Principles of Virology

1034 Pages·2008·84.94 MB·English

by  S. Jane Flint

PRINCIPLES OF
Virology
THIRD EDITION
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Molecular Biology
V O L U M E I
P R I N C I P L E S O F
Virology
T H I R D E D I T I O N
S. J. FLINT V. R. RACANIELLO
Department of Molecular Biology Department of Microbiology
Princeton University College of Physicians and Surgeons
Princeton, New Jersey Columbia University
New York, New York
L. W. ENQUIST
A. M. SKALKA
Department of Molecular Biology
Princeton University Fox Chase Cancer Center
Princeton, New Jersey Philadelphia, Pennsylvania
WASHINGTON, DC
Front cover illustration: A model of the atomic
structure of the poliovirus type 1 Mahoney
strain. The model has been highlighted by
radial depth cuing so that the portions of the
model that are farthest from the center are
bright. Prominent surface features include
a star-shaped mesa at each of the fivefold
axes and a propeller-shaped feature at each
of the threefold axes. A deep cleft or canyon
surrounds the star-shaped feature. This can-
yon is the receptor-binding site. Courtesy of
Robert Grant, Stéphane Crainic, and James
Hogle (Harvard Medical School).
Back cover illustration: Progress in the global
eradication of poliomyelitis has been strik-
ing, as illustrated by maps showing areas of
known or probable circulation of wild-type
poliovirus in 1988, 1998, and 2008. Dark red
indicates the presence of virus. In 1988, the
virus was present on all continents except
Australia. By 1998, the Americas were free Address editorial correspondence to ASM Press, 1752 N St. NW, Washington,
of wild-type poliovirus, and transmission DC 20036-2904, USA
was interrupted in the western Pacific region
(including the People’s Republic of China) Send orders to ASM Press, P.O. Box 605, Herndon, VA 20172, USA
and in the European region (with the excep- Phone: [phone] or [phone]
tion of southeastern Turkey). By 2008, the Fax: [phone]
number of countries reporting endemic E-mail: [email protected]
circulation of poliovirus had been reduced Online: estore.asm.org
to four: Afghanistan, Pakistan, India, and
Nigeria. Copyright © 2000, 2004, 2009 ASM Press
American Society for Microbiology
1752 N St. NW
Washington, DC 20036-2904
Library of Congress Cataloging-in-Publication Data
Principles of virology / S.J. Flint ... [et al.]. — 3rd ed.
p. ; cm.
Includes bibliographical references and index.
ISBN 978-1-55581-443-4 (pbk. : set) — ISBN 978-1-55581-479-3
(pbk. : v. 1) — ISBN 978-1-55581-480-9 (pbk. : v. 2)
1. Virology. I. Flint, S. Jane. II. American Society for Microbiology.
[DNLM: 1. Viruses. 2. Genetics, Microbial. 3. Molecular Biology.
4. Virology—methods. QW 160 P957 2009]
QR360.P697 2009
579.2—dc22
2008030964
10 9 8 7 6 5 4 3 2 1
ISBN 978-1-55581-479-3
All Rights Reserved
Printed in the United States of America
Illustrations and illustration concepting: Patrick Lane, ScEYEnce Studios
Cover and interior design: Susan Brown Schmidler
We dedicate this book to the students, current and future scientists
and physicians, for whom it was written.
We kept them ever in mind.
We also dedicate it to our families:
Jonn, Gethyn, and Amy Leedham
Kathy and Brian
Doris, Aidan, Devin, and Nadia
Rudy, Jeanne, and Chris
Oh, be wiser thou!
Instructed that true knowledge leads to love.
WILLIAM WORDSWORTH
Lines left upon a Seat in a Yew-tree
1888
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Contents
Preface xv
Acknowledgments xix
The Science of Virology 1
1 Foundations 2
Luria’s Credo 3
Why We Study Viruses 3
Viruses Are Everywhere 3
Viruses Cause Human Disease 4
Viruses Infect All Living Things 4
Viruses Can Cross Species Boundaries 4
Viruses “R” Us 4
Viruses Are Uniquely Valuable Tools with Which To Study Biology 4
Viruses Can Also Be Used To Manipulate Biology 5
Virus Prehistory 5
Viral Infections in Antiquity 5
The First Vaccines 7
Microorganisms as Pathogenic Agents 8
Discovery of Viruses 10
The Definitive Properties of Viruses 12
The Structural Simplicity of Viruses 12
The Intracellular Parasitism of Viruses 13
Viruses Defined 17
Cataloging Animal Viruses 18
The Classical System 20
Classification by Genome Type 20
The Baltimore Classification System 21
vii
viii CONTENTS
A Common Strategy for Viral Propagation 21
Perspectives 21
References 23
2 The Infectious Cycle 24
Introduction 25
The Infectious Cycle 25
The Cell 27
The Architecture of Cell Surfaces 28
The Extracellular Matrix: Components and Biological Importance 28
Properties of the Plasma Membrane 30
Cell Membrane Proteins 31
Entering Cells 32
Making Viral RNA 32
Making Viral Proteins 33
Making Viral Genomes 33
Forming Progeny Virions 33
Viral Pathogenesis 33
Overcoming Host Defenses 33
Cultivation of Viruses 34
Cell Culture 34
Embryonated Eggs 36
Laboratory Animals 36
Assay of Viruses 37
Measurement of Infectious Units 37
Efficiency of Plating 40
Measurement of Virus Particles and Their Components 42
Viral Growth: the Burst Concept 44
The One-Step Growth Cycle 45
Initial Concept 45
One-Step Growth Analysis: a Valuable Tool for Studying Animal Viruses 46
Perspectives 48
References 48
Molecular Biology 51
3 Genomes and Genetics 52
Introduction 53
Genome Principles and the Baltimore System 53
Structure and Complexity of Viral Genomes 54
DNA Genomes 55
RNA Genomes 57
What Do Viral Genomes Look Like? 58
CONTENTS ix
Coding Strategies 60
What Can Viral Sequences Tell Us? 60
The Origin of Viral Genomes 62
The “Big and Small” of Viral Genomes: Does
Size Matter? 62
Genetic Analysis of Viruses 66
Classic Genetic Methods 66
Engineering Mutations into Viral Genomes 68
Genetic Interference by Double-Stranded RNA 74
Engineering Viral Genomes: Viral Vectors 74
Perspectives 79
References 80
4 Structure 82
Introduction 83
Functions of the Virion 83
Nomenclature 85
Methods for Studying Virus Structure 85
Building a Protective Coat 88
Helical Structures 88
Capsids or Nucleocapsids with Icosahedral Symmetry 92
Packaging the Nucleic Acid Genome 106
Direct Contact of the Genome with a Protein Shell 107
Packaging by Specialized Virion Proteins 110
Packaging by Cellular Proteins 111
Viruses with Envelopes 112
Viral Envelope Components 112
Simple Enveloped Viruses: Direct Contact of External Proteins with the Capsid
or Nucleocapsid 116
Enveloped Viruses with an Additional Protein Layer 117
Complex Viruses 119
Bacteriophage T4 119
Herpesviruses 119
Poxviruses 121
Other Components of Virions 122
Virion Enzymes 122
Other Viral Proteins 123
Nongenomic Viral Nucleic Acid 123
Cellular Macromolecules 124
Perspectives 125
References 125
5 Attachment and Entry 128
Introduction 129
Attachment of Viruses to Cells 130
General Principles 130
Identification of Cell Receptors for Virus Particles 131
Examples of Cell Receptors 132
How Virions Attach to Receptors 138