VIROLOGY PRINCIPLES AND APPLICATIONS WILEY. John B. Carter and Venetia A. Saunders

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1 VIROLOGY PRINCIPLES AND APPLICATIONS John B. Carter and Venetia A. Saunders WILEY

2 -urief 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 Chapter 2 Chapter 3 Chapter 4 Chapter 5 Chapter 6 Chapter 7 Chapter 8 Chapter 9 Chapter 10 Chapter 11 Chapter 12 Chapter 13 Chapter 14 Chapter 15 Chapter 16 Chapter 17 Chapter 18 Chapter 19 Chapter 20 Chapter 21 Chapter 22 Viruses and Their Importance Methods Used in Virology 9 Virus Structure 27 Virus Transmission 45 Attachment and Entry of Viruses into Cells 55 Transcription, Translation, and Transport 65 Virus Genome Replication 83 Assembly and Exit of Virions from Cells 93 Outcomes of Infection for the Host 101 Classification and Nomenclature of Viruses 115 Herpesviruses (and Other dsdna Viruses) 121 Parvoviruses (and Other ssdna Viruses) 135 Reoviruses (and Other dsrna Viruses) 145 Picornaviruses (and Other Plus-Strand RNA Viruses) 155 Rhabdoviruses (and Other Minus-Strand RNA Viruses) 169 Influenza Virus 183 Retroviruses 195 Human Immunodeficiency Viruses 207 Hepadnaviruses (and Other Reverse-Transcribing DNA Viruses) 223 Bacterial Viruses 237 Origins and Evolution of Viruses 263 Emerging Viruses 277 vii

3 Cha Chi Viii BRIEF CONTENTS Chapter 23 Chapter 24 Viruses and Cancer Survival of Infectivity Chapter 25 Chapter 26 Virus Vaccines Anti-viral Drugs Chapter 27 Prions 327 Virologists' Vocabulary 335 Index 347 Pref Pref Ab~ Gre Col

4 ~wcontents 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 Viruses Are Ubiquitous on Earth Reasons for Studying Viruses Some viruses cause disease Some viruses are useful Virus studies have contributed to knowledge The Nature of Viruses Viruses are small particles Viruses have genes Viruses are parasites Some viruses are dependent on other viruses Are viruses living or nonliving? The Remainder of the Book 7 Chapter 2 Methods Used in Virology Introduction to Methods Used in Virology Cultivation of Viruses Animal cell culture Isolation of Viruses Centrifugation Differential centrifugation Density gradient centrifugation Structural Investigations of Celts and Virions Light microscopy Electron microscopy X-ray crystallography Electrophoretic Techniques Detection of Viruses and Virus Components Detection of virions Detection of infectivity using cell cultures Detection of virus antigens Detection of virus nucleic acids 18 ix

5 X CONTENTS 2.8 Infectivity Assays Quantitative assays Ouantal assays One-step growth curve Virus Genetics Genome sequencing Genome manipulation Investigation of gene function and expression Investigation of Protein-Protein Interactions 25 Chi Chapter 3 Virus Structure Introduction to Virus Structure Virus Genomes Genome size Secondary and tertiary structure Modifications at the ends of virus genomes Proteins non-covalently associated with virus genomes Segmented genomes Repeat sequences Virus Proteins Capsids Capsids with helical symmetry Capsids with icosahedral symmetry Conical and rod-shaped capsids Virion Membranes Enveloped virions 41 Virions with internal membranes 42 Membrane lipids Occlusion Bodies Other Virion Components Virus RNA in DNA viruses Cell molecules in virions 43 Cl Chapter 4 Virus Transmission Introduction to Virus Transmission Transmission via vectors: general principles Transmission of Plant Vi ruses Transmission of Vertebrate Viruses Non-vector transmission of vertebrate viruses Vector transmission of vertebrate viruses Virus survival in a new vertebrate host Transmission of Invertebrate Viruses Permissive Cells 52 c Chapter 5 Attachment and Entry of Viruses into Cells Overview of Virus Replication Animal Viruses 57

6 p CONTENTS Xi Cell receptors and co-receptors Virus attachment sites Attachment of virions to receptors Entry of animal viruses into cells Intracellular transport Genome uncoating Bacteriophages 63 Chapter 6 Transcription, Translation, and Transport Introduction to Transcription, Translation, and Transport Transcription of Virus Genomes Modifications to the central dogma Transcription in Eukaryotes Promoters and enhancers Transcription factors Transcriptases Capping transcripts Polyadenylation of transcripts Splicing transcripts Translation in Eukaryotes Initiation of translation Translation from bicistronic mrnas Co- and post-translational modification of proteins Transport of Molecules in Eukaryotic Cells Transcription and Translation in Bacteria 80 Chapter 7 Virus Genome Replication Overview of Virus Genome Replication Locations of Virus Genome Replication in Eukaryotic Cells Initiation of Genome Replication RNA and protein primers Poly me rases DNA Replication Double-Stranded RNA Replication Single-Stranded RNA Replication Reverse Transcription 91 Chapter 8 Assembly and Exit of Virions from Cells Introduction to Assembly and Exit of Virions from Cells Nucleocapsid Assembly Helical viruses Icosahedral viruses Genome packaging Assembly mechanisms 96

7 Xii CONTENTS 8.3 Formation of Virion Membranes Budding through cell membranes De novo synthesis of viral membranes Virion Exit From the Infected Cell 99 -Chapte Chapter 9 Outcomes of Infection for the Host Introduction to Outcomes of Infection for the Host Factors Affecting Outcomes of Infection Innate immunity in vertebrates Adaptive immunity in vertebrates RNA silencing Programmed cell death Non-Productive Infections Latent infections Abortive infections Productive Infections Spread of infections within multicellular hosts Disease 111 Chapt Chapter 10 Classification and Nomenclature of Viruses History of Virus Classification and Nomenclature International Committee on Taxonomy of Viruses Modern Virus Classification and Nomenclature Classification based on genome sequences Nomenclature of viruses and taxonomic groups Baltimore Classification of Viruses 119 Chapter 11 Herpesviruses (and Other dsdna Viruses) Introduction to Herpesviruses The Human Herpesviruses Herpes simplex viruses 1 and Varicella-zoster virus Epstein-Barr virus Human cytomegalovirus Human herpesvirus Human herpesvirus Kaposi's sarcoma-associated herpesvirus The Herpesvirus Virion HSV-1 Genome Organization HSV-1 Replication Attachment and entry Transcription and translation Genome replication Assembly and exit of virions from the cell Overview of HSV-1 replication Latent Herpesvirus Infection Other dsdna Viruses 132 Chap

8 CONTENTS Xiii Chapter 12 Chapter 13 Parvoviruses (and Other ssdna Viruses) Introduction to Parvoviruses Examples of Parvoviruses Dependoviruses Autonomous parvoviruses Parvovirus Virion Capsid Genome Parvovirus Replication Attachment and entry Single-stranded DNA to double-stranded DNA Transcription and translation DNA replication and virion assembly Overview of parvovirus replication Dependovirus replication Other ssdna Viruses 141 Reoviruses (and Other dsrna Viruses) Introduction to Reoviruses Rotavirus Virion Rotavirus Replication Attachment and entry Early events Late events Overview of rotavirus replication Rotavirus disease Other dsrna Viruses 153 Chapter 14 Picornaviruses (and Other Plus-Strand RNA Viruses) Introduction to Picornaviruses Some Important Picornaviruses Hepatitis A virus Poliovirus Coxsackieviruses Rhinoviruses Foot and mouth disease virus Picornavirus Virion Capsid Genome Picornavirus Replication Attachment Entry Translation and post-translational modifications Transcription/ genome replication Assembly and exit Inhibition of host gene expression Overview of picornavirus replication 164

9 XiV CONTENTS 14.5 Picornavirus Recombination Picornavirus Experimental Systems Reverse genetics Cell-free synthesis of infectious virus Other Plus-Strand RNA Viruses 167 Chapter 15 Rhabdoviruses (and Other Minus-Strand RNA Viruses) Introduction to Rhabdoviruses Some Important Rhabdoviruses Rabies virus Vesicular stomatitis virus The Rhabdovirus Virion and Genome Organization Rhabdovirus Replication Attachment and entry Transcription Translation Genome replication and secondary transcription Assembly of virions and exit from the cell Inhibition of host gene expression Role of the nucleus Overview of rhabdovirus replication Other Minus-Strand RNA Viruses and Viruses with Ambisense Genomes Reverse Genetics 180 Chi Chapter 16 Influenza Virus Introduction to Influenza Viruses The Influenza Virion Influenza A Virus Replication Attachment and entry RNA replication Translation and transport of proteins Virion assembly and release Overview of influenza virus replication Importance of Influenza Viruses Reverse Genetics 192 Chapter 17 Retroviruses Introduction to Retroviruses Retrovirus Virion Retrovirus Replication Attachment and entry Reverse transcription Integration of the provirus Transcription and genome replication Translation and post-translational modifications 201

10 CONTENTS XV Assembly and release of virions Overview of retrovirus replication Examples of Retroviruses Retroviruses as Gene Vectors Endogenous Retroviruses 205 Chapter 18 Chapter 19 Human Immunodeficiency Viruses Introduction to HIV HIV Virion HIV Genome HIV-1 Replication Attachment and entry Reverse transcription and transport to the nucleus Early gene expression Late gene expression Assembly and exit of virions Overview of HIV-1 replication HIV-1 Variability Antigens Host cell range Resistance to drugs Progression of HIV Infection Prevention of HIV Transmission 220 Hepadnaviruses (and Other Reverse-Transcribing DNA Viruses) Introduction to Hepadnaviruses Importance of HBV HBV Virion DNA P (polymerase) protein Capsid Envelope Non-Infectious Particles Soluble Virus Protein HBV Genome HBV Genetic Groups HBV Replication Attachment Entry Transcription Translation Nucleocapsid assembly Genome synthesis Envelope acquisition and exit Overview of HBV replication cycle Prevention and Treatment of HBV Infection Other Reverse-Transcribing DNA Viruses 236

11 XVi CONTENTS Chapter 20 Bacterial Viruses Introduction to Bacterial Viruses (Bacteriophages) Single-Stranded RNA Phages Virion structure of ssrna phages Genome of ssrna phages Replication cycle of ssrna phages Double-Stranded RNA Phages Single-Stranded DNA Phages Icosahedral ssdna phages Filamentous ssdna phages Double-Stranded DNA Phages Phage T Phage T Phage lambda (A.) 257 Chap Chapter 21 Origins and Evolution of Viruses Introduction to Origins and Evolution of Viruses Origins of Viruses Molecular precursors of cellular organisms Components of cells Intracellular micro-organisms How did viruses originate? Evolution of Viruses Viruses from the past Monitoring virus evolution Mechanisms of virus evolution Evolution of new viruses Co-evolution of viruses and their hosts 273 Chan Chapter 22 Emerging Viruses Introduction to Emerging Viruses Viruses in New Host Species Bunyaviruses Paramyxoviruses Viruses in New Areas West Nile virus Chikungunya virus Bluetongue virus Viruses in New Host Species and in New Areas Filoviruses Monkeypox virus New viruses SARS coronavirus Recently Discovered Viruses Human metapneumovirus 285 Chap

12 CONTENTS XVii 22.7 Re-Emerging Viruses Measles and mumps viruses Bioterrorism Virus Surveillance Dealing with Outbreaks 286 Chapter 23 Viruses and Cancer Introduction to Viruses and Cancer Papillomavirus-Linked Cancers Polyomavirus-Linked Cancers Epstein-Barr Virus-Linked Cancers Kaposi's Sarcoma Adult T Cell Leukemia Hepatocellular Carcinoma Virus-Associated Cancers in Animals Cell Lines Derived From Virus-Associated Cancers How Do Viruses Cause Cancer? "Deliberate" interference with control of cell activities "Accidental" activation of cell genes Retroviral oncogenes Damage to immune defenses Overview of cancer induction by viruses Prevention of Virus-Induced Cancers 299 Chapter 24 Survival of Infectivity Preservation of Virus Infectivity Destruction of Virus Infectivity Inactivation Targets in Virions Inactivation Kinetics Agents that Inactivate Virus Infectivity Physical agents Chemical agents 304 Chapter 25 Virus Vaccines Introduction to Virus Vaccines Live Attenuated Virus Vaccines Inactivated Virus Vaccines Virion Subunit Vaccines Live Recombinant Virus Vaccines Mass-Production of Viruses for Vaccines Virus-Like Particles Synthetic Peptide Vaccines DNA Vaccines Storage and Transport of Vaccines 313

13 ~ lr XViii CONTENTS Chapter 26 Chapter 27 Anti-viral Drugs Introduction to Anti-viral Drugs Development of Anti-viral Drugs Screening compounds for anti-viral activity Rational design of anti-viral drugs Safety of anti-viral drugs Examples of Anti-viral Drugs Nucleoside analogs Non-nucleoside inhibitors of reverse transcription HIV protease inhibitors HIV attachment and fusion inhibitors HIV integrase inhibitors Influenza virus neuraminidase inhibitors Drug Resistance Anti-viral Drug Research 324 Prions Introduction to Prions Transmissible Spongiform Encephalopathies The Nature of Prions Prion replication Prion Diseases Prion diseases in animals Prion diseases in humans Prion Strains Prion Transmission The Protein-Only Hypothesis 332 Virc 320 dev< I abo of e: new pub cry man thes con1 tion to i: rewi redl ard acid Virologists' Vocabulary 335 Index 347

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