Viruses: Molecular Biology, Host Interactions, and Applications to Biotechnology

Viruses
Copyright
List of Contributors
Preface
1 Introduction: A Short History of Virology
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	From Filterable Agent to Genetic Parasite
	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
	Further Reading
2 Virion Structure, Genome Organization, and Taxonomy of Viruses
	What Is a virus?—Perhaps There Is a Simple Answer, Not an Easy Answer
	Virion Morphologies
		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
		dsDNA viruses
		ssDNA viruses—No Polarity or Mixed Polarity
		ssDNA(−) viruses
		ssDNA(+) viruses
		ssDNA(+/−) viruses
		dsRNA viruses
		ssRNA (Viroids)
		ssRNA(−) viruses
		ssRNA(+) viruses
		ssRNA(+/−) viruses
	Virus Taxonomy: Organization of the Vast Diversity Among Viruses
		Baltimore Classification
		The International Committee on Taxonomy of Viruses
		The Goal of Virus Taxonomy
	Further Reading
3 Replication and Expression Strategies of Viruses
	Overview of Virus Genome Transcription and Replication
	Polymerases
		Initiation, Elongation, and Termination
		Initiation
		Elongation
		Termination
	Mechanisms of Genome Transcription and Replication
		Rolling Circle Replication
		Rolling-Hairpin Replication
		dsDNA Bidirectional Replication
		dsDNA (RT) Transcription and Replication
		ssRNA (RT) 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
	Viral Genome Expression
		Disruption of Transcription Initiation Complex Assembly
		Termini Maturation and Modification
		Internal Ribosome Entry
		Poly(A) Tailing
		RNA Editing
		Alternative Splicing
		Suppression of Termination
		Programmed Ribosomal Frameshifting
		Leaky Scanning and Translation Reinitiation
		Ribosomal Shunting
		“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
	Further reading
4 Origins and Evolution of Viruses
	Are Viruses Living Organisms?
		Classic Virus Concept
		The Virocell Concept
		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
		Recombination
		Reassortment
		Horizontal Gene Transfer
	Where Do Viruses Come From?
		Hypotheses on Virus Origin
			Precellular Theory (Virus-First Hypothesis)
			Endogenous Hypothesis (Escape Hypothesis)
			Viral-Oncogene Hypothesis
			Reductive Theory
		Evidence for Viruses Being Ancient
		Extreme Chimerism and Modularity
		What Are Metagenomics Studies Telling Us?
		Virus Hallmark Genes
		Viral Capsid Proteins and Their Relatedness
		Viroids and Mavericks
	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?
	Further Reading
5 Host Range, Host–Virus Interactions, and Virus Transmission
	Defining the Host Range
	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
		Horizontal Transmission
		Airborne Viruses
		Waterborne Viruses
		Soilborne Viruses
		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
	Further Reading
6 Viruses as Pathogens: Plant Viruses
	Geminiviruses: Cassava mosaic geminiviruses, Maize streak virus, Wheat dwarf virus
		Cassava mosaic geminiviruses
		Maize streak virus
		Wheat dwarf virus
	Potyviruses and Criniviruses: Sweet potato feathery mottle virus, Sweet potato chlorotic stunt virus, and Sugarcane mosaic ...
		Sugarcane mosaic virus
	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
	Further Reading
7 Viruses as Pathogens: Animal Viruses, With Emphasis on Human Viruses
	Retroviridae: Human Immunodeficiency Virus 1
		Structure and Genomic Organization
		Genetic Diversity
		Replication and Pathogenesis
		Surveillance and Detection
		Treatment
	Flaviviridae: DENGUE VIRUS and Other Members
		Structure and Genomic Organization
		Dengue virus
			Genetic Diversity
			Pathogenesis
			Diagnosis
			Treatment and Prevention
		Yellow fever virus
			Genetic Diversity
			Clinical Features
			Diagnosis
			Treatment and Prevention
		Zika virus
			Genetic Diversity
			Clinical Features and Complications
			Treatment and Prevention
		Hepacivirus C
			Genetic Diversity
			Clinical Features and Pathogenesis
			Treatment and Prevention
	Togaviridae: CHIKUNGUNYA VIRUS
		Characteristics and Diversity
		Clinical Aspects
		Transmission and Epidemiology
		Diagnosis and Treatment
	Filoviridae: Ebola and Marburg Viruses
		Structure and Genomic Organization
		Genetic Diversity
		Replication Cycle
		Pathogenesis and Clinical Manifestations
		Diagnosis and Detection
		Treatment and Prevention
	Orthomyxoviridae: Influenza Viruses
		Structure and Genomic Organization
		Genetic Diversity
		Host Range and Distribution
		Viral Replication
		Pathogenesis
		Treatment
	Papillomaviridae: Human Papillomavirus
		Genetic Organization, Diversity, and Replication
		Oncogenic Potential of Papillomaviruses
		Diagnosis and Treatment
	Rhabdoviridae: RABIES LYSSAVIRUS
		Structure and Organization
		Genetic Diversity
		Replication and Pathogenesis
		Clinical Symptoms
		Prevention and Treatment
	Further Reading
8 Viruses as Pathogens: Animal Viruses Affecting Wild and Domesticated Species
	Animal Influenza Viruses
		Genetic Diversity and Epidemiology
		Pathogenesis
			Avian influenza
			Swine influenza
			Equine influenza
		Diagnosis, Treatment, and Management
	African swine fever
		Structure and Genomic Organization
		Genetic Diversity
		Replication
		Pathogenesis
		Detection, Prevention, and Control
	Equine Infectious Anemia
		Structure, Genomic Organization, and Diversity
		Pathogenesis and Replication
		Diagnosis, Prevention, and Control
	Equine Encephalitis
		Structure and Genomic Organization
		Pathogenesis and Replication
		Eastern Equine Encephalitis
		Western Equine Encephalitis
		Venezuelan Equine Encephalitis
		Diagnosis, Prevention, and Treatment
	African Horse Sickness
		Structure, Genomic Organization, and Genetic Diversity
		Pathogenesis and Replication
		Diagnosis, Prevention, and Treatment
	Marek’s Disease
		Structure, Genomic Organization, and Genetic Diversity
		Pathogenesis
		Virus Replication
		Diagnosis, Prevention, and Treatment
	Foot-and-Mouth Disease
		Structure, Genomic Organization, and Genetic Diversity
		Pathogenesis and Replication
		Diagnosis, Control, Prevention, and Treatment
	Further Reading
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
		Escherichia virus P1
		Escherichia virus Lambda
	Viruses Infecting Fungi
		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
	Further Reading
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 Uncoating
		Virus Factories for Virus Replication and Assembly
		Virion Assembly and Egress
		Virus-Induced Changes in Selected Metabolic Pathways
			Glycolysis
			Fatty Acid Synthesis
			Glutaminolysis
			Photosynthesis
			Hormone Synthesis and Signaling
		Virus-Induced Changes in Selected Structures and Functions of the Cell
			Endoplasmic Reticulum
			Cytoskeleton
			Nucleus
			Mitochondria
			Chloroplasts
			Ribosomes
			Ubiquitin-Proteasome Machinery
		Other Host–Virus Interactions and Immune Evasion
		Innate Immunity
		Hormone Action in Many Facets of Plant Virus Resistance
		RNA Silencing
		Other Innate Immune Responses Against Viruses
			Nonsense-Mediated mRNA Decay
			RNA Exosome
		Adaptive Immunity
	Further Reading
11 Beneficial Interactions with Viruses
	Phage–Host Interactions
		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
	Virus–Plant Interactions
		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
	Further Reading
12 Viruses as Tools of Biotechnology: Therapeutic Agents, Carriers of Therapeutic Agents and Genes, Nanomaterials, and More
	Phage Therapy and Related Techniques
		Phage Display
	Virus-Based Vaccine Technologies
	Mammalian Viruses With Inherent Cytotoxic Activity as Therapeutic Agents
	Mammalian Viruses as Gene Delivery Vehicles
		γ-Retroviral Vectors
		Lentivirus Vectors
		Adenovirus Vectors
		Adeno-associated virus Vectors
	Plant Viral Vectors
	Viruses as Biological Control Agents
	Viruses as Scaffolds and Templates for Nanomaterials
		Imaging Molecules
		Scaffolds for Tissue Engineering
		Templates for Materials Synthesis
	Further Reading
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
		Metagenomics Approaches
	Detection of Viruses and Diagnosis of Virus Infections
		Culture Systems: Whole Organisms- and Cell-Based Methods
		Immunological 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
			RNA-Mediated Resistance
		CRISPR/Cas9 and Other Targets for Engineering Virus Resistance
	Further Reading
Conclusion It’s a Viral World
	Further Reading
Index