Studies in Viral Ecology E-Book
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- Herausgeber: John Wiley & Sons
- Kategorie: Wissenschaft und neue Technologien
- Sprache: Englisch
This second edition of Studies in Viral Ecology is designed to serve as a means of updating the knowledge of virologists regarding the broader aspects of viral ecology. As with the first edition, this book explains the ecology of viruses by examining their interactive dynamics with their hosting species (covering both animals and plants), including the types of transmission cycles that viruses have evolved encompassing principal and alternate hosts, vehicles and vectoring species. Examining virology from an organismal biology approach and focusing on the concept that viral infections represent areas of overlap in the ecologies of the involved species, Viral Ecology is essential for students and professionals who either may be non-virologists or virologists whose previous familiarity has been very specialized.This second edition of Studies in Viral Ecology is designed to serve as a means of updating the knowledge of virologists regarding the broader aspects of viral ecology. As with the first edition, this book explains the ecology of viruses by examining their interactive dynamics with their hosting species (covering both animals and plants), including the types of transmission cycles that viruses have evolved encompassing principal and alternate hosts, vehicles and vectoring species. Examining virology from an organismal biology approach and focusing on the concept that viral infections represent areas of overlap in the ecologies of the involved species, Viral Ecology is essential for students and professionals who either may be non-virologists or virologists whose previous familiarity has been very specialized. Now in its second edition, Studies in Viral Ecology explores the intricate interactions between viruses and other organisms from a "virocentric" perspective. Divided into five sections, the book opens with a thorough introduction to the ecology of all viruses, followed by detailed examinations that individually consider the viruses of other microorganisms, viruses of vascular plants, and viruses of vertebrate and invertebrate animals. The chapters have been written by leading scientists in their respective research fields and cover topics such as the evolution of fungal viruses, viruses affecting insects, viruses of terrestrial and marine mammals, and the relationship between humans, their viruses, and prions. Studies in Viral Ecology, Second Edition remains required reading for virologists and virology instructors and students who study the interactions between virus and host at the individual species and higher taxonomic levels.
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Table of Contents
COVER
TITLE PAGE
COPYRIGHT PAGE
DEDICATION PAGE
PREFACE
CONTRIBUTORS
CITATION FOR COVER IMAGE, STUDIES IN VIRAL ECOLOGY, SECOND EDITION
SECTION I: AN INTRODUCTION TO THE ECOLOGY OF VIRUSES
CHAPTER 1: DEFINING THE ECOLOGY OF VIRUSES
*
1.1 INTRODUCTION
1.2 SURVIVING THE GAME: THE VIRUS AND IT'S HOST
1.3 STEPPIN' OUT AND TAKING THE A TRAIN: REACHING OUT AND TOUCHING SOMEONE BY VECTOR OR VEHICLE
1.4 WHY THINGS ARE THE WAY THEY ARE
1.5 SUMMARY (CAN THERE BE CONCLUSIONS?)
ACKNOWLEDGEMENT
A REMEMBRANCE OF RICARDO FLORES
REFERENCES
SECTION II: VIRUSES OF OTHER MICROORGANISMS
CHAPTER 2: BACTERIOPHAGE AND VIRAL ECOLOGY IN THE “OMICS AGE”
2.1 VIRAL DIVERSITY AND DISTRIBUTIONS
2.2 BACTERIOPHAGE IMPACTS ON BACTERIAL COMMUNITIES
2.3 BACTERIOPHAGE–HOST INTERACTIONS AND COEVOLUTION
2.4 VIRAL INFORMATICS: PAST, PRESENT, AND FUTURE CHALLENGES
REFERENCES
CHAPTER 3: VIRUSES OF EUKARYOTIC MICROALGAE
3.1 INTRODUCTION
3.2 DNA VIRUSES – PHYCODNAVIRIDAE: VIRUS LEVIATHANS OF THE AQUATIC WORLD
3.3 OTHER DNA VIRUSES
3.4 RNA VIRUSES
3.5 DETECTION AND DISCOVERY METHODS
3.6 FUTURE PERSPECTIVES
3.7 INDEX OF VIRUSES
REFERENCES
CHAPTER 4: VIRUSES OF SEAWEEDS
4.1 INTRODUCTION
4.2 DIVERSITY OF VIRUSES IN SEAWEEDS
4.3 DIVERSITY OF PHAEOVIRUSES
4.4 LIFE CYCLE OF PHAEOVIRUSES
4.5 ECOLOGY OF PHAEOVIRUSES
4.6 GENOMES
4.7 GENOME INTEGRATION
4.8 SUMMARY
REFERENCES
CHAPTER 5: THE ECOLOGY AND EVOLUTION OF FUNGAL VIRUSES
5.1 INTRODUCTION
5.2 BIOLOGY AND DIVERSITY OF FUNGAL VIRUSES
5.3 TRANSMISSION OF FUNGAL VIRUSES
5.4 EFFECTS OF VIRUSES ON FUNGAL FITNESS
5.5 POPULATION BIOLOGY OF FUNGAL VIRUSES
5.6 BIOLOGICAL CONTROL OF FUNGI WITH VIRUSES
5.7 FUTURE DIRECTIONS
REFERENCES
SECTION III: VIRUSES OF VASCULAR PLANTS
CHAPTER 6: ECOLOGY OF PLANT INFECTING VIRUSES, WITH SPECIAL REFERENCE TO GEMINIVIRUSES
6.1 INTRODUCTION
6.2 VIRUS‐VECTOR‐PLANT ECOSYSTEMS
6.3 CONTROL OF VIRUS DISEASES
6.4 ROLE OF MAN AND CLIMATE CHANGE IN VIRUS ECOLOGY
6.5 EMERGENCE OF NEW RECOMBINANT GEMINIVIRUSES
6.6 CONCLUSIONS
ACKNOWLEDGMENT
DECLARATION
REFERENCES
CHAPTER 7: VIROIDS AND VIROID DISEASES OF PLANTS
7.1 INTRODUCTION
7.2 STRUCTURE AND CLASSIFICATION
7.3 REPLICATION AND MOVEMENT
7.4 HOST RANGE, SPECIFICITY, AND DEFENSE
7.5 PATHOGENESIS
7.6 INTERACTIONS BETWEEN VIROIDS AND VIRUSES
7.7 TRANSMISSION
7.8 EPIDEMIOLOGY AND CONTROL
7.9 CONCLUSIONS
ACKNOWLEDGMENTS
REFERENCES
SECTION IV: VIRUSES OF INVERTEBRATE ANIMALS
CHAPTER 8: VIRUSES INFECTING MARINE MOLLUSKS
8.1 INTRODUCTION
8.2 HISTORY, CLASSIFICATION, AND VIRUS MORPHOLOGY
8.3 CLINICAL FEATURES, LESIONS, AND TISSUE DISTRIBUTION
8.4 EPIDEMIOLOGY AND VIRUS ECOLOGY
8.5 HOST–PATHOGEN INTERACTIONS AND IMMUNE RESPONSE
8.6 CONCLUSION
REFERENCES
CHAPTER 9: VIRUSES AFFECTING CRUSTACEANS
9.1 INTRODUCTION
9.2 UNDERSTANDING THE BASICS OF CRUSTACEAN VIRAL ECOLOGY
9.3 VIRUSES OF SPECIFIC HOST GROUPS
9.4 CASE STUDY
9.5 CONCLUSIONS
ACKNOWLEDGMENTS
REFERENCES
CHAPTER 10: VIRUSES OF INSECTS
10.1 INTRODUCTION
10.2 DIVERSITY OF INSECT VIRUSES
10.3 ECOLOGY OF DEFORMED WING VIRUS
10.4 SUMMARY
REFERENCES
SECTION V: VIRUSES OF VERTEBRATE ANIMALS
CHAPTER 11: VIRUSES OF FISH
11.1 INTRODUCTION
11.2 FISH AS VIRAL HOSTS
11.3 THE VIRUS
11.4 THE IMPACT OF ENVIRONMENTAL FACTORS
11.5 IMPACT OF VIRUS FOR WILD FISH POPULATIONS
11.6 THE IMPACT OF VIRAL DISEASES FOR FISH FARMING
11.7 INDIRECT IMPACT OF VIRUSES ON FISH
11.8 VACCINES AND VACCINATION
11.9 SELECTED VIRUS SPECIES FROM THE VARIOUS BALTIMORE GROUPS
11.10 SUMMARY
REFERENCES
CHAPTER 12: ECOLOGY OF VIRUSES INFECTING ECTOTHERMIC VERTEBRATES
12.1 INTRODUCTION TO VIRUS DIVERSITY IN AMPHIBIANS
12.2 VIRAL PATHOGENS INFECTING AMPHIBIANS
12.3 CONCLUSIONS
ACKNOWLEDGMENTS
REFERENCES
CHAPTER 13: VIRUSES OF REPTILES
13.1 INTRODUCTION
13.2 GENERAL REPTILE TAXONOMY
13.3 VIRUSES OF REPTILES
13.4 REPTILIAN IMMUNE SYSTEM
13.5 MECHANISMS OF INFECTION
13.6 DETERMINANTS OF DISEASE
13.7 IMPACT OF VIRAL INFECTIONS ON REPTILE POPULATIONS
13.8 SELECTED VIRAL SPECIES ACCORDING TO GENOME ORGANIZATION
13.9 SUMMARY AND FUTURE PERSPECTIVES
REFERENCES
CHAPTER 14: ECOLOGY OF AVIAN VIRUSES
14.1 INTRODUCTION
14.2 AN EXAMPLE: INFLUENZA A VIRUSES
14.3 AVIAN INFLUENZA VIRUS HOSTS
14.4 HOST AND VIRUS TRAITS ASSOCIATED WITH TRANSMISSION OF AVIAN INFLUENZA VIRUSES
14.5 HOST PRE‐EXISTING IMMUNITY AND AVIAN INFLUENZA VIRUSES
14.6 HOST ECOLOGY AND PERSISTENCE OF AVIAN INFLUENZA VIRUSES
14.7 HIGHLY PATHOGENIC AVIAN INFLUENZA VIRUSES AND WILD BIRDS
14.8 CONCLUSION
REFERENCES
CHAPTER 15: VIRUSES OF TERRESTRIAL MAMMALS
15.1 INTRODUCTION
15.2 ECOLOGY AND DISEASE
15.3 SUMMARY
ACKNOWLEDGMENT
REFERENCES
CHAPTER 16: VIRUSES OF MARINE MAMMALS
16.1 INTRODUCTION
16.2 INFLUENZA A AND B VIRUSES
16.3 MORBILLIVIRUSES
16.4 OTHER VIRUSES
REFERENCES
CHAPTER 17: THE RELATIONSHIP BETWEEN HUMANS, THEIR VIRUSES AND PRIONS
*
17.1 INTRODUCTION
17.2 ACHIEVING THE GOAL OF VIRAL REPRODUCTION
17.3 ACHIEVING THE GOAL OF VIRAL TRANSMISSION BETWEEN HOSTS
17.4 SUMMARY OF VIRAL FAMILIES THAT AFFLICT HUMANS
17.5 SUMMARY OF PRIONS THAT AFFLICT HUMANS
17.6 CONCLUSIONS
ACKNOWLEDGEMENT
REFERENCES
INDEX
END USER LICENSE AGREEMENT
List of Tables
Chapter 1
TABLE 1.1 Categories of Physical Barriers
TABLE 1.2 Categories of Chemical Barriers
TABLE 1.3 Categories of Biological Barriers
Chapter 2
TABLE 2.1 Bacteriophage Taxa Recognized by the International Committee on Taxonom...
Chapter 3
TABLE 3.1 Index of the Virus Genera Covered in this Chapter, and the Types of...
Chapter 4
TABLE 4.1 Reports of Viruses in Seaweeds
TABLE 4.2 Features of Phaeovirus Subgroups
Chapter 5
TABLE 5.1 Overview of Fungal Virus Families and Groups Discussed in This Chapter.
Chapter 6
TABLE 6.1 Plant Viruses and their Taxonomic Classification.
Chapter 7
TABLE 7.1 Classification of Viroids
TABLE 7.2 New Viroids and Viroid‐like RNAs Identified by High‐throughput Sequenci...
Chapter 8
TABLE 8.1 Viruses Infecting Marine Mollusks
Chapter 9
TABLE 9.1 Summary of known DNA viruses of crustacea, sorted alphabetically by vi...
TABLE 9.2 Summary of known RNA viruses of crustacea, sorted alphabetically by vir...
Chapter 10
TABLE 10.1 Viruses of Insects
TABLE 10.2 Physiochemical Properties of Insect Viruses
Chapter 11
TABLE 11.1 Examples of Viruses from the Various Groups of the Baltimore Class...
Chapter 12
TABLE 12.1 Viral Families Containing Members Infecting Fish, Amphibians, and ...
TABLE 12.2 Cellular and Molecular Elements of the Larval and Adult
Xenopus
Imm...
TABLE 12.3 First Reports of Amphibian Ranavirus Infections in Wild, Captive, ...
Chapter 13
TABLE 13.1 Virus Families Described in Reptiles
TABLE 13.2 Viruses Commonly Found in Reptiles and Discussed in this Text and ...
TABLE 13.3 Overview of Reported Prevalence of Common Viral Infections in Pet ...
Chapter 14
TABLE 14.1 Avian Virus Families and Respective Viruses Isolated from Domestic...
TABLE 14.2 List of Wild Bird Orders and Families in which Influenza A Viruses...
Chapter 15
TABLE 15.1 Listing of Viral Families Affecting Vertebrates
TABLE 15.2 Viral Pathogens That Have Jumped Species by Year Reported
TABLE 15.3 Genetic Changes and Recent Evidence of Viral Evolution
TABLE 15.4 The More Important Arboviruses Causing Human Disease
Chapter 17
TABLE 17.1 Terminology of Human Illnesses Induced by Viruses and Prions
List of Illustrations
Chapter 1
FIGURE 1.1 Image of Sekhmet, “Bust Fragment from a colossal statue of Sekhme...
FIGURE 1.2 Drawing of a helical capsid structure showing how the capsid prot...
FIGURE 1.3 Photograph of the assembled model published by Hurst et al. (1987...
FIGURE 1.4 Drawing of an icosahedral capsid structure showing what would be ...
FIGURE 1.5 Transmission electron micrograph of coronaviruses. Viruses have g...
FIGURE 1.6 Transmission electron micrograph of bacterial viruses, termed bac...
FIGURE 1.7 Interactions between organisms (biological entities) occur in the...
FIGURE 1.8 Generalized biological life cycle. Ecologically, the life cycles ...
FIGURE 1.9 The lines connecting the four vertices of this tetrahedron repres...
FIGURE 1.10 Viral ecology can be represented by this diagram, which represen...
FIGURE 1.11 Viruses can arrive at their new host (filled arrows) either dire...
FIGURE 1.12 Epidemic transmission of a virus within a host population is rep...
FIGURE 1.13 Endemic transmission of a virus within a host population is repr...
FIGURE 1.14 This figure addresses viral association with a biological vector...
FIGURE 1.15 The transmission of a virus via a biological vector can be repre...
FIGURE 1.16 This figure represents a generalization of the ecological intera...
FIGURE 1.17 This figure addresses viral association with a vehicle and repre...
FIGURE 1.18 The transmission of virus via vehicles can be represented by thi...
FIGURE 1.19 This figure integrates the concepts of host, vehicle and biologi...
FIGURE 1.20 This figure presents a hypothetical example of the way in which ...
FIGURE 1.21 This figure represents the question of how the success of a viru...
Chapter 2
FIGURE 2.1 Overview of the lytic and lysogenic cycles. Potential outcomes of...
Chapter 3
FIGURE 3.1 The viral shunt and shuttle. The viral shunt is represented by th...
FIGURE 3.2 Evolutionary relationships of large DNA viruses based on DNA poly...
FIGURE 3.3 Viral infection of
E. huxleyi
. Virus particle (approx. 190 nm dia...
FIGURE 3.4 True color satellite image of a milky
E. huxleyi
bloom in the Eng...
FIGURE 3.5 Crystalline arrays of marnavirus (HaRNAV) particles within the cy...
Chapter 4
FIGURE 4.1 Life histories of (a)
Ectocarpus siliculosus
(Ectocarpales) and E...
Chapter 5
FIGURE 5.1 Vegetative incompatibility in filamentous fungi results in progra...
FIGURE 5.2 Effects of alleles at six vegetative incompatibility (
vic
) loci i...
FIGURE 5.3 Expected transmission of CHV‐1 in populations of
Cryphonectria pa
...
FIGURE 5.4 Cultures of isolate W2 of the Dutch elm disease fungus,
Ophiostom
...
FIGURE 5.5 Superficial canker on a European chestnut tree (
Castanea sativa
) ...
FIGURE 5.6 Healthy stand of European chestnut trees (
Castanea sativa
) in Por...
FIGURE 5.7 American chestnut tree (
Castanea dentata
) in a stand in northern ...
Chapter 6
FIGURE 6.1 Schematic representation of the genome organization of members of...
FIGURE 6.2 Symptoms caused by several geminiviruses: cassava mosaic disease ...
FIGURE 6.3 Typical stem curling phenotypes obtained when DNA‐β is co‐inocula...
FIGURE 6.4 Change in symptom patterns exhibited by
Nicotiana benthamiana
aft...
FIGURE 6.5 Inter‐relationships between the various environmental factors tha...
FIGURE 6.6 Different symptom recovery phenotypes displayed by cassava mosaic...
FIGURE 6.7 Example of synergism between two geminiviruses, African cassava m...
FIGURE 6.8 (a and b) Correlation between ACMV incidence and monthly mean tem...
FIGURE 6.9 This diagram represents a world map on which are depicted each of...
Chapter 7
FIGURE 7.1 Structure of viroids. Upper and middle panels, schemes of the cha...
FIGURE 7.2 Rolling‐circle mechanism for viroid replication. The (+) polarity...
FIGURE 7.3 Viroid movement pathways. (a) Schematic drawing illustrating the ...
FIGURE 7.4 Secondary structure of potato spindle tuber viroid (PSTVd) showin...
FIGURE 7.5 Convergent evolution of two natural isolates of HSVd during prolo...
Chapter 8
FIGURE 8.1 Transmission electron micrographs of OsHV‐1 infected cells from P...
FIGURE 8.2 Intranuclear capsids presenting a variety of morphological types ...
FIGURE 8.3 Integration of genetic material into empty capsids in the nucleus...
FIGURE 8.4 An extracellular enveloped particle with a central electron‐dense...
FIGURE 8.5 Phylogenetic tree generated by the maximum likelihood method. Boo...
Chapter 9
FIGURE 9.1 (a) Penaeus monodon Nudivirus infection of the hepatopancreas tub...
FIGURE 9.2 Schematic representation of the genome organization of (a) Penaeu...
Chapter 10
FIGURE 10.1 Two drone pupae of the Western honey bee with
Varroa
mites.
FIGURE 10.2 Example of deformed wing virus in a honey bee. Note the stumpy, ...
Chapter 11
FIGURE 11.1 Schematic anatomic drawing of a teleost. Abbreviations: CNS: cen...
FIGURE 11.2 The ontogeny of the immune system of Atlantic halibut (see text)...
FIGURE 11.3 (a) Electron microscopic pictures of Lymphocystis disease virus ...
FIGURE 11.4 (a) Immuno‐histo‐chemical (IHC) staining of paraffin wax section...
Chapter 12
FIGURE 12.1 Ranavirus life cycle. Virions bind target cells and enter cells ...
FIGURE 12.2 Transmission electron micrograph (TEM) of an FV3‐infected fathea...
FIGURE 12.3 Distribution of amphibian ranaviruses. Dark shaded areas are tho...
Chapter 13
FIGURE 13.1 Number of publications recorded in the Web of Science using “vir...
FIGURE 13.2 Severe diphtheroid necrotizing stomatitis and glossitis with pla...
FIGURE 13.3 Increased amounts of mucous in the oral cavity of a ball python ...
FIGURE 13.4 Pancreas of a boa constrictor (Boa constrictor) with inclusion b...
FIGURE 13.5 Juvenile green turtle (
Chelonia mydas
) captured off the coast of...
Chapter 14
FIGURE 14.1 Migratory flyways of wild bird populations. A world map with the...
FIGURE 14.2 Wild migratory birds are the original virus reservoir of most in...
FIGURE 14.3 Electron micrograph image of an avian influenza H7N7 virus respo...
FIGURE 14.4 Virus binding pattern of avian influenza H7N7 virus to epithelia...
FIGURE 14.5 Distribution of hemagglutinin and neuraminidase subtypes in infl...
FIGURE 14.6 Annual influenza A virus prevalence in mallards during fall migr...
FIGURE 14.7 Mallard (
Anas platyrhynchos
) with a GPS transmitter. Radio‐ and ...
FIGURE 14.8 Phylogeny of the hemagglutinin (HA) protein of American and Eura...
FIGURE 14.9 In wild birds, influenza A viruses of 16 different hemagglutinin...
FIGURE 14.10 Waders foraging at horseshoe crabs in Delaware Bay during their...
FIGURE 14.11 Sample size dependent on expected prevalence. The number of bir...
Chapter 15
FIGURE 15.1 Routes of transmission and human exposure to zoonotic viruses. V...
Chapter 16
FIGURE 16.1 Interspecies transmission of influenza viruses between marine ma...
FIGURE 16.2 Influenza virus outbreaks and infections reported during 1975–20...
Chapter 17
FIGURE 17.1 This figure shows the viral ecology of
Rabies lyssairus
(species...
Guide
COVER PAGE
TITLE PAGE
COPYRIGHT PAGE
DEDICATION PAGE
PREFACE
CONTRIBUTORS
CITATION FOR COVER IMAGE, STUDIES IN VIRAL ECOLOGY, SECOND EDITION
TABLE OF CONTENTS
BEGIN READING
INDEX
WILEY END USER LICENSE AGREEMENT
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STUDIES IN VIRAL ECOLOGY
Second Edition
Edited by
CHRISTON J. HURST
Cincinnati, OH, USAUniversidad del Valle, Santiago de Cali, Valle, Colombia
This second edition first published 2021© 2021 John Wiley & Sons Ltd
Edition HistoryWiley‐Blackwell (1e 2011)
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Library of Congress Cataloging‐in‐Publication Data
Names: Hurst, Christon J. (Christon James), 1954– editor.Title: Studies in viral ecology / edited by Christon J. Hurst.Description: Second edition. | Hoboken, NJ : Wiley‐Blackwell, 2021. | Includes bibliographical references and index.Identifiers: LCCN 2021058741 (print) | LCCN 2021058742 (ebook) | ISBN 9781119608363 (cloth) | ISBN 9781119608400 (adobe pdf) | ISBN 9781119608417 (epub)Subjects: MESH: Viruses | Ecosystem | Disease Vectors | Host‐Pathogen InteractionsClassification: LCC QR478.A1 (print) | LCC QR478.A1 (ebook) | NLM QW 160 | DDC 579.2–dc23LC record available at https://lccn.loc.gov/2021058741LC ebook record available at https://lccn.loc.gov/2021058742
Cover Design: WileyCover Image: Composite courtesy of Christon J. Hurst
DEDICATION
I dedicate this volume 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 Medellín and tragically orphaned as a young child after which he was lovingly raised by an aunt in Bogotá. 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 parent Henry adopted the child and eventually even helped to pay for her college tuition. The second daughter came through Henrys' 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 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.
Photo caption: Henry Hanssen Villamizar 1945–2007
PREFACE
Viral ecology is a field of study which has grown and expanded greatly since the viruses as a group first received their name in 1898. The viruses are highly evolved biological entities with an organismal biology that is complex and interwoven with the biology of their hosting species.
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 microorganisms and the viruses of macroorganisms 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 they utilize, as well as their relationship to the availability of suitable vehicles that can transport the different viral groups.
Three of my fellow authors for this book, V. Gregory Chinchar, Claude M. Fauquet, and Robert A. Owens, have been part of this project since 1996 when we began planning the initial version of this book, titled Viral Ecology. We achieved publication of Viral Ecology in 2000. Most of the authors who have contributed their words and knowledge to this project subsequently joined us in 2008 and 2009 as we began preparing the first edition of Studies in Viral Ecology, which appeared in 2011. Together, as a group, we have welcomed additional authors who newly are joining us for this second edition of Studies in Viral Ecology. Our collective hope is that you will enjoy reading the information presented in this book as much as we 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. HurstCincinnati, Ohio
CONTRIBUTORS
Michael J. Allen, University of Exeter, Exeter; Plymouth Marine Laboratory, Plymouth, United Kingdom
Ellen Ariel, James Cook University, Townsville, Australia
Kelly S. Bateman, International Centre of Excellence for Aquatic Animal Diseases, Weymouth, Dorset, United Kingdom
Jesse L. Brunner, Washington State University, Pullman, Washington, United States of America
V. Gregory Chinchar, The University of Mississippi Medical Center, Jackson, Mississippi, United States of America
Jessica Chopyk, University of California at San Diego, San Diego, California, United States of America
Francesco Di Serio, Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
Amanda L. J. Duffus, Gordon State College, Barnesville, Georgia, United States of America
Nuria Duran‐Vila, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
Claude M. Fauquet, International Center for Tropical Agriculture, Cali, Colombia
Sasan Fereidouni, University of Vienna, Vienna, Austria
Ricardo Flores, Universidad Politécnica de Valencia‐Consejo Superior de Investigaciones Científicas, Valencia, Spain
Bradley I. Hillman, Rutgers University, New Brunswick, New Jersey, United States of America
Christon J. Hurst, Cincinnati, Ohio, United States of America; Universidad del Valle, Cali, Colombia
Victoria L. N. Jackson, University of Exeter, Exeter, United Kingdom
Jessica L. Kevill, University of Minnesota, Saint Paul, Minnesota, United States of America
Laura D. Kramer, Wadsworth Center, New York State Department of Health, Albany, New York; Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, United States of America
Rachel E. Marschang, Laboklin GmbH & Co, KG, Bad Kissingen, Germany
Dean A. McKeown, Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
Jonathan I. Meddings, James Cook University, Townsville, Australia
Michael G. Milgroom, Cornell University, Ithaca, New York, United States of America
Adam Monier, University of Exeter, Exeter, United Kingdom
Daniel J. Nasko, University of Maryland, College Park, Maryland, United States of America
Beatriz Navarro, Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
Audun Helge Nerland, University of Bergen, Bergen; Institute of Marine Research, Bergen, Norway
Aina‐Cathrine Øvergård, University of Bergen, Bergen, Norway
Robert A. Owens, United States Department of Agriculture, Beltsville, Maryland, United States of America
Sonal Patel, Institute of Marine Research, Bergen; Norwegian Veterinary Institute, Bergen, Norway
Basavaprabhu L. Patil, ICAR‐Indian Institute of Horticultural Research, Bengaluru, India
Tristan Renault, Institut Français de Recherche pour L’exploitation de la Mer, Nantes, France
Eric G. Sakowski, Mount St. Mary’s University, Emmitsburg, Maryland, United States of America
Declan C. Schroeder, University of Minnesota, Saint Paul, Minnesota, United States of America; University of Reading, Reading, United Kingdom
Norma P. Tavakoli, Wadsworth Center, New York State Department of Health, Albany, New York; Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, United States of America
Josanne H. Verhagen, National Influenza Center, Erasmus Medical Center, Rotterdam, the Netherlands
CITATION FOR COVER IMAGE, STUDIES IN VIRAL ECOLOGY, SECOND EDITION
Citation
“A World Filled with Viruses” montage image created in 2020 and used with permission of the artist, Christon J. Hurst. Those images incorporated into this montage as a clockwise inward spiral beginning from upper left were: Akha couple.JPG by (author Weltenbummler84, Creative Commons Attribution‐Share Alike 2.0 Germany); Grib skov.jpg (author Malene Thyssen, Creative Commons Attribution‐Share Alike 3.0 Unported license); Red‐tailed Hawk with moon over Estero Bay CA ‐ composition red‐tail‐moon‐composite‐2630s (323660913).jpg (author Mike Baird Creative Commons Attribution 2.0 Generic license); Bee‐apis.jpg (Maciej A. Czyzewski, Creative Commons Attribution‐Share Alike 1.0 Generic license); Reinbukken på frisk grønt beite. ‐ panoramio.jpg (Are G Nilsen, Creative Commons Attribution‐Share Alike 3.0 Unported license); Sanc0063 ‐ Flickr ‐ NOAA Photo Library.jpg (Claire Fackler, CINMS, NOAA, Public Domain image); Phage.jpg (Dr Graham Beards, Creative Commons Attribution‐Share Alike 3.0 Unported license); Heterocarpus ensifer.jpg (NOAA, Public Domain image); Gadus morhua Cod‐2b‐Atlanterhavsparken‐Norway.JPG (Hans‐Petter Fjeld, Creative Commons Attribution‐Share Alike 2.5 Generic license); Killerwhales jumping.jpg (Robert Pittman, Public domain image); CornishMussels.JPG (Wilson44691 at English Wikipedia, Public domain image); Agaricus bisporus mushroom.jpg (, Public Domain image); Eastern box turtle.jpg (Matt Reinbold, Creative Commons Attribution 2.0 Generic license; Dendropsophus microcephalus ‐ calling male (Cope, 1886).jpg (Brian.gratwicke, Creative Commons Attribution 2.0 Generic license); Cassava1 (3945716612).jpg (CIAT, Creative Commons Attribution‐Share Alike 2.0 Generic license); Weisse‐Fliege.jpg (gaucho, Creative Commons Attribution‐Share Alike 3.0 Unported license); Porto Covo February 2009‐2.jpg (Alvesgaspar, Creative Commons Attribution‐Share Alike 3.0 Unported license); Gephyrocapsa oceanica.jpg (ja:User:NEON, Creative Commons Attribution‐Share Alike 2.5 Generic license).
SECTION IAN INTRODUCTION TO THE ECOLOGY OF VIRUSES
CHAPTER 1DEFINING THE ECOLOGY OF VIRUSES*
CHRISTON J. HURST1,2
1 Consulting Microbiologist, Cincinnati, OH, USA
2 Engineering Faculty, Universidad del Valle, Ciudad Universitaria Meléndez, Santiago de Cali, Valle, Colombia
CONTENTS
1.1 Introduction
1.1.1 What is a Virus?
1.1.2 What is Viral Ecology?
1.1.3 Why Study Viral Ecology
1.2 Surviving the Game: The Virus and it’s Host
1.2.1 Cell Sweet Cell, and Struggles at Home
1.2.2 I Want a Niche, Just Like the Niche, That Nurtured Dear Old Mom and Dad
1.2.3 Being Societal
1.3 Steppin' Out and Taking The A Train: Reaching Out and Touching Someone by Vector or Vehicle
1.3.1 “Down and Dirty” (Just Between Us Hosts)
1.3.2 “The Hitchhiker” (Finding a Vector)
1.3.3 “In a Dirty Glass” (Going There by Vehicle)
1.3.4 Bringing Concepts Together
1.3.5 Is There No Hope?
1.4 Why Things Are the Way They Are
1.4.1 To Kill or Not to Kill – A Question of Virulence
1.4.2 Genetic Equilibrium (versus Disequilibrium)
1.4.3 Evolution
1.5 Summary (Can There be Conclusions?)
Acknowledgement
A Remembrance of Ricardo Flores
References
1.1 INTRODUCTION
The goal of virology is to understand the viruses and their behavior. Virology is an interesting subject and even has contributed to the concepts of what we consider to represent dieties and art. Sekhmet, an ancient Egyptian goddess, was for a time considered to be the source of both causation and cure for many of the diseases that we now know to be caused by viruses (Figure 1.1). Influenza, a viral‐induced disease of vertebrates, was once assumed to be caused by the influence of the stars, and that is represented by the origin of it’s name which is derived from Italian. The following was a rhyme which children in the United Sates sang while skipping rope during the influenza pandemic of 1918–1919:
FIGURE 1.1 Image of Sekhmet, “Bust Fragment from a colossal statue of Sekhmet,” Cincinnati Art Museum, John J. Emery Fund, Accession #1945.65 Cincinnati, Ohio. Originally the warrior goddess of Upper Egypt, Sekhmet was for a time believed to be the bringer of disease. She would inflict pestilence if not properly appeased, and if appeased could cure such illness.
I had a little bird
And its name was Enza
I opened the door
And in‐flew‐Enza.
(Source: The flu of 1918, by Eileen A Lynch, The Pennsylvania Gazette November/December 1998 (http://www.upenn.edu/gazette/1198/lynch.html).
And a bit more recently an interesting poem was written about viruses (Source: Michael Newman, 1984):
“The Virus”
Observe this virus: think how small
Its arsenal, and yet how loud its call;
It took my cell, now takes your cell,
And when it leaves will take our genes as well.
Genes that are master keys to growth
That turn it on, or turn it off, or both;
Should it return to me or you
It will own the skeleton keys to do
A number on our tumblers; stage a coup.
But would you kill the us in it,
The sequence that it carries, bit by bit?
The virus was the first to live,
Or lean in that direction; now we give
Attention to its way with locks,
And how its tickings influence our clocks;
Its gears fit in our clockworking,
Its habits of expression have a ring
That makes our carburetors start to ping.
This happens when cells start to choke
As red cells must in monoxidic smoke,
Where membranes get the guest‐list wrong
And single‐file becomes a teeming throng,
And growth exists for its own sake;
Then soon enough the healthy genes must break;
If we permit this with our cells,
With molecules abet the clanging bells;
Lend our particular tone to our death knells.
The purpose of this book is to define the ecology of viruses and, in so doing, try to approach the question of what life is like from a “virocentric” (as opposed to our normal anthropocentric) point of view. 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 geographic distribution of the organism of interest. The objective of this chapter is to introduce the main concepts of viral ecology. The remaining chapters of this book will then address those concepts in greater detail and illustrate the way in which those concepts apply to various host systems.
1.1.1 What is a Virus?
Viruses are biological entities which possess a genome composed of either ribonucleic acid (RNA) or deoxyribonucleic acid (DNA). Some virus groups produce single stranded genomes, and other virus groups produce either fully or partially double stranded genomes. Viruses are infectious agents which do not possess a cellular structure of their own, and hence they are “acellular infectious agents.” In 2000, (Hurst, 2000) I proposed a biological domain that would represent the acellular infectious agents which possess nucleic acid genomes (termed “genomic acellular infectious agents”), and its constituent members would be the infectious agents commonly termed to be either viruses, satellite viruses, virusoids or viroids. The proposed domain title was Akamara (ακαμαρα), whose derivation from Greek (α + καμαρα) would translate as meaning “without chamber” or “without vault,” and I suggested that name as describing the fact that these agents lack a cellular structure of their own. I feel honored by the recognition that my suggestion has received https://es.wikipedia.org/wiki/Akamara;https://prezi.com/accqbr5jjusj/christon‐j‐hurst/;https://www.timetoast.com/timelines/historia‐de‐la‐clasificacion‐de‐los‐seres‐vivos‐2b8474a8‐2d53‐45ba‐8516‐5338c25fd224.
Furthermore, the viruses are obligate intracellular parasites, meaning that they live (if that can be said of viruses) and replicate within living host cells at the expense of those host cells. Viruses accomplish their replication by usurping control of the host cell's biomolecular machinery. Those which are termed “classical viruses” will form a physical structure termed a “virion” or viral particle that consists of their RNA or DNA genome surrounded by a layer of proteins (termed “capsid proteins”) which form a shell or “capsid” that protects the genomic material. Together, this capsid structure and its enclosed genomic material are often referred to as being a “nucleocapsid”. If the question becomes one of “Which came first, the virus or the capisd proteins?,” then Jalasvuori and coauthors (2015) have suggested that capsid proteins came first as a means of facilitating horizontal gene transfer.
Two of the most basic categories of capsid structures are those described as being helical versus icosahedral. The genetic coding for the capsid proteins generally is carried by the viral genome. Most of the presently known virus types code for their own capsid proteins. However, there are some viruses which are termed as being “satellite viruses.” The satellite viruses encapsidate with proteins that are coded for by the genome of another virus which coinfects (simultaneously infects) that same host cell. That virus which loans its help by giving its capsid proteins to the satellite virus is termed as being a “helper virus.” The capsid or nucleocapsid is, in the case of some groups of viruses, surrounded in turn by one or more concentric lipid bilayer membranes which are obtained from the host cell. Viruses are grouped taxonomically from the levels of species and genus, on upward through to higher taxonomic levels. The basis for those taxonomic designations includes viral morphology, host range, and replication strategy. Viral taxonomic designations historically incorporated distinctions that were based upon viral antigenic cross reactivity. The usage of antigenic cross reactivity has largely been replaced by taxonomic designations that reflect viral genomic analysis.
Figure 1.2 is a drawing of a helical nucleocapsid structure showing how the capsid proteins attach to the helical coil of the viral nucleic acid genome. Presumably, all of the capsid proteins are identical to one another in a helical structure. Those viruses that possess helical capsid structures generally have single stranded RNA genomes. Some of the virus families which possess single stranded RNA genomes have a genome that is positive sense, which means that their genome has the coding of a messenger RNA molecule and can be translated. There also are virus families that have negative sense single stranded RNA genomes, which means that their genome must be copied to produce complimentary strands, and those complimentary strands can be translated.
FIGURE 1.2 Drawing of a helical capsid structure showing how the capsid proteins attach to the helical coil of the viral nucleic acid genome. Presumably, all of the capsid proteins are identical to one another in a helical structure.
Figure 1.3 is a photograph of the assembled model published by Hurst et al. (1987) showing the protein arrangement in an icosahedral capsid structure. As mentioned above, viruses have genus and species names, plus higher viral taxonomy levels also exist. This particular structure is a representation of the viral family Picornaviridae. The members of this family have a single stranded RNA genome that is positive sense. Picornaviruses produce capsids that contain multiple copies of three major (larger‐sized, numbered 1, 2, and 3) capsid proteins and one minor (smaller‐sized) capsid protein. The relative positions of the three major capsid proteins are shown in Figure 1.3 as trapezoids numbered 1, 2, and 3. The trapezoidal shape is used for illustrative purposes, as the true shapes of these proteins is more complex and not truly trapezoidal.
FIGURE 1.3 Photograph of the assembled model published by Hurst et al. (1987) showing the protein arrangement in an icosahedral capsid structure. This particular structure is a representation of the viral family Picornaviridae. The members of this family produce capsids that contain multiple copies of three major (larger‐sized, numbered 1, 2, and 3) capsid proteins and one minor (smaller‐sized, numbered 4) capsid protein. The relative positions of the three major capsid proteins are shown in this illustration as trapezoids numbered 1, 2, and 3. The trapezoidal shape is used for illustrative purposes, as the true shapes of these proteins is more complex and not truly trapezoidal. The darkly outlined triangle represents one of the twenty sides of the viral capsid. Although these sides are often referred to as “faces,” the term icosahedron literally interprets from the Greek as meaning that this structure has twenty surfaces upon which it could rest.
FIGURE 1.4 Drawing of an icosahedral capsid structure showing what would be a mirror image of the shape of the capsid proteins for the viral family Bromoviridae. Unlike the picornaviral model, the bromoviral capsid seems to contain multiple copies of only one type of capsid protein. Presumably, those copies of the same protein would be rotated into different relative positions such that they can arrange into an icosahedron. This drawing shows how those capsid proteins combine to produce the twofold (left), threefold (center), and fivefold (right) axes of symmetry that define an icosahedral structure.
Figure 1.4 is a drawing of an icosahedral capsid structure showing what would be a mirror image of the shape of the capsid proteins for the viral family Bromoviridae. The bromoviruses have a single stranded RNA genome that is positive sense. Unlike the picornaviral model, the bromoviral capsid seems to contain multiple copies of only one type of capsid protein. Presumably, those copies of the same protein would be rotated into different relative positions such that they can arrange into an icosahedron. An icosahedral structure is defined by having twofold (left), threefold (center), and fivefold (right) axes of symmetry. Figure 1.3 shows a fivefold axis of symmetry.
Figure 1.5 is an electron micrograph of coronaviruses and these particular virions belong to the species Gammacoronavirus avian coronavirus. The coronaviruses are members of the viral family Coronaviridae, and they have a single stranded RNA genome that is positive sense. The coronavirus has a helical nucleocapsid, and its mature virions possess a outer lipid membrane with characteristic club‐shaped spikes that protrude from the membrane. The Latin origin of the name, corona, given to this virus group means crown or wreath and refers to an item worn on the head as adornment. Those spikes enable the coronavirus virions to bind onto the host cell molecule which the virus uses as a receptor. Virus groups differ with respect to which host cell component they have evolved to use as their receptor, but the commonality is that a receptor will be part of a molecule that is exposed on the surface of their targeted host cells. Binding to its receptor is a necessary initial step, after which the viral nucleic acid genome enters the host cell and the virus can then begin its replicative process. For many virus groups, that replicative process may result in the immediate production of progeny virions. Other virus groups incorporate reproductive strategies in which progeny virions are produced less often, with the virus instead using such maintenance strategies as latency, endogeny and lysogeny, as will be explained later in this chapter.
FIGURE 1.5 Transmission electron micrograph of coronaviruses. Viruses have genus and species names, plus higher taxonomy levels also exist. The virus shown in this image is designated Gammacoronavirus avian coronavirus, and it belongs to the family Coronaviridae. Viruses are designated taxonomically on the basis of their morphology and host range. Viral taxonomic designations also used to include distinctions that were based upon viral antigenic cross reactivity. The usage of antigenic cross reactivity has largely been replaced by taxonomic designations that reflect viral genomic analysis. The title of this image is “Coronaviruses 004 lores.jpg,” it is a Public Domain image from the Centers for Disease Control and Prevention’s Public Health Image Library (PHIL), with identification number #4814.
Figure 1.6 is a transmission electron micrograph of multiple bacteriophage attached to the cell wall of a bacterial host. The term phage refers to viruses that infect microorganisms. There are many viral families that include members which are infectious for bacteria, and those members are known as bacteriophage. I would guess that these particular virions belong to the viral family Siphoviridae. Siphoviruses have double‐stranded DNA genomes packaged within an icosahedral structure. The siphoviral icosahedron has a flexible non‐contractile tail and short fibers that extend outward from the bottom, distal end, of the tail.
There also exist many other types of acellular infectious agents which have commonalities with the classical viruses in terms of their ecology. Two of these other types of acellular infectious agents, the viroids and prions, are included in this book and are addressed within their own respective chapters (chapter 7 by Flores, Di Serio, Navarro, Duran‐Vila and Owens, chapter 17 on viruses of humans by Hurst). Viroids are biological entities akin to the classical viruses and likewise can replicate only within host cells. The viroids possess RNA genomes but lack capsid proteins. The agents which we refer to as prions were once considered to be nonclassical viruses. However, we now know that the prions appear to be aberrant cellular protein products which, at least in the case of those afflicting mammals, have acquired the potential to be environmentally transmitted. The natural environmental acquisition of a prion infection occurs when a susceptible host mammal ingests the bodily material of an infected host mammal. The reproduction of prions is not a replication, but rather seems to result from a conversion of a normal host protein into an abnormal form (Hurst chapter 17 on viruses of humans). A prion would be a ‘non‐genomic acellular infectious agent’.
FIGURE 1.6 Transmission electron micrograph of bacterial viruses, termed bacteriophage, attached to a bacterial cell wall. My guess, based upon their taxonomic structure, would be that the viruses shown in this image belong to the family Siphoviridae.
This image is titled “Phage.jpg” by author Dr. Graham Beards, and it is being used under a Creative Commons Attribution‐Share Alike 3.0 Unported license. The magnification is approximately 200,000. https://en.wikipedia.org/wiki/File:Phage.jpg.
All members of the known virus families complete their reproduction when they are internal to a host cell, with one exception. That unique exception is the species Acidianus two‐tailed virus (genus Bicaudavirus, family Bicaudaviridae) which undergoes a morphological maturation following its release from a host cell (Hochstein et al. 2018). This uniqueness of the Acidianus two‐tailed virus suggests that it may represent the initial discovery of an entirely new category of biological entities.
1.1.2 What is Viral Ecology?
Ecology is the study of the relationships between organisms and their surroundings. Viral ecology is, therefore, the relationship between viruses, other organisms, and the environments which a virus must face as it attempts to comply with the basic biological imperatives of genetic survival and replication. As shown in Figure 1.7, interactions between species and their constituent individual organisms (biological entities) occur in the areas where there exist overlaps in the temporal, physical, and biomolecular (or biochemical) aspects of the ecological zones of those different species. Many types of interactions can develop between species as they share an environment. One of the possible types of interactions is predation. When a microorganism is the predator, that predator is referred to as being a pathogen and the prey is referred to as being a host. Viruses are predators, and later in this chapter I will return to explaining that concept.
FIGURE 1.7 Interactions between organisms (biological entities) occur in the areas where the physical and chemical ecologies of the involved organisms overlap. Infectious disease is a type of interaction in which a microorganism acts as a parasitic predator. The microorganism is referred to as a pathogen in these instances.
When we study viral ecology we can view the two genetic imperatives that every biological entity must face, namely, that it survive and that it reproduce, in the perspective of a biological life cycle. A generalized biological life cycle is presented in Figure 1.8. This type of cycle exists, in its most basic form, at the level of the individual virus or individual cellular being. However, it must be understood that in the case of a multicellular being this biological life cycle exists not only at the level of each individual cell, but also at the tissue or tissue system level, and at the organ level. This biological life cycle likewise exists on even larger scales, where it operates at levels which describe the existence of each species as a whole, at the biological genus level, and also seems to operate further upward to at least the biological family level. Ecologically, the life cycles of those different individuals and respective species which affect one another will become interconnected both temporarily, geographically, and biologically. Thus, there will occur an evolution of the entire biological assemblage and, in turn, this process of biotic evolution will be obliged to adapt to any abiotic changes that occur in the environment which those organisms share. While a species physiologic capacities establish the potential limits of the niche which it could occupy within this shared environment, the actual operational boundaries of it's niche are more restricted and defined by it's interspecies connections and biological competitions. The concepts of evolution, habitat and niche, including the difference between a potential niche versus an operational niche, recently have been discussed by Hurst (2016, 2021).
FIGURE 1.8 Generalized biological life cycle. Ecologically, the life cycles of different organisms which affect one another are temporally interconnected.
1.1.3 Why Study Viral Ecology?
The interplay which occurs between a virus and the living organisms which surround it, while all simultaneously pursue their own biological drive to achieve genetic survival and replication, creates an interest for studying the ecology of viruses (Larson, 1998). While examining this topic, we improve our understanding of the behavioral nature of viruses as predatory biological entities. It is important to realize that in nature both the viruses of macroorganisms and the viruses of microorganisms normally exist in a cycle with their respective hosts. Under normal conditions, the impact of viruses upon their natural hosts may be barely apparent due to factors such as evolutionary coadaptation between the virus and its host (evolutionary coadaptation is the process by which species try to achieve a mutually acceptable coexistence by evolving in ways which enable them to adapt to one another). 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 term “biological invasion” is used to describe some of these catastrophic encounters. Biological invasions will be discussed in Section 1.2 of this chapter.
As we study viral ecology we come to understand not only those interconnections which exist between the entities of virus and host, but also the interconnections between these two entities and any vectors or vehicles which the virus may utilize. As shown in Figure 1.9, this interplay can be represented by the four vertices of a tetrahedron. The possible routes by which a virus may move from one host organism to another host organism can be illustrated as the interconnecting lines between those vertices which represent two hosts (present and proximate) plus one vertice apiece representing the concepts of vector and vehicle. Figure 1.10, which represents a flattened form of the tetrahedron shown in the previous figure (Figure 1.9) can be considered our point of reference as we move forward in examining viral ecology. The virus must survive when in association with the present host and then successfully move from that (infected) host organism (center of Figure 1.10) to another host organism. This movement, or transmission, may occur via direct contact between the two host organisms or via routes which involve vectors and vehicles (Hurst and Murphy 1996). Vectors are, by definition, animate (living) objects. Vehicles are, by definition, inanimate (non‐living) objects. Any virus which utilizes either vectors or vehicles must possess the means to survive when in association with those vectors and vehicles in order to sustain its cycle of transmission within a population of host organisms. If a virus replicates enough to increase its population while in association with a vector, then that vector is termed to be “biological” in nature. If the virus population does not increase while in association with a vector, then that vector is termed to be “mechanical” in nature. Because viruses are obligate intracellular parasites, and vehicles are by definition non‐living, then we must assume that the virus cannot increase its population while in association with a vehicle.
FIGURE 1.9 The lines connecting the four vertices of this tetrahedron represent the possible routes by which a virus can move from one host organism to another host organism.
Environmentally, there are several organizational levels at which a virus must function. The first and most basic of those levels is the individual host cell. That one cell may comprise the entire host organism. Elsewise, that host cell may be part of a tissue. If within a tissue, then the tissue will be contained within a larger structure termed either a tissue system (plant terminology) or an organ (plant and animal terminology). That tissue system or organ will be contained within an organism. The host organism is exposed to the open (ambient) environment, where it is but one part of a population of other organisms belonging to its same species. The members of that host species will be surrounded by populations of other types of organisms. Those populations of other types of organisms will be serving as hosts and vectors for either the same or other viruses. Each one of these organizational levels represents a different environment which the virus must successfully confront. A virus' affects upon it's hosts and vectors will draw responses against which the virus must defend itself if the virus is to survive. Also, the virus must always be ready to do battle with it's potential biological competitors. Contrariwise, the virus must be open to considering newly encountered (or reencountered) species as possible hosts or vectors. Because of their acellular nature, when viruses are viewed in the ambiental environments (air, soil and water) they appear to exist in a form that essentially is biologically inert. However, they have a very actively involved behavior when viewed in these many other organismal environments.
FIGURE 1.10 Viral ecology can be represented by this diagram, which represents a flattened form of the tetrahedron shown in the previous figure (Figure 1.9). The virus must successfully move from an infected host organism (center of figure) to another host organism. This movement, or transmission, may occur via direct transfer or via routes which involve vehicles and vectors. In order to sustain this cycle of transmission within a population of host organisms, the virus must survive when in association with the subsequently encountered hosts, vehicles and vectors.
Considering the fact that viruses are obligate intracellular parasites, their ecology must be presented in terms which also include aspects of the ecology of their hosts and any vectors which they may utilize. Those factors or aspects of viral ecology which we study, and thus which will be considered in this book, include the following:
Host Related Issues
what are the principal and alternate hosts for the viruses;
what types of replication strategies do the viruses employ on a host cellular level, host tissue or tissue system level, host organ level, the level of the host as a whole being, and the host population level;
