M ETHODS IN MOLECULAR BIOLOGY

Transcription

1 M ETHODS IN MOLECULAR BIOLOGY Series Editor John M. Walker School of Life Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK For further volumes:

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3 Animal Influenza Virus Second Edition Edited by Erica Spackman Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, US Department of Agriculture, Agricultural Research Service, Athens, GA, USA

4 Editor Erica Spackman Exotic and Emerging Avian Viral Diseases Unit Southeast Poultry Research Laboratory US Department of Agriculture Agricultural Research Service Athens, GA, USA ISSN ISSN (electronic) ISBN ISBN (ebook) DOI / Springer New York Heidelberg Dordrecht London Library of Congress Control Number: Springer Science+Business Media New York 2014 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. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher s location, in its current version, and permission for use must always be obtained from Springer. Permissions for use may be obtained through RightsLink at the Copyright Clearance Center. Violations are liable to prosecution under the respective Copyright Law. 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. While the advice and information in this book are believed to be true and accurate at the date of publication, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein. Printed on acid-free paper Humana Press is a brand of Springer Springer is part of Springer Science+Business Media (

5 Pref ace Influenza A viruses are among the most important pathogens for humans, food animals, and companion animals. Of the animal influenza viruses, avian, swine, and equine influenza are likely to have the greatest economic impact internationally because of their value as food animals or, with horses due to a large sport competition industry. Also, although the risk is truly unknown, as domestic animals, poultry, swine, and horses have extended contact with humans, which provides an interface for interspecies transmission, there is always the potential for these animal influenza viruses to become threats to public health. Regardless of the possible implications for public health, influenza is highly significant to poultry, swine, and equine health. Research and diagnostics with animal influenza viruses are critical to animal health in its own right and it should be recognized that the needs and goals of animal agriculture and veterinary medicine are not always the same as those of public health. Even within these three examples of animal influenza viruses there are differences in the approach which may need to be taken, as the structure of the poultry, swine, and equine industries are different and there are some biological differences of influenza virus from each animal group as well. One of the aims of this book is to sort out those differences and to provide host, strain, and lineage specific guidance and procedures. The reader will also recognize that in some cases the same method is described for all three of these animal viruses, for example real-time RT-PCR or hemagglutination inhibition (HI) assay. At first glance this may seem redundant; however there are often seemingly minor, but crucial differences in the assay, such as sample processing for each species (e.g., how to treat for sera the HI assay) or the specificity of reagents (e.g., primer sequences for RT-PCR; optimal laboratory host system for virus isolation). In contrast there are some methods that will be unique to an animal influenza virus group and parameters will necessarily vary. Certainly, assays may be adapted to individual study needs with proper optimization or can simply be used as they are described. The aim of this book is to provide the essential methods used in working with animal influenza viruses, and to compile more advanced information that will guide the user in designing influenza studies. Most importantly this book would not have been possible without the contributions of the authors. The contributors are experts in their fields; therefore their input and knowledge is invaluable with the details they provide from their extensive experience. I want to gratefully acknowledge each of them for taking time from their busy schedules to contribute to this book. I would also like to thank the editorial team at Springer: John Walker, MIMB series editor, and both Patrick Marton and David Casey for all their time and help with completing this book. Happy pipetting. Athens, GA, USA Erica Spackman v

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7 Contents Preface Contributors v xi PART I GENERAL 1 Hemagglutination Assay for Influenza Virus Mary Lea Killian 2 Hemagglutination-Inhibition Assay for Influenza Virus Subtype Identification and the Detection and Quantitation of Serum Antibodies to Influenza Virus Janice C. Pedersen 3 Neuraminidase-Inhibition Assay for the Identification of Influenza A Virus Neuraminidase Virus Subtype or Neuraminidase Antibody Specificity Janice C. Pedersen 4 Reverse Genetics of Influenza Virus Chang-Won Lee 5 Immunohistochemical Staining of Influenza Virus in Tissues Mary J. Pantin-Jackwood PART II AVIAN INFLUENZA 6 A Brief Introduction to Avian Influenza Virus Erica Spackman 7 Wild Bird Surveillance for Avian Influenza Virus Justin D. Brown, Rebecca Poulson, and David E. Stallknecht 8 Avian Influenza Virus Sample Types, Collection, and Handling Mary Lea Killian 9 Avian Influenza Virus RNA Extraction Erica Spackman and Scott A. Lee 10 Avian Influenza Virus Detection and Quantitation by Real- Time RT-PCR Erica Spackman 11 Influenza Subtype Identification with Molecular Methods Erica Spackman 12 Avian Influenza Virus Isolation, Propagation, and Titration in Embryonated Chicken Eggs Erica Spackman and Mary Lea Killian 13 Agar Gel Immunodiffusion Assay to Detect Antibodies to Type A Influenza Virus Terra A. Jenson vii

8 viii Contents 14 Detection of Influenza A Antibodies in Avian Serum Samples by ELISA Len Chappell, Mary Lea Killian, and Erica Spackman 15 Conducting Influenza Virus Pathogenesis Studies in Avian Species Carol J. Cardona, David A. Halvorson, Justin D. Brown, and Mary J. Pantin-Jackwood 16 Laboratory Methods for Assessing and Licensing Influenza Vaccines for Poultry David E. Swayne 17 Detection of Cell-Mediated Immune Response to Avian Influenza Viruses Darrell R. Kapczynski 18 Characterization of Cytokine Expression Induced by Avian Influenza Virus Infection with Real-Time RT-PCR Darrell R. Kapczynski, Hai Jun Jiang, and Michael H. Kogut 19 Newcastle Disease Virus Detection and Differentiation from Avian Influenza Patti J. Miller and Mia Kim Torchetti PART III SWINE INFLUENZA 20 A Brief Introduction to Influenza A Virus in Swine Amy L. Vincent, Kelly M. Lager, and Tavis K. Anderson 21 Sample Types, Collection, and Transport for Influenza A Viruses of Swine Marie R. Culhane and Susan E. Detmer 22 Isolation of Swine Influenza Virus in Cell Cultures and Embryonated Chicken Eggs Jianqiang Zhang and Phillip C. Gauger 23 RNA Extraction from Swine Samples and Detection of Influenza A Virus in Swine by Real-Time RT-PCR Jianqiang Zhang and Karen M. Harmon 24 Hemagglutinin Inhibition Assay with Swine Sera Pravina Kitikoon, Phillip C. Gauger, and Amy L. Vincent 25 Enzyme-Linked Immunosorbent Assay for Detection of Serum or Mucosal Isotype-Specific IgG and IgA Whole- Virus Antibody to Influenza A Virus in Swine Phillip C. Gauger, Crystal L. Loving, and Amy L. Vincent 26 Serum Virus Neutralization Assay for Detection and Quantitation of Serum-Neutralizing Antibodies to Influenza A Virus in Swine Phillip C. Gauger and Amy L. Vincent 27 Microneutralization Assay for Swine Influenza Virus in Swine Serum Pravina Kitikoon and Amy L. Vincent

9 Contents ix 28 Analyzing Swine Sera for Functional Antibody Titers Against Influenza A Neuraminidase Proteins Using an Enzyme-Linked Lectin Assay (ELLA) Matthew R. Sandbulte and Maryna C. Eichelberger 29 Antibody Secreting Cell Assay for Influenza A Virus in Swine Pravina Kitikoon, Crystal L. Loving, and Amy L. Vincent 30 In Vivo Models for Pathotyping and Vaccine Efficacy for Swine Influenza Kelly M. Lager and Amy L. Vincent PART IV EQUINE INFLUENZA 31 A Brief Introduction to Equine Influenza and Equine Influenza Viruses Thomas M. Chambers 32 Equine Influenza Diagnosis: Sample Collection and Transport Thomas M. Chambers and Stephanie E. Reedy 33 RNA Extraction from Equine Samples for Equine Influenza Virus Udeni B. R. Balasuriya 34 Type A Influenza Virus Detection from Horses by Real-Time RT-PCR and Insulated Isothermal RT-PCR Udeni B. R. Balasuriya 35 Equine Influenza Culture Methods Thomas M. Chambers and Stephanie E. Reedy 36 Equine Influenza Serological Methods Thomas M. Chambers and Stephanie E. Reedy Index

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11 Contributors TAVIS K. ANDERSON Department of Biology, Georgia Southern University, Statesboro, GA, USA UDENI B. R. BALASURIYA Department of Veterinary Science, Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY, USA JUSTIN D. BROWN Department of Population Health, Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA, USA CAROL J. CARDONA College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, USA THOMAS M. CHAMBERS Department of Veterinary Science, Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY, USA LEN CHAPPELL Georgia Poultry Laboratory Network, Oak wood, GA, USA MARIE R. CULHANE Veterinary Diagnostic Laboratory, University of Minnesota, St. Paul, MN, USA SUSAN E. DETMER Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada MARYNA C. EICHELBERGER Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD, USA PHILLIP C. GAUGER Veterinary Diagnostic Laboratory, Iowa State University, Ames, IA, USA DAVID A. HALVORSON Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA KAREN M. HARMON Veterinary Diagnostic Laboratory, Iowa State University, Ames, IA, USA TERRA A. JENSON Diagnostic Virology Laboratory, U.S. Department of Agriculture, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, Ames, IA, USA HAI JUN JIANG Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, US Department of Agriculture, Agricultural Research Service, Athens, GA, USA DARRELL R. KAPCZYNSKI Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, US Department of Agriculture, Agricultural Research Service, Athens, GA, USA MARY LEA KILLIAN Diagnostic Virology Laboratory, U.S. Department of Agriculture, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, Ames, IA, USA PRAVINA KITIKOON Virus and Prion Research Unit, U.S. Department of Agriculture, National Animal Disease Center, Agricultural Research Service, Ames, IA, USA MICHAEL H. KOGUT Food and Feed Safety Research Unit, U.S. Department of Agriculture, Southern Plains Agricultural Research Center, Agricultural Research Service, College Station, TX, USA xi

12 xii Contributors KELLY M. LAGER Virus and Prion Research Unit, U.S. Department of Agriculture, National Animal Disease Center, Agricultural Research Service, Ames, IA, USA CHANG-WON LEE Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, USA SCOTT A. LEE Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, US Department of Agriculture, Agricultural Research Service, Athens, GA, USA CRYSTAL L. LOVING Virus and Prion Research Unit, U.S. Department of Agriculture, National Animal Disease Center, Agricultural Research Service, Ames, IA, USA PATTI J. MILLER Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, US Department of Agriculture, Agricultural Research Service, Athens, GA, USA MARY J. PANTIN-JACKWOOD Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, US Department of Agriculture, Agricultural Research Service, Athens, GA, USA JANICE C. PEDERSEN Diagnostic Virology Laboratory, U.S. Department of Agriculture, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, Ames, IA, USA REBECCA POULSON Department of Population Health, Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA, USA STEPHANIE E. REEDY Department of Veterinary Science, Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY, USA MATTHEW R. SANDBULTE Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA ERICA SPACKMAN Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, US Department of Agriculture, Agricultural Research Service, Athens, GA, USA DAVID E. STALLKNECHT Department of Population Health, Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA, USA DAVID E. SWAYNE Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, US Department of Agriculture, Agricultural Research Service, Athens, GA, USA MIA KIM TORCHETTI Diagnostic Virology Laboratory, U.S. Department of Agriculture, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, Ames, IA, USA AMY L. VINCENT Virus and Prion Research Unit, U.S. Department of Agriculture, National Animal Disease Center, Agricultural Research Service, Ames, IA, USA JIANQIANG ZHANG Veterinary Diagnostic Laboratory, Iowa State University, Ames, IA, USA