Principles of Molecular VirologyFifth Edition

Principles of MolecularVirology

Fifth Edition

Alan J. CannUniversity of Leicester, UK

AMSTERDAM • BOSTON • HEIDELBERG • LONDONNEW YORK • OXFORD • PARIS • SAN DIEGO

SAN FRANCISCO • SINGAPORE • SYDNEY • TOKYO

Academic Press is an imprint of Elsevier

Academic Press is an imprint of Elsevier225 Wyman Street, Waltham, MA 02451, USAThe Boulevard, Langford Lane, Kidlington, Oxford, OX5 1GB, UK

First Edition 1993Second Edition 1997Third Edition 2001Fourth Edition 2005

Fifth Edition

Copyright � 2012, Elsevier Ltd. All rights reserved.

No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, includingphotocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher.Details on how to seek permission, further information about the Publisher’s permissions policies and our arrangements withorganizations such as the Copyright Clearance Center and the Copyright Licensing Agency, can be found at our website: www.elsevier.com/permissions.

This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as may benoted herein).

NoticesKnowledge and best practice in this field are constantly changing. As new research and experience broaden our understanding,changes in research methods, professional practices, or medical treatment may become necessary.

Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information,methods, compounds, or experiments described herein. In using such information or methods they should be mindful of theirown safety and the safety of others, including parties for whom they have a professional responsibility.

To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume any liability for any injuryand/or damage to persons or property as amatter of products liability, negligence or otherwise, or from any use or operation of anymethods, products, instructions, or ideas contained in the material herein.

Library of Congress Cataloging-in-Publication DataCann, Alan.Principles of molecular virology/Alan J. Cann.

p. cm.Includes index.ISBN 978-0-12-384939-71. Molecular virology. I. Title.QR389.C36 2012579.2–dc22

2011010880

British Library Cataloguing-in-Publication DataA catalogue record for this book is available from the British Library.

ISBN: 978-0-12-384939-7

For information on all Academic Press publications visit ourWeb site at www.elsevierdirect.com

Printed in Canada

11 12 13 14 15 9 8 7 6 5 4 3 2 1

Contents

PREFACE TO THE FIFTH EDITION .......................................................... ix

CHAPTER 1 Introduction.......................................................................... 1What Are Viruses? ......................................................................... 2

Are viruses alive? ....................................................................... 3The History of Virology.................................................................. 4Living Host Systems....................................................................... 6Cell Culture Methods ..................................................................... 8Serological/Immunological Methods ..........................................10Ultrastructural Studies ................................................................. 11Molecular Biology ......................................................................... 18Summary........................................................................................ 23

CHAPTER 2 Particles .............................................................................. 25The Function and Formation of Virus Particles ........................25

Capsid symmetry and virus architecture ..............................27Helical capsids .......................................................................... 28Icosahedral (isometric) capsids ..............................................33Enveloped viruses .................................................................... 39Complex virus structures ........................................................ 42Proteinenucleic acid interactions and genome

packaging ............................................................................. 48Virus receptors: recognition and binding .............................52Other interactions of the virus capsid with the host cell ....53

Summary........................................................................................ 53

CHAPTER 3 Genomes............................................................................. 55The Structure and Complexity of Virus Genomes....................55

Molecular genetics ................................................................... 57Virus genetics ........................................................................... 61Virus mutants ........................................................................... 63Genetic interactions between viruses ...................................66Nongenetic interactions between viruses.............................69 v

Small DNA genomes ................................................................ 70Large DNA genomes................................................................ 75Positive-strand RNA viruses ................................................... 78Negative-strand RNA viruses .................................................81Segmented and multipartite virus genomes.........................84Reverse transcription and transposition ...............................88Evolution and epidemiology.................................................... 97

Summary......................................................................................100

CHAPTER 4 Replication........................................................................ 103Overview of Virus Replication ..................................................103Investigation of Virus Replication ............................................105The Replication Cycle ................................................................109

Attachment..............................................................................110Penetration ..............................................................................117Uncoating ................................................................................118Genome replication and gene expression ...........................121Assembly .................................................................................125Maturation...............................................................................127Release.....................................................................................129

Summary......................................................................................131

CHAPTER 5 Expression........................................................................ 133Expression of Genetic Information...........................................133Control of Prokaryote Gene Expression...................................134Control of Expression in Bacteriophage l ...............................135Control of Eukaryote Gene Expression....................................140Genome Coding Strategies........................................................142

Class I: Double-stranded DNA..............................................143Class II: Single-stranded DNA..............................................145Class III: Double-stranded RNA ...........................................146Class IV: Single-stranded (þ)sense RNA.............................148Class V: Single-stranded (e)sense RNA..............................151Class VI: Single-stranded (þ)sense RNA with DNAintermediate............................................................................153Class VII: Double-stranded DNA with RNA

intermediate .......................................................................153Transcriptional Control of Expression .....................................154Posttranscriptional Control of Expression ...............................158Summary......................................................................................167

CHAPTER 6 Infection............................................................................ 169Virus Infections of Plants...........................................................169Immune Responses to Virus Infections in Animals ...............174

vi Contents

Viruses and Apoptosis...............................................................179Interferons ...................................................................................181Evasion of Immune Responses by Viruses .............................186

Inhibition of MHC-I-restricted antigen presentation .........186Inhibition of MHC-II-restricted antigen presentation ........187Inhibition of natural killer cell lysis ......................................187Interference with apoptosis ..................................................187Inhibition of cytokine action..................................................187Evasion of humoral immunity ...............................................188Evasion of the complement cascade....................................188

ViruseHost Interactions ............................................................188The Course of Virus Infections .................................................196

Abortive infection...................................................................196Acute infection........................................................................198Chronic infection ....................................................................198Persistent infection ................................................................198Latent infection.......................................................................200

Prevention and Therapy of Virus Infection .............................201RNA Interference (RNAi) ...........................................................205Virus Vectors and Gene Therapy .............................................206Chemotherapy of Virus Infections............................................208Summary......................................................................................213

CHAPTER 7 Pathogenesis.................................................................... 215Mechanisms of Cellular Injury ..................................................216Viruses and Immunodeficiency ................................................220Virus-Related Diseases ..............................................................224Bacteriophages and Human Disease .......................................227Cell Transformation by Viruses ................................................228Cell Transformation by Retroviruses .......................................232Cell Transformation by DNAViruses.......................................235Viruses and Cancer ....................................................................238New and Emergent Viruses ......................................................243Zoonoses......................................................................................250Bioterrorism.................................................................................251Summary......................................................................................252

CHAPTER 8 Subviral Agents: Genomes without Viruses,Viruses without Genomes.............................................. 255Satellites and Viroids .................................................................255Prions ...........................................................................................259

Pathology of prion diseases ..................................................260TSE in Animals ...........................................................................260

viiContents

Scrapie .....................................................................................260Transmissible mink encephalopathy (TME) .......................262Feline spongiform encephalopathy (FSE)............................262Chronic wasting disease (CWD)...........................................262Bovine spongiform encephalopathy (BSE) ..........................263

Human TSES ................................................................................264Molecular Biology of Prions.......................................................267Summary......................................................................................272

APPENDIX 1: GLOSSARY AND ABBREVIATIONS ............................... 275APPENDIX 2: CLASSIFICATION OF SUBCELLULAR

INFECTIOUS AGENTS..................................................... 285APPENDIX 3: THE HISTORY OF VIROLOGY........................................ 291INDEX......................................................................................................... 297

viii Contents

Preface to the Fifth Edition

This is the book I nearly didn't write. Quite a lot has changed for me since thefourth edition was published, and when discussions began as to whether toproduce a new edition, I had my doubts. Frommy perspective, one of the mainthings that has changed is MicrobiologyBytes.comdthere, and in related spacessuch as the MicrobiologyBytes page on Facebook, in the words of ElvisCostello, “Every day I write the book.” So why are you reading this? Althoughthe Internet is far better than printed books for many things, there is clearly stilla strong demand for this book because sometimes it’s good to have a core ofknowledge in one place (e.g., when it comes to revision for exams). Add to thatthe translations into other languages (including Chinese) that the last editionreceived, plus the Amazon Kindle version, and I can reach a wide and appre-ciative audience in this format.

Once I had agreed to write a new edition, I wanted to do two things. I wanted toupdate the technical knowledge throughout, but I also needed to completelyrewrite the whole book to make it far more accessible, based on the experience Ihave gained writing online over the past few years. Hopefully I have achievedthat.

I would like to thank all the staff of Elsevier, without whose hard work andpersuasion this edition would never have appeared. Although we have nevermet face to face, they reside inmy inbox, constantly remindingme that chaptersare overdue.

Alan J. CannUniversity of Leicester, UKalan.cann@leicester.ac.uk

January 2011

ix