2ND EDITION FUNDAMENTALS OF MOLECULAR VIROLOGY NICHOLAS H ACHESON John Wiley & Sons, Inc ffirs.indd i 19/05/11 10:33 AM Vice President and Publisher Acquisitions Editor Associate Editor Assistant Editor Marketing Manager Senior Media Editor Media Specialist Production Manager Senior Production Editor Designer Kaye Pace Kevin Witt Michael Palumbo/Lauren Morris Jenna Paleski Clay Stone Linda Muriello Daniela DiMaggio Janis Soo Joyce Poh Maddy Lesure/Seng Ping Ngieng Cover images: Enterobacteria Phage Phi X174, Human Rhinovirus 3, Simian Virus 40 Images created by Jean-Yves Sgro, University of Wisconsin, Madison, with software Qutemol and VMD This book was set in 10/12 Janson Text Roman by MPS Limited, a Macmillan Company, and printed and bound by Markono Print Media Pte Ltd The cover was printed by Markono Print Media Pte Ltd This book is printed on acid free paper Founded in 1807, John Wiley & Sons, Inc has been a valued source of knowledge and understanding for more than 200 years, helping people around the world meet their needs and fulfill their aspirations Our company is built on a foundation of principles that include responsibility to the communities we serve and where we live and work In 2008, we launched a Corporate Citizenship Initiative, a global effort to address the environmental, social, economic, and ethical challenges we face in our business Among the issues we are addressing are carbon impact, paper specifications and procurement, ethical conduct within our business and among our vendors, and community and charitable support For more information, please visit our website: www.wiley.com/go/citizenship Copyright © 2011, 2007 John Wiley & Sons, Inc 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, mechanical, photocopying, recording, scanning or otherwise, except as permitted under Sections 107 or 108 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher, or authorization through payment of the appropriate percopy fee to the Copyright Clearance Center, Inc 222 Rosewood Drive, Danvers, MA 01923, website www.copyright com Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030-5774, (201)748-6011, fax (201)748-6008, website http://www.wiley com/go/permissions Evaluation copies are provided to qualified academics and professionals for review purposes only, for use in their courses during the next academic year These copies are licensed and may not be sold or transferred to a third party Upon completion of the review period, please return the evaluation copy to Wiley Return instructions and a free of charge return shipping label are available at www.wiley.com/go/returnlabel Outside of the United States, please contact your local representative Library of Congress Cataloging-in-Publication Data Acheson, N H Fundamentals of molecular virology / Nicholas H Acheson.—2nd ed p ; cm Includes bibliographical references and index ISBN 978-0-470-90059-8 (pbk : alk paper) Molecular virology I Title [DNLM: Viruses Virus Physiological Phenomena Viruses—genetics QW 160] QR389.A24 2011 616.9'101—dc22 2011002024 Printed in Asia 10 ffirs.indd ii 19/05/11 10:33 AM I dedicate this book to four mentors whose enthusiasm for virology stimulated my interest when I was a student, and who encouraged me to follow my own path Johns Hopkins III James D Watson Igor Tamm Purnell Choppin ffirs.indd iii 19/05/11 10:33 AM ffirs.indd iv 19/05/11 10:33 AM B R I E F C O N T E N T S SECTION I: INTRODUCTION TO VIROLOGY Introduction to Virology Nicholas H Acheson, McGill University Virus Structure and Assembly 18 Stephen C Harrison, Harvard University Virus Classification: The World of Viruses 31 Nicholas H Acheson, McGill University Virus Entry 45 Ari Helenius, Swiss Federal Institute of Technology, Zurich SECTION II: VIRUSES OF BACTERIA AND ARCHAEA Single-Stranded RNA Bacteriophages 59 Jan van Duin, University of Leiden Microviruses 69 Bentley Fane, University of Arizona Bacteriophage T7 77 William C Summers, Yale University Bacteriophage Lambda 85 Michael Feiss, University of Iowa Viruses of Archaea 97 David Prangishvili, Institut Pasteur 11 Picornaviruses 125 Bert L Semler, University of California, Irvine 12 Flaviviruses 137 Richard Kuhn, Purdue University 13 Togaviruses 148 Milton Schlesinger, Washington University in St Louis Sondra Schlesinger, Washington University in St Louis Revised by: Richard Kuhn, Purdue University 14 Coronaviruses 159 Mark Denison, Vanderbilt University Michelle M Becker, Vanderbilt University SECTION IV: NEGATIVE-STRAND AND DOUBLE-STRANDED RNA VIRUSES OF EUKARYOTES 15 Paramyxoviruses and Rhabdoviruses 175 Nicholas H Acheson, McGill University Daniel Kolakofsky, University of Geneva Christopher Richardson, Dalhousie University Revised by: Laurent Roux, University of Geneva 16 Filoviruses 188 Heinz Feldmann, Division of Intramural Research, NIAID, NIH Hans-Dieter Klenk, University of Marburg Nicholas H Acheson, McGill University 17 Bunyaviruses 200 Richard M Elliott, University of St Andrews SECTION III: POSITIVE-STRAND RNA VIRUSES OF EUKARYOTES 18 Influenza Viruses 210 10 Cucumber Mosaic Virus 112 19 Reoviruses 225 Ping Xu, J Noble Research Institute Marilyn J Roosinck, J Noble Research Institute Dalius J Briedis, McGill University Terence S Dermody, Vanderbilt University James D Chappell, Vanderbilt University v TOC.indd v 13/05/11 2:11 PM vi Brief Contents SECTION V: SMALL DNA VIRUSES OF EUKARYOTES 20 Parvoviruses 238 Peter Beard, Swiss Institute for Experimental Cancer Research 21 Polyomaviruses 247 Nicholas H Acheson, McGill University 22 Papillomaviruses 263 Greg Matlashewski, McGill University Revised by: Lawrence Banks, International Centre for Genetic Engineering and Biotechnology, Trieste 29 Human Immunodeficiency Virus 354 Alan Cochrane, University of Toronto 30 Hepadnaviruses 365 Christopher Richardson, Dalhousie University SECTION VIII: VIROIDS AND PRIONS 31 Viroids and Hepatitis Delta Virus 378 Jean-Pierre Perreault, Université de Sherbrooke Martin Pelchat, University of Ottawa 32 Prions 387 SECTION VI: LARGER DNA VIRUSES OF EUKARYOTES 23 Adenoviruses 274 Philip Branton, McGill University Richard C Marcellus, McGill University 24 Herpesviruses 285 Bernard Roizman, University of Chicago Gabriella Campadelli-Fiume, University of Bologna Richard Longnecker, Northwestern University 25 Baculoviruses 302 Eric B Carstens, Queen’s University 26 Poxviruses Dalius J Briedis, McGill University SECTION IX: HOST DEFENSES AGAINST VIRUS INFECTION 33 Intrinsic Cellular Defenses Against Virus Infection 398 Karen Mossman, McMaster University Pierre Genin, University Paris Descartes John Hiscott, McGill University 34 Innate and Adaptive Immune Responses to Virus Infection 415 Malcolm G Baines, McGill University Karen Mossman, McMaster University 312 Richard C Condit, University of Florida 27 Viruses of Algae and Mimivirus 325 Michael J Allen, Plymouth Marine Laboratory William H Wilson, Bigelow Laboratory for Ocean Sciences SECTION X: ANTIVIRAL AGENTS AND VIRUS VECTORS 35 Antiviral Vaccines 428 Brian Ward, McGill University 36 Antiviral Chemotherapy 444 Donald M Coen, Harvard University SECTION VII: VIRUSES THAT USE A REVERSE TRANSCRIPTASE 28 Retroviruses 342 Alan Cochrane, University of Toronto TOC.indd vi 37 Eukaryotic Virus Vectors 456 Rénald Gilbert, NRC Biotechnology Research Institute, Montreal Bernard Massie, NRC Biotechnology Research Institute, Montreal 13/05/11 2:11 PM C O N T E N T S SECTION I: INTRODUCTION TO VIROLOGY Introduction to Virology THE NATURE OF VIRUSES Viruses consist of a nucleic acid genome packaged in a protein coat Viruses are dependent on living cells for their replication Virus particles break down and release their genomes inside the cell Virus genomes are either RNA or DNA, but not both WHY STUDY VIRUSES? Viruses are important disease-causing agents Viruses can infect all forms of life Viruses are the most abundant form of life on Earth The study of viruses has led to numerous discoveries in molecular and cell biology A BRIEF HISTORY OF VIROLOGY: THE STUDY OF VIRUSES The scientific study of viruses is very recent Viruses were first distinguished from other microorganisms by filtration The crystallization of tobacco mosaic virus challenged conventional notions about genes and the nature of living organisms The “phage group” stimulated studies of bacteriophages and helped establish the field of molecular biology Study of tumor viruses led to discoveries in molecular biology and understanding of the nature of cancer DETECTION AND TITRATION OF VIRUSES Most viruses were first detected and studied by infection of intact organisms The plaque assay arose from work with bacteriophages Eukaryotic cells cultured in vitro have been adapted for plaque assays Hemagglutination is a convenient and rapid assay for many viruses 10 Virus particles can be seen and counted by electron microscopy 10 The ratio of physical virus particles to infectious particles can be much greater than 11 THE VIRUS REPLICATION CYCLE: AN OVERVIEW 11 The single-cycle virus replication experiment 11 An example of a virus replication cycle: mouse polyomavirus 12 Analysis of viral macromolecules reveals the detailed pathways of virus replication 13 STEPS IN THE VIRUS REPLICATION CYCLE 13 Virions bind to receptors on the cell surface 13 The virion (or the viral genome) enters the cell 14 Early viral genes are expressed: the Baltimore classification of viruses 14 The seven groups in the Baltimore classification system 14 Early viral proteins direct replication of viral genomes 15 Late messenger RNAs are made from newly replicated genomes 15 Late viral proteins package viral genomes and assemble virions 16 Progeny virions are released from the host cell 16 Virus Structure and Assembly 18 BASIC CONCEPTS OF VIRUS STRUCTURE 18 Virus structure is studied by electron microscopy and X-ray diffraction 19 Many viruses come in simple, symmetrical packages 19 CAPSIDS WITH ICOSAHEDRAL SYMMETRY 21 Some examples of virions with icosahedral symmetry The concept of quasi-equivalence 21 Larger viruses come in more complex packages 23 21 CAPSIDS WITH HELICAL SYMMETRY 25 VIRAL ENVELOPES 26 Viral envelopes are made from lipid bilayer membranes Viral glycoproteins are inserted into the lipid membrane to form the envelope 27 26 PACKAGING OF GENOMES AND VIRION ASSEMBLY 28 Multiple modes of capsid assembly 28 Specific packaging signals direct incorporation of viral genomes into virions 28 Core proteins may accompany the viral genome inside the capsid 28 Formation of viral envelopes by budding is driven by interactions between viral proteins 28 DISASSEMBLY OF VIRIONS: THE DELIVERY OF VIRAL GENOMES TO THE HOST CELL 29 Virions are primed to enter cells and release their genome 29 vii TOC.indd vii 13/05/11 2:11 PM viii Contents Virus Classification: The World of Viruses 31 VIRUS CLASSIFICATION 31 Many different viruses infecting a wide variety of organisms have been discovered 31 Virus classification is based on molecular architecture, genetic relatedness, and host organism 31 Viruses are grouped into species, genera, and families 32 Distinct naming conventions and classification schemes have developed in different domains of virology 33 MAJOR VIRUS GROUPS 33 Study of the major groups of viruses leads to understanding of shared characteristics and replication pathways 33 Viruses with single-stranded DNA genomes are small and have few genes 34 Viruses with double-stranded DNA genomes include the largest known viruses 35 Most plant viruses and many viruses of vertebrates have positive-strand RNA genomes 35 Viruses with negative-strand RNA genomes have helical nucleocapsids; some have fragmented genomes 38 Viruses with double-stranded RNA genomes have fragmented genomes and capsids with icosahedral symmetry 38 Viruses with a reverse transcription step in their replication cycle can have either RNA or DNA genomes 39 Satellite viruses and satellite nucleic acids require a helper virus to replicate 40 Viroids not code for proteins, but replicate independently of other viruses 40 THE EVOLUTIONARY ORIGIN OF VIRUSES 40 The first steps in the development of life on Earth: the RNA world 40 Viroids and RNA viruses may have originated in the RNA world 41 The transition to the DNA-based world 42 Retroviruses could have originated during the transition to DNA-based cells 43 Small- and medium-sized DNA viruses could have arisen as independently replicating genetic elements in cells 43 Large DNA viruses could have evolved from cellular forms that became obligatory intracellular parasites 43 These arguments about the origin of viruses are only speculations 44 Virus Entry 45 How virions get into cells? 45 Enveloped and non-enveloped viruses have distinct penetration strategies 46 Some viruses can pass directly from cell to cell 46 TOC.indd viii A variety of cell surface proteins can serve as specific virus receptors 47 Receptors interact with viral glycoproteins, surface protrusions, or “canyons” on the surface of the virion 48 Many viruses enter the cell via receptor-mediated endocytosis 48 Passage from endosomes to the cytosol is often triggered by low pH 49 Membrane fusion is mediated by specific viral “fusion proteins” 50 Fusion proteins undergo major conformational changes that lead to membrane fusion 50 Non-enveloped viruses penetrate by membrane lysis or pore formation 51 Virions and capsids are transported within the cell in vesicles or on microtubules 52 Import of viral genomes into the nucleus 52 The many ways in which viral genomes are uncoated and released 54 SECTION II: VIRUSES OF BACTERIA AND ARCHAEA Single-Stranded RNA Bacteriophages 59 The discovery of RNA phages stimulated research into messenger RNA function and RNA replication 59 RNA phages are among the simplest known organisms 59 Two genera of RNA phages have subtle differences 60 RNA phages bind to the F-pilus and use it to insert their RNA into the cell 60 Phage RNA is translated and replicated in a regulated fashion 61 RNA secondary structure controls translation of lysis and replicase genes 61 Ribosomes translating the coat gene disrupt secondary structure, allowing replicase translation 62 Ribosomes terminating coat translation can reinitiate at the lysis gene start site 63 Replication versus translation: competition for the same RNA template 64 Genome replication requires four host cell proteins plus the replicase 64 A host ribosomal protein directs polymerase to the coat start site 65 Polymerase skips the first A residue but adds a terminal A to the minus-strand copy 65 Synthesis of plus-strands is less complex and more efficient than that of minus-strands 65 The start site for synthesis of maturation protein is normally inaccessible to ribosomes 65 Synthesis of maturation protein is controlled by delayed RNA folding 66 Assembly and release of virions 67 13/05/11 2:11 PM Contents Microviruses 69 ϕX174: a tiny virus with a big impact 69 Overlapping reading frames allow efficient use of a small genome 70 ϕX174 binds to glucose residues in lipopolysaccharide on the cell surface 70 ϕX174 delivers its genome into the cell through spikes on the capsid surface 71 Stage I DNA replication generates double-stranded replicative form DNA 72 Gene expression is controlled by the strength of promoters and transcriptional terminators 72 Replicative form DNAs are amplified via a rolling circle mechanism 72 Summary of viral DNA replication mechanisms 73 Procapsids are assembled by the use of scaffolding proteins 73 Scaffolding proteins have a flexible structure 74 Single-stranded genomes are packaged into procapsids as they are synthesized 74 Role of the J protein in DNA packaging 75 Cell lysis caused by E protein leads to release of phage 75 Did all icosahedral ssDNA virus families evolve from a common ancestor? 75 Bacteriophage T7 77 T7: a model phage for DNA replication, transcription, and RNA processing 77 T7 genes are organized into three groups based on transcription and gene function 78 Entry of T7 DNA into the cytoplasm is powered by transcription 79 Transcription of class II and III genes requires a novel T7-coded RNA polymerase 79 Class II genes code for enzymes involved in T7 DNA replication 80 T7 RNAs are cleaved by host cell ribonuclease III to smaller, stable mRNAs 80 Class III gene expression is regulated by delayed entry and by promoter strength 80 DNA replication starts at a unique internal origin and is primed by T7 RNA polymerase 80 Large DNA concatemers are formed during replication 81 Concatemer processing depends on transcription by T7 RNA polymerase and occurs during DNA packaging into preformed proheads 82 Special features of the T7 family of phages 82 Bacteriophage Lambda 85 Roots 85 Phage adsorption and DNA entry depend on cellular proteins involved in sugar transport 86 TOC.indd ix ix The lytic transcription program is controlled by termination and antitermination of RNA synthesis at specific sites on the genome 87 The CI repressor blocks expression of the lytic program by regulating three nearby promoters: PL, PR, and PRM 88 Cleavage of CI repressor in cells with damaged DNA leads to prophage induction 89 The Cro repressor suppresses CI synthesis and regulates early gene transcription 89 Making the decision: go lytic or lysogenize? 90 A quick review 90 Breaking and entering: the insertion of prophage DNA into the bacterial chromosome 90 Excision of DNA from the bacterial chromosome 92 Int synthesis is controlled by retroregulation 93 DNA replication is directed by O and P, but carried out by host cell proteins 93 Assembly of heads involves chaperones and scaffolding proteins 93 DNA is inserted into preformed proheads by an ATP-dependent mechanism 94 Host cell lysis 94 Viruses of Archaea 97 Archaea, the third domain of life 97 Viruses of Archaea have diverse and unusual morphologies 99 Fuselloviridae are temperate viruses that produce virions without killing the host cell 99 Genomes of fuselloviruses are positively supercoiled 101 Transcription of SSV-1 DNA is temporally controlled 101 Filamentous enveloped viruses of the Lipothrixviridae come in many lengths 102 A droplet-shaped virus is the only known member of the Guttaviridae (from the Latin gutta, “droplet”) 103 Acidianus bottle-shaped virus (ABV): its name says it all! 103 The genome of Pyrobaculum spherical virus has nearly all open reading frames encoded on one DNA strand 104 Viruses in the family Rudiviridae (from the Latin rudis, “small rod”) are non-enveloped, helical rods 105 Rudiviruses escape from the cell by means of unique pyramidal structures 106 Acidianus two-tailed virus (ATV) has a virion with tails that spontaneously elongate 106 Infection with ATV at high temperatures leads to lysogeny 106 Two related viruses of hyperhalophiles resemble fuselloviruses by morphology but not by genetics 108 Two unusual viruses with icosahedral capsids and prominent spikes 108 A virus with a single-stranded DNA genome is closely related to a virus with a double-stranded DNA genome 108 Comparative genomics of archaeal viruses 109 Conclusion 110 13/05/11 2:11 PM x Contents SECTION III: POSITIVE-STRAND RNA VIRUSES OF EUKARYOTES 10 Cucumber Mosaic Virus 112 Mosaic disease in cucumber plants led to the discovery of cucumber mosaic virus (CMV) 113 Cucumber mosaic virus has a positive-strand RNA genome enclosed in a compact capsid with icosahedral symmetry 113 The genome of cucumber mosaic virus consists of three distinct RNA molecules 113 The three genome RNAs and a subgenomic RNA are encapsidated in separate but otherwise identical particles 114 The 3'-terminal regions of cucumber mosaic virus genome segments can fold to form a transfer RNA-like structure 114 Cucumber mosaic virus is transmitted in nature by aphids 115 The genome of cucumber mosaic virus encodes five multifunctional proteins 116 Replication of viral RNA is associated with intracellular membranes, and requires coordinated interaction of viral RNAs, proteins, and host proteins 117 Brome mosaic virus RNA replication has been analyzed in yeast cells 117 Brome mosaic virus RNA synthesis takes places on cytoplasmic membranes 117 Packaging of viral genomes 117 Cucumber mosaic virus requires protein 3a (movement protein) and coat protein for cell-to-cell movement and for long-distance spread within infected plants via the vasculature 118 Tobacco mosaic virus movement protein can direct movement of cucumber mosaic virus in infected plants 119 Mutation, recombination, reassortment, and genetic bottlenecks are involved in the evolution of cucumber mosaic virus 120 Host responses to cucumovirus infections reflect both a battle and adaptation between viruses and hosts 120 Plants respond to virus infection by RNA silencing, and cucumber mosaic virus protein 2b suppresses silencing 121 Cucumber mosaic virus supports replication of defective and satellite RNAs 122 Satellite RNAs can either attenuate or increase severity of symptoms in infected plants 122 11 Picornaviruses 125 Picornaviruses cause a variety of human and animal diseases including poliomyelitis and the common cold 125 Poliovirus: a model picornavirus for vaccine development and studies of replication 126 TOC.indd x Picornavirus virions bind to cellular receptors via depressions or loop regions on their surface 127 Genome RNA may pass through pores formed in cell membranes by capsid proteins 128 Translation initiates on picornavirus RNAs by a novel internal ribosome entry mechanism 128 Essential features of picornavirus IRES elements 130 Interaction of picornavirus IRES elements with host cell proteins 131 Picornavirus proteins are made as a single precursor polyprotein that is autocatalytically cleaved by viral proteinases 131 Picornaviruses make a variety of proteinases that cleave the polyprotein and some cellular proteins 131 Replication of picornavirus RNAs is initiated in a multiprotein complex bound to proliferated cellular vesicles 131 RNA synthesis is primed by VPg covalently bound to uridine residues 133 Virion assembly involves cleavage of VP0 to VP2 plus VP4 133 Inhibition of host cell macromolecular functions 134 12 Flaviviruses 137 Flaviviruses cause several important human diseases 137 Yellow fever is a devastating human disease transmitted by mosquitoes 138 A live, attenuated yellow fever virus vaccine is available and widely used 139 Hepatitis C virus: a recently discovered member of the Flaviviridae 139 The flavivirus virion contains a lipid bilayer and envelope proteins arranged with icosahedral symmetry 139 Flavivirus E protein directs both binding to receptors and membrane fusion 140 Flaviviruses enter the cell by pH-dependent fusion 141 Flavivirus genome organization resembles that of picornaviruses 141 The polyprotein is processed by both viral and cellular proteinases 142 Nonstructural proteins organize protein processing, viral RNA replication, and capping 144 Flavivirus RNA synthesis is carried out on membranes in the cytoplasm 144 Virus assembly also takes place at intracellular membranes 145 13 Togaviruses 148 Most togaviruses are arthropod borne, transmitted between vertebrate hosts by mosquitoes 148 Togavirus virions contain a nucleocapsid with icosahedral symmetry wrapped in an envelope of the same symmetry 149 Togaviruses enter cells by low pH-induced fusion inside endosome vesicles 150 13/05/11 2:11 PM ... subject of intense research interest 313 13 /05 /11 2 :11 PM Contents Linear vaccinia virus genomes have covalently sealed hairpin ends and lack introns 314 Two forms of vaccinia virions have different... “stuttering” transcription 216 Two influenza A mRNAs undergo alternative splicing in the nucleus 216 Genome replication begins when newly synthesized NP protein enters the nucleus 217 Nucleocapsids... proteins catalyze synthesis of full-length antigenome RNA 15 1 Replication and transcription: synthesis of genome and subgenomic RNAs 15 3 Structural proteins are cleaved during translation and directed