Jane Flint - Principles of Virology

RNA from RNA Templates Introduction The Nature of the RNA Template The RNA Synthesis Machinery Mechanisms of RNA Synthesis Paradigms for Viral RNA Synthesis Origins of Diversity in RNA Virus Genomes Perspectives References 7 Synthesis of RNA from DNA Templates Introduction Transcription by RNA Polymerase II Transcription of Viral DNA Templates by the Cellular Machinery Alone Viral Proteins That Govern Transcription of DNA Templates Transcription of Viral Genes by RNA Polymerase III Inhibition of the Cellular Transcriptional Machinery Unusual Functions of Cellular Transcription Components in Virus-Infected Cells Viral DNA-Dependent RNA Polymerases Perspectives References 8 Processing Introduction Covalent Modification during Viral Pre-mRNA Processing Export of RNAs from the Nucleus Posttranscriptional Regulation of Viral or Cellular Gene Expression by Viral Proteins Regulation of Turnover of Viral and Cellular mRNAs in the Cytoplasm Noncoding RNAs Perspectives References 9 Replication of DNA Genomes Introduction DNA Synthesis by the Cellular Replication Machinery Mechanisms of Viral DNA Synthesis Exponential Accumulation of Viral Genomes Limited Replication of Viral DNA Genomes Origins of Genetic Diversity in DNA Viruses Perspectives References 10 Reverse Transcription and Integration Retroviral Reverse Transcription Retroviral DNA Integration Hepadnaviral Reverse Transcription Perspectives References 11 Protein Synthesis Introduction Mechanisms of Eukaryotic Protein Synthesis The Diversity of Viral Translation Strategies Regulation of Translation during Viral Infection Perspectives References 12 Intracellular Trafficking Introduction Assembly within the Nucleus Assembly at the Plasma Membrane Interactions with Internal Cellular Membranes Transport of Viral Genomes to Assembly Sites Perspectives References 13 Assembly, Release, and Maturation Introduction Methods of Studying Virus Assembly and Egress Assembly of Protein Shells Selective Packaging of the Viral Genome and Other Components of Virus Particles Acquisition of an Envelope Release of Virus Particles Maturation of Progeny Virus Particles Cell-to-Cell Spread Perspectives References 14 The Infected Cell Introduction Signal Transduction Gene Expression Metabolism Remodeling of Cellular Organelles Perspectives References APPENDIX: Structure, Genome Organization, and Infectious Cycles of Viruses Featured in This BookAdenoviruses Arenaviruses Coronaviruses Filoviruses Flaviviruses Hepadnaviruses Herpesviruses Orthomyxoviruses Paramyxoviruses Parvoviruses Picornaviruses Polyomaviruses Poxviruses Reoviruses Retroviruses Rhabdoviruses Togaviruses Glossary Index

3 Volume II Preface Acknowledgments About the Authors Key of Repetitive Elements 1 Infections of Populations: History and Epidemiology Introduction to Viral Pathogenesis A Brief History of Viral Pathogenesis Viral Epidemics in History Epidemiology Parameters That Govern the Ability of a Virus to Infect a Population Perspectives References 2 Barriers to Infection Introduction An Overview of Infection and Immunity Successful Infections Must Modulate or Bypass Host Defenses Viral Tropism Spread throughout the Host Organ Invasion Shedding of Virus Particles Perspectives References 3 The Early Host Response: Cell Autonomous and Innate Immunity Introduction The First Critical Moments: How Do Individual Cells Detect a Virus Infection? Cell-Intrinsic Defenses Secreted Mediators of the Innate Immune Response The Innate Immune Response Perspectives References 4 Adaptive Immunity and Establishment of Memory Introduction Attributes of the Host Response Lymphocyte Development, Diversity, and Activation Events at the Site of Infection Set the Stage for the Adaptive Response Antigen Processing and Presentation The CTL (Cell-Mediated) Response The Humoral (Antibody) Response Immunological Memory Perspectives References 5 Patterns and Pathogenesis Introduction Animal Models of Human Diseases Patterns of Infection Viral Virulence Pathogenesis Perspectives References 6 Cellular Transformation and Oncogenesis Introduction Oncogenic Viruses Activation of Cellular Signal Transduction Pathways by Viral Transforming Proteins Disruption of Cell Cycle Control Pathways by Viral Transforming Proteins Transformed Cells Increase in Size and Survive Tumorigenesis Requires Additional Changes in the Properties of Transformed Cells Other Mechanisms of Transformation and Oncogenesis by Human Tumor Viruses Perspectives References 7 Vaccines Introduction The Origins of Vaccination Vaccine Basics The Science and Art of Making Vaccines Vaccine Technology: Delivery and Improving Antigenicity The Ongoing Quest for an AIDS Vaccine Perspectives References 8 Antiviral Drugs Introduction Discovering Antiviral Compounds Drug Resistance Examples of Antiviral Drugs Expanding Targets for Antiviral Drug Development Two Stories of Antiviral Success Perspectives References 9 Therapeutic Viruses Introduction Phage Therapy Oncolytic Animal Viruses Gene Therapy Vaccine Vectors Perspectives References 10 Virus Evolution Virus Evolution How Do Virus Populations Evolve? The Origin of Viruses Host-Virus Relationships Drive Evolution Lessons from Paleovirology Perspectives References 11 Emergence The Spectrum of Host-Virus Interactions Encountering New Hosts: Humans Constantly Provide New Venues for Infection Common Sources for Animal-to-Human Transmission Viral Diseases That Illustrate the Drivers of Emergence The Contribution to Emergence of Mutation, Recombination, or Reassortment New Technologies Uncover Previously Unrecognized Viruses Perceptions and Possibilities Perspectives References 12 Human Immunodeficiency Virus Type I Pathogenesis Introduction HIV-1 Is a Lentivirus Entry and Transmission The Course of Infection Virus Reproduction Immune Responses to HIV-1 HIV-1 and Cancer Prospects for Treatment and Prevention Perspectives References 13 Unusual Infectious Agents Introduction Viroids Satellite Viruses and RNAs Prions and Transmissible Spongiform Encephalopathies Perspectives References APPENDIX: Epidemiology and Pathogenesis of Selected Human Viruses Adenoviruses Arenaviruses Bunyaviruses Caliciviruses Coronaviruses Filoviruses Flaviviruses Flaviviruses Flaviviruses Hepadnaviruses Herpesviruses Herpesviruses Herpesviruses Orthomyxoviruses Papillomaviruses Paramyxoviruses Paramyxoviruses Picornaviruses Picornaviruses Picornaviruses Polyomaviruses Poxviruses Reoviruses Reoviruses Retroviruses Retroviruses Rhabdoviruses Togaviruses Togaviruses Glossary Index

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1 Chapter 2 Table 2.1 Particle-to-PFU ratios of some animal viruses

2 Chapter 3 Table 3.1 Some viral vectors

3 Chapter 4 Table 4.1 Functions of virion proteins Table 4.2 Nomenclature used in description of virus structure Table 4.3 Some virion enzymes

4 Chapter 7 Table 7.1 Strategies of transcription of viral DNA templates Table 7.2 Eukaryotic RNA polymerases synthesize different classes of cellular an... Table 7.3 Properties and functions of some viral transcriptional regulatorsTable 7.4 Viral RNA polymerase III transcription units

5 Chapter 9Table 9.1 Viral origin recognition proteinsTable 9.2 Replication systems of large DNA virusesTable 9.3 Viral enzymes of nucleic acid metabolism

6 Chapter 10Table 10.1 Comparison of retroviral integration site preferences in human cellsTable 10.2 Comparison of retroviral and hepadnaviral reverse transcription

7 Chapter 12Table 12.1 Some viral envelope glycoprotein precursors processed by secretory pa...

8 Chapter 13Table 13.1 Common sequence motifs required for budding of enveloped virus partic...

9 Chapter 17Table 3.1 Some viral modulators of the interferon responseTable 3.2 Some chemokine receptors and their ligands

10 Chapter 19Table 5.1 Incubation periods of some common virusesTable 5.2 Some persistent viral infections of humansTable 5.3 Epstein-Barr latency programs

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