospitalier Universitaire de Caen, Caen Cedex, France

MATTI KIUPEL • Diagnostic Center for Population and Animal Health, College of

Veterinary Medicine , Michigan State University , East Lansing , MI , USA; Department of
Pathobiology and Diagnostic Investigation, College of Veterinary Medicine , Michigan
State University , East Lansing , MI , USA

Contributors