Chapter
Viruses Have Contributed to Our Understanding of a Gene and How It Works
Viruses Have Allowed Us to Understand How Genes Are Regulated
Viruses Have Contributed to Our Understanding of How Genomes Are Organized
Viruses Have Contributed to Our Understanding of the Mechanisms Underlying RNAi
Viruses That Cause Diseases Represent a Small Fraction of the Viral Community
Viruses Can Be Beneficial to Their Hosts
Viruses Can Function as Tools for Biotechnology
2 Virion Structure, Genome Organization, and Taxonomy of Viruses
What Is a virus?—Perhaps There Is a Simple Answer, Not an Easy Answer
Icosahedral/Spherical Virions
Filamentous/Bacilliform Virions
Amazing Forms Among Old and New Comers
Do Viruses Really Need a Coat?
Types and Function of the Virus Envelope
Genomes: The Nucleic Acids Space Exploited by Viruses
ssDNA viruses—No Polarity or Mixed Polarity
Virus Taxonomy: Organization of the Vast Diversity Among Viruses
The International Committee on Taxonomy of Viruses
The Goal of Virus Taxonomy
3 Replication and Expression Strategies of Viruses
Overview of Virus Genome Transcription and Replication
Initiation, Elongation, and Termination
Mechanisms of Genome Transcription and Replication
Rolling Circle Replication
Rolling-Hairpin Replication
dsDNA Bidirectional Replication
dsDNA (RT) Transcription and Replication
Positive-Strand RNA Virus Replication
Double-Strand RNA Virus Transcription and Replication
Negative-Strand RNA Virus Transcription and Replication
dsDNA Template Transcription and Replication
Disruption of Transcription Initiation Complex Assembly
Termini Maturation and Modification
Suppression of Termination
Programmed Ribosomal Frameshifting
Leaky Scanning and Translation Reinitiation
“2A” Oligopeptides and “Stop-Carry On” Recoding
Subversion of Host Gene Expression
Inhibition of Cellular RNA Polymerase
Disruption of Cellular mRNA Export Pathways
Decay of Host mRNAs by Viruses
Circumvention of Cellular RNA Decay Machinery
Shutoff of Cellular mRNA Translation
Recruitment of Cellular Hsp70 Chaperones for Viral Protein Folding
Compromising Cellular Lipid Metabolism
Cell Cycle Disruption for Preferential Viral Replication
Virus Genome Replication Complexes
4 Origins and Evolution of Viruses
Are Viruses Living Organisms?
Virocell Versus Ribocell: Are Giant Viruses the Missing Link?
Sources of Variation in Virus Genomes: The Many Ways By Which Viruses Change
Mutation and High Viral Replication Error Rates
Where Do Viruses Come From?
Hypotheses on Virus Origin
Precellular Theory (Virus-First Hypothesis)
Endogenous Hypothesis (Escape Hypothesis)
Viral-Oncogene Hypothesis
Evidence for Viruses Being Ancient
Extreme Chimerism and Modularity
What Are Metagenomics Studies Telling Us?
Viral Capsid Proteins and Their Relatedness
Evolution of Viruses With Their Hosts
Arms Race Between Hosts and Parasites, and Unplanned Mutualism
Viruses and the Tree of Life: Tree of Life or Tree of Viruses?
5 Host Range, Host–Virus Interactions, and Virus Transmission
Interactions Between a Virus and Its Host(s) May Have Different Outcomes
The Many Ways of Virus Transmission
Cell-to-Cell Transmission
Virus Survival in the Environment
Transplantation, Anastomosis, and Grafting
Zoonosis in the Spread of Viruses
Virus Transmission by Vectors
Noncirculative Transmission of Viruses
Circulative, Nonpropagative Transmission of Viruses
Circulative, Propagative Transmission of Viruses
Vertical Transmission: Parent to Offspring Transmission of Viruses
6 Viruses as Pathogens: Plant Viruses
Geminiviruses: Cassava mosaic geminiviruses, Maize streak virus, Wheat dwarf virus
Cassava mosaic geminiviruses
Potyviruses and Criniviruses: Sweet potato feathery mottle virus, Sweet potato chlorotic stunt virus, and Sugarcane mosaic ...
Babuviruses: Banana bunchy top virus
Cucumoviruses: Cucumber mosaic virus
Tungroviruses and Waikaviruses: Rice tungro bacilliform virus and Rice tungro spherical virus
Rice tungro bacilliform virus
Rice tungro spherical virus
7 Viruses as Pathogens: Animal Viruses, With Emphasis on Human Viruses
Retroviridae: Human Immunodeficiency Virus 1
Structure and Genomic Organization
Replication and Pathogenesis
Surveillance and Detection
Flaviviridae: Dengue Virus and Other Members
Structure and Genomic Organization
Clinical Features and Complications
Clinical Features and Pathogenesis
Togaviridae: Chikungunya Virus
Characteristics and Diversity
Transmission and Epidemiology
Filoviridae: Ebola and Marburg Viruses
Structure and Genomic Organization
Pathogenesis and Clinical Manifestations
Orthomyxoviridae: Influenza Viruses
Structure and Genomic Organization
Host Range and Distribution
Papillomaviridae: Human Papillomavirus
Genetic Organization, Diversity, and Replication
Oncogenic Potential of Papillomaviruses
Rhabdoviridae: Rabies Lyssavirus
Structure and Organization
Replication and Pathogenesis
8 Viruses as Pathogens: Animal Viruses Affecting Wild and Domesticated Species
Genetic Diversity and Epidemiology
Diagnosis, Treatment, and Management
Structure and Genomic Organization
Detection, Prevention, and Control
Structure, Genomic Organization, and Diversity
Pathogenesis and Replication
Diagnosis, Prevention, and Control
Structure and Genomic Organization
Pathogenesis and Replication
Eastern Equine Encephalitis
Western Equine Encephalitis
Venezuelan Equine Encephalitis
Diagnosis, Prevention, and Treatment
Structure, Genomic Organization, and Genetic Diversity
Pathogenesis and Replication
Diagnosis, Prevention, and Treatment
Structure, Genomic Organization, and Genetic Diversity
Diagnosis, Prevention, and Treatment
Structure, Genomic Organization, and Genetic Diversity
Pathogenesis and Replication
Diagnosis, Control, Prevention, and Treatment
9 Viruses of Prokaryotes, Protozoa, Fungi, and Chromista
Viruses Infecting Archaea
Sulfolobus islandicus rod-shaped virus 1
Sulfolobus turreted icosahedral virus 1
Viruses Infecting Bacteria
Cryphonectria hypovirus 1
Sclerotinia sclerotiorum betaendornavirus 1
Viruses Infecting Protozoa
RNA viruses of Leishmania
Acanthamoeba polyphaga mimivirus
Viruses Infecting Chromista
Plasmopara halstedii virus A
Phytophthora infestans RNA viruses
P. infestans Viruses With a dsRNA Genome
P. infestans Viruses With an ssRNA Genome
10 Host–Virus Interactions: Battles Between Viruses and Their Hosts
Types of Virus–Host Relationships: Terrorism vs Guerilla Warfare
Weapons and Defenses I: Prokaryotic Virus–Host Interactions
Weapons and Defenses II: Eukaryotic Virus–Host Interactions
Virus Recognition, Attachment, and Entry
Virus Factories for Virus Replication and Assembly
Virion Assembly and Egress
Virus-Induced Changes in Selected Metabolic Pathways
Hormone Synthesis and Signaling
Virus-Induced Changes in Selected Structures and Functions of the Cell
Ubiquitin-Proteasome Machinery
Other Host–Virus Interactions and Immune Evasion
Hormone Action in Many Facets of Plant Virus Resistance
Other Innate Immune Responses Against Viruses
Nonsense-Mediated mRNA Decay
11 Beneficial Interactions with Viruses
Phages Affect Host Population Sizes and Biogeochemical Cycles
Phages Manipulate Host Metabolism
Phages Contribute to Microbial–Metazoan Symbioses That Affect Metazoan Fitness
Virus–Fungus Interactions
Mycoviruses Increase Their Hosts’ Fitness
Mycoviruses as Modulators of Symbiotic Associations
Interactions Between Mycoviruses and Nonhosts
Virus–Arthropod Interactions
Arthropod Viruses Protect Their Hosts
Arthropod Viruses Mediate Host Responses
Unexpected Outcomes in Virus–Mammal Interactions
Animal Viruses Can Protect Against Other Viruses
Retroviruses and Emergence of Placental Mammals
Animal Viruses as Drivers of Protein Adaptation
Viruses Help Plants Cope With Abiotic Stress
Viruses Help Plants Cope With Biotic Stress
Plant Viruses as Modulators of Symbioses
Interactions Between Vectors, Nonvectors, and Plant Viruses
12 Viruses as Tools of Biotechnology: Therapeutic Agents, Carriers of Therapeutic Agents and Genes, Nanomaterials, and More
Phage Therapy and Related Techniques
Virus-Based Vaccine Technologies
Mammalian Viruses With Inherent Cytotoxic Activity as Therapeutic Agents
Mammalian Viruses as Gene Delivery Vehicles
Adeno-associated virus Vectors
Viruses as Biological Control Agents
Viruses as Scaffolds and Templates for Nanomaterials
Scaffolds for Tissue Engineering
Templates for Materials Synthesis
13 Viruses as Targets for Biotechnology: Diagnosis and Detection, Transgenesis, and RNAi- and CRISPR/Cas-Engineered Resistance
Uncovering the Virosphere and Hidden World of Viruses
Classic Sequence-Based Methodologies
Next Generation Sequencing
Detection of Viruses and Diagnosis of Virus Infections
Culture Systems: Whole Organisms- and Cell-Based Methods
Molecular Methods Based on Detection of Nucleic Acids
Viral Targets for Engineered Resistance
Local and Systemic Movement of Viruses
CP-Mediated Resistance in Plants
CRISPR/Cas9 and Other Targets for Engineering Virus Resistance
Conclusion: It’s a Viral World
Viruses
：Molecular Biology, Host Interactions, and Applications to Biotechnology
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