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STUDIES IN VIRAL ECOLOGY
STUDIES IN VIRAL ECOLOGY Animal Host Systems Volume 2
Edited By CHRISTON J. HURST Xavier University Cincinnati, Ohio USA and Universidad del Valle Santiago de Cali, Valle Colombia
Copyright Ó 2011 by Wiley-Blackwell. All rights reserved Published by John Wiley & Sons, Inc., Hoboken, New Jersey Published simultaneously in Canada No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning, or otherwise, except as permitted under Section 107 or 108 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher, or authorization through payment of the appropriate per-copy fee to the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, (978) 750-8400, fax (978) 750-4470, or on the web at www.copyright.com. Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, (201) 748-6011, fax (201) 748-6008, or online at http://www.wiley.com/go/permission. Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or fitness for a particular purpose. No warranty may be created or extended by sales representatives or written sales materials. The advice and strategies contained herein may not be suitable for your situation. You should consult with a professional where appropriate. Neither the publisher nor author shall be liable for any loss of profit or any other commercial damages, including but not limited to special, incidental, consequential, or other damages. For general information on our other products and services or for technical support, please contact our Customer Care Department within the United States at (800) 762-2974, outside the United States at (317) 572-3993 or fax (317) 572-4002. Wiley also publishes its books in a variety of electronic formats. Some content that appears in print may not be available in electronic formats. For more information about Wiley products, visit our web site at www.wiley.com. Library of Congress Cataloging-in-Publication Data: Studies in viral ecology / edited by Christon J. Hurst. v. cm. Includes index. Contents: v.1. Microbial and Botanical Host Systems (ISBN 978-0-470-62396-1) – v.2. Animal Host Systems (ISBN 978-0-470-62429-6). ISBN (set) 978-1-118-02458-4 (cloth) 1. Viruses–Ecology. I. Hurst, Christon J. QR478.A1S78 2011 579.2–dc22 2010046370 Printed in Singapore. oBook ISBN: 978-1-118-02571-0 ePDF ISBN: 978-1-118-02567-3 ePub ISBN: 978-1-118-02569-7 10 9 8 7 6
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CONTENTS
VOLUME
1
DEDICATION
ix
PREFACE
xi
CONTRIBUTORS
xiii
ATTRIBUTION CREDITS FOR COVER AND SPINE ARTWORK
xv
SECTION I
1
AN INTRODUCTION TO THE STRUCTURE AND BEHAVIOR OF VIRUSES
Defining the Ecology of Viruses
1 3
Christon J. Hurst
2
An Introduction to Viral Taxonomy with Emphasis on Microbial and Botanical Hosts and the Proposal of Akamara, a Potential Domain for the Genomic Acellular Agents
41
Christon J. Hurst
3
Virus Morphology, Replication, and Assembly
67
Debi P. Nayak
v
vi
4
CONTENTS
The (Co)Evolutionary Ecology of Viruses
131
Michael J. Allen
SECTION II 5
VIRUSES OF OTHER MICROORGANISMS
Bacteriophage and Viral Ecology as Seen Through the Lens of Nucleic Acid Sequence Data
145
147
Eric Sakowski, William Kress, and K. Eric Wommack
6
Viruses of Cyanobacteria
169
Lauren D. McDaniel
7
Viruses of Eukaryotic Algae
189
William H. Wilson and Michael J. Allen
8
Viruses of Seaweeds
205
Declan C. Schroeder
9
The Ecology and Evolution of Fungal Viruses
217
Michael G. Milgroom and Bradley I. Hillman
10
Prion Ecology
255
Reed B. Wickner
SECTION III VIRUSES OF MACROSCOPIC PLANTS
271
11
273
Ecology of Plant Viruses, with Special Reference to Geminiviruses Basavaprabhu L. Patil and Claude M. Fauquet
12
Viroids and Viroid Diseases of Plants
307
Ricardo Flores, Francesco Di Serio, Beatriz Navarro, Nuria Duran-Vila, and Robert A. Owens
INDEX
VOLUME
343
2
DEDICATION
ix
PREFACE
xi
CONTRIBUTORS
xiii
ATTRIBUTION CREDITS FOR COVER AND SPINE ARTWORK
xv
CONTENTS
SECTION I
1
AN INTRODUCTION TO THE STRUCTURE AND BEHAVIOR OF VIRUSES
Defining the Ecology of Viruses
vii
1 3
Christon J. Hurst
2
An Introduction to Viral Taxonomy with Emphasis on Animal Hosts and the Proposal of Akamara, a Potential Domain for the Genomic Acellular Agents
41
Christon J. Hurst
3
Virus Morphology, Replication, and Assembly
63
Debi P. Nayak
4
The (Co)evolutionary Ecology of Viruses
127
Michael J. Allen
SECTION II 5
VIRUSES OF MACROSCOPIC ANIMALS
Coral Viruses
141 143
William H. Wilson
6
Viruses Infecting Marine Molluscs
153
Tristan Renault
7
The Viral Ecology of Aquatic Crustaceans
177
Leigh Owens
8
Viruses of Fish
191
Audun Helge Nerland, Aina-Cathrine Øverga rd, and Sonal Patel
9
Ecology of Viruses Infecting Ectothermic Vertebrates—The Impact of Ranavirus Infections on Amphibians
231
V. Gregory Chinchar, Jacques Robert, and Andrew T. Storfer
10
Viruses of Insects
261
Declan C. Schroeder
11
Viruses of Terrestrial Mammals
273
Laura D. Kramer and Norma P. Tavakoli
12
Viruses of Cetaceans
309
Marie-Franc¸oise Van Bressem and Juan A. Raga
13
The Relationship Between Humans, Their Viruses, and Prions
333
Christon J. Hurst
14
Ecology of Avian Viruses
365
Josanne H. Verhagen, Ron A.M. Fouchier, and Vincent J. Munster
INDEX
395
DEDICATION
I dedicate these two volumes to the memory of my brother in spirit, Henry Hanssen. To me, he seemed a hero and I remember him most for his unfailing ability to present a sense of humanity in times of tragedy. We first met while studying together for our doctorates in Houston, Texas. Henry was born in Colombia near Medellı´n and tragically orphaned as a young child after which he was lovingly raised by an aunt in Bogota´. Henry may have gained his tremendous sense of humanity from that experience. He had no biological children of his own but helped to raise two daughters. The first of those came into his life by a twist of luck while one day Henry was walking along a street in Colombia and heard what he thought might be a cat trapped inside of a garbage bin. Henry went over to free the cat and discovered
instead a crying infant child in a plastic bag, presumably discarded there by a distraught mother. Henry took the baby to the police, and when no one stepped forward as a parent Henry adopted the child and eventually even helped to pay for her college tuition. The second daughter came through Henry’s marriage to the love of his life. When there arose need for representing humanity, Henry was undaunted by circumstance. His accomplishments included establishing an infant vaccination program against poliomyelitis in Angola at the personal request of Jonas Salk. Angola was in a state of civil war at that time and no one else was willing to undertake the necessary but frightening task. Henry showed equal humanitarianism to civilians and military on both sides of that conflict. Subsequently, Henry initiated
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DEDICATION
a similar poliomyelitis vaccination program during a period of civil war in Central America and for his efforts was awarded honorary citizenship by one of the countries there. He then initiated a poliomyelitis vaccination program in his native Colombia, while that country’s continuing civil war was in full strength. I was proud to address Henry by the name of “brother” and always will think of him in that way. He addressed me by that same term of affection and he is lovingly remembered by everyone whom his life touched.
HENRY HANSSEN VILLAMIZAR (1945–2007)
PREFACE
Virology is a field of study which has grown and expanded greatly since the viruses as a group first received their name in 1898. Many of the people who presently are learning virology have come to perceive these acellular biological entities as being merely trinkets of nucleic acid to be cloned, probed, and spliced. However, the viruses are much more than merely trinkets to be played with in molecular biology laboratories. The viruses are indeed highly evolved biological entities with an organismal biology that is complex and interwoven with the biology of their hosting species. Ecology is defined as the branch of science which addresses the relationships between an organism of interest and the other organisms with which it interacts, the interactions between the organism of interest and its environment, and the geographical distribution of the organism of interest. The purpose of this book is to help define and explain the ecology of viruses, i.e., to examine what life might seem like from a
“virocentric” point of view, as opposed to our normal “anthropocentric” perspective. As we begin our examination of the virocentric life, it is important to realize that in nature both the viruses of macroorganisms and the viruses of microorganisms exist in cycles with their respective hosts. Under normal conditions, the impact of viruses upon their natural host populations may be barely apparent due to factors such as evolutionary coadaptation between the virus and those natural hosts. However, when viruses find access to new types of hosts and alternate transmission cycles, or when they encounter a concentrated population of susceptible genetically similar hosts such as occurs in densely populated human communities, communities of cultivated plants or animals, or algal blooms, then the impact of the virus upon its host population can appear catastrophic. The key to understanding these types of cycles lies in understanding the viruses and how their ecology relates to the ecology of their hosts, their alternate hosts, and any vectors which
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PREFACE
they utilize, as well as their relationship to the availability of suitable vehicles that can transport the different viral groups. I hope that you will enjoy the information presented in this book set as much as I and the other authors have enjoyed presenting it to you.
The written word is a marvelous thing, able to convey understanding and enthusiasm across unimaginable distances and through time. CHRISTON J. HURST Cincinnati, Ohio
CONTRIBUTORS
MICHAEL J. ALLEN, Plymouth Marine Laboratory, Plymouth, UK V. GREGORY CHINCHAR, Department of Microbiology, University of Mississippi Medical Center, Jackson, MS RON A.M. FOUCHIER, Department of Virology, National Influenza Center, Erasmus Medical Center, Rotterdam, The Netherlands CHRISTON J. HURST, Departments of Biology and Music, Xavier University, Cincinnati, OH; Engineering Faculty, Universidad del Valle, Ciudad Universitaria Melendez, Santiago de Cali, Valle, Colombia LAURA D. KRAMER, Wadsworth Center, New York State Department of Health, University of Albany, Albany, NY; Department of Biomedical Sciences, School of Public Health, University of Albany, Albany, NY VINCENT J. MUNSTER, Laboratory of Virology, Rocky Mountain Laboratories, Division of
Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT DEBI P. NAYAK, Department of Microbiology and Immunology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA AUDUN HELGE NERLAND, The Gade Institute, University of Bergen, Bergen, Norway; Institute of Marine Research, University of Bergen, Bergen, Norway AINA-CATHRINE ØVERGA˚RD, The Gade Institute, University of Bergen, Bergen, Norway; Institute of Marine Research, University of Bergen, Bergen, Norway LEIGH OWENS, Discipline of Microbiology and Immunology, School of Veterinary and Biomedical Sciences, James Cook University, Townsville, Australia SONAL PATEL, Institute of Marine Research, University of Bergen, Bergen, Norway
xiii
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CONTRIBUTORS
JUAN A. RAGA, Marine Zoology Unit, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
University of Albany, Albany, NY; Department of Biomedical Sciences, School of Public Health, University of Albany, Albany, NY
TRISTAN RENAULT, Laboratoire de Genetique et Pathologie, Ifremer La Tremblade, France
MARIE-FRANC¸OISE VAN BRESSEM, Cetacean Conservation Medicine Group (CMED/ CEPEC), Bogota, Colombia; Centro Peruano de Estudios Cetolo´gicos (CEPEC), Museo de Delfines, Pucusana, Lima 20, Peru
JACQUES ROBERT, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY DECLAN C. SCHROEDER, Marine Biological Association of the UK, Plymouth, UK ANDREW T. STORFER, School of Biological Sciences, Washington State University, Pullman, WA NORMA P. TAVAKOLI, Wadsworth Center, New York State Department of Health,
JOSANNE H. VERHAGEN, Department of Virology, National Influenza Center, Erasmus Medical Center, Rotterdam, The Netherlands WILLIAM H. WILSON, Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, ME
ATTRIBUTION CREDITS FOR COVER AND SPINE ARTWORK
Cover credits “Montage showing animal hosts”, montage image used with permission of the artist, Christon J. Hurst. Those images incorporated into this montage were: Honeybees - Snapshot of a comb within a husbanded honeybee colony (source: image courtesy of S. J. Martin, provided by Declan C. Schroeder); Big eared townsend bat (Corynorhinus townsendii) File:Big-eared-townsend-fledermaus.jpg (author unknown; public domain image, Bureau of Land Management, U. S. Federal Government); Laughing Kookaburra – Dacelo novaeguineae waterworks.jpg (author: Wikipedia user name Noodle snacks; Creative Commons Attribution-Share Alike 3.0 Unported license); Cotton Rat - File:Sigmodon hispidus1.jpg (author unknown; Centers for Disease Control and Prevention, U.S. Federal Government, public domain image); Heterocarpus shrimp - File: Heterocarpus ensifer.jpg (author unknown; National Oceanic and Atmospheric Administration, U.S. Federal Government, public domain image); Pillar coral - File:PillarCoral.jpg (author: Commander William Harrigan, NOAA Corps (ret.); National Oceanic and
Atmospheric Administration, U.S. Federal Government, public domain image); Zebra striped Gorgonian wrapper, colonial anemone - File:Colonial anemone zebra.jpg (author: Nick Hobgood; Creative Commons Attribution-Share Alike 3.0 Unported license); Humpback whale - File:Humpback stellwagen edit.jpg (author: Whit Welles; Creative Commons Attribution 3.0 Unported license); Killer whales - File:Killerwhales jumping.jpg (author: Pittman; National Oceanic and Atmospheric Administration, U.S. Federal Government, public domain image); School of Goldband Fusilier, Pterocaesio chrysozona File:School of Pterocaesio chrysozona in Papua New Guinea 1.jpg (author: Mila Zinkova; Creative Commons Attribution-Share Alike 3.0 Unported license); Abalone - File:Abalone OCA.jpg (author: Wikipedia user name Little Mountain 5; Creative Commons AttributionShare Alike 3.0 Unported license.); and Giant Malaysian prawn Macrobrachium rosenbergii - File:Giant Malaysian Prawn.JPG (author: Wikipedia user name Syrist; Creative Commons Attribution-Share Alike 3.0 Unported license). xv
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ATTRIBUTION CREDITS FOR COVER AND SPINE ARTWORK
Spine credits “Montage showing animal, botanical and microbial hosts”, montage image used with permission of the artist, Christon J. Hurst. Those images incorporated into this montage were: Calliope Hummingbird - File:Calliopenest.jpg (author: Wolfgang Wander; Creative Commons Attribution-Share Alike 3.0 Unported license); Cassava - File:Casava.jpg (author: Bob Walker; Creative Commons Attribution-ShareAlike 2.5 License); Tiger Salamander (Ambystoma tigrinum) - File: Salamandra Tigre.png (author: Carla Isabel
Ribeiro; Creative Commons Attribution-Share Alike 3.0 Unported license); Volvox tertius (author: Matthew D. Herron; image supplied by and used with author’s permission); Volvox aureus (author: Matthew D. Herron; image supplied by and used with author’s permission); Molluscs (mostly bivalves) harvested from contaminated water in Zulia, Venezuela (author: Christon J. Hurst; image provided for use in this montage); and giant clam - File: Tridacna crocea.jpg (author: Nick Hobgood; Creative Commons Attribution-Share Alike 3.0 Unported license).
