The Biological Role of a Virus

Series Preface
Volume Preface
Contents
Part I: Viral Control of Community Energetics
	Chapter 1: Viral Nature of the Aquatic Ecosystems
		1.1 Introduction
		1.2 Viral Influence on Biogeochemical Cycle
			1.2.1 Viral Modulation on Patterns of Geochemical Cycling in the Ocean
			1.2.2 Virus-Host Interactions-Mediated Modification of Host Cell Metabolism
		1.3 Viral Infection Shaping Microbial Community Diversity
			1.3.1 Contribution of Lytic Infection to Microbial Diversity Maintenance
			1.3.2 Potential Contribution of Lysogenic Infection to Microbial Diversity Maintenance
		1.4 Evolutionary Roles of Viruses that Generate Genotype-Level Microbial Diversification
		1.5 Conclusion
		References
	Chapter 2: Life Continues as Viruses Close Land, Water and Atmosphere Nutrient Cycle
		2.1 Our `Love-Hate´ Relationship with Viruses
		2.2 The Open Ocean
			2.2.1 Autotrophy Dominates
			2.2.2 Heterotrophic Bacterial Production Does Not Move Up the Food Chain
		2.3 Freshwater
			2.3.1 Heterotrophy Dominates
			2.3.2 Carbon Sources Entering the DOC Pool
			2.3.3 Dissolved Organic Carbon [DOC] Pool
			2.3.4 [DOC] Pool Versus DOC Turnover: Flux
		2.4 Viral Lysis Is Recycling DOC Through the DOC Pool
			2.4.1 Low Bacterial Growth Efficiencies Coupled with Viral Lysis
			2.4.2 DOC-Bacterial Respiration-Viral Lysis
		2.5 Viral-Bacterial Nutrient Recycling Supports Primary Production
		2.6 Conclusion
		References
Part II: Understanding the Genetic Partnership Between a Host and Its Viruses
	Chapter 3: Cataloging the Presence of Endogenous Viruses
		3.1 Introduction: Defining Endogeny and Lysogeny
		3.2 Endogenous Viruses of Eukaryotic Hosts
		3.3 Groups of Viruses for Which Endogenous Sequences Have Been Identified at the Level of Viral Family
			3.3.1 Amalgaviridae
			3.3.2 Asfarviridae
			3.3.3 Baculoviridae
			3.3.4 Betaflexiviridae
			3.3.5 Bornaviridae
			3.3.6 Bromoviridae
			3.3.7 Bunyaviridae
			3.3.8 Caulimoviridae
			3.3.9 Chrysoviridae
			3.3.10 Chuviridae (and Unspecified Mono-Chu)
			3.3.11 Circoviridae
			3.3.12 Endornaviridae
			3.3.13 Filoviridae
			3.3.14 Flavivridae
			3.3.15 Geminiviridae
			3.3.16 Hepadnaviridae
			3.3.17 Hypoviridae
			3.3.18 Lavidaviridae
			3.3.19 Metaviridae
			3.3.20 Mimiviridae
			3.3.21 Molliviridae
			3.3.22 Nairoviridae
			3.3.23 Nanoviridae
			3.3.24 Nodaviridae
			3.3.25 Nudiviridae
			3.3.26 Nimaviridae
			3.3.27 Nyamiviridae
			3.3.28 Orthomyxoviridae
			3.3.29 Partitiviridae
			3.3.30 Parvoviridae
			3.3.31 Phenuiviridae
			3.3.32 Phycodnaviridae
			3.3.33 Pithoviridae
			3.3.34 Polydnaviridae
			3.3.35 Potyviridae
			3.3.36 Poxviridae
			3.3.37 Pseudoviridae
			3.3.38 Qinviridae
			3.3.39 Reoviridae
			3.3.40 Retroviridae
			3.3.41 Rhabdoviridae
			3.3.42 Totiviridae
			3.3.43 Virgaviridae (Includes Former Tobamoviridae)
		3.4 Groups of Viruses for Which Endogenous Sequences Were Not Identified at the Level of Viral Family
			3.4.1 Unspecified Bunya-Arena
			3.4.2 Unspecified Hepe-Virga
			3.4.3 Unspecified Iridoviridae/Marseilleviridae Group
			3.4.4 Unspecified Mononegavirales
			3.4.5 Unspecified Mononegavirales-Like Virus
			3.4.6 Unspecified Narna-Levi
			3.4.7 Unspecified Nucleocytoviricota
			3.4.8 Unclassified Riboviria
			3.4.9 Unspecified Partiti-Picobirna
			3.4.10 Unspecified Toti-Chryso
			3.4.11 Unspecified Virga-Like
		3.5 Groups of Viruses for Which Lysogenous Sequences Have Been Identified at the Level of Viral Family
			3.5.1 Inoviridae
			3.5.2 Microviridae
			3.5.3 Myoviridae
			3.5.4 Podoviridae
			3.5.5 Siphoviridae
		3.6 Summary Thoughts
		References
	Chapter 4: Do the Biological Roles of Endogenous and Lysogenous Viruses Represent Faustian Bargains?
		4.1 Introduction
			4.1.1 Viruses as Genomic Partners of Their Hosts
			4.1.2 Viruses as Transfer Agents for Genomic Information
		4.2 What Is a Faustian Bargain
			4.2.1 The Devil and Daniel Webster
			4.2.2 Do Endogeny and Lysogeny Represent Faustian Bargains that Have Been Forged with Viruses?
		4.3 General Benefits Versus Detriments of Endogenous and Lysogenous Interactions
		4.4 Viruses as a Means of Horizontal Gene Transfer
		4.5 What Is the Functional Role of Retrotransposons?
			4.5.1 Non-LTR Retrotransposons
			4.5.2 The LTR Retrotransposons
			4.5.3 The Role of Mammalian Apparent LTR Retrotransposons (MaLRs) in Humans
		4.6 An Example Regarding the Importance of Endogenous Viral Sequences in Health and Disease of Unicellular Eukaryotes
			4.6.1 Lavidaviridae
		4.7 Examples Regarding the Importance of Endogenous Viral Sequences in Morphological Development, Health and Disease of Animals
			4.7.1 Bornaviridae
			4.7.2 Filoviridae
			4.7.3 Metaviridae
			4.7.4 Nudiviridae
			4.7.5 Parvoviridae
			4.7.6 Polydnaviridae
			4.7.7 Retroviridae
				4.7.7.1 The Importance of Endogenous Retroviridae in Health and Disease of Their Human Hosts
					4.7.7.1.1 The Beneficial Role of Endogenous Retroviridae in Placentation and Gestation
					4.7.7.1.2 Other Involvements of Endogenous Retroviridae in Health Versus Disease
				4.7.7.2 The Parallel Roles of Endogenous Retroviridae in Health and Disease of Animals
		4.8 Examples Regarding the Importance of Non-endogenous and Endogenous Viral Sequences in Health and Disease of Plants and fun...
			4.8.1 The Role of Non-endogenous Viruses in Plant Health
			4.8.2 The Role of Endogenous Viruses in Plant Health
				4.8.2.1 Caulimoviridae
				4.8.2.2 Endornaviridae
				4.8.2.3 Metaviridae and Pseudoviridae
		4.9 Understanding How Partnership with an Endogenous Fungal Virus Can Reduce the Phytopathogenicity of its Fungal Host
		4.10 Lysogenous Viruses of Prokaryotic Hosts
			4.10.1 Some of the Benefits and Detriments Associated with Lysogenic Archaelphage and Bacteriophage
			4.10.2 Examples Regarding the Ecology of Lysogenous Viral Sequences in Prokaryotes
				4.10.2.1 Inoviridae
				4.10.2.2 Microviridae
				4.10.2.3 Myoviridae
				4.10.2.4 Podoviridae
				4.10.2.5 Siphoviridae
			4.10.3 Tailocins, Type VI Secretion Systems, and Gene Transfer Agents Represent the Concept of Retaining and Subsequently Usin...
				4.10.3.1 R-Type Tailocins
				4.10.3.2 F-Type Tailocins
				4.10.3.3 Type VI Secretion Systems
				4.10.3.4 Gene Transfer Agents
		4.11 Summary
		References
	Chapter 5: Einstein´s Capsid: Bacteriophages Solve the Problems of Space and Time for Bacteria with Emergency Dead to Alive Ho...
		5.1 Introduction
		5.2 Approach
		5.3 Defining the Hypothesis
			5.3.1 Sensing Impending Death
			5.3.2 The Probability of Lysis over Lysogeny
			5.3.3 Superinfection Immunity and CRISPR
			5.3.4 Other Supporting Evidence
		5.4 What Is the Advantage of EDA-HGT (Viruses)?
		5.5 Potential Ontogeny of the Bacteriophage Related Systems
			5.5.1 Progressive Capture of Supplementary DNA by EDA-HGT
			5.5.2 The Effects of Plasmids
		5.6 Bacteria Encoding for Their Own Infection with HGTA
			5.6.1 Integration Host Factor
			5.6.2 Type IV Secretion Systems and Type IV Pili
		5.7 Derivatives of EDA-HGT
			5.7.1 Gene Transfer Agents
			5.7.2 Bacteriocins: Type F and R Pyocins of Pseudomonas aeruginosa
		5.8 Biological Implications if EDA-HGT Theory Is Correct
			5.8.1 Benthic Biofilm as the Ancestral State for Bacteria?
			5.8.2 Lysogeny vs Lysis Revisited
		5.9 Testing the Hypothesis
		5.10 Conclusions
		References
	Chapter 6: Diverse Phage-Encoded Toxins and Their Role in Bacterial Ecology
		6.1 Bacteriophage and Bacteria: A Fine Line Between Friend and Foe
		6.2 Impact of Lysogenic Phages on Bacterial Hosts
		6.3 Lysogeny and Toxigenicity in Bacterial Pathogens
			6.3.1 Phage-Conversion and Toxigenicity in Vibrio cholerae
			6.3.2 The Rise of a Lethal Pathogen: Lysogenic Conversion and Toxigenicity in Escherichia coli
			6.3.3 Lysogenic Conversion and Toxin-Production in Clostridium botulinum
			6.3.4 Phage-Conversion and Toxigenicity in Corynebacterium diphtheriae
		6.4 Insects, Symbionts, and Phage-Encoded ToxinsOh My!
		6.5 Summary
		References
	Chapter 7: Mycoviruses as Antivirulence Elements of Fungal Pathogens
		7.1 Introduction
		7.2 Mycoviruses
		7.3 Plant Pathogenic Fungi as Hosts of Mycoviruses
		7.4 Mycoviruses as Biological Control Agents
			7.4.1 Hypovirulence in the Chestnut Blight Fungus, Cryphonectria parasitica
				7.4.1.1 Mycovirus Species Belonging to the Genus Hypovirus
				7.4.1.2 Cryphonectria hypovirus 1 Subtypes
				7.4.1.3 Phenotypic Effects of Cryphonectria hypovirus 1 on Its Fungal Host
				7.4.1.4 Effects of Cryphonectria hypovirus 1 at the Molecular Level
				7.4.1.5 Effect of Cryphonectria hypovirus 1 on the Cryphonectria parasitica Secretome and Enzyme Activities
				7.4.1.6 Trilateral Interaction Between Chestnut Tree, Cryphonectria parasitica and Cryphonectria hypovirus 1
				7.4.1.7 Cryphonectria hypovirus 1 Transmission and Spread
				7.4.1.8 Human-Mediated Biological Control of Chestnut Blight
				7.4.1.9 Other Viruses Belonging to the Genus Hypovirus
				7.4.1.10 Other Viruses Infecting Cryphonectria parasitica
			7.4.2 Hypoviruses in Other Fungal Genera
			7.4.3 Hypovirulence in Magnaporthe oryzae (Magnaporthe grisea)
			7.4.4 Hypovirulence in Alternaria alternata
			7.4.5 Hypovirulence in Rhizoctonia solani
			7.4.6 Hypovirulence in Fusarium Species
			7.4.7 Hypovirulence in Heterobasidion Species
			7.4.8 Hypovirulence in Ophiostoma novo-ulmi
			7.4.9 Hypovirulence in Botrytis Species
			7.4.10 Hypovirulence in Rosellinia necatrix
			7.4.11 Hypovirulence in Helminthosporium victoriae
			7.4.12 Hypovirulence in Sclerotinia sclerotiorum
		7.5 Mycoviruses Related to Plant Viruses
		7.6 Conclusion
		References
Part III: Defending the Health of Its Hosts
	Chapter 8: The Contribution of Viruses to Immune Systems
		8.1 Introduction
		8.2 The Greater Virus World
		8.3 Viruses as Drivers of Evolution
		8.4 Immune Systems: An Evolutionary Perspective
			8.4.1 What Is an Immune System?
			8.4.2 A Simple Immune System Based on RNA?
			8.4.3 Innate and Adaptive Immunity
		8.5 Viruses Against Viruses: Superinfection Exclusion, a Simple Immune System
			8.5.1 Endogenous Retrovirus-Mediated Immunity in Eukaryotes: The Envelope Protein
			8.5.2 Endogenous Retrovirus-Mediated Immunity in Eukaryotes: The Gag Protein
			8.5.3 Evolution of Retrovirus-Mediated Immunity in Real Time?
			8.5.4 Superinfection Exclusion by Other Endogenized Eukaryotic Viruses
			8.5.5 piRNA-Guided CRISPR-Cas-Like Immunity in Eukaryotes Based on Endogenous Viral Sequences
			8.5.6 Do Endogenous Viruses Render Bats Resistant to Viral Infections?
			8.5.7 Superinfection Exclusion by Endogenized Viruses in Prokaryotes
		8.6 The Enemy of My Enemy Is My Friend: Harnessing Viruses for Complex Immune Systems
			8.6.1 A Small Virus Against a Giant Virus in the Protist Cafeteria roenbergensis: An Adaptive Immune System at the Population ...
			8.6.2 CRISPR-Cas Immunity Largely Originates from Viruses and Mobile Genetic Elements
			8.6.3 At the Heart of Adaptive Immunity in Jawed Vertebrates Is an Ancient Mobile Genetic Element
		8.7 Discussion
		References
	Chapter 9: Application of Viruses for Gene Therapy and Vaccine Development
		9.1 Introduction
		9.2 Gene Therapy and Vaccine Targets
		9.3 Viral Vectors
			9.3.1 Adenoviruses
			9.3.2 Adeno-associated Viruses
			9.3.3 Alphaviruses
			9.3.4 Flaviviruses
			9.3.5 Measles Virus
			9.3.6 Rhabdoviruses
			9.3.7 Herpes Simplex Viruses
			9.3.8 Retroviruses
			9.3.9 Lentiviruses
			9.3.10 Newcastle Disease Virus
			9.3.11 Reoviruses
			9.3.12 Poxviruses
			9.3.13 Picornaviruses
			9.3.14 Polyoma Viruses
			9.3.15 Chimeric Vectors
		9.4 Preclinical Evaluation
			9.4.1 Cancer
			9.4.2 Metabolic Diseases
			9.4.3 Cardiovascular Diseases
			9.4.4 Hematological Disorders
			9.4.5 Neurological Disorders
			9.4.6 Infectious Diseases
			9.4.7 Ophthalmological Diseases
			9.4.8 Muscular Diseases
			9.4.9 Lung Diseases
		9.5 Clinical Trials
		9.6 COVID-19
		9.7 Approved Drugs
		9.8 Conclusions and Future Aspects
		References
	Chapter 10: Eukaryotic Virus Interactions with Bacteria: Implications for Pathogenesis and Control
		10.1 An Introduction to Virus Interactions with Bacteria
		10.2 Evidence for Direct Interactions Between Viruses and Microbiota
			10.2.1 Respiratory Syncytial Virus-Bacterial Interactions Facilitate Streptococcus pneumoniae Infection
			10.2.2 Gut Microbiota in the Pathogenesis of Intestinal Viruses
		10.3 Circadian Rhythms of the Microbiota: Potential Implications for Viral Infection
		10.4 Role of Viruses in Enhancing Bacterial Superinfections
		10.5 Role of Microbiome in Shielding from Viral Infections
		10.6 Effects of Virus Binding on Bacteria
		10.7 Enteric Virus-Bacteria Interactions
			10.7.1 Direct Interactions
			10.7.2 Indirect Immune-Mediated Interactions
			10.7.3 Respiratory Virus-Bacteria Interactions
		10.8 The Respiratory System: Microbiome Shifts
			10.8.1 The Upper Respiratory System: Direct Interactions
			10.8.2 The Lower Respiratory System: Microbiome Shifts
			10.8.3 The Lower Respiratory System: Direct Interactions
		10.9 SARS-CoV-2 Interaction with Bacteria
		References