Principles of Virology

Volume I
Cover
Title Page
Copyright Page
Table of Contents
Preface
Acknowledgments
About the Authors
Key of Repetitive Elements
PART I The Science of Virology
Chapter 1 Foundations
Luria’s Credo
Viruses Defined
Why We Study Viruses
Viruses Are Everywhere
Viruses Infect All Living Things
Viruses Can Cause Human Disease
Viruses Can Be Beneficial
Viruses “R” Us
Viruses Can Cross Species Boundaries
Viruses Are Unique Tools To Study Biology
Virus Prehistory
Viral Infections in Antiquity
The First Vaccines
Microorganisms as Pathogenic Agents
Discovery of Viruses
The Defining Properties of Viruses
The Structural Simplicity of Virus Particles
The Intracellular Parasitism of Viruses
Cataloging Animal Viruses
The Classical System
Classification by Genome Type: the Baltimore System
A Common Strategy for Viral Propagation
Perspectives
References
Study Questions
Chapter 2 The Infectious Cycle
Introduction
The Infectious Cycle
The Cell
Entering Cells
Viral RNA Synthesis
Viral Protein Synthesis
Viral Genome Replication
Assembly of Progeny Virus Particles
Viral Pathogenesis
Overcoming Host Defenses
Cultivation of Viruses
Cell Culture
Embryonated Eggs
Laboratory Animals
Assay of Viruses
Measurement of Infectious Units
Efficiency of Plating
Measurement of Virus Particles
Viral Reproduction: The Burst Concept
The One-Step Growth Cycle
One-Step Growth Analysis: a Valuable Tool for Studying Animal Viruses
Global Analysis
DNA Microarrays
Mass Spectrometry
Protein-Protein Interactions
Single-Cell Virology
Perspectives
References
Study Questions
PART II Molecular Biology
Chapter 3 Genomes and Genetics
Introduction
Genome Principles and the Baltimore System
Structure and Complexity of Viral Genomes
DNA Genomes
RNA Genomes
What Do Viral Genomes Look Like?
Coding Strategies
What Can Viral Sequences Tell Us?
The “Big and Small” of Viral Genomes: Does Size Matter?
The Origin of Viral Genomes
Genetic Analysis of Viruses
Classical Genetic Methods
Engineering Mutations into Viral Genomes
Engineering Viral Genomes: Viral Vectors
Perspectives
References
Study Questions
Chapter 4 Structure
Introduction
Functions of the Virion
Nomenclature
Methods for Studying Virus Structure
Building a Protective Coat
Helical Structures
Capsids with Icosahedral Symmetry
Other Capsid Architectures
Packaging the Nucleic Acid Genome
Direct Contact of the Genome with a Protein Shell
Packaging by Specialized Viral Proteins
Packaging by Cellular Proteins
Viruses with Envelopes
Viral Envelope Components
Simple Enveloped Viruses: Direct Contact of External Proteins with the Capsid or Nucleocapsid
Enveloped Viruses with an Additional Protein Layer
Large Viruses with Multiple Structure Elements
Particles with Helical or Icosahedral Parts
Alternative Architectures
Other Components of Virions
Enzymes
Other Viral Proteins
Cellular Macromolecules
Mechanical Properties of Virus Particles
Investigation of Mechanical Properties of Virus Particles
Stabilization and Destabilization of Virus Particles
Perspectives
References
Study Questions
Chapter 5 Attachment and Entry
Introduction
Attachment of Virus Particles to Cells
General Principles
Identification of Receptors for Virus Particles
Virus-Receptor Interactions
Entry into Cells
Virus-Induced Signaling via Cell Receptors
Routes of Entry
Membrane Fusion
Intracellular Trafficking and Uncoating
Movement of Viral and Subviral Particles within Cells
Uncoating of Enveloped Virus Particles
Uncoating of Nonenveloped Viruses
Import of Viral Genomes into the Nucleus
The Nuclear Pore Complex
Nuclear Localization Signals
Nuclear Import of RNA Genomes
Nuclear Import of DNA Genomes
Import of Retroviral Genomes
Perspectives
References
Study Questions
Chapter 6 Synthesis of RNA from RNA Templates
Introduction
The Nature of the RNA Template
Secondary Structures in Viral RNA
Naked or Nucleocapsid RNA
The RNA Synthesis Machinery
Identification of RNA-Dependent RNA Polymerases
Three-Dimensional Structures of RNA-Dependent RNA Polymerases
Mechanisms of RNA Synthesis
Initiation
Capping
Elongation
Functions of Additional Polymerase Domains
RNA Polymerase Oligomerization
Template Specificity
Unwinding the RNA Template
Role of Cellular Proteins
Paradigms for Viral RNA Synthesis
(+) Strand RNA
Synthesis of Nested Subgenomic mRNAs
(-) Strand RNA
Ambisense RNA
Double- Stranded RNA
Unique Mechanisms of mRNA and Genome Synthesis of Hepatitis Delta Virus
Do Ribosomes and RNA Polymerases Collide?
Origins of Diversity in RNA Virus Genomes
Misincorporation of Nucleotides
Segment Reassortment and RNA Recombination
RNA Editing
Perspectives
References
Study Questions
Chapter 7 Synthesis of RNA from DNA Templates
Introduction
Properties of Cellular RNA Polymerases That Transcribe Viral DNA
Some Viral Genomes Must Be Converted to Templates Suitable for Transcription
Transcription by RNA Polymerase II
Regulation of RNA Polymerase II Transcription
Common Properties of Proteins That Regulate Transcription
Transcription of Viral DNA Templates by the Cellular Machinery Alone
Viral Proteins That Govern Transcription of DNA Templates
Patterns of Regulation
The Human Immunodeficiency Virus Type 1 Tat Protein Autoregulates Transcription
The Transcriptional Cascades of DNA Viruses
Entry into One of Two Alternative Transcriptional Programs
Transcription of Viral Genes by RNA Polymerase III
The VA-RNA I Promoter
Inhibition of the Cellular Transcriptional Machinery
Unusual Functions of Cellular Transcription Components in Virus- Infected
Cells
Viral DNA-Dependent RNA Polymerases
Perspectives
References
Study Questions
Chapter 8 Processing
Introduction
Covalent Modification during Viral Pre-mRNA Processing
Capping the 5' Ends of Viral mRNA
Synthesis of 3' Poly(A) Segments of Viral mRNA
Internal Methylation of Adenosine Residues
Splicing of Viral Pre-mRNA
Regulated Processing of Viral Pre-mRNA
Editing of Viral mRNAs
Export of RNAs from the Nucleus
The Cellular Export Machinery
Export of Viral mRNA
Posttranscriptional Regulation of Viral or Cellular Gene Expression by Viral Proteins
Temporal Control of Viral Gene Expression
Viral Proteins Can Inhibit Cellular mRNA Production
Regulation of Turnover of Viral and Cellular mRNAs in the Cytoplasm
Intrinsic Turnover
Regulation of mRNA Stability by Viral Proteins
mRNA Stabilization Can Facilitate Transformation
Nonsense-Mediated mRNA Decay
Noncoding RNAs
Small Interfering RNAs and Micro-RNAs
Long Noncoding RNAs
Circular RNAs
Perspectives
References
Study Questions
Chapter 9 Replication of DNA Genomes
Introduction
DNA Synthesis by the Cellular Replication Machinery
Eukaryotic Replicons
Cellular Replication Proteins
Mechanisms of Viral DNA Synthesis
Lessons from Simian Virus 40
Replication of Other Viral DNA Genomes
Properties of Viral Replication Origins
Recognition of Viral Replication Origins
Viral DNA Synthesis Machines
Resolution and Processing of Viral Replication Products
Exponential Accumulation of Viral Genomes
Viral Proteins Can Induce Synthesis of Cellular Replication Proteins
Synthesis of Viral Replication Machines and Accessory Enzymes
Viral DNA Replication Independent of Cellular Proteins
Delayed Synthesis of Structural Proteins Prevents Premature Packaging of DNA Templates
Inhibition of Cellular DNA Synthesis
Synthesis of Viral DNA in Specialized Intracellular Compartments
Limited Replication of Viral DNA Genomes
Integrated Parvoviral DNA Can Be Replicated as Part of the Cellular Genome
Different Viral Origins Regulate Replication of Epstein-Barr Virus
Limited and Amplifying Replication from a Single Origin: the Papillomaviruses
Origins of Genetic Diversity in DNA Viruses
Fidelity of Replication by Viral DNA Polymerases
Modulation of the DNA Damage Response
Recombination of Viral Genomes
Perspectives
References
Study Questions
Chapter 10 Reverse Transcription and Integration
Retroviral Reverse Transcription
Discovery
Impact
The Process of Reverse Transcription
General Properties and Structure of Retroviral Reverse Transcriptases
Other Examples of Reverse Transcription
Retroviral DNA Integration
The Pathway of Integration: Integrase-Catalyzed Steps
Integrase Structure and Mechanism
Hepadnaviral Reverse Transcription
A DNA Virus with Reverse Transcriptase
The Process of Hepadnaviral Reverse Transcription
Perspectives
References
Study Questions
Chapter 11 Protein Synthesis
Introduction
Mechanisms of Eukaryotic Protein Synthesis
General Structure of Eukaryotic mRNA
The Translation Machinery
Initiation
Elongation and Termination
The Diversity of Viral Translation Strategies
Polyprotein Synthesis
Leaky Scanning
Reinitiation
StopGo Translation
Suppression of Termination
Ribosomal Frameshifting
Bicistronic mRNAs
Regulation of Translation during Viral Infection
Inhibition of Translation Initiation after Viral Infection
Regulation of eIF4F
Regulation of Poly(A)-Binding Protein Activity
Regulation of eIF3
Interfering with RNA
Stress-Associated RNA Granules
Perspectives
References
Study Questions
Chapter 12 Intracellular Trafficking
Introduction
Assembly within the Nucleus
Import of Viral Proteins for Assembly
Assembly at the Plasma Membrane
Transport of Viral Membrane Proteins to the Plasma Membrane
Sorting of Viral Proteins in Polarized Cells
Disruption of the Secretory Pathway in Virus-Infected Cells
Signal Sequence-Independent Transport of Viral Proteins to the Plasma Membrane
Interactions with Internal Cellular Membranes
Localization of Viral Proteins to Compartments of the Secretory Pathway
Localization of Viral Proteins to the Nuclear Membrane
Transport of Viral Genomes to Assembly Sites
Transport of Genomic and Pregenomic RNA from the Nucleus to the Cytoplasm
Transport of Genomes from the Cytoplasm to the Plasma Membrane
Perspectives
References
Study Questions
Chapter 13 Assembly, Release, and Maturation
Introduction
Methods of Studying Virus Assembly and Egress
Structural Studies of Virus Particles
Visualization of Assembly and Exit by Microscopy
Biochemical and Genetic Analyses of Assembly Intermediates
Methods Based on Recombinant DNA Technology
Assembly of Protein Shells
Formation of Structural Units
Capsid and Nucleocapsid Assembly
Self-Assembly and Assisted Assembly Reactions
Selective Packaging of the Viral Genome and Other Components of Virus Particles
Concerted or Sequential Assembly
Recognition and Packaging of the Nucleic Acid Genome
Incorporation of Enzymes and Other Nonstructural Proteins
Acquisition of an Envelope
Sequential Assembly of Internal Components and Budding from a Cellular Membrane
Coordination of the Assembly of Internal Structures with Acquisition of the Envelope
Release of Virus Particles
Assembly and Budding at the Plasma Membrane
Assembly at Internal Membranes: the Problem of Exocytosis
Release of Nonenveloped Virus Particles
Maturation of Progeny Virus Particles
Proteolytic Processing of Structural Proteins
Other Maturation Reactions
Cell-to-Cell Spread
Perspectives
References
Study Questions
Chapter 14 The Infected Cell
Introduction
Signal Transduction
Signaling Pathways
Signaling in Virus-Infected Cells
Gene Expression
Inhibition of Cellular Gene Expression
Differential Regulation of Cellular Gene Expression
Metabolism
Methods To Study Metabolism
Glucose Metabolism
The Citric Acid Cycle
Electron Transport and Oxidative Phosphorylation
Lipid Metabolism
Remodeling of Cellular Organelles
The Nucleus
The Cytoplasm
Perspectives
References
Study Questions
Appendix Structure, Genome Organization, and Infectious Cycles of Viruses Featured in This Book
Glossary
Index
Volume II
Cover
Title Page
Copyright Page
Table of Contents
Preface
Acknowledgments
About the Authors
Key of Repetitive Elements
Chapter 1 Infections of Populations: History and Epidemiology
Introduction to Viral Pathogenesis
A Brief History of Viral Pathogenesis
The Relationships among Microbes and the Diseases They Cause
The First Human Viruses Identified and the Role of Serendipity
New Methods Facilitate the Study of Viruses as Causes of Disease
Viral Epidemics in History
Epidemics Shaped History: the 1793 Yellow Fever Epidemic in Philadelphia
Tracking Epidemics by Sequencing: West Nile Virus Spread to the Western Hemisphere
Zoonotic Infections and Epidemics Caused by “New” Viruses
The Economic Toll of Viral Epidemics in Livestock
Population Density and World Travel Are Accelerators of Viral Transmission
Focus on Frontline Health Care: Ebolavirus in Africa
Emergence of a Birth Defect Associated with Infection: Zika Virus in Brazil
Epidemiology
Fundamental Concepts
Methods Used by Epidemiologists
Surveillance
Network Theory and Practical Applications
Parameters That Govern the Ability of a Virus to Infect a Population
Geography and Population Density
Climate
Perspectives
References
Study Questions
Chapter 2 Barriers to Infection
Introduction
An Overview of Infection and Immunity
A Game of Chess Played by Masters
Initiating an Infection
Successful Infections Must Modulate or Bypass Host Defenses
Skin
Respiratory Tract
Alimentary Tract
Eyes
Urogenital Tract
Placenta
Viral Tropism
Accessibility of Viral Receptors
Other Host-Virus Interactions That Regulate the Infectious Cycle
Spread throughout the Host
Hematogenous Spread
Neural Spread
Organ Invasion
Entry into Organs with Sinusoids
Entry into Organs That Lack Sinusoids
Organs with Dense Basement Membranes
Skin
Shedding of Virus Particles
Respiratory Secretions
Saliva
Feces
Blood
Urine
Semen
Milk
Skin Lesions
Tears
Perspectives
References
Study Questions
Chapter 3 The Early Host Response: Cell Autonomous and Innate Immunity
Introduction
The First Critical Moments: How Do Individual Cells Detect a Virus Infection?
Cell Signaling Induced by Viral Entry Receptor Engagement
Receptor-Mediated Recognition of Microbe-Associated Molecular Patterns
Cell- Intrinsic Defenses
Apoptosis (Programmed Cell Death)
Programmed Necrosis (Necroptosis)
Autophagy
Epigenetic Silencing
Host Proteins That Restrict Virus Reproduction (Restriction Factors)
RNA Interference
CRISPR
The Continuum between Intrinsic and Innate Immunity
Secreted Mediators of the Innate Immune Response
Overview of Cytokine Functions
Interferons, Cytokines of Early Warning and Action
Chemokines
The Innate Immune Response
Monocytes, Macrophages, and Dendritic Cells
Complement
Natural Killer Cells
Other Innate Immune Cells Relevant to Viral Infections
Perspectives
References
Study Questions
Chapter 4 Adaptive Immunity and Establishment of Memory
Introduction
Attributes of the Host Response
Speed
Diversity and Specificity
Memory
Self- Control
Lymphocyte Development, Diversity, and Activation
The Hematopoietic Stem Cell Lineage
The Two Arms of Adaptive Immunity
The Major Effectors of the Adaptive Response: B and T Cells
Diverse Receptors Impart Antigen Specificity to B and T Cells
Events at the Site of Infection Set the Stage for the Adaptive Response
Acquisition of Viral Proteins by Professional Antigen-Presenting Cells Enables Production of Proinflammatory Cytokines and Establishment of Inflammation
Activated Antigen-Presenting Cells Leave the Site of Infection and Migrate to Lymph Nodes
Antigen Pro cessing and Presentation
Professional Antigen-Presenting Cells Induce Activation via Costimulation
Presentation of Antigens by Class I and Class II MHC Proteins
Lymphocyte Activation Triggers Massive Cell Proliferation
The CTL (Cell-Mediated) Response
CTLs Lyse Virus-Infected Cells
Control of CTL Proliferation
Control of Infection by CTLs without Killing
Rashes and Poxes
The Humoral (Antibody) Response
Antibodies Are Made by Plasma Cells
Types and Functions of Antibodies
Virus Neutralization by Antibodies
Antibody-Dependent Cell-Mediated Cytotoxicity: Specific Killing by Nonspecific Cells
Immunological Memory
Perspectives
References
Study Question Puzzle
Chapter 5 Patterns and Pathogenesis
Introduction
Animal Models of Human Diseases
Patterns of Infection
Incubation Periods
Mathematics of Growth Correlate with Patterns of Infection
Acute Infections
Persistent Infections
Latent Infections
Abortive Infections
Transforming Infections
Viral Virulence
Measuring Viral Virulence
Approaches To Identify Viral Genes That Contribute to Virulence
Viral Virulence Genes
Pathogenesis
Infected Cell Lysis
Immunopathology
Immunosuppression Induced by Viral Infection
Oncogenesis
Molecular Mimicry
Perspectives
References
Study Question Puzzle
Chapter 6 Cellular Transformation and Oncogenesis
Introduction
Properties of Transformed Cells
Control of Cell Proliferation
Oncogenic Viruses
Discovery of Oncogenic Viruses
Viral Genetic Information in Transformed Cells
The Origin and Nature of Viral Transforming Genes
Functions of Viral Transforming Proteins
Activation of Cellular Signal Transduction Pathways by Viral Transforming Proteins
Viral Signaling Molecules Acquired from the Cell
Alteration of the Production or Activity of Cellular Signal Transduction Proteins
Disruption of Cell Cycle Control Pathways by Viral Transforming Proteins
Abrogation of Restriction Point Control Exerted by the RB Protein
Production of Virus-Specific Cyclins
Inactivation of Cyclin-Dependent Kinase Inhibitors
Transformed Cells Increase in Size and Survive
Mechanisms That Permit Survival of Transformed Cells
Tumorigenesis Requires Additional Changes in the Properties of Transformed Cells
Inhibition of Immune Defenses
Other Mechanisms of Transformation and Oncogenesis by Human Tumor Viruses
Nontransducing Oncogenic Retroviruses: Tumorigenesis with Very Long Latency
Oncogenesis by Hepatitis Viruses
Perspectives
References
Study Questions
Chapter 7 Vaccines
Introduction
The Origins of Vaccination
Smallpox: a Historical Perspective
Worldwide Vaccination Programs Can Be Dramatically Effective
Vaccine Basics
Immunization Can Be Active or Passive
Active Vaccination Strategies Stimulate Immune Memory
The Fundamental Challenge
The Science and Art of Making Vaccines
Inactivated Virus Vaccines
Attenuated Virus Vaccines
Subunit Vaccines
Virus- Like Particles
Nucleic Acid Vaccines
Vaccine Technology: Delivery and Improving Antigenicity
Adjuvants Stimulate an Immune Response
Delivery and Formulation
Immunotherapy
The Ongoing Quest for an AIDS Vaccine
Perspectives
References
Study Question Puzzle
Chapter 8 Antiviral Drugs
Introduction
A Brief History of Antiviral Drug Discovery
Discovering Antiviral Compounds
The Lexicon of Antiviral Discovery
Screening for Antiviral Compounds
Computational Approaches to Drug Discovery
The Difference between “R” and “D”
Drug Resistance
Examples of Antiviral Drugs
Inhibitors of Virus Attachment and Entry
Inhibitors of Viral Nucleic Acid Synthesis
Inhibition of Viral Polyprotein Processing and Assembly
Inhibition of Virus Particle Release
Expanding Targets for Antiviral Drug Development
Attachment and Entry Inhibitors
Nucleic Acid-Based Approaches
Proteases and Nucleic Acid Synthesis and Processing Enzymes
Virus Particle Assembly
Microbicides
Two Stories of Antiviral Success
Combination Therapy
Challenges Remaining
Perspectives
References
Study Questions
Chapter 9 Therapeutic Viruses
Introduction
Phage Therapy
History
Some Advantages and Limitations of Phage Therapy
Applications in the Clinic and for Disease Prevention
Future Prospects
Oncolytic Animal Viruses
From Anecdotal Reports to Controlled Clinical Trials
Rational Design of Oncolytic Viruses
Two Clinically Approved Oncolytic Viruses
Future Directions
Gene Therapy
Introduction
Retroviral Vectors
Adenovirus-Associated Virus Vectors
Future Prospects
Vaccine Vectors
DNA Viruses
RNA Viruses
Perspectives
References
Study Questions
Chapter 10 Virus Evolution
Virus Evolution
How Do Virus Populations Evolve?
Two General Virus Survival Strategies Can Be Distinguished
Large Numbers of Viral Progeny and Mutants Are Produced in Infected Cells
The Quasispecies Concept
Genetic Shift and Genetic Drift
Fundamental Properties of Viruses That Constrain Evolution
Two General Pathways for Virus Evolution
Evolution of Virulence
The Origin of Viruses
When and How Did They Arise?
Evolution of Contemporary Eukaryotic Viruses
Host-Virus Relationships Drive Evolution
DNA Virus-Host Relationships
RNA Virus-Host Relationships
The Host-Virus “Arms Race”
Lessons from Paleovirology
Endogenous Retroviruses
DNA Fossils Derived from Other RNA Viral Genomes
Endogenous Sequences from DNA Viruses
Short-versus Long-Term Rates of Viral Evolution
Perspectives
References
Study Questions
Chapter 11 Emergence
The Spectrum of Host-Virus Interactions
Stable Interactions
The Evolving Host-Virus Interaction
The Dead-End Interaction
The Resistant Host
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
Poliomyelitis: Unexpected Consequences of Modern Sanitation
Introduction of Viruses into Naïve Populations
Hantavirus Pulmonary Syndrome: Changing Animal Populations
Severe Acute and Middle East Respiratory Syndromes (SARS and MERS): Zoonotic Coronavirus Infections
The Contribution to Emergence of Mutation, Recombination, or Reassortment
Canine Parvoviruses: Cat-to-Dog Host Range Switch by Two Amino Acid Changes
Influenza Epidemics and Pandemics: Escaping the Immune Response by Reassortment
New Technologies Uncover Previously Unrecognized Viruses
Hepatitis Viruses in the Human Blood Supply
A Revolution in Virus Discovery
Perceptions and Possibilities
Virus Names Can Be Misleading
All Viruses Are Important
Can We Predict the Next Viral Pandemic?
Preventing Emerging Virus Infections
Perspectives
References
Study Questions
Chapter 12 Human Immunodeficiency Virus Type I Pathogenesis
Introduction
Worldwide Impact of AIDS
HIV-1 Is a Lentivirus
Discovery and Characterization
Distinctive Features of the HIV-1 Reproduction Cycle and the Functions of HIV-1 Proteins
The Viral Capsid Counters Intrinsic Defense Mechanisms
Entry and Transmission
Entry in the Cell
Entry into the Body
Transmission in Human Populations
The Course of Infection
The Acute Phase
The Asymptomatic Phase
The Symptomatic Phase and AIDS
Effects of HIV-1 on Other Tissues and Organs
Virus Reproduction
Dynamics in the Absence of Treatment
Dynamics of Virus Reproduction during Treatment
Latency
Immune Responses to HIV-1
Innate Response
Humoral Responses
HIV-1 and Cancer
Kaposi’s Sarcoma
B- Cell Lymphomas
Anogenital Carcinomas
Prospects for Treatment and Prevention
Antiviral Drugs
Confronting the Problems of Persistence and Latency
Gene Therapy Approaches
Immune System-Based Therapies
Antiviral Drug Prophylaxis
Perspectives
References
Study Questions
Chapter 13 Unusual Infectious Agents
Introduction
Viroids
Replication
Sequence Diversity
Movement
Pathogenesis
Satellite Viruses and RNAs
Replication
Pathogenesis
Hepatitis Delta Virus
Prions and Transmissible Spongiform Encephalopathies
Scrapie
Physical Properties of the Scrapie Agent
Human TSEs
Hallmarks of TSE Pathogenesis
Prions and the prnp Gene
Prion Strains
Bovine Spongiform Encephalopathy
Chronic Wasting Disease
Treatment of Prion Diseases
Perspectives
References
Study Questions
Appendix Epidemiology and Pathogenesis of Selected Human Viruses
Glossary
Index
EULA