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Virology: Principles and Applications
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Mô tả chi tiết
Principles and
Applications
Contents
Preface to Second Edition
Preface to First Edition
Abbreviations Used in This Book
Greek Letters Used in This Book
Color Coding for Molecules
Chapter 1: Viruses and Their Importance
1.1 Viruses are Ubiquitous on Earth
1.2 Reasons for Studying Viruses
1.3 The Nature of Viruses
1.4 The Remainder of the Book
Learning Outcomes
Sources of Further Information
Chapter 2: Methods Used in Virology
2.1 Introduction to Methods Used in Virology
2.2 Cultivation of Viruses
2.3 Isolation of Viruses
2.4 Centrifugation
2.5 Structural Investigations of Cells and Virions
2.6 Electrophoretic Techniques
2.7 Detection of Viruses and Virus Components
2.8 Infectivity Assays
2. 9 Virus Genetics
2.10 Investigation of ProteinslJ"Protein Interactions
Learning Outcomes
Sources of Further Information
Chapter 3: Virus Structure
3.1 Introduction to Virus Structure
3.2 Virus Genomes
3.3 Virus Proteins
3.4 Capsids
3.5 Virion Membranes
3.6 Occlusion Bodies
3.7 Other Virion Components
Learning Outcomes
Sources of Further Information
Chapter 4: Virus Transmission
4. 1 Introduction to Virus Transmission
4.2 Transmission of Plant Viruses
4.3 Transmission of Vertebrate Viruses
4.4 Transmission of Invertebrate Viruses
4.5 Permissive Cells
Learning Outcomes
Sources of Further Information
Chapter 5: Attachment and Entry of Viruses into Cells
5.1 Overview of Virus Replication
5.2 Animal Viruses
5.3 Bacteriophages
Learning Outcomes
Sources of Further Information
Chapter 6: Transcription, Translation, and Transport
6. 1 Introduction to Transcription, Translation, and Transport
6.2 Transcription of Virus Genomes
6.3 Transcription in Eukaryotes
6.4 Translation in Eukaryotes
6.5 Transport of Molecules in Eukaryotic Cells
6.6 Transcription and Translation in Bacteria
Learning Outcomes
Sources of Further Information
Chapter 7: Virus Genome Replication
7 .1 Overview of Virus Genome Replication
7.2 Locations of Virus Genome Replication in Eukaryotic Cells
7 .3 Initiation of Genome Replication
7. 4 Polymerases
7.5 DNA Replication
7 .6 Double-Stranded RNA Replication
7.7 Single-Stranded RNA Replication
7.8 Reverse Transcription
Learning Outcomes
Sources of Further Information
Chapter 8: Assembly and Exit of Virions from Cells
8.1 Introduction to Assembly and Exit of Virions from Cells
8.2 Nucleocapsid Assembly
8.3 Formation of Virion Membranes
8.4 Virion Exit From the Infected Cell
Learning Outcomes
Sources of Further Information
Chapter 9: Outcomes of Infection for the Host
9.1 Introduction to Outcomes of Infection for the Host
9.2 Factors Affecting Outcomes of Infection
9.3 Non-Productive Infections
9.4 Productive Infections
Learning Outcomes
Sources of Further Information
Chapter 10: Classification andl Nomenclature of Viruses
10. 1 History of Virus Classification and Nomenclature
10.2 Modern Virus Classification and Nomenclature
10.3 Baltimore Classification of Viruses
Learning Outcomes
Sources of Further Information
Chapter 11: Herpesviruses (and Other dsDNA Viruses)
11.1 Introduction to Herpesviruses
11.2 The Human Herpesviruses
11.3 The Herpesvirus Virion
11.4 HSV-1 Genome Organization
11. 5 HSV-1 Rep I ication
11.6 Latent Herpesvirus Infection
11.7 Other dsDNA Viruses
Learning Outcomes
Sources of Further Information
Chapter 12: Parvoviruses (and Other ssDNA Viruses)
12.1 Introduction to Parvoviruses
12.2 Examples of Parvoviruses
12.3 Parvovirus Virion
12.4 Parvovirus Replication
12.5 Other ssDNA Viruses
Learning Outcomes
Sources of Further Information
Chapter 13: Reoviruses (and Other dsRNA Viruses)
13.l Introduction to Reoviruses
13.2 Rotavirus Virion
13.3 Rotavirus Repl ication
13.4 Other dsRNA Viruses
Learning Outcomes
Sources of Further Information
Chapter 14: Picornaviruses (and Other Plus-Strand RNA Viruses)
14. 1 Introduction to Picornaviruses
14.2 Some Important Picornaviruses
14.3 Picornavirus Virion
14.4 Picornavirus Replication
14.5 Picornavirus Recombination
14.6 Picornavirus Experimental Systems
14.7 Other Plus-Strand RNA Viruses
Learning Outcomes
Sources of Further Information
Chapter 15: Rhabdoviruses (and Other Minus-Strand RNA Viruses)
15. 1 Introduction to Rhabdoviruses
15.2 Some Important Rhabdoviruses
15.3 The Rhabdovirus Virion and Genome Organization
15.4 Rhabdovirus Replication
15.5 Other Minus-Strand RNA Viruses and Viruses with Ambisense Genomes
15.6 Reverse Genetics
Learning Outcomes
Sources of Further Information
Chapter 16: Influenza Virus
16.1 Introduction to Influenza Viruses
16.2 The Influenza Virion
16.3 Influenza A Virus Replication
16.4 Importance of Influenza Viruses
16.5 Reverse Genetics
Learning Outcomes
Sources of Further Information
Chapter 17: Retroviruses
17 .1 Introduction to Retroviruses
17.2 Retrovirus Virion
17.3 Retrovirus Replication
17.4 Examples of Retroviruses
17.5 Retroviruses as Gene Vectors
17 .6 Endogenous Retroviruses
Learning Outcomes
Sources of Further Information
Chapter 18: Human Immunodeficiency Viruses
18.1 Introduction to HIV
18.2 HIV Virion
18.3 HIV Genome
18.4 HIV-1 Replication
18.5 HIV-1 Variability
18.6 Progression of HIV Infection
18.7 Prevention of HIV Transmission
Learning Outcomes
Sources of Further Information
Chapter 19: Hepadnaviruses (and Other Reverse-Transcribing DNA Viruses)
19.1 Introduction to Hepadnaviruses
19.2 Importance of HBV
19.3 HBV Virion
19. 4 Non-Infectious Particles
19.5 Soluble Virus Protein
19.6 HBV Genome
19.7 HBV Genetic Groups
19.8 HBV Replication
19.9 Prevention and Treatment of HBV Infection
19.10 Other Reverse-Transcri bing DNA Viruses
Learning Outcomes
Sources of Further Information
Chapter 20: Bacterial Viruses
20.1 Introduction to Bacterial Viruses (Bacteriophages)
20.2 Single-Stranded RNA Phages
20.3 Double-Stranded RNA Phages
20.4 Single-Stranded DNA Phages
20.5 Double-Stranded DNA Phages
Learning Outcomes
Sources of Further Information
Chapter 21: Origins and Evolution of Viruses
21.1 Introduction to Origins and Evolution of Viruses
21.2 Origins of Viruses
21.3 Evolution of Viruses
Learning Outcomes
Sources of Further Information
Chapter 22: Emerging Viruses
22.1 Introduction to Emerging Viruses
22.2 Viruses in New Host Species
22.3 Viruses in New Areas
22.4 Viruses in New Host Species and in New Areas
22.5 New viruses
22.6 Recently Discovered Viruses
22. 7 Re-Emerging Viruses
22.8 Virus Surveillance
22.9 Dealing with Outbreaks
Learning Outcomes
Sources of Further Information
Chapter 23: Viruses and Cancer
23.1 Introduction to Viruses and Cancer
23.2 Papillomavirus-Linked Cancers
23.3 Polyomavirus-Linked Cancers
23.4 Epsteinsl.>"Barr Virus-Linked Cancers
23.5 Kaposisl.>™s Sarcoma
23.6 Adult T Cell Leukemia
23.7 Hepatocellular Carcinoma
23.8 Virus-Associated Cancers in Animals
23.9 Cell Lines Derived From Virus-Associated Cancers
23.10 How Do Viruses Cause Cancer?
23. 11 Prevention of Virus-Induced Cancers
Learning Outcomes
Sources of Further Information
Chapter 24: Survival of Infectivity
24.1 Preservation of Virus Infectivity
24.2 Destruction of Virus Infectivity
24.3 Inactivation Targets in Virions
24.4 Inactivation Kinetics
24. 5 Agents that Inactivate Virus Infectivity
Learning Outcomes
Sources of Further Information
Chapter 25: Virus Vaccines
25.1 Introduction to Virus Vaccines
25.2 Live Attenuated Virus Vaccines
25.3 Inactivated Virus Vaccines
25.4 Virion Subunit Vaccines
25.5 Live Recombinant Virus Vaccines
25.6 Mass-Production of Viruses for Vaccines
25.7 Virus-Like Particles
25.8 Synthetic Peptide Vaccines
25.9 DNA Vaccines
25.10 Storage and Transport of Vaccines
Learning Outcomes
Sources of Further Information
Chapter 26: Anti-viral Drugs
26.1 Introduction to Anti-viral Drugs
26.2 Development of Anti-viral Drugs
26.3 Examples of Anti-viral Drugs
26.4 Drug Resistance
26.5 Anti-vira l Drug Research
Learni ng Outcomes
Sou rces of Fu rther Information
Chapter 27: Pri ons
27 . l Introd uction to Prions
27.2 Transmissible Spongiform Encephalopathies
27 .3 The Nature of Prions
27.4 Prion Di seases
27.5 Prion Strains
27 .6 Prion Tra nsmission
27. 7 The Protei n-Only Hypothesis
Learni ng Outcomes
Sources of Further Information
Virologistss1> TM Vocabulary
Index
VIROLOGY
PRINCIPLES AND APPLICATIONS
John B. Carter
and
Venelia A. Saunders
[S ormRG]
KATI TPB I ET I h33
y
This edition first published 2013 by John Wiley & Sons Ltd
Copyright © 2013, 2007 John Wiley & Sons Ltd
Cover image: Glass Sculpture of HIV virus courtesy of Wellcome Images
All effort has been made to trace and acknowledge ownership of copyright. The
publisher would be glad to hear from any copyright holders whom it has not been
possible to contact.
Registered office
John Wiley & Sons Ltd, The Atrium, Southern Gate, Chichester, West Sussex, P019
8SQ, United Kingdom
For details of our global editorial offices, for customer services, and for information
about how to apply for permission to reuse the copyright material in this book
please see our website at www.wiley.com.
The rights of John Carter and Venetia Saunders to be identified as the authors of
this work has been asserted in accordance with the UK Copyright, Designs and
Patents Act 1988.
All rights reserved. No part of this publication may be reproduced, stored in a
retrieval system, or transmitted, in any form or by any means, electronic,
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Copyright, Designs and Patents Act 1988, without the prior permission of the
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that the publisher is not engaged in rendering professional services. If professional
advice or other expert assistance is required, the services of a competent
professiional should be sought.
Library of Congress Cataloging-in-Publication Data
Carter, John B., 1944-
Virology : principles and applications / John Carter, Venetia Saunders. - 2nd ed.
p.; cm.
Includes bibliographical references and index.
ISBN 978-1-119-99143-4 (cloth) - ISBN 978-1-1 19-99142-7 (pbk.)
I. Sau nders, Venetia A., 1949- II. Title.
[DNLM : 1. Viruses. 2. Virus Diseases . QW 160]
616.9'101-dc23
201 2041 238
ISBN 978-1-1186-2979-6 ( ebk)
ISBN 978- 1-1186-2977-2 (ebk)
ISBN 978-1-1186-2976-5 (ebk)
ISBN 978-1-1199-9 14 2-7 (pbk. )
ISBN 978-1-1199-9143-4 (hbk)
A catalogue record for this book is available from the Briti sh Library
Senior Commissioning Editor: Andrew McAleer
Assistant Ed itor: Kathari ne Earwaker
Marketi ng Managers: Fran Hunt and Jo Underwood
Project Editor: Jul iet Booker
To Myra, Robert, Jon, and Mark
Preface to Second Ed ition
Virology conti nues to be an exciti ng subject and to develop at a rapid pace. The
introduction of new la boratory techn iq ues a nd th e conti n ued applicati on of
esta bl ished techni ques are prod ucing a wealth of new information . There has been
an explosion in the publication of virology papers reporting the di scovery of new
viruses and providi ng deeper insights into many facets of the subject. We have
tried to reflect these developments in the second edition, which contai ns much new
material, incl uding an add itional chapter (on infl uenza virus). In an attem pt to
improve cl arity, sections of the text have been rewritten .
In the diagrams, many of which have been redrawn for inclusion in this ed ition,
there is a sta ndard color code to differentiate va rious types of nuclei c acid and
protein molecules. Please note that, in the interests of cla rity, there have been
some mod ifications to the color code used in the first edition. There is a key to the
c o l or cod e on pag e xxi x . In add itio n, t h e book has a w e b s ite
(www . wi ley.co m/college/ca rter) w ith a ccompa nyi ng tea ch ing and learning
resources, including animations of virus replication cycles.
We are grateful to the many people who provided feedback on the first edition and
to those who made suggestions for the second edition . We have i ncorporated many
of the suggestions for new material, thoug h space constrai nts prevented us from
i ncorporating them all. Again, we would be grateful to receive feed back.
We thank the team at John Wi ley & Sons Ltd for all their help with this new ed ition
and to our famil ies for their conti nuing support.
John B. Carters€-
John .Carter147@ntlworld .com
Venetia A. Sau nderss€-
s€-Authors are now retired; both were previously at School of Pharmacy &
Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool,
L3 3AF, UK.
Preface to First Edition
Virology is a fascinating and rapidly developing subject, and is worthy of study
purely because viruses are interesting! Furthermore, virology is a branch of science
that is of immense relevance to mankind for a host of reasons, not least of which
are the threats to human health caused by viruses, such as HIV, hepatitis B virus,
papillomaviruses, measles, and influenza viruses, to mention just a few. There is a
continuing need for trained virologists and it is hoped that this book will play a
small role in helping to fulfill that need. To a large extent the material in the book is
based on virology taught at Uverpool John Moores University.
This is not a textbook of fundamental virology, medical virology, veterinary virology,
plant virology or of bacteriophages, but a bit of each of these! The general pattern
of the book is that principles of virology are covered earlier and applications are
covered later. There is no strict demarcation between the two, however, so the
reader may be made aware of important applications while principles are being
introduced.
The first 10 chapters cover basic aspects of virology. A chapter on methods used in
virology comes early in the book, but could be skimmed to gain an overview of its
contents and thereafter used for reference. There is one chapter on each of the
seven Baltimore classes, concentrating mainly on animal viruses. There is a chapter
devoted entirely to HIV and an extended chapter on phages, reflecting the renewed
interest in their biology and applications. After a chapter on origins and evolution of
viruses, there follow five chapters covering various aspects of applied virology,
including vaccines and antiviral drugs. The final chapter is on prions, which are not
viruses but are often considered along with the viruses.
Each chapter starts with s"Dt-bAt a glance,s"DK a brief summary with the dual aim of
giving a flavor of what is coming up and providing a revision aid. Each chapter ends
with a list of learning outcomes and a guide to further reading in books and
journals. The references are mainly from the twenty-first century, but there is a
selection of important papers from the last century.
The book has a web site (www.wiley.com/go/carter) where you can find:
• many references additional to those in the book;
• links to the journal references (to the full text where this is freely available,
otherwise to the abstract);
• links to virology web sites;
• self-assessment questions and answers for each chapter, to reinforce and
extend concepts developed in the book.
A key feature of our book is a standard color code to differentiate various types of
nucleic acid and protein molecules in the diagrams. The color code is explained in
the following pages. It is appreciated that color coding may be of limited value to
individuals who have difficulty in differentiating colors, so we have also labeled
many of the molecules.
A number of virus replication cycles are described and the reader should be aware
that these are models based on evidence to date; the models may have to be
modified in the light of future evidence. We present the virus replication cycles as
fitting within a general framework of seven steps:
1. Attachment of a virion to a cell
2. Entry into the cell
3. Transcription of virus genes into mRNAs
4. Translation of virus mRNAs into virus proteins
5. Genome replication
6. Assembly of the virus proteins and genomes into virions
7. Exit of the virions from the cell.
We hope that this helps in appreciating how virus replication fits into a general
pattern, and in comparing the replication cycles of different types of virus. For
some groups of viruses the framework has to be modified, and we make clear
when that is the case.
If you come across an unfam iliar term please consult the Virolog istss"f> ™
Vocabulary at the back of the book. This glossary i111cludes not only virology-specific
terms, but also a selection of terms from cell biology, molecular biology,
immunology, and medicine.
A list of abbreviations that are used throughout this book appears on the following
pages.
We wish to thank the many people who have made the production of this book
possible. We thanl< all those who supplied images and those who gave permission
for the use of their images; we are especially g rateful to David Bhella, Tom
Goddard, Kathryn Newton, and Jean-Yves Sgro. Thanks also to Robert Carter for
assistance with images. We acknowledge the contributions of the many students
who have acted as guinea pigs for our teaching materials and who have provided
us with feedback. Grateful thanks also to those who reviewed material for the book
and provided valuable feedback. We are sorry that we were unable to include all
the topics suggested, but if we had done so the book would have run to several
volumes! Many thanks to Rachael Ballard and all at John Wiley & Sons Ltd who
helped the book come to fruition. Finally, thanks to our families for their support
and for their patience during those many hours we spent ensconced in the study.
We hope you find the book useful and we would be interested to hear what you
think of it. We have tried to ensure that there are no errors, but it is probable that
some h.ave slipped through; if you come across any errors please inform us.
John B. Carter
John.Carter! [email protected]