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Brief Contents Preface to Second Edition xix Preface to First Edition xxi Abbreviations Used in This Book xxiii Greek Letters Used in This Book xxvii Color Coding for Molecules xxix Chapter 1 Viruses and Their Importance 1 Chapter 2 Methods Used in Virology 9 Chapter 3 Virus Structure 27 Chapter 4 Virus Transmission 45 Chapter 5 Attachment and Entry of Viruses into Cells 55 Chapter 6 Transcription, Translation, and Transport 65 Chapter 7 Virus Genome Replication 83 Chapter 8 Assembly and Exit of Virions from Cells 93 Chapter 9 Outcomes of Infection for the Host 101 Chapter 10 Classifi cation and Nomenclature of Viruses 115 Chapter 11 Herpesviruses (and Other dsDNA Viruses) 121 Chapter 12 Parvoviruses (and Other ssDNA Viruses) 135 Chapter 13 Reoviruses (and Other dsRNA Viruses) 145 Chapter 14 Picornaviruses (and Other Plus-Strand RNA Viruses) 155 Chapter 15 RhabdovirusesCOPYRIGHTED (and Other Minus-Strand RNA Viruses) MATERIAL 169 Chapter 16 Infl uenza Virus 183 Chapter 17 Retroviruses 195 Chapter 18 Human Immunodefi ciency Viruses 207 Chapter 19 Hepadnaviruses (and Other Reverse-Transcribing DNA Viruses) 223 Chapter 20 Bacterial Viruses 237 Chapter 21 Origins and Evolution of Viruses 263 Chapter 22 Emerging Viruses 277 vii fftoc.inddtoc.indd vviiii 118/01/138/01/13 55:26:26 PPMM viii BRIEF CONTENTS Chapter 23 Viruses and Cancer 289 Chapter 24 Survival of Infectivity 301 Chapter 25 Virus Vaccines 307 Chapter 26 Anti-viral Drugs 315 Chapter 27 Prions 327 Virologists’ Vocabulary 335 Index 347 fftoc.inddtoc.indd vviiiiii 118/01/138/01/13 55:26:26 PPMM Contents Preface to Second Edition xix Preface to First Edition xxi Abbreviations Used in This Book xxiii Greek Letters Used in This Book xxvii Color Coding for Molecules xxix Chapter 1 Viruses and Their Importance 1 1.1 Viruses Are Ubiquitous on Earth 2 1.2 Reasons for Studying Viruses 3 1.2.1 Some viruses cause disease 3 1.2.2 Some viruses are useful 3 1.2.3 Virus studies have contributed to knowledge 4 1.3 The Nature of Viruses 4 1.3.1 Viruses are small particles 4 1.3.2 Viruses have genes 5 1.3.3 Viruses are parasites 6 1.3.4 Some viruses are dependent on other viruses 6 1.3.5 Are viruses living or nonliving? 6 1.4 The Remainder of the Book 7 Chapter 2 Methods Used in Virology 9 2.1 Introduction to Methods Used in Virology 11 2.2 Cultivation of Viruses 11 2.2.1 Animal cell culture 11 2.3 Isolation of Viruses 12 2.4 Centrifugation 14 2.4.1 Differential centrifugation 14 2.4.2 Density gradient centrifugation 14 2.5 Structural Investigations of Cells and Virions 15 2.5.1 Light microscopy 15 2.5.2 Electron microscopy 15 2.5.3 X-ray crystallography 16 2.6 Electrophoretic Techniques 16 2.7 Detection of Viruses and Virus Components 16 2.7.1 Detection of virions 16 2.7.2 Detection of infectivity using cell cultures 16 2.7.3 Detection of virus antigens 18 2.7.4 Detection of virus nucleic acids 18 ix fftoc.inddtoc.indd iixx 118/01/138/01/13 55:26:26 PPMM x CONTENTS 2.8 Infectivity Assays 20 2.8.1 Quantitative assays 20 2.8.2 Quantal assays 21 2.8.3 One-step growth curve 22 2.9 Virus Genetics 23 2.9.1 Genome sequencing 23 2.9.2 Genome manipulation 24 2.9.3 Investigation of gene function and expression 24 2.10 Investigation of Protein–Protein Interactions 25 Chapter 3 Virus Structure 27 3.1 Introduction to Virus Structure 28 3.2 Virus Genomes 28 3.2.1 Genome size 28 3.2.2 Secondary and tertiary structure 28 3.2.3 Modifi cations at the ends of virus genomes 29 3.2.4 Proteins non-covalently associated with virus genomes 32 3.2.5 Segmented genomes 33 3.2.6 Repeat sequences 33 3.3 Virus Proteins 33 3.4 Capsids 35 3.4.1 Capsids with helical symmetry 35 3.4.2 Capsids with icosahedral symmetry 36 3.4.3 Conical and rod-shaped capsids 40 3.5 Virion Membranes 40 3.5.1 Enveloped virions 41 3.5.2 Virions with internal membranes 42 3.5.3 Membrane lipids 42 3.6 Occlusion Bodies 42 3.7 Other Virion Components 43 3.7.1 Virus RNA in DNA viruses 43 3.7.2 Cell molecules in virions 43 Chapter 4 Virus Transmission 45 4.1 Introduction to Virus Transmission 46 4.1.1 Transmission via vectors: general principles 46 4.2 Transmission of Plant Viruses 47 4.3 Transmission of Vertebrate Viruses 49 4.3.1 Non-vector transmission of vertebrate viruses 49 4.3.2 Vector transmission of vertebrate viruses 50 4.3.3 Virus survival in a new vertebrate host 51 4.4 Transmission of Invertebrate Viruses 51 4.5 Permissive Cells 52 Chapter 5 Attachment and Entry of Viruses into Cells 55 5.1 Overview of Virus Replication 56 5.2 Animal Viruses 57 fftoc.inddtoc.indd x 118/01/138/01/13 55:26:26 PPMM CONTENTS xi 5.2.1 Cell receptors and co-receptors 57 5.2.2 Virus attachment sites 58 5.2.3 Attachment of virions to receptors 58 5.2.4 Entry of animal viruses into cells 58 5.2.5 Intracellular transport 60 5.2.6 Genome uncoating 63 5.3 Bacteriophages 63 Chapter 6 Transcription, Translation, and Transport 65 6.1 Introduction to Transcription, Translation, and Transport 66 6.2 Transcription of Virus Genomes 66 6.2.1 Modifi cations to the central dogma 68 6.3 Transcription in Eukaryotes 68 6.3.1 Promoters and enhancers 68 6.3.2 Transcription factors 70 6.3.3 Transcriptases 70 6.3.4 Capping transcripts 71 6.3.5 Polyadenylation of transcripts 72 6.3.6 Splicing transcripts 73 6.4 Translation in Eukaryotes 73 6.4.1 Initiation of translation 73 6.4.2 Translation from bicistronic mRNAs 75 6.4.3 Co- and post-translational modifi cation of proteins 77 6.5 Transport of Molecules in Eukaryotic Cells 77 6.6 Transcription and Translation in Bacteria 80 Chapter 7 Virus Genome Replication 83 7.1 Overview of Virus Genome Replication 84 7.2 Locations of Virus Genome Replication in Eukaryotic Cells 86 7.3 Initiation of Genome Replication 86 7.3.1 RNA and protein primers 86 7.4 Polymerases 88 7.5 DNA Replication 88 7.6 Double-Stranded RNA Replication 90 7.7 Single-Stranded RNA Replication 90 7.8 Reverse Transcription 91 Chapter 8 Assembly and Exit of Virions from Cells 93 8.1 Introduction to Assembly and Exit of Virions from Cells 94 8.2 Nucleocapsid Assembly 95 8.2.1 Helical viruses 95 8.2.2 Icosahedral viruses 95 8.2.3 Genome packaging 96 8.2.4 Assembly mechanisms 96 fftoc.inddtoc.indd xxii 118/01/138/01/13 55:26:26 PPMM xii CONTENTS 8.3 Formation of Virion Membranes 96 8.3.1 Budding through cell membranes 96 8.3.2 De novo synthesis of viral membranes 98 8.4 Virion Exit From the Infected Cell 99 Chapter 9 Outcomes of Infection for the Host 101 9.1 Introduction to Outcomes of Infection for the Host 103 9.2 Factors Affecting Outcomes of Infection 103 9.2.1 Innate immunity in vertebrates 103 9.2.2 Adaptive immunity in vertebrates 105 9.2.3 RNA silencing 108 9.2.4 Programmed cell death 108 9.3 Non-Productive Infections 109 9.3.1 Latent infections 109 9.3.2 Abortive infections 110 9.4 Productive Infections 110 9.4.1 Spread of infections within multicellular hosts 110 9.4.2 Disease 111 Chapter 10 Classifi cation and Nomenclature of Viruses 115 10.1 History of Virus Classifi cation and Nomenclature 116 10.1.1 International Committee on Taxonomy of Viruses 116 10.2 Modern Virus Classifi cation and Nomenclature 116 10.2.1 Classifi cation based on genome sequences 117 10.2.2 Nomenclature of viruses and taxonomic groups 117 10.3 Baltimore Classifi cation of Viruses 119 Chapter 11 Herpesviruses (and Other dsDNA Viruses) 121 11.1 Introduction to Herpesviruses 122 11.2 The Human Herpesviruses 122 11.2.1 Herpes simplex viruses 1 and 2 122 11.2.2 Varicella-zoster virus 122 11.2.3 Epstein–Barr virus 122 11.2.4 Human cytomegalovirus 123 11.2.5 Human herpesvirus 6 123 11.2.6 Human herpesvirus 7 123 11.2.7 Kaposi’s sarcoma-associated herpesvirus 123 11.3 The Herpesvirus Virion 123 11.4 HSV-1 Genome Organization 125 11.5 HSV-1 Replication 125 11.5.1 Attachment and entry 125 11.5.2 Transcription and translation 126 11.5.3 Genome replication 126 11.5.4 Assembly and exit of virions from the cell 128 11.5.5 Overview of HSV-1 replication 129 11.6 Latent Herpesvirus Infection 129 11.7 Other dsDNA Viruses 132 fftoc.inddtoc.indd xxiiii 118/01/138/01/13 55:26:26 PPMM CONTENTS xiii Chapter 12 Parvoviruses (and Other ssDNA Viruses) 135 12.1 Introduction to Parvoviruses 136 12.2 Examples of Parvoviruses 136 12.2.1 Dependoviruses 136 12.2.2 Autonomous parvoviruses 137 12.3 Parvovirus Virion 137 12.3.1 Capsid 137 12.3.2 Genome 138 12.4 Parvovirus Replication 138 12.4.1 Attachment and entry 138 12.4.2 Single-stranded DNA to double-stranded DNA 139 12.4.3 Transcription and translation 139 12.4.4 DNA replication and virion assembly 140 12.4.5 Overview of parvovirus replication 140 12.4.6 Dependovirus replication 140 12.5 Other ssDNA Viruses 141 Chapter 13 Reoviruses (and Other dsRNA Viruses) 145 13.1 Introduction to Reoviruses 146 13.2 Rotavirus Virion 146 13.3 Rotavirus Replication 147 13.3.1 Attachment and entry 147 13.3.2 Early events 148 13.3.3 Late events 151 13.3.4 Overview of rotavirus replication 152 13.3.5 Rotavirus disease 152 13.4 Other dsRNA Viruses 153 Chapter 14 Picornaviruses (and Other Plus-Strand RNA Viruses) 155 14.1 Introduction to Picornaviruses 156 14.2 Some Important Picornaviruses 156 14.2.1 Hepatitis A virus 156 14.2.2 Poliovirus 156 14.2.3 Coxsackieviruses 156 14.2.4 Rhinoviruses 157 14.2.5 Foot and mouth disease virus 157 14.3 Picornavirus Virion 157 14.3.1 Capsid 158 14.3.2 Genome 159 14.4 Picornavirus Replication 160 14.4.1 Attachment 160 14.4.2 Entry 160 14.4.3 Translation and post-translational modifi cations 161 14.4.4 Transcription/genome replication 161 14.4.5 Assembly and exit 164 14.4.6 Inhibition of host gene expression 164 14.4.7 Overview of picornavirus