Virus Infected Cells

Preface
Contents
Part I: General/Technical Aspects
	Chapter 1: In Situ Imaging of Virus-Infected Cells by Cryo-Electron Tomography: An Overview
		Introduction
		Sample Preparation
		Data Collection and Image Processing
		Integrative Techniques
			Cryo-serial Block Face Scanning Electron Microscopy
			Cryo-soft X-Ray Tomography
			Cryo-correlative Light and Electron Microscopy
		Cryo-ET Studies of Enveloped Viruses and Their Interactions Within the Host Cell
			Cryo-ET of Purified Enveloped Viruses
				Human Immunodeficiency Virus (HIV-1)
				Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)
				Other Enveloped Viruses
		In Situ Cellular Cryo-ET Enables Peering into the Cell
			Probing Enveloped Viral Infections and Molecular Mechanisms of Virus-Host Interactions
				Viral Disassembly and Genome Release
				Viral Factories Are Sites of Viral Replication
					Enveloped Positive-Strand RNA Viruses
					Enveloped Negative-Strand RNA Viruses
				Viral Assembly and Egress
		Concluding Remarks and Perspectives
		References
	Chapter 2: Approaches to Evaluating Necroptosis in Virus-Infected Cells
		Introduction
		Necroptosis Pathway and Players
		Necroptosis Inhibitors
		In Vitro Necroptosis in Cultured Cells
		In Vivo Models of Necroptosis
		Cellular Patterns and Methods to Evaluate Necroptosis
			Metabolic Viability Assays
			Membrane Integrity Assays
			Necroptosis Morphology
			Immuno-techniques
		The Viruses That Activate or Inhibit Necroptosis
			DNA Viruses
				Herpesviruses
				Murine Cytomegalovirus
				Human Cytomegalovirus
				Herpes Simplex Viruses
				Poxviruses
			RNA Viruses
				Influenza A
				Reovirus
				Respiratory Syncytial Virus
				SARS-CoV-2
				Flaviviruses
				Rotavirus
		Conclusion
		References
	Chapter 3: Apoptosis and Phagocytosis as Antiviral Mechanisms
		Introduction
		Virus Life Cycle, Classification, and Infection
		Changes in Host Cells After Viral Infection
			Alteration of Gene Expression
			Changes in Cell Surface Structures
			Apoptosis and Viral Resistance to Apoptosis
			Cellular and Humoral Immune Responses Against Virus Infection and the Possible Induction of Cytokine Storm
		Roles for Phagocytosis in the Prevention and Progression of Viral Diseases
			Phagocytosis of Virus-Infected Cells as Innate Immune Response
			Consequences of Apoptosis-Dependent Phagocytosis of Virus-Infected Cells
		Perspectives
		References
	Chapter 4: The Art of Viral Membrane Fusion and Penetration
		General Terminology and Mechanisms of How Viruses Cross Host Membranes
		Viral Membrane Fusion and Membrane Fusion Proteins
		Conformational States of Viral Fusion Proteins
		Membrane Penetration by Non-enveloped Viruses
			Proteinaceous Pore-Forming Viruses
				Viruses Utilizing Lytic Peptide-Driven Membrane Penetration
				Lipid-Modifying Membrane Rupturing Viruses
		Visualization of Viral Membrane Fusion and Penetrations Using Cryo-electron Tomography
		Endosomal Lipids as Regulators of Membrane Fusion
			Effect of Lipid Curvature
			Effect of Lipid Charge
		Host Restriction Factors Controlling Viral Membrane Fusion and Penetration by Modulating the Endosomal Lipid Composition
		Role of Viral Uncoating in Membrane Fusion
		Inhibitors of Viral Membrane Fusion
		Conclusion
		Glossary
		References
	Chapter 5: Single-Particle Tracking of Virus Entry in Live Cells
		Introduction
		Dynamic Entry of Viruses into Host Cells
			Virus-Receptor Interactions
			Virus Internalization
			Virus Transport
			Virus Uncoating
		Fluorescent Labeling of Viruses and Cellular Components
			Fluorescent Proteins
			Organic Dyes
			Quantum Dots
		Microscopy Methods and Image Processing
			Microscopy Configurations
			Image Processing
		Concluding Remarks
		References
	Chapter 6: Correlative Cryo-imaging Using Soft X-Ray Tomography for the Study of Virus Biology in Cells and Tissues
		Soft X-Ray Technique
			SXT Principles and Advantages
			SXT Data Collection
		Use of SXT in Viral Studies
		Extending the Information Content of SXT Data in the Context of Correlative Microscopy Schemes
		Sample Preparation and B24 Experimental Workflow
		SXT Correlative Schemes in the Service of Virus Research
			Reovirus
			Hepatitis C Virus
		Challenges and Prospects
		References
	Chapter 7: The Virus-Induced Cytopathic Effect
		Introduction
		Cytopathic Effects across Viral Species
		Approaches to Studying the Cytopathic Effect
			Bright-Field Microscopy
			Fluorescence Microscopy
				Immunofluorescence Assay (IFA)
				Labeling with Fluorescent Dyes
			Plaque Assay
		Monitoring of the Cytopathic Effect and Its Relevance
			Cellular Tropism Evaluation
			Antiviral Drug Screening
			Neutralizing Antibodies Assessment
		Conclusions
		References
Part II: Specific Viruses
	Chapter 8: Human Papilloma Virus-Infected Cells
		Introduction
		HPV Entry into Its Target Cells
			HPV Endocytosis as a Journey to the Nucleus
		Replication and Transcription of the HPV Genome
		Exocytosis and Exit toward a New Infection
		Conclusions
		References
	Chapter 9: Defining the Assembleome of the Respiratory Syncytial Virus
		Respiratory Syncytial Virus Infection Is a Global Health Problem
		The Genetic Structure of RSV
		RSV Particle Morphogenesis at the Assembleome
			Interactions between the Virus Membrane Structural Proteins at the Assembleome
			RSV Particles Form as Filamentous Structures at the Assembleome on Infected Cells
			The Assembleome Forms at Lipid Raft Microdomains on the Surface of Infected Cells
			Filamentous Actin (F-Actin) Remodeling at Lipid Raft Microdomains at the Assembleome Drives Virus Filament Formation
			Trafficking of the rac1 and rhoA Proteins to the Assembleome Is Required for Virus Filament Formation
		Future Perspectives
		References
	Chapter 10: Japanese Encephalitis Virus-Infected Cells
		Introduction
		Epidemiology
		Transmission Cycle
		Clinical Features
		JEV Molecular Biology
		Infection Route: A Cellular Overview
		Cellular Response to Infection
			Alteration of Signalling Pathways
			PKR Activation and Formation of Stress Granules
			Induction of Oxidative Stress
			Activation of the Unfolded Protein Response
			Upregulation of Autophagy
			Innate Immune Activation
			Cell Death Pathways
			Downregulation of Cell Adhesion Molecules
			Metabolic Reprogramming
		Infection Route: A Host Overview
			Infection Route in the Periphery
			Peripheral Immune Response to Infection
			Virus Entry into the CNS
			CNS Response to Infection
		Perspectives
		References
	Chapter 11: African Swine Fever Virus Host-Pathogen Interactions
		Introduction
		Virus Replication
			Virion Structure
			Virus Entry
			Early Steps in Replication
			Virus Factories
			Membranes
			Cytoskeleton
		Programmed Cell Death
		Autophagy
		Interferon Response
			Type I Interferons
			Induction of Type I Interferon Expression
			Interferon Regulatory Factors
			Nuclear Factor κB
			Transmembrane Pathogen Recognition Receptors
			Cytosolic Pathogen Recognition Receptors
			IFN-Mediated Signalling
			ASFV Modulation of the IFN Response
			Inhibition of IFN Induction at the Level of Transcription Factors or Their Activation
			Inhibition of Specific PRRs Pathways
			Inhibition of IFN-Mediated Signalling
		Cellular Stress
			Secretory Pathway
		Concluding Remarks
		References
	Chapter 12: Coronavirus and the Cytoskeleton of Virus-Infected Cells
		Introduction to the Cytoskeleton
			Cytoskeleton
			Actin Filaments
			Microtubules
			Intermediate Filaments
		Coronavirus
			The Structure and Life Cycle of Coronavirus
			SARS-CoV-2 and COVID-19 Infection
			Hazards of Other Virus Infections
		Response of the Host Cell Cytoskeleton Network Following Coronavirus Infection
			Coronavirus Infection Induces Expression Level or Posttranslational Modification Changes of the Cytoskeleton and its Related P...
			Coronavirus Infection Induces Actin Filament Rearrangement
			Microtubules Are Hijacked by Coronavirus for Trafficking
			Detection of Intermediate Filament Changes upon Infection
		Host Cytoskeleton Participates in Coronavirus Life Cycle
			Host Cytoskeleton Protein Facilitates Coronaviral Internalization
			Host Cytoskeleton Affects Coronaviral Replication
			Host Cytoskeleton Participates in the Coronaviral Assembly Process
			Coronaviral Release Can Be Promoted by Cytoskeleton Proteins
		Cytoskeleton and Pathogenesis
			The Ciliary Structure Is Involved in the Pathogenic Process
			Lung Injury Caused by SARS-CoV-2 Is Related to Endothelial Cell Permeability Regulation
			Relationship with the Nervous System
		Possibilities of Cytoskeleton-Related Treatment of COVID-19
		Summary
		References
	Chapter 13: Viral RNA Is a Hub for Critical Host-Virus Interactions
		Introduction: RNA-Binding Proteins Are at the Core of Virus Infection
		RNA-Binding Proteins, Structure and Function
		The Expanding Universe of Cellular RNA-Binding Proteins
		The Essential Roles of Viral RBPs in Infection
		Virus Infection Profoundly Remodels the Cellular RNA-Binding Proteome (RBPome)
			How Are Cellular RBPs Regulated by a Virus Infection?
		New Methods to Uncover the Viral RNA Interactome
			Methods to Uncover the Viral RNA Interactome
		Viral RNA Is a Hub for Critical and Conserved Host-Virus Interactions
			RBPs Involved in Innate Immunity
			RNA Stability and Degradation
			Protein Synthesis
		Outlook
		References
	Chapter 14: Influenza A Virus: Cellular Entry
		Molecular Mechanisms of Influenza A Virus Entry
		Uncoating Reaction In Vitro
		Application to Coronavirus Endosomal Uncoating
		Conclusions
		References
	Chapter 15: Human Endogenous Retroviruses in Diseases
		HERV Functions
			Introduction to ERVs
			Classification of HERVs
				Human Endogenous Retrovirus-K (HML-2)
				HERV-H
			Replication of HERVs
			HERVs as Transcriptional Regulators
				HERVs as Promoters or Enhancers
				HERV-Encoded Proteins
				HERV-Derived ncRNAs or dsRNAs
				HERVs May Alter Gene Structure or Yield Antisense Sequences
			HERV Biological Functions
				Physiological Functions Involving HERVs
				HERVs Involved in Human Diseases
		HERV Involvement in Viral Diseases
			HERVs Associated with Retroviral Infections
			HERVs Associated with RNA Virus Infections
			HERVs Associated with DNA Virus Infections
		HERVs and Epigenetic Modifications
			Retroviruses and Epigenetics
			HERVs and DNA Methylation
				Epigenetic Suppression of HERV Expression
				Epigenetic Activation of HERVs
			HERVs and DNA Acetylation
		The Mechanisms of HERVs in Antiviral Immunity
		The Roles of HERVs in Therapy
			Therapies Targeting HERVs
				Specific Monoclonal Antibodies (mAbs)
				Chimeric Antigen Receptor T Cells (CAR-T)
				Epigenetic Modifications
			Therapies Utilizing HERV Tools
				HERVs as Vaccine Carriers
				LTR as a Retrotransposon Homolog
		References
	Chapter 16: Cholesterol and M2 Rendezvous in Budding and Scission of Influenza A Virus
		Introduction
		Methods
			Experimental Techniques
			Theoretical Modeling and Simulation
		Biomolecules and Interactions Driving Budding and Scission
			Initiation of Budding
			Virion Assembly
			Scission of the Budding Neck
		A Contemporary Hypothesis on the Roles of Cholesterol and M2
		Conclusion
		References
			Further Reading
Correction to: In Situ Imaging of Virus-Infected Cells by Cryo-Electron Tomography: An Overview
	Correction to: Chapter 1 in: S. Vijayakrishnan et al. (eds.), Virus Infected Cells, Subcellular Biochemistry 106, https://doi....