CLINICAL VIROLOGY MANUAL
FIFTH EDITION
CLINICAL VIROLOGY MANUAL
FIFTH EDITION
Editor in Chief
Michael J. Loeffelholz
Professor in the Department of Pathology, Director of the Clinical Microbiology Laboratory at the University of Texas Medical Branch (UTMB) at Galveston.
Editors
Richard L. Hodinka
Professor in the Microbiology Department and Chair of the Department of Biomedical Sciences at the University of South Carolina School of Medicine
Stephen A. Young
Director of Research and Clinical Trials at TriCore Reference Laboratories
Benjamin A. Pinsky
Assistant Professor in the Departments of Pathology and Medicine, Division of Infectious Diseases and Geographic Medicine, at the Stanford University School of Medicine
Copyright © 2016 by ASM Press. ASM Press is a registered trademark of the American Society for Microbiology. All rights reserved. No part of this publication may be reproduced or transmitted in whole or in part or reutilized in any form or by any means, electronic or mechanical, including photocopying and recording, or by any information storage and retrieval system, without permission in writing from the publisher.
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Library of Congress Cataloging-in-Publication Data
Names: Loeffelholz, Michael J., editor. | Hodinka, Richard L., editor. | Young, Stephen A., editor.| Pinsky, Benjamin A., editor.
Title: Clinical Virology Manual Fifth Edition / editor in chief, Michael J. Loeffelholz; editors, Richard L. Hodinka, Stephen A. Young, Benjamin A. Pinsky.
Description: Fifth edition. | Washington, DC: ASM Press, [2016]
Identifiers: LCCN 2016020815| ISBN 9781555819149 (hard cover) | ISBN 9781683673187 (e-ISBN)
Subjects: LCSH: Diagnostic virology—Handbooks, manuals, etc.
Classification: LCC QR387 .C48 2016 | DDC 616.9/101—dc23 LC record available at https://lccn.loc.gov/2016020815
ISBN 978-1-55581-914-9
e-ISBN 978-1-68367-318-7
doi:10.1128/9781555819156
Printed in Canada
10 9 8 7 6 5 4 3 2 1
Address editorial correspondence to: ASM Press, 1752 N St., N.W., Washington, DC 20036-2904, USA.
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Phone: 800-546-2416; 703-661-1593. Fax: 703-661-1501.
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DEDICATION
We dedicate this edition of the Clinical Virology Manual to our families for their patience and support during this and our other professional endeavors. We are truly blessed to be part of their lives and to receive their unconditional love.
We would also like to thank, and gratefully acknowledge the support and leadership of, our close colleague, mentor, and friend, Dr. Steven Specter, who has worked tirelessly over the years in delivering the first four editions of the Manual, to advance the field of viral diagnostics, and to provide a forum for clinical virologists, academicians, and clinicians to present and discuss the latest scientific discoveries. We will be forever appreciative of his unwavering efforts.
Contents
Contributors
Editor Biographies
Preface to the Fifth Edition
SECTION I
GENERAL TOPICS IN CLINICAL VIROLOGY
1 The Taxonomy, Classification, and Characterization of Medically Important Viruses
STEVEN J. DREWS
2 Quality Assurance and Quality Control in Clinical and Molecular Virology
MATTHEW J. BANKOWSKI
3 Regulatory Compliance
LINOJ SAMUEL
4 Laboratory Safety
K. SUE KEHL
5 Laboratory Design
MATTHEW J. BINNICKER
SECTION II
LABORATORY PROCEDURES FOR DETECTING VIRUSES
6 Specimen Requirements Selection, Collection, Transport, and Processing
REETI KHARE AND THOMAS E. GRYS
7 Primary Isolation of Viruses
MARIE L. LANDRY AND DIANE LELAND
8 Viral Antigen Detection
DIANE S. LELAND AND RYAN F. RELICH
9 Serologic (Antibody Detection) Methods
DONGXIANG XIA, DEBRA A. WADFORD, CHRISTOPHER P. PREAS, AND DAVID P. SCHNURR
10 Nucleic Acid Extraction in Diagnostic Virology
RAYMOND H. WIDEN AND SUZANE SILBERT
11 Nucleic Acid Amplification by Polymerase Chain Reaction
ANA MARÍA CÁRDENAS AND KEVIN ALBY
12 Isothermal Nucleic Acid Amplification Methods
HARALD H. KESSLER AND EVELYN STELZL
13 Quantitative Molecular Methods
NATALIE N. WHITFIELD AND DONNA M. WOLK
14 Signal Amplification Methods
YUN (WAYNE) WANG
15 DNA Sequencing for Clinical and Public Health Virology: Some Assembly Required
JOANNE BARTKUS
16 Phenotypic and Genotypic Antiviral Susceptibility Testing
MARTHA T. VAN DER BEEK AND ERIC C. J. CLAAS
17 Point-of-Care Diagnostic Virology
JAMES J. DUNN AND LAKSHMI CHANDRAMOHAN
18 Future Technology
ERIN MCELVANIA TEKIPPE AND CAREY-ANN D. BURNHAM
SECTION III
VIRAL PATHOGENS
19 Respiratory Viruses
CHRISTINE ROBINSON, MICHAEL J. LOEFFELHOLZ, AND BENJAMIN A. PINSKY
20 Enteroviruses and Parechoviruses
M. STEVEN OBERSTE AND MARK A. PALLANSCH
21 Measles, Mumps, and Rubella Viruses
WILLIAM J. BELLINI, JOSEPH P. ICENOGLE, AND CAROLE J. HICKMAN
22 Gastrointestinal Viruses
MICHAEL D. BOWEN
23 Hepatitis A and E Viruses
GILBERTO VAUGHAN AND MICHAEL A. PURDY
24 Hepatitis B and D Viruses
REBECCA T. HORVAT
25 Hepatitis C Virus
MELANIE MALLORY AND DAVID HILLYARD
26 Herpes Simplex Viruses and Varicella Zoster Virus
SCOTT H. JAMES AND MARK N. PRICHARD
27 Cytomegalovirus
PREETI PANCHOLI AND STANLEY I. MARTIN
28 Epstein-Barr Virus
DERRICK CHEN AND BELINDA YEN-LIEBERMAN
29 Human Herpesviruses 6, 7, and 8
SHEILA C. DOLLARD AND TIMOTHY M. KARNAUCHOW
30 Human Papillomaviruses
SUSAN NOVAK-WEEKLEY AND ROBERT PRETORIUS
31 Human Polyomaviruses
REBECCA J. ROCKETT, MICHAEL D. NISSEN, THEO P. SLOOTS, AND SEWERYN BIALASIEWICZ
32 Parvoviruses
RICHARD S. BULLER
33 Poxviruses
ASHLEY V. KONDAS AND VICTORIA A. OLSON
34 Rabies Virus
ROBERT J. RUDD AND APRIL D. DAVIS
35 Arboviruses
LAURA D. KRAMER, ELIZABETH B. KAUFFMAN, NORMA P. TAVAKOLI
36 Animal-Borne Viruses
GREGORY J. BERRY, MICHAEL J. LOEFFELHOLZ, AND GUSTAVO PALACIOS
37 Human Immunodeficiency Viruses and Human T-lymphotropic Viruses
JÖRG SCHÜPBACH
38 Chlamydiae
BARBARA VAN DER POL AND CHARLOTTE A. GAYDOS
39 The Human Virome
MATTHEW C. ROSS, NADIM J. AJAMI, AND JOSEPH F. PETROSINO
40 Human Susceptibility and Response to Viral Diseases
VILLE PELTOLA AND JORMA ILONEN
APPENDIXES: REFERENCE VIROLOGY LABORATORIES
APPENDIX 1 Reference Virology Laboratory Testing Performed at the Centers for Disease Control
ROBERTA B. CAREY
APPENDIX 2 Public Health Laboratory Virology Services
JANE GETCHELL
APPENDIX 3 International Reference Laboratories Offering Virology Services
ARIEL I. SUAREZ AND CRISTINA VIDELA
INDEX
Contributors
NADIM AJAMI
Baylor College of Medicine, Department of Molecular Virology and Microbiology, Alkek Center for Metagenomics and Microbiome Research Houston, TX 77030
KEVIN ALBY
University of Pennsylvania, Department of Pathology and Laboratory Medicine, Philadelphia, PA 19104
MATTHEW J. BANKOWSKI
Diagnostic Laboratory Services (The Queen’s Medical Center) Aiea, HI 96701
JOHN A. BURNS
School of Medicine, Department of Pathology, University of Hawaii at Manoa Honolulu, HI 96813
JOANNE BARTKUS
Minnesota Department of Health, Public Health Laboratory St Paul, MN 55164
WILLIAM BELLINI
Centers for Disease Control and Prevention, MMRHLB/DVD/NCIRD Atlanta, GA 30329
GREGORY BERRY
University of Texas Medical Branch, Clinical Microbiology Laboratory Galveston, TX 77555
SEWERYN BIALASIEWICZ
Centre for Children’s Health Research, Children’s Health Queensland, and the Child Health Research Centre, The University of Queensland South Brisbane, QLD 4101 Australia
MATTHEW J. BINNICKER
Mayo Clinic, Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology Rochester, MN 55905
MICHAEL D. BOWEN
Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases Atlanta, GA 30333
RICHARD BULLER
Washington University School of Medicine, Department of Pediatrics Saint Louis, MO 63110
CAREY-ANN BURNHAM
Washington University School of Medicine, Department of Pathology & Immunology Saint Louis, MO 63110
ANA MARIA CARDENAS
University of Pennsylvania, Department of Pathology and Laboratory Medicine Philadelphia, PA 19103
ROBERTA CAREY
Centers for Disease Control and Prevention, Laboratory Quality Management Atlanta, GA 30333
LAKSHMI CHANDRAMOHAN
Texas Children’s Hospital, Department of Pathology Houston, TX 77030
DERRICK CHEN
Mayo Clinic, Laboratory Medicine and Pathology Rochester, MN 55905
ERIC C.J. CLAAS
Leiden University Medical Centre, Medical Microbiology Leiden 2333 ZA
APRIL DAVIS
New York State Health Department, Wadsworth Center Slingerlands, NY 12159
SHEILA C. DOLLARD
Centers for Disease Control and Prevention, Division of Viral Diseases Atlanta, GA 30329
STEVEN J. DREWS
ProvLab Alberta, Diagnostic Virology University of Alberta, Department of Laboratory Medicine and Pathology Edmonton, AB Canada
JAMES DUNN
Texas Children’s Hospital, Department of Pathology Houston, TX 77030
CHARLOTTE GAYDOS
Johns Hopkins University School of Medicine, Division of Infectious Diseases Baltimore, MD 21205
JANE GETCHELL
Public Health Laboratory Consultant Bethany Beach, DE 19930
THOMAS GRYS
Mayo Clinic in Arizona, Department of Laboratory Medicine and Pathology Phoenix, AZ 85054
CAROLE HICKMAN
Centers for Disease Control and Prevention, MMRHLB/DVD/NCIRD Atlanta, GA 30329
REBECCA HORVAT
University of Kansas Medical Center, Department of Pathology Kansas City, Kansas 66160
JOSEPH ICENOGLE
Centers for Disease Control and Prevention, MMRHLB/DVD/NCIRD Atlanta, GA 30329
JORMA ILONEN
University of Turku, The Immunogenetics Laboratory Turku, Finland
SCOTT JAMES
University of Alabama at Birmingham, Department of Pediatrics Birmingham, AL 35233
TIMOTHY KARNAUCHOW
Children’s Hospital of Eastern Ontario, Division of Virology Ottawa, Ontario K1H 8L1 Canada
ELIZABETH KAUFFMAN
New York State Department of Health, Wadsworth Center Slingerlands, NY 12159
SUE KEHL
Medical College of Wisconsin, Department of Pathology Milwaukee, WI 53226
HARALD KESSLER
Medical University of Graz Graz, Austria
REETI KHARE
Northwell Health Laboratories, Department of Pathology and Laboratory Medicine Lake Success, NY 11042
ASHLEY KONDAS
Centers for Disease Control and Prevention, Poxvirus and Rabies Branch Atlanta, GA 30333
LAURA KRAMER
New York State Department of Health, Wadsworth Center, and Department of Biomedical Sciences, SUNY Albany Slingerlands, NY 12159
MARIE LOUISE LANDRY
Yale University, Departments of Laboratory Medicine and Internal Medicine (Infectious Diseases) New Haven, CT 06520
DIANE LELAND
Indiana University School of Medicine, Department of Pathology and Laboratory Medicine Indianapolis, IN 46202
MICHAEL LOEFFELHOLZ
University of Texas Medical Branch, Clinical Microbiology Laboratory Galveston, TX 77555
STANLEY MARTIN
The Ohio State University Wexner Medical Center, Division of Infectious Diseases; Transplant Infectious Diseases Service Columbus, OH 43210
MICHAEL NISSEN
Children’s Health Queensland, Queensland Children’s Medical Research Institute Brisbane, Queensland 4029 Australia
SUSAN NOVAK-WEEKLEY
Southern California Permanente Medical Group, Regional Reference Laboratories, Microbiology North Hollywood, CA 91605
M. STEVEN OBERSTE
Centers for Disease Control and Prevention, Poxvirus and Rabies Branch Atlanta, GA 30333
VICTORIA OLSON
Centers for Disease Control and Prevention, Poxvirus and Rabies Branch Atlanta, GA 30333
GUSTAVO PALACIOS
USAMRIID, Center for Genome Sciences Frederick, MD 21702
MARK PALLANSCH
Centers for Disease Control and Prevention, Division of Viral Diseases Atlanta, GA 30329
PREETI PANCHOLI
The Ohio State University Wexner Medical Center, Department of Pathology Columbus, OH 43205
VILLE PELTOLA
Turku University Hospital, Department of Pediatrics and Adolescent Medicine Turku 20521 Finland
JOSEPH PETROSINO
Baylor College of Medicine, Department of Molecular Virology and Microbiology, Alkek Center for Metagenomics and Microbiome Research Houston, TX 77030
CHRISTOPHER PREAS
California Department of Public Health, Viral and Rickettsial Disease Laboratory Richmond, CA 94804
ROBERT PRETORIUS
Southern California Permanente Medical Group— Fontana, Obstetrics and Gynecology Fontana, CA 92445
MARK PRICHARD
University of Alabama at Birmingham, Department of Pediatrics Birmingham, AL 35233
MICHAEL PURDY
Centers for Disease Control and Prevention, Division of Viral Hepatitis Atlanta, GA 30329
RYAN RELICH
Indiana University School of Medicine, Department of Pathology and Laboratory Medicine Indianapolis, IN 46202
REBECCA ROCKETT
Centre for Infectious Diseases & Microbiology - Public Health (CIDM-PH) Institute of Clinical Pathology & Medical Research (ICPMR) Westmead Hospital, Westmead NSW, 2145, Sydney, Australia
MATTHEW ROSS
Baylor College of Medicine, Department of Molecular Virology and Microbiology, Alkek Center for Metagenomics and Microbiome Research Houston, TX 77030
ROBERT RUDD
New York State Health Department, Wadsworth Center Slingerlands, NY 12159
LINOJ SAMUEL
Henry Ford Health System, Department of Pathology Detroit, MI 48202
DAVID SCHNURR
California Department of Public Health, Viral and Rickettsial Disease Laboratory Richmond, CA 94804
JÖRG SCHÜPBACH
University of Zurich, Institute of Medical Virology, Swiss National Center for Retroviruses Zurich CH-8057 Switzerland
SUZANE SILBERT
Tampa General Hospital, Department of Pathology, Esoteric Testing/R&D Tampa, FL 33606
THEO SLOOTS
Centre for Children’s Health Research, Children’s Health Queensland, and the Child Health Research Centre, The University of Queensland South Brisbane, QLD 4101 Australia
EVELYN STELZL
Medical University of Graz Graz, Austria
ARIEL SUAREZ
IACA Laboratorios, Molecular Biología Bahia Blanca, Buenos Aires B8000FIB Argentina
NORMA TAVAKOLI
New York State Department of Health, Wadsworth Center, And Department of Biomedical Sciences, State University of New York Albany, NY 12208
ERIN MCELVANIA TEKIPPE
University of Texas Southwestern Medical Center, Department of Pathology and Pediatrics Dallas, TX
MARTHA T. VAN DER BEEK
Leiden University Medical Centre, Medical Microbiology Leiden 2333 ZA Netherlands
BARBARA VAN DER POL
University of Alabama at Birmingham School of Medicine, Division of Infectious Diseases Birmingham, AL 35294
GILBERTO VAUGHAN
Centers for Disease Control and Prevention, Division of Viral Hepatitis Atlanta, GA 30329
CRISTINA VIDELA
CEMIC Virology Buenos Aires C1431FWO Argentina
DEBRA WADFORD
California Department of Public Health, Viral and Rickettsial Disease Laboratory Richmond, CA 94804
YUN F. WANG
Emory University School of Medicine, Department of Pathology & Laboratory Medicine Atlanta, GA 30303
NATALIE WHITFIELD
OpGen Clinical Services Laboratory Gaithersburg, MD 20878
RAYMOND WIDEN
Tampa General Hospital, Pathology Department, Esoteric Testing/R&D Tampa, FL 33606
DONNA WOLK
Geisinger Health Systems, Dept. of Laboratory Medicine Danville, PA 17822
DONGXIANG XIA
California Department of Public Health, Viral and Rickettsial Disease Laboratory Richmond, CA 94804
BELINDA YEN-LIEBERMAN
Cleveland Clinic, Laboratory Medicine Cleveland, OH 44195
Editor Biographies
Michael J. Loeffelholz is a Professor in the Department of Pathology, Director of the Clinical Microbiology Laboratory at the University of Texas Medical Branch (UTMB) at Galveston, and Director of the American Society for Microbiology (ASM) CPEP-accredited Medical Microbiology Fellowship program at UTMB. Dr. Loeffelholz is also an editor of the Journal of Clinical Microbiology. He has served on a number of committees, including the Pan American Society for Clinical Virology (PASCV), ASM Committee on Professional Affairs, CDC Board of Scientific Counselors/Office of Infectious Diseases, and the Association of Public Health Laboratories Board of Directors. Dr. Loeffelholz is a diplomate of the American Board of Medical Microbiology (ABMM).
Richard L. Hodinka is a Professor in the Microbiology Department and Chair of the Department of Biomedical Sciences at the University of South Carolina School of Medicine, Greenville. Dr. Hodinka's clinical and research interests involve pediatric viral diseases, detection and monitoring of viral infections in pediatric and adult immunocompromised hosts, and the development and study of rapid and accurate methods for the diagnosis of infectious diseases; current emphasis is on molecular technologies and automated instrumentation for the greatest impact on the care and management of ill patients. Dr. Hodinka has served as President and a Council Member for the PASCV, as a member of the International Scientific Advisory Committee for the Asia Pacific Congress of Medical Virology, and on a number of ASM committees. Dr. Hodinka has published extensively and is the author of a number of original scientific publications, review articles, and book chapters.
Stephen A. Young is Director of Research and Clinical Trials at TriCore Reference Laboratories and Professor (emeritus) in the Department of Pathology at the University of New Mexico. Dr. Young served as a collaborator in the Multi-Center AIDS Cohort Study for 25 years and is a co-investigator on two NIH grants affiliated with the cohort. He is involved in an active research program to evaluate and develop diagnostic products for clinical microbiology and has completed approximately 100 FDA in vitro diagnostic device trials or market evaluations of diagnostic tests. Dr. Young is a diplomate of the ABMM.
Benjamin A. Pinsky is an Assistant Professor in the Departments of Pathology and Medicine, Division of Infectious Diseases and Geographic Medicine, at the Stanford University School of Medicine and is the Medical Director of the Clinical Virology Laboratory for Stanford Health Care and Stanford Children's Health. Dr. Pinsky is on the editorial boards of several journals including the Journal of Clinical Microbiology and Clinical Microbiology Reviews. He has also served on a number of committees, including the PASCV, College of American Pathologists Microbiology Resource Committee, and the Association for Molecular Pathology Clinical Practice Committee. Dr. Pinsky is board certified in Clinical Pathology by the American Board of Pathology.
Preface to the Fifth Edition
The aims of the fifth edition of the Clinical Virology Manual remain the same as prior editions and include serving as a reference source to healthcare professionals and laboratorians in providing clinical and technical information regarding viral diseases and the diagnosis of viral infections.
This new edition includes 40 chapters and 3 appendices and, similar to the organization of prior additions, consists of the four sections: general topics, laboratory procedures, viral pathogens, and the appendices. We have modified the content of the appendices to provide basic but practical information on reference virology laboratories at both the national and international levels. The viral pathogen chapters have a consistent organization, with proportionally more content dedicated to diagnostics and testing. Additionally, a new section, with the heading of “Diagnostic Best Practices”, has been included in each viral pathogens chapter. The section summarizes recommendations for diagnostic testing and cites evidence-based guidelines when available.
The past several years have been very challenging, as well as exciting, for diagnostic virologists, with outbreaks of enterovirus D68, measles virus, mumps virus, norovirus, Ebola virus, and, most recently, Zika virus. In addition, there is continued emergence of chikungunya, dengue, and influenza viruses, highlighted by the influenza pandemic of 2009. The landscape of hepatitis C virus has changed, and will continue to change dramatically, with the availability of new classes of direct-acting antiviral drugs that provide an excellent probability of cure.
This edition has incorporated these significant events to the extent allowed by the production schedule. We thank the authors for their contributions, particularly during this very busy time for virologists. We also thank the staff of the American Society for Microbiology Press for their support and hard work in bringing this edition to fruition.
The fifth edition of the Manual also brings a major change in editors, as a new editor has been added and a previous editor has cycled off. Also, after successfully leading this series through four editions, Dr. Steven Specter has passed on the reins of Editor-in-Chief. We hope that this edition is a credit to Dr. Specter, as well as to other prior editors, Drs. Lancz and Wiedbrauk.
MICHAEL J. LOEFFELHOLZ
RICHARD L. HODINKA
STEPHEN A. YOUNG
BENJAMIN A. PINSKY
SECTION I
General Topics in Clinical Virology