Basic Virology, 3rd Edition

581 Pages·2007·17.66 MB·English

by  Edward K. Wagner

BASIC VIROLOGY
In Memoriam
Edward K. Wagner
(May 4, 1940 to January 21, 2006)
It was one of those telephone calls that you do not want to receive. Each of us, that weekend
in late January, heard of the untimely passing of our colleague, co-author, collaborator, mentor,
and friend, Ed Wagner. Ed will be remembered for his many contributions to the teaching of
virology and for his research contributing to our understanding of the intricacies of the
herpesviruses. From his graduate work at MIT, through his postdoctoral research at the
University of Chicago, and on to his professorship at the University of California, Irvine,
Ed was a passionate champion for the most rigorous and critical thinking and the most
dedicated teaching, setting a standard for the discipline of virology. Beyond the laboratory
and the classroom, Ed loved life to the fullest, with his family and friends. The last time we
were together as a writing team, in the fall of 2005, we all remember an intense day of work
in a conference room at UCI, followed by an evening of touring some of Ed’s favorite haunts
in the Southern California coastal towns he called home. It is with those thoughts etched
into our memories that we dedicate this edition of Basic Virology to Edward K. Wagner.
Basic Virology
Third
Edition
Edward K. Wagner
Department of Molecular Biology and Biochemistry
University of California, Irvine
Martinez J. Hewlett
Department of Molecular and Cellular Biology
University of Arizona
David C. Bloom
Department of Molecular Genetics and Microbiology
University of Florida
David Camerini
Department of Molecular Biology and Biochemistry
University of California, Irvine
© 1999, 2004, 2008 by Blackwell Publishing
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First edition published 1999
Second edition published 2004
Third edition published 2008 by Blackwell Publishing Ltd
1 2008
Library of Congress Cataloging-in-Publication Data
Basic virology / Edward K. Wagner . . . [et al.]. – 3rd ed.
p. ; cm.
Rev. ed. of: Basic virology / Edward K. Wagner, Martinez J. Hewlett. 2nd ed. 2004.
Includes bibliographical references and index.
ISBN-13: 978-1-4051-4715-6 (pbk. : alk. paper)
ISBN-10: 1-4051-4715-6 (pbk. : alk. paper)
1. Viruses. 2. Virus diseases. 3. Virology. 4. Medical virology. I. Wagner, Edward K.
II. Wagner, Edward K. Basic virology.
[DNLM: 1. Virus Diseases–virology. 2. Genome, Viral. 3. Virus Replication.
4. Viruses–pathogenicity. WC 500 B311 2008]
QR360.W26 2008
579.2–dc22
2007019839
A catalogue record for this title is available from the British Library.
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Brief Contents
Preface xxi
Acknowledgments xxix
PART I VIROLOGY AND VIRAL DISEASE 1
Chapter 1 Introduction – The Impact of Viruses on Our View of Life 3
Chapter 2 An Outline of Virus Replication and Viral Pathogenesis 15
Chapter 3 Virus Disease in Populations and Individual Animals 27
Chapter 4 Patterns of Some Viral Diseases of Humans 41
PART II BASIC PROPERTIES OF VIRUSES AND VIRUS–
CELL INTERACTION 63
Chapter 5 Virus Structure and Classifi cation 65
Chapter 6 The Beginning and End of the Virus Replication Cycle 79
Chapter 7 H ost Immune Response to Viral Infection – The Nature of the Vertebrate
Immune Response 97
Chapter 8 Strategies to Protect Against and Combat Viral Infection 119
PART III WORKING WITH VIRUS 145
Chapter 9 Visualization and Enumeration of Virus Particles 147
Chapter 10 Replicating and Measuring Biological Activity of Viruses 155
Chapter 11 Physical and Chemical Manipulation of the Structural Components of
Viruses 173
Chapter 12 Characterization of Viral Products Expressed in the Infected Cell 193
Chapter 13 Viruses Use Cellular Processes to Express their Genetic
Information 213
PART IV REPLICATION PATTERNS OF SPECIFIC
VIRUSES 243
Chapter 14 Replication of Positive-sense RNA Viruses 245
Chapter 15 Replication Strategies of RNA Viruses Requiring RNA-directed mRNA
Transcription as the First Step in Viral Gene Expression 273
Chapter 16 Replication Strategies of Small and Medium-sized DNA Viruses 303
vi BRIEF CONTENTS
Chapter 17 Replication of Some Nuclear-replicating Eukaryotic DNA Viruses with
Large Genomes 331
Chapter 18 Replication of Cytoplasmic DNA Viruses and “Large” Bacteriophages 359
Chapter 19 Retroviruses: Converting RNA to DNA 381
Chapter 20 Human Immunodefi ciency Virus Type 1 (HIV-1) and Related
Lentiviruses 399
Chapter 21 Hepadnaviruses: Variations on the Retrovirus Theme 413
PART V VIRUSES: NEW APPROACHES AND NEW
PROBLEMS 433
Chapter 22 The Molecular Genetics of Viruses 435
Chapter 23 Molecular Pathogenesis 463
Chapter 24 Viral Bioinformatics and Beyond 473
Chapter 25 Viruses and the Future – Problems and Promises 485
Appendix Resource Center 501
Technical Glossary 507
Index 533
Contents
Preface xxi
Preface to the second edition xxii
Preface to the third edition xxii
Text organization xxiii
Specifi c features of this text designed to aid instructors and
students in pursuing topics in greater depth xxvi
Depth of coverage xxvi
Sources for further study xxvi
The Internet xxvii
Chapter outlines xxvii
Case studies xxvii
Review material xxvii
Glossary xxvii
Acknowledgments xxix
PART I VIROLOGY AND VIRAL DISEASE 1
CHAPTER 1 Introduction – The Impact of Viruses on Our View of Life 3
The science of virology 3
The effect of virus infections on the host organism and populations
– viral pathogenesis, virulence, and epidemiology 4
The interaction between viruses and their hosts 6
The history of virology 7
Examples of the impact of viral disease on human history 8
Examples of the evolutionary impact of the virus–host
interaction 9
The origin of viruses 9
Viruses have a constructive as well as destructive impact on
society 12
Viruses are not the smallest self-replicating pathogens 13
Questions for Chapter 1 14
CHAPTER 2 An Outline of Virus Replication and Viral Pathogenesis 15
Virus replication 15
Stages of virus replication in the cell 17
Pathogenesis of viral infection 19
Stages of virus-induced pathology 19
viii CONTENTS
Initial stages of infection – entry of the virus into the host 20
The incubation period and spread of virus through the host 21
Multiplication of virus to high levels – occurrence of disease
symptoms 23
The later stages of infection – the immune response 24
The later stages of infection – virus spread to the next
individual 24
The later stages of infection – fate of the host 24
Questions for Chapter 2 25
CHAPTER 3 Virus Disease in Populations and Individual Animals 27
The nature of virus reservoirs 27
Some viruses with human reservoirs 28
Some viruses with vertebrate reservoirs 30
Viruses in populations 30
Viral epidemiology in small and large populations 30
Factors affecting the control of viral disease in populations 33
Animal models to study viral pathogenesis 34
A mouse model for studying poxvirus infection and spread 35
Rabies: where is the virus during its long incubation period? 37
Herpes simplex virus latency 37
Murine models 39
Rabbit models 40
Guinea pig models 40
Questions for Chapter 3 40
CHAPTER 4 Patterns of Some Viral Diseases of Humans 41
The dynamics of human–virus interactions 42
The stable association of viruses with their natural host places
specifi c constraints on the nature of viral disease and mode of
persistence 42
Classifi cation of human disease-causing viruses according to
virus–host dynamics 44
Viral diseases leading to persistence of the virus in the host are
generally associated with viruses having long associations with
human populations 44
Viral diseases associated with acute, severe infection are
suggestive of zoonoses 48
Patterns of specifi c viral diseases of humans 49
Acute infections followed by virus clearing 49
Colds and respiratory infections 49
Infl uenza 49
Variola 49
Infection of an “accidental” target tissue leading to permanent
damage despite effi cient clearing 50
Persistent viral infections 50
Papilloma and polyomavirus infections 50
Herpesvirus infections and latency 52
Other complications arising from persistent infections 52
Viral and subviral diseases with long incubation periods 53
Rabies 53
CONTENTS ix
HIV–AIDS 53
Prion diseases 54
Some viral infections targeting specifi c organ systems 54
Viral infections of nerve tissue 54
Examples of viral encephalitis with grave prognosis 55
Rabies 55
Herpes encephalitis 55
Viral encephalitis with favorable prognosis for recovery 56
Viral infections of the liver (viral hepatitis) 56
Hepatitis A 57
Hepatitis B 57
Hepatitis C 57
Hepatitis D 57
Hepatitis E 58
Questions for Chapter 4 58
Problems for Part I 59
Additional Reading for Part I 61
PART II BASIC PROPERTIES OF VIRUSES AND
VIRUS–CELL INTERACTION 63
CHAPTER 5 Virus Structure and Classifi cation 65
The features of a virus 65
Viral genomes 69
Viral capsids 69
Viral envelopes 72
Classifi cation schemes 72
The Baltimore scheme of virus classifi cation 75
Disease-based classifi cation schemes for viruses 75
The virosphere 77
Questions for Chapter 5 78
CHAPTER 6 The Beginning and End of the Virus Replication Cycle 79
Outline of the virus replication cycle 79
Viral entry 80
Animal virus entry into cells – the role of the cellular receptor 80
Mechanisms of entry of nonenveloped viruses 83
Entry of enveloped viruses 84
Entry of virus into plant cells 85
Injection of bacteriophage DNA into Escherichia coli 87
Nonspecifi c methods of introducing viral genomes into cells 89
Late events in viral infection: capsid assembly and virion release 89
Assembly of helical capsids 89
Assembly of icosahedral capsids 92
Generation of the virion envelope and egress of the enveloped
virion 93
Questions for Chapter 6 96
CHAPTER 7 Host Immune Response to Viral Infection – The Nature of the
Vertebrate Immune Response 97
The innate immune response – early defense against pathogens 98
Toll-like receptors 99