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دانلود کتاب - Encyclopaedia of Virology FOURTH EDition 4th
دانلود کتاب - دایره المعارف ویروس شناسی ویرایش چهارم
مشخصات کتاب
- Encyclopaedia of Virology FOURTH EDition 4th
ویرایش: نویسندگان: dennis Bamford , Mark Zuckerman, encyclopedia 4TH سری: ISBN (شابک) : 9780128145159 ناشر: ap سال نشر: 2022 تعداد صفحات: [4621] زبان: English فرمت فایل : PDF (درصورت درخواست کاربر به PDF، EPUB یا AZW3 تبدیل می شود) حجم فایل: 112 Mb
قیمت کتاب (تومان) : 33,000
در صورت تبدیل فایل کتاب - Encyclopaedia of Virology FOURTH EDition 4th به فرمت های PDF، EPUB، AZW3، MOBI و یا DJVU می توانید به پشتیبان اطلاع دهید تا فایل مورد نظر را تبدیل نمایند.
توجه داشته باشید کتاب - دایره المعارف ویروس شناسی ویرایش چهارم نسخه زبان اصلی می باشد و کتاب ترجمه شده به فارسی نمی باشد. وبسایت اینترنشنال لایبرری ارائه دهنده کتاب های زبان اصلی می باشد و هیچ گونه کتاب ترجمه شده یا نوشته شده به فارسی را ارائه نمی دهد.
توضیحاتی در مورد کتاب - دایره المعارف ویروس شناسی ویرایش چهارم
دایره‌المعارف ویروس‌شناسی، ویرایش چهارم، بر پایه‌ی محکمی است که توسط نسخه‌های قبلی گذاشته شده بود و دامنه آن را با موضوعات جدید و به موقع گسترش می‌دهد. پوشش جامع کتاب از کل ویروس کره، آن را به منبعی منحصربفرد تبدیل می‌کند، با محتوایی که در مورد ویروس‌های موجود در محیط و ویروس‌های بیماری‌زای انسان‌ها، حیوانات، گیاهان و میکروارگانیسم‌ها کاوش می‌کند. حوزه‌ها و مفاهیم کلیدی مربوط به طبقه‌بندی ویروس، ساختار، اپیدمیولوژی، پاتوژنز، تشخیص، درمان و پیشگیری مورد بحث قرار می‌گیرند و خواننده را از طریق فصل‌هایی که در سطح قابل دسترس ارائه شده‌اند، همراه با خواندن بیشتر برای کسانی که به اطلاعات خاص‌تری نیاز دارند، راهنمایی می‌کنند. به دانش‌آموزان و محققان یک فروشگاه یک‌جا برای اطلاعات در مورد ویروس‌شناسی ارائه می‌دهد که به راحتی در جاهای دیگر در دسترس نیست، شکاف مهمی از اطلاعات را در زمینه‌ای که در سال‌های گذشته پیشرفت چشمگیری داشته است پر می‌کند. ، بنابراین یک استاندارد با کیفیت بالا را تضمین می کند
توضیحاتی درمورد کتاب به خارجی
Encyclopedia of Virology, Fourth Edition, builds on the solid foundation laid by the previous editions, expanding its reach with new and timely topics. The book's comprehensive coverage of the whole virosphere makes it a unique resource, with content exploring viruses present in the environment and the pathogenic viruses of humans, animals, plants and microorganisms. Key areas and concepts concerning virus classification, structure, epidemiology, pathogenesis, diagnosis, treatment and prevention are discussed, guiding the reader through chapters that are presented at an accessible level, with included further reading for those needing more specific information. Offers students and researchers a one-stop shop for information on virology not easily available elsewhere Fills a critical gap of information in a field that has seen significant progress in past years Authored and edited by recognized experts in the field, with a range of different expertise, thus ensuring a high-quality standard
فهرست مطالب
e9780128145159v1_WEB Cover ENCYCLOPEDIA OF VIROLOGY FOURTH EDITION EDITORS IN CHIEF EDITORIAL BOARD SECTION EDITORS FOREWORD PREFACE HOW TO USE THE ENCYCLOPEDIA LIST OF CONTRIBUTORS CONTENT OF ALL VOLUMES FUNDAMENTALS OFVIROLOGY A Brief History of Virology Introduction Previrology Dawn of Virology The Physico-Chemical Phase - Plant Viruses The Biochemical Phase - Bacterial Viruses The Cell Biology Phase - Animal Viruses Viral Diversity The Structural Phase The Sequencing Phase Pathogenicity and Host Defense Mechanisms Epidemiology Viral Control Vaccines Drugs Virus Emergence and Human Activities Concluding Remarks Further Reading Relevant Websites The Origin of Viruses Introduction The Evolutionary Connection Between Viruses and Mobile Genetic Elements The Origin of RNA Viruses The Origin of Selfish RNA Replicons and Their Relationships With Modern RNA Viruses A Scenario for the Origin of Riboviria The Origin of RNA Viruses Infecting Eukaryotes The Origin of Reverse-Transcribing RNA and DNA Viruses The Origin of DNA Viruses The Origin of Giant Viruses and Megaphages Conclusion Further Reading The Virocell Concept The Virion/Virus Paradigm Critics of the Virion/Virus Paradigm Critics of the Virocell Concept Diversity of Virocells Virocells and Ribovirocells Virocells With Nucleus Implications of the Virocell Concept Viruses as Cradles of New Genes Enumeration of Viruses in the Environment Are Viruses Living? Conclusions Further Readings Virus Taxonomy Glossary History of Virus Taxonomy Early Taxonomic Developments (1886-1971) Baltimore Classification (1971) Current Virus Taxonomy (1971-Present) The International Committee on Taxonomy of Viruses (ICTV) Organization Taxonomic Process Virus Classification Differentiating Taxa and Viruses Nomenclature Virus Taxa Viruses Future Developments Acknowledgement Further Reading Relevant Websites The Greater Virus World and Its Evolution Introduction Virus Hallmark Genes Evolutionary Relationships Within and Between the Baltimore Classes RNA viruses Reverse-Transcribing Viruses Single-stranded DNA viruses Double-stranded DNA viruses The Evolutionary Status of the Baltimore Classes, Global Organization of the Virus World and Higher Level Virus Taxonomy The Global Network Organization of the Virus World and the Key Events in Virus Evolution Conclusions Further Reading The Virus Species Concept Glossary Species in Biology Assignment of Viruses to Species The Development of the Species Level in Virus Taxonomy Species Assignments and Genetic Relationships Criteria Used in Species Definitions Species and Genotypes Classification of Metagenomically Characterized Viruses Emergence of a Genomics-Based Taxonomy of Viruses Species Nomenclature What are Species? Summary References Further Reading Relevant Websites Genetic Diversity and Evolution of Viral Populations Glossary Introduction Error-Prone Replication Intrinsic Selectivity of Viral Polymerases Other Factors Determining Polymerase Selectivity Lack of Proofreading Role of Post-Replicative Repair Repair Avoidance Error-Prone Repair Polymerases Diversity-Generating Retroelements Viral Hyper-Mutation Mediated by Host Enzymes Cellular Cytidine Deaminases Cellular Adenosine Deaminases Recombination Reassortment Template Switching Recombination in DNA Viruses Basic Population Genetic Processes Shaping Viral Diversity Mutation-Selection Balance Viral Quasispecies Error Catastrophe and Lethal Mutagenesis of Viruses Adaptation via Directional Selection of Beneficial Mutations Frequency-Dependent Selection Random Genetic Drift Implications for Viral Disease Short-Term Pathogenesis Immune Escape Drug Resistance Conclusions Further Reading Mechanisms of RNA Virus Evolution Glossary RNA Viruses Have High Mutation Rates Genetic Exchange Recombination Reassortment Rates of Recombination Detecting Recombination Evolutionary Outcomes for Recombination and Reassortment Natural Selection in Viruses Coevolution With Hosts Viruses are Under Selection by Factors Other Than Host Cells Genetic Drift The Quasispecies Concept Additional Constraints on RNA Virus Evolution Conclusions Further Reading Relevant Websites Mechanisms of DNA Virus Evolution Glossary Introduction Diversity of DNA Virus Genome Types Host Cell Biology and Availability of Host Enzymes Constrains Virus Evolution Time Frames: Viral Adaptation Within a Host vs. Evolution Over Multiple Generations DNA Virus Hosts Vary From Single Cells to Complex Multi-Cellular Organisms The Contributions of DNA Virus Persistence and Chronic Infections Co-Divergence With Hosts as a Driver of DNA Diversification Single Nucleotide Differences as a Measure of Evolutionary Change In Vivo Observations of Within-Host Diversity and Adaptation of DNA Viruses Fluctuations in Tandem Repeat Copy Number as a Mechanism of Evolution Large DNA Viruses Undergo Frequent Recombination Recombination at Different Frequencies for Small DNA Virus Genomes Duplication and Deletions of Genes and Genome Segments Host-Virus Exchange via Horizontal Gene Transfer and Transposable Elements Conclusions Acknowledgments Further Reading Paleovirology Introduction Patterns and Mechanisms Underlying Viral Integration Calibrating the Long-Term Evolutionary History of Extant Viral Families Evolutionary Impact of Endogenous Retroviruses Evolutionary Impact of Non-Retroviral EVE Ecology of Host-Virus Interactions Other Contributions of Paleovirology to Our Understanding of Host-Virus Interactions Further Reading Evolution Steered by Structure Glossary The Evolution of Viruses Viral Evolutionary Relationships From Sequence Analysis A Change of Paradigm: Structure-Based Virus Classification Inferring Viral Evolutionary Relationship Through Structure-Based Classification The Fold of Some Viral Envelope Glycoproteins Recapitulates That of Cellular Proteins Architectural and Functional Similarities With Cellular Structures: Are Exosomes Reminiscent of Enveloped Viruses? Conclusions Acknowledgments See also References Further Reading Relevant Websites Pairwise Sequence Comparison in Virology Virus Classification Methods, the Increase Use of Sequences for Virus Classification Sequence Comparison Methods Sequence-Based Virus Classification Methods Review DEmARC Natural Vector SDT GRAViTy ViPTree ViCTree PASC Description and Application Advantages of PASC Compared to Other Methods Limitations of PASC Conclusion Further Reading Relevant Websites Computational Analysis of Recombination in Viral Nucleotide Sequences Introduction Computational Estimation of Recombination Rapid Tests to Detect the Presence of Recombination Identification of Recombination Breakpoints Estimation of Recombination Rates Reconstruction of Phylogenetic Recombination Networks Analyzing Recombination in Sequences Derived From Next Generation Sequencing Illustrative Case Studies of Analysis of Recombination in Virus Genetic Data Recombination in the Design of HIV-1 Centralized Vaccines The Influence of Recombination on HIV-1 Fitness Recovery Recombination Among Hepatitis B Virus Genotypes Analyzing Adaptation of HIV-1 gp120 Under Recombination Concluding Remarks Acknowledgments References Relevant Websites Phylogeny of Viruses Introduction: Evolution, Phylogeny, and Viruses Tree Definitions Phylogenetic Analysis Applications of Phylogeny in Virology Acknowledgments Further Reading Virus Bioinformatics What is up in Virus Bioinformatics Technology and Bioinformatics Drive Discoveries Tools for Diagnostics Genome Sequencing RNA Secondary Structures in Viruses Viral Metagenomics Evolution and Phylogenetics Virus-Host Interactions Machine Learning as an Opportunity Host Transcriptomics Conclusions Further Reading Relevant Websites Metagenomics in Virology Glossary Metagenomics Applied to Viruses Pioneering Viral Metagenomics, One Gene at a Time Scaling up From Fragmented Genes to Complete Genomes Viral Metagenomics in the Clinic Metagenomic Discovery of New Viral Pathogens Epidemiological Surveillance and Environmental Monitoring Characterizing the Global Viral Diversity Identifying Globally Dominant Bacteriophages Unveiling New Uncultivated Giant Viruses Revealing the Extraordinary Diversity of ssDNA and RNA Viruses Leveraging Time Series to Track Virus Populations Dynamics Future of Viral Metagenomics: Major Challenges and Upcoming Innovations Further Reading Relevant Websites Database and Analytical Resources for Viral Research Community Significance of Viral Databases Overview of Viral Databases and Analytical Tools Types of Databases Types of Bioinformatics Webtools Virus Pathogen Database and Analysis Resource (ViPR) and Influenza Research Database (IRD) Sources of Data Data Aggregated From Public Data Archives Direct Submission of Novel Data Derived and Predictive Data Data Summary Data Curation Data Retrieval Search Interface Application Programming Interfaces (API) Analysis and Visualization Capabilities Sequence Annotation Sequence Search and Alignments Phylogenetic Tree Reconstruction Metadata-Driven Comparative Genomics Analysis and Visualization of 3D Protein Structures Genome Annotation Using VIGOR Virus Genotype/Clade Classification HA Subtype Numbering Conversion Workbench User Support Usage Statistics Summary and Conclusions Further Reading Relevant Websites Classification of the Viral World Based on Atomic Level Structures Glossary Introduction Methods to Compare (Viral) Proteins Incorporating Different Levels of Data to Structural Alignment and Classification Databases for Structure-Based Classification Inferring Phylogeny Based on Structural Data Case Study: Past and Present of the Structure-Based PRD1-Adenovirus Viral Lineage Conclusions and Future Perspectives - New Methods for Classifying Biological Entities Including Viruses Acknowledgments Further Reading Relevant Websites Isolating, Culturing, and Purifying Viruses With a Focus on Bacterial and Archaeal Viruses Glossary Bacterial and Archaeal Viruses Come in Different Sizes and Form a Polyphyletic Group of Viruses Isolation and Culturing of Bacterial and Archaeal Viruses Purification of Viruses Ultrafiltration Methods Precipitation Methods Preparative Ultracentrifugation Methods Chromatographic Methods Flow Field-Flow Fractionation Methods Assessing Purification Performance Conclusions Further Reading Relevant Websites High Throughput Sequencing and Virology Glossary Introduction First Sequencing Methods Next Generation Sequencing and Applications in Virology 454 (Pyrosequencing) Illumina Sequencing Applications of High-Throughput Sequencing in Virology Metagenomic Approaches RNA Sequencing DNA Sequencing - Amplicon Sequencing Enrichment Strategies Positive Selection-Based Enrichment Negative Selection-Based Enrichment Single Cell Sequencing Using Single Cell Sequencing to Investigate Cellular Heterogeneity and its Impact on Viral Infection Using Single Cell Sequencing to Investigate Viral Heterogeneity Single Molecule Sequencing (Pacific Biosciences and Nanopore) Pacific Biosciences Oxford Nanopore Technologies Merging SRS and LRS Discussion/Conclusions Further Reading Single-Virus Genomics: Studying Uncultured Viruses, One at a Time Glossary Single-Virus Genomics: A New Tool for Viral Discovery Best Practices and Protocol for Single-Virus Genomics Sample Size and Preservation Staining and Single-Virus Separation (Sorting) Viral Capsid Lysis and Whole Genome Amplification Sequencing Detailed Protocol Sample Collection and Preservation Viral Staining Fluorescence-Activated Virus Sorting DNA decontamination and fluorescence-activated virus sorting preparation Preparation of 384-well plates for sorting Sorting Whole-Genome Amplification DNA decontamination Reagent preparation DLB preparation Stop solution DNA decontamination of DLB and stop solution Master mix preparation The whole genome reaction procedure References Further Reading Biophysical Characterizations in the Solution State Introduction Solution-State Small Angle X-Ray Scattering SAXS as a Structural Tool (Theoretical Considerations) Time-Resolved SAXS Diffracted X-Ray Tracking X-Ray Footprinting Mass Spectrometry Concluding Remarks Further Reading Virus Crystallography Introduction The Nitty Gritty: How do you do Virus Crystallography Targets, Virus Families and Predisposition to Crystallization (Biosafety Levels 2 and 3) Crystallization and Automation (Additives and Aids) Crystal Handling and Cryoprotection (Notes for Enveloped and Non-Enveloped Viruses) Data Collection (In-House and Synchrotron) and Automation Structure Solution and Model Building Understanding Evolution through Structural Anatomy Synergies Vaccines, Anti-Virals and Therapeutics Future Outlook Acknowledgments Further Reading Relevant Websites Advanced Light and Correlative Microscopy in Virology Glossary Introduction Virus Labeling Advanced Light Microscopy Approaches Real-Time Single Virus Tracking in Live cells Quantitative Spectral Imaging Multiphoton Imaging Cryo Electron Tomography Correlative Light and Cryo Tomography in Cells Discussion and Outlook Further Reading Atomic-Force Microscopy (AFM) Investigation of Viruses Atomic Force Microscopy Principles and Technology AFM of Biological Specimens Initial Observations From AFM Triangulation Numbers of Icosahedra Recombinant and Mutant Virus Particles Virus Fibers and Membranes Infection and Budding From Host Cells Specific and Special Structural Features Dissection of Complex Viruses Visualization of Viral Nucleic Acid Viral Assembly Further Reading Cryo-Electron Microscopy (CEM) Structures of Viruses Historical Background Cryo-EM at Near-Atomic Resolution Data Collection and Image Reconstruction Interpretation of Near-Atomic Resolution Maps Side Chain Interactions and Virus Assembly Beyond Global Symmetry Symmetry Mismatch in DNA Portals Envelope Glycoproteins Genome Structures In-Situ Structural Virology Cellular Electron Cryotomography Acknowledgment References Further Reading Analysis of Viruses in the Cellular Context by Electron Tomography Glossary Introduction Sample Preparation Chemical Fixation Cryo-Immobilization Room Temperature-Electron Tomography Cryo-Electron Tomography Cryo-ET of Cell Periphery Cryo-ET of Cell Lamellae or Vitreous Sections Acknowledgments References Further Reading Relevant Websites Mathematical Modeling of Virus Architecture Glossary Introduction The Principle of Genetic Economy Viral Geometry and Icosahedral Symmetry Mathematical Models of Icosahedral Capsid Architecture Quasi-Equivalence Theory Predictions and Limitations of Quasi-Equivalence Theory Viral Tiling Theory Practical Applications An Overarching Framework for Icosahedral Architectures Non-Quasi-Equivalent Trihexagonal Lattice Architectures Implications for Viral Evolution Virus Structure in 3D - The Hamiltonian Paths Approach Applications of the Hamiltonian Paths Approach An Assembly Code Embedded Within the Viral Genetic Message Virus Assembly Mechanisms Beyond Icosahedral Symmetry Conclusion References Further Reading Relevant Websites Principles of Virus Structure Glossary Introduction General Principles of Capsid Architecture Icosahedral Symmetry Helical Symmetry Methods for Studying Virus Structures Structural Folds of Capsid Proteins Jelly-Roll beta-Barrel The Immunoglobulin-like Fold The Serine Protease Fold The Four-helix Bundle The HK97 Fold Capsid Assembly Non-Enveloped Icosahedral RNA Viruses Enveloped Icosahedral RNA Viruses Small Icosahedral ssDNA Viruses Large Icosahedral dsDNA Viruses Tailed Bacteriophages Conclusion Acknowledgments References Further Reading Relevant Websites Structures of Small Icosahedral Viruses Glossary Introduction Basic Structure Diversity Picornaviruses as an Exemplar Family Capsid Assembly Genome Encapsidation Host Interactions Uncoating Antiviral Drugs Antigenicity and Antibody Interactions Conclusion Further Reading Relevant Websites Structural Principles of the Flavivirus Particle Organization and of Its Conformational Changes Introduction The Flavivirus Precursor Polyprotein and the Derived Structural Proteins The Immature Flavivirus Particle Acid Sensitivity Mature Particle Organization Physical Principles of the Flavivirus Particle Organization Thermodynamic Transition Between Icosahedral Surface Lattices Discussion Acknowledgement References Reoviruses (Reoviridae) and Their Structural Relatives Introduction Overall Structure of the Reoviridae Family Viruses The Non-Turreted Subfamily Sedoreovirinae Rotavirus Orbivirus Phytoreovirus The Turreted Subfamily Spinareovirinae Orthoreovirus Aquareovirus Cypovirus General Features of the Viral Genome Structural Organization of the Capsid Layers The Outer Capsid Layer Cell Entry of the dsRNA Viruses The dsRNA Virus Core and Endogenous Transcription Viral Innermost Capsid Layer That Encloses the Genome Viral RNA-Dependent RNA Polymerase (RdRp) Viral RNA Capping Genome Replication and Packaging Viroplasm or Replication Factories Replication and Packaging Other dsRNA Virus Families Conclusions Acknowledgments References Structures of Tailed Phages and Herpesviruses (Herpesviridae) Glossary Introduction Tailed Phages Icosahedral Head or Capsid Tail Podoviridae Siphoviridae Myoviridae Herpesviruses Structural Comparison of Tailed Phages and Herpesviruses MCP Fold Portal Protein Structural Insights Into the Infective Viral Cycle Genome Ejection Genome Replication Procapsid Morphogenesis Genome Packaging Final Virion Assembly Conclusions Further Reading Adenoviruses (Adenoviridae) and Their Structural Relatives Glossary General Features of Adenoviruses Structure of Human Adenovirus Type 5 Hexon Penton Base Fiber Minor Coat Proteins Protein IIIa Protein VI Protein VIII Protein IX Core Proteins Variants: Other Adenoviruses Fiber Shafts and Heads External Minor Coat Proteins Adenovirus Structural Relatives The Double Jelly Roll Lineage Variants of the Double Jelly Roll Fold: PRD1-Like Viruses With Authentic Hexameric Capsomers (Paired Orthogonal Single... Vertex Structures in the Double Jelly Roll Lineage Membranes and Membrane Proteins Genomes in the Double Jelly Roll Lineage Asymmetric Features Capsid Size Determination in the DJR Lineage Polintons and the Evolutionary Pathway of DJR Viruses Further Reading Relevant Websites Negative Single-Stranded RNA Viruses (Mononegavirales): A Structural View Glossary Prologue Classification of NSRVs and Genome Organization General Features of NSRV Virion Structures Structure of the Virion Surface Structure and Function of Virion Glycoproteins Accessory Proteins in the Virion Surface Inside the Virion The Matrix Proteins The Viral Ribonucleoproteins/Nucleocapsids Assemblies The Nucleoproteins The Polymerase Phosphoproteins Concluding Remarks Further Reading Relevant Websites Structure of Retrovirus Particles (Retroviridae) Gag Proteins and Retroviral Virion Structure Structures of Individual Gag Domains Matrix Protein (MA) Capsid Protein (CA) Nucleocapsid Protein (NC) Linker Peptides Assembly of the Immature Retroviral Virion Leading to Maturation and Release of Virus Structure of ENV Conclusions References Structure of Helical Viruses Glossary Introduction Rod-Shaped Helical Plant Viruses Flexible, Filamentous Plant Viruses Filamentous Bacteriophage Hemorrhagic Filoviridae Viruses of the Archaea, Rudiviridae and Lipothrixviridae Claviviridae Spindle-Shaped Viruses: Bicaudaviridae and Fuselloviridae Conclusion Further Reading Relevant Websites Giant Viruses and Their Virophage Parasites Glossary Introduction The Serendipitous Discovery of Giant Viruses of Amoebae Diversity and Distribution of Giant Viruses in the World The Life Style of the Giants Genomics and Proteomics of Giant Viruses Origin and Evolution: An Intriguing Enigma Parasites of Viruses: The Nature of Virophages and the Genetic Mobilome Perspectives Further Reading Viral Replication Cycle Glossary Attachment Entry Uncoating Transcription and Genome Replication Group I: Double-Stranded DNA Group II: Single-Stranded DNA Group III: Double-Stranded RNA Group IV: Single-Stranded (plus)-Sense RNA Group V: Single-Stranded (-)-Sense RNA Group VI: Single-Stranded RNA with DNA Intermediate Group VII: Double-Stranded DNA with RNA Intermediate Assembly Maturation Release Further Reading Viral Receptors Glossary Introduction Virus Receptors in Virus Cell Entry Attachment Receptor-mediated virus uncoating Receptor-mediated endocytosis The Identification of Virus Receptors Glycan Receptors, Interactions with Viruses Sialic Acid Receptors Influenza Viruses Polyomaviruses Enteroviruses Histo-Blood Group Antigen Receptors Noroviruses Rotaviruses Glycosaminoglycan Receptors Glycan-Based Antiviral Strategies Protein Receptors, Interactions With Viruses Immunoglobulin Superfamily Proteins Virus interactions with IgSF receptors Complement Control Proteins Ectoenzymes CoV-ectoenzyme interactions Co-Receptors for Infection Attachment Factors, Molecules That Facilitate Infection Evolution of Virus-Receptor Interactions and Viral Tropism Summary Further Reading Bacterial and Archeal Virus Entry Glossary Introduction Host Cell Barriers Virion as a Genome Delivery Devise Host Recognition and Adsorption Viral Enzymes in Capsule and Cell Wall Penetration Genome Delivery Mechanisms of Phages Icosahedral Tailed dsDNA Bacterial Viruses Icosahedral DNA Viruses With an Internal Membrane Pleomorphic DNA Viruses Icosahedral ssDNA Bacterial Viruses (With no Membrane) Filamentous DNA Viruses Icosahedral Enveloped dsRNA Bacterial Viruses Icosahedral ssRNA Bacterial Viruses Summary Further Reading Nonenveloped Eukaryotic Virus Entry Preamble Simple Non-Enveloped Viruses Complex Non-Enveloped Viruses Exploitation of the Virus Entry Pathway Concluding Remarks Further Reading Enveloped Virus Membrane Fusion Glossary Introduction General Considerations Viral Fusion Site in the Cell Specific Lipid Requirements Structure of Viral Fusion Glycoproteins Class I fusion glycoproteins Influenza HA, the prototype of class I fusion glycoproteins Class I common characteristics Class II Fusion Glycoproteins TBEV E, the prototype of class II fusion glycoproteins Class II common characteristics Several cellular fusogens have the class II fold Class III Fusion Glycoproteins VSV G, the prototype of class III fusion glycoproteins Class III common characteristics Other Viral Fusion Glycoproteins Regulating the Conformational Change to Avoid Premature Triggering Working of the Fusion Machinery A Common Mechanism of Fusion Interaction With the Target Membrane Structural Intermediates During the Conformational Changes An elongated trimeric intermediate for class I and class II fusion glycoproteins Monomeric intermediates for vesiculovirus G Cooperativity Conclusions Further Reading Genome Replication of Bacterial and Archaeal Viruses Glossary Genomes of Prokaryotic Viruses Genome Replication of Prokaryotic dsDNA Viruses RNA-Primed DNA Replication Protein-Primed DNA Replication Rolling Circle DNA Replication Other DNA Replication Mechanisms Genome Replication of Prokaryotic ssDNA Viruses Rolling Circle Replication Genome Replication of Prokaryotic RNA Viruses Replication Using an RNA-Dependent RNA Polymerase Concluding Remarks Acknowledgments Further Reading Relevant Websites Viral Transcription Introduction General Principles of Viral Transcription Degree of Dependence on Host Transcription Machinery Features of Viral Transcripts at the 5prime and 3prime Ends Promote Translation Transcription Strategies Determine Mechanisms of Host Shutoff Overall Genome Organization Orchestrates Viral Transcriptional Program RNA Viruses Encode a RdRp that Transcribes and Replicates Their Genome RdRps Contain an Evolutionarily Conserved Architecture Different RdRp and Template Conformations Distinguish Transcription from Replication RdRps Can Coordinate Transcription, Capping, and Polyadenylation Prospective Further Reading Translation of Viral Proteins Introduction Canonical or Cap-Dependent mRNA Translation The Initiation Phase Protein Kinase R (PKR) Initiation factor eIF4E Scanning and assembly of the 80S ribosome Elongation and Termination Phases Canonical (Cap-Dependent) Initiation of Virus mRNA Translation ‘Imprisonment’ of Cellular mRNAs Within the Nucleus Non-Canonical (Cap-Independent) Initiation of Virus mRNA Translation Internal Ribosome Entry Sites (IRESes) Cap-Independent Translation Enhancers (CITEs) Virus Alternatives to Components of Initiation An Alternative to the m7G Cap Structure: Virus Protein, Genome Linked (VPg) An alternative to eIF4F Ribosome ‘Shunting’ (Discontinous Scanning) Leaky Scanning Initiation at Non-AUGs Ribosome Reinitation Translational ‘Recoding’: Non-Canonical Elongation and Termination Ribosomal Bypassing (‘Hopping’) Ribosomal ‘Frame-Shifting’ ‘StopGo’/‘Stop Carry-On’/Ribosomal ‘Skipping’ Ribosome Stop Codon ‘Read-Through’ Virus-Encoded Proteinases MicroRNAs (miRNAs) References Further Reading Relevant Websites Recombination Introduction Recombination in DNA Viruses Recombination in RNA Viruses Defective-Interfering RNAs Summary and Conclusions See also Further Reading Assembly of Viruses: Enveloped Particles Glossary Introduction Viral Envelope Icosahedral Enveloped Viruses: Alphaviruses and Flaviviruses Alphavirus Assembly Alphavirus life cycle Alphavirus virion structure Alphavirus assembly and budding Flavivirus Assembly Flavivirus life cycle Flavivirus virion structure Flavivirus assembly and budding Conclusion See also Further Reading Assembly of Viruses: Nonenveloped Particles Architecture of Viruses Methods of Structure Determination Atomic Structure of Helical Viruses Atomic Structure of Spherical Viruses Nucleic Acid-Protein Interaction Evolution Assembly Host Receptor Recognition Site Antigenic Sites Antiviral Agents See also Further Reading Virion Assembly: From Small Picornaviruses (Picornaviridae) to Large Herpesviruses (Herpesviridae) Introduction Structural Principles in Icosahedral Capsid Assembly Synthesis of Nascent Capsid Assembly and Assembly Intermediates Modes of Assembly Capsid Self-Assembly Scaffolding Protein-Assisted Capsid Assembly Viral Genome-Assisted Capsid Assembly Concluding Remarks Acknowledgments Further Readings Genome Packaging Glossary Introduction Energy-independent Genome Packaging in Small Single-Stranded Viruses Energy-independent Genome Packaging in Larger (ss)RNA Viruses Double-Stranded RNA Viruses Energy-Driven Genome Packaging in Double-Stranded DNA and Giant Viruses Conclusion References Relevant Websites Virus Factories Glossary Introduction Methods to Study Virus Factories Representative Examples of Virus Factories Viral Factories as Targets for Antiviral Therapies Further Reading Relevant Websites Release of Phages From Prokaryotic Cells Glossary Introduction The Definition of Phage Lysis The Cell Envelope Multigene Lysis (MGL) Systems The Lambda Prophage as a Lysis Platform The Lambda Lysis Cassette Operational Outline of Lambda MGL Looking Under the Hood of Lambda Lysis A Second Strategy: Pinholins and SAR Endolysins A Second Type of Spanin Regulation of MGL Dual start holin genes: Holin-antiholin pairs Real-Time Regulation of Holin Function: Phage T4 Lysis Inhibition MGL Diversity Holin Diversity Endolysin Diversity Spanin Diversity MGL in Gram-Positive Hosts Lysis in Mycobacteria Single Gene Lysis (SGL) Systems phiX174 E: The First “Protein Antibiotic” Sgl The SGLs of the Leviviridae The Mysterious L Extrusion Phage Egress in Archaea Further Reading Virus Budding Overview Assembly Envelopment Budding ESCRT-dependent budding ESCRT-independent budding Intracellular budding Quasi-enveloped viruses Maturation Cell-to-Cell Transmission Conclusions Acknowledgments References Vesicle-Mediated Transcytosis and Export of Viruses Glossary Introduction Transcytosis In vitro Models of Viral Transcytosis Endocytic Mechanisms Leading to Transcytosis Caveolin-Dependent Endocytosis Macropinocytosis Receptor-Mediated, Clathrin-Dependent Endocytosis Immunoglobulins as Mediators of Transcytosis Endocytic Sorting and Vectorial Transport of Vesicles Secretion of Cargo Transcytosis and Viral Pathogenesis Breaching Epithelial Barriers Neuroinvasion Viral Hepatitis Fetal Infections Extracellular Vesicle-mediated Export of Viruses Nonlytic Release of Virus in Extracellular Vesicles Exosome-Like Release of Quasi-enveloped Viruses Autophagy-Related Vesicle-Mediated Release of Virus References Further Reading Vector Transmission of Animal Viruses Glossary Introduction Arthropod Vectors of Animal Arboviruses Co-Evolution of Viruses and Vectors: Vector-Only, Vector-Borne Viruses and Non-Vectored Viruses Environmental/Anthropogenic Factors Contributing to Vector-Borne Virus Spread Replication and Transmission of Arboviruses in Their Arthropod Vector and the Role of Arthropods in Maintenance and... Virus-Vector Interactions and Role of the Arthropod Innate Immune Response Co-Infection of Arthropods With Symbiotic Bacteria and How It Influences Virus Replication Role of the Vector in the Genetic Diversity of Animal Arboviruses Further Reading Relevant Websites The Human Virome Glossary Definition of the Human Virome Technological Development and Limits for the Description of the Human Virome Composition and Diversity of the Human Virome by Body Compartments Gastrointestinal Tract Virome Skin Virome Oral Cavity and Respiratory Tract Viromes Blood Virome Genital and Urinary Tract Viromes Implication of the Virome in Human Health and Immunity Conclusion Further Reading Relevant Websites Epidemiology of Human and Animal Viral Diseases Glossary Introduction Factors Influencing the Spread of Viral Diseases Perpetuation of Viruses in Nature Virus Entry Virus Shedding Modes of Virus Transmission Influence of the Clinical Status of the Host Influence of Virulence of the Virus Influence of Host Population Immunity Influence of Population Size Influence of Zoonotic Transmission Cycles Influence of Arthropod Transmission Cycles Assessment of Disease Occurrence and Outcome Epidemiological Studies Case-control studies and cohort studies Time series analysis Qualitative studies Molecular Epidemiology Seroepidemiologic Studies Digital Epidemiology Sentinel Studies Vaccine Trials Mathematical Modeling Data Sharing, Data Privacy and Ethics Proof of Causation Conclusion: Implications for Disease Prevention See also Further Reading Zoonosis, Emerging and Re-Emerging Viral Diseases Glossary Introduction Factors in Interspecies Transmission Epidemiological or Ecological Barriers Host-Pathogen Interactions Viral Factors Receptor specificity Ability to adapt Virulence Factors in Increasing Emergence of Viral Diseases Prevention and Control of Emerging Viruses Diagnosis Treatment Vaccination Control of Mosquito Vectors Concluding Remarks Further Reading Antiviral Innate Immunity: Introduction Glossary Introduction Defensins Complement System Cellular Innate Immunity Antiviral Cytokines: The Type I Interferons New Kids in the Gut: The Type III Interferons Interferon Induction Type I IFN Signaling Direct Antiviral Effects of Type I IFNs Indirect Antiviral Effects of Type I IFNs Innate Immunity Memory Tonic IFN Levels Viral Counterstrategies Good Cop-Bad Cop Concluding Remarks Further Reading Humoral and T Cell-Mediated Immunity to Viruses Role of the Innate Immune System in the Initiation of the Adaptive Immune Response Introduction to Barrier Immunity Innate Immune Effectors are Poised to Respond to Viruses That Overcome Barrier Protection Innate Immune Recognition of Viruses Crosstalk Between Innate and Adaptive Immune Cells The Adaptive Immune Response to Viral Infections Overview T Cell Recognition of Viral Antigens T Cell Effectors in the Response to Viral Infections CD4plus T Cells T Helper 1 (Th1) Cells T Follicular Helper (Tfh) Cells Regulatory T Cells (Tregs) Cytotoxic CD4plus T Cells CD8plus Cytotoxic T Cells (CTL) Mounting an Effective T Cell-Mediated Immune Response to Viral Infections T Cell Priming T Cell Help Cytotoxicity Contraction of Cellular Immune Responses and the Formation of Immune Memory The Humoral Immune Response to Viral Infections B Cells are the Drivers of Humoral Immunity Antibodies Play an Essential Role in Antiviral Humoral Immunity Neutralization Opsonization Antibody-Dependent Cellular Cytotoxicity (ADCC) Induction of Immunity to Viruses by Vaccination Dysregulation of Immune Response to Viruses Conclusions Further Reading Antigenicity and Antigenic Variation Introduction Influenza A Virus Hemagglutinin Dengue Virus Envelope Human Immunodeficiency Virus Type 1 Envelope Glycoprotein Enterovirus A71 Capsid Conclusion Further Reading Antigen Presentation Introduction Antigen-Presenting Cells Major Pathways of Antigen Presentation MHC-I Antigen Presentation MHC-II Antigen Presentation Viral Subversion of Antigen Presentation Concluding Remarks Further Reading Defense Against Viruses and Other Genetic Parasites in Prokaryotes Introduction Classification and Diversity of Defense Systems Toxins-Antitoxins: PCD or Dormancy Systems Self Versus Nonself Recognition Innate Immunity Systems CRISPR-Cas – The Adaptive Immunity System Unclassified Defense Systems Genomic Organization and Evolution of Defense Systems Defense Islands and a Tight Link between Defense and Mobilome Genes Gene and Domain Shuffling and Sharing Association of Defense Systems With Programmed Cell Death Components Concluding Remarks Further Reading Relevant Websites Defective-Interfering Viruses History Structure Generation of DI Genomes Defectiveness Interference Defective Interfering versus Defective Viruses Cyclic Variations of Defective Interference Assay for DI Particles Biological Effects DI Particles in Experimental Animals DI Particles in Natural Infections Future Perspectives See also Further Reading Ecology and Global Impacts of Viruses Glossary Introduction Methods for Studying Viral Community Ecology Virus-Host Linkages and Ecology Viral Impacts on Carbon, Nutrient, and Biogeochemical Cycling Drivers of Viral Community Composition Further Reading The Role of Retroviruses in Cellular Evolution Glossary Introduction Molecular Consequences of Retrovirus Integration Retroviruses Can Drive Evolution of Host Genes Host dependency factors (HDFs) Restriction factors (RFs) Host immunity Host genes with indirect effects on retrovirus infection, spread or disease Germline Insertions (Endogenous Retroviruses) Can Generate Genetic Novelty Exaptation of ERVs Exaptation of ERV-encoded envelope glycoproteins Exaptation of ERV-derived non-coding elements Exaptation of other ERV-derived proteins Summary Further Reading Relevant Websites The Role of Bacteriophages in Bacterial Evolution Antagonistic Phage-Bacterium Relationships Synergistic Phage-Bacterium Relationships Lysis-Lysogeny Decision: An Ecophysiological Perspective Coevolution: Polylysogeny Coevolution: Prophage Remnants Coevolution: Integration Sites Coevolution: In the Patient Coevolution: Defense Mechanisms Coevolution: War and Peace Further Reading Viruses and Their Potential for Bioterrorism Glossary Introduction Unconventional Bioweapons Use of Diseases in Early History 20th Century State Sponsored Biological Weapons Programs Viruses as Bioweapons Entomological Warfare Agro-Warfare Biological Agents for Good or Evil Effects of Viral Introductions Conclusion References Further Reading The Use of Viral Promoters in Expression Vectors An Introduction to Promoters Viral Promoters Viral Promoter Examples Further Viral Promoter Use Further Reading Oncolytic Viruses Glossary Introduction Modes of Action Tumor Targeting by OVs Combination Therapies Conclusion Further Reading Relevant Websites Biotechnology Approaches to Modern Vaccine Design Introduction to Virus-Like Particles Immunological Properties of Virus-Like Particles VLPs and the Induction of the Cellular Immune Response VLPs and the Induction of the Humoral Immune Response VLPs and the Stimulation of Toll-Like Receptors Expression Systems to Produce Virus-Like Particles Bacteria Yeast Mammalian Cells Insect Cells Plants and Plant Cell Culture Cell-Free Expression Systems Virus-Like Particles as Nano-Carriers Conjugation of Antigens and Virus-Like Particles Genetic fusion Chemical and affinity conjugation The SpyTag/SpyCatcher system Loading of Virus-Like Particles by Encapsulation VLP-Based Vaccines for Humans HPV and HBV Influenza Polio VLPs as Cancer Vaccines and Therapeutics Further Reading Viruses: Impact on Science and Society Introduction Virus: Meanings and Metaphor Etymology and Evolution of the Meaning of Virus Virus as Metaphor Viruses and Science Impact of Science and Technology on Virology Impact of Viruses on Science Harnessing of Viruses by Humans Commerce and Tulip Mania Vaccines Phage therapy Gene therapy and cancer therapy Bioweapons Impact of Viruses on Society Impact on Human Disease The origins and historical demographics of viral infections in humans Viral epidemics in the past century Impact on human capital in the era of COVID-19 Impact of Viruses on Livestock and Crops Viruses in Art and Literature Further Reading e9780128145159v2_WEB Cover ENCYCLOPEDIA OF VIROLOGY FOURTH EDITION EDITORS IN CHIEF EDITORIAL BOARD SECTION EDITORS FOREWORD PREFACE HOW TO USE THE ENCYCLOPEDIA LIST OF CONTRIBUTORS CONTENT OF ALL VOLUMES HUMAN AND ANIMALVIRUSES Adenoviruses (Adenoviridae) Glossary Classification Virion Structure Genome Life Cycle Epidemiology Clinical Features HAdV-A HAdV-B1 HAdV-B2 HAdV-C HAdV-D HAdV-E HAdV-F HAdV-G Epizootiology Simian Adenoviruses Canine and Other Carnivoran Adenoviruses Porcine Adenoviruses Equine Adenoviruses Bovine, Ovine, Caprine, and Other Ruminant Adenoviruses Avian Adenoviruses Reptilian Adenoviruses Frog and Fish Adenoviruses Pathogenesis Diagnosis Treatment Prevention Adenoviruses as Vectors Further Reading Relevant Websites African Horse Sickness Virus (Reoviridae) Classification Virion Structure and Genome Life Cycle Epidemiology Clinical Features Pathology Diagnosis Treatment, Control, and Prevention Further Reading African Swine Fever Virus (Asfarviridae) Glossary African Swine Fever Virus Classification Virion Structure Genome Organisation Multigene families Polymerases DNA replication Helicases Nucleotide metabolism DNA repair Virion morphogenesis and structural proteins Proteins that inhibit host defences Inhibitors of apoptosis Inhibitors of type I interferon and inflammatory responses Other enzymes Life Cycle Entry Transcription DNA replication Assembly and morphogenesis Epidemiology Clinical Features Pathogenesis Immune Responses Diagnosis and Control Further Reading Akabane Virus and Schmallenberg Virus (Peribunyaviridae) Glossary Introduction Classification Virion Structure Genome Viral Replication Epidemiology Clinical Features Pathogenesis Diagnosis Prevention Further Reading Relevant Websites Alphaviruses Causing Encephalitis (Togaviridae) Glossary History Taxonomy and Classification Virion and Genome Structure Properties of the Virion Properties of the Genome Properties of the Viral Proteins Nonstructural proteins Structural proteins Replication Geographic and Seasonal Distribution Host Range and Virus Propagation Genetics Evolution Epidemiology Transmission and Tissue Tropism Pathogenicity Clinical Features of Infection Pathology and Histopathology Prevention, Treatment and Control Future Further Reading Anelloviruses (Anelloviridae) Glossary Introduction Classification Virion Structure and Genome Life Cycle Epidemiology Clinical Features Pathogenesis Diagnosis Treatment and Prevention Further Reading Animal Lentiviruses (Retroviridae) Glossary Introduction Classification Virion Structure Genome Encoded Proteins Replication Cycle Reverse Transcription Biological Properties Variability Natural Hosts Transmission Tropism Pathogenic Processes Immune Deficiency Inflammation Cell Defenses and Viral Mechanisms to Evade Them Animal Lentiviral Infections Feline Immunodeficiency and Puma Lentiviral Infections Bovine Immunodeficiency (BI) and Jembrana Disease (JD) Visna-maedi (VM) and Caprine Arthritis and Encephalitis (CAE) Equine Infectious Anemia (EIA) Further Reading Animal Morbilliviruses (Paramyxoviridae) Classification Virion Structure Genome Proteins Life Cycle Epidemiology and Host Range RPV PPRV CDV Aquatic Mammal Morbilliviruses Emerging Morbilliviruses Clinical Features Pathogenesis Diagnosis and Prevention Treatment Rinderpest Eradication: A Success Story Further Reading Animal Papillomaviruses (Papillomaviridae) Glossary Classification Virion Structure Genome Life Cycle Epidemiology Clinical Features Papillomas Ruminants Horses Dogs Cats Viral Plaques Horses Dogs Cats Squamous Cell Carcinomas Ruminants Horses Dogs Cats Rabbits Sarcoids Horses Cats Other Neoplasms Pathogenesis Diagnosis Papillomas Viral Plaques Squamous Cell Carcinomas and Other Neoplasms Sarcoids Treatment Papillomas Viral Plaques Squamous Cell Carcinomas and Sarcoids Prevention Further Reading Relevant Websites Astroviruses (Astroviridae) Glossary Classification Virion Structure Genome Life Cycle Binding and Entry Uncoating and Replication Assembly and Release Epidemiology Classical HAstV Novel HAstV Clinical Features Human Disease Animal Disease Pathogenesis Obstacles Mechanism of Disease Immune Response Diagnosis Treatment Prevention Further Reading Avian Hepadnaviruses (Hepadnaviridae) Glossary Classification Virus Structure Genome Life Cycle Epidemiology Pathogenesis and Clinical Features Diagnosis Treatment Endogenous Avian Hepadnavirus Elements Acknowledgments References Further Reading Avian Herpesviruses (Herpesviridae) Classification Host Range Virion Structure Genome Replication Cycle Epidemiology Clinical Features Pathogenesis Diagnosis Prevention Further Reading Avian Influenza Viruses (Orthomyxoviridae) Glossary Introduction Taxonomy Virion Structure and Genome Life Cycle Epidemiology Clinical Features and Pathogenesis Prevention Further Reading Relevant Websites Avian Leukosis and Sarcoma Viruses (Retroviridae) Glossary History Classification Virion Structure Genome Life Cycle Epidemiology Clinical Features Pathogenesis Diagnosis Treatment Endogenous Retroviruses Further Reading Bluetongue Virus (Reoviridae) Introduction Classification Virion Structure and Genome Life Cycle Virus Attachment and Entry Into Cells Transcription and Replication Core Assembly Assembly of Genomic RNA and Packaging Virion Maturation and Egress Epidemiology Pathogenesis and Clinical Features Diagnosis Vaccination and Control Future Perspectives Further Reading Borna Disease Virus and Related Bornaviruses (Bornaviridae) Introduction Classification Virus Structure Genome Life Cycle Epidemiology and Clinical Features Borna Disease Staggering Disease in Cats Bornavirus Associated Encephalitis in Humans Proventricular Dilatation Disease of Birds Endogenous Bornavirus-Like Elements Pathogenesis Diagnosis Control and Prevention Future Prospects Further Reading Bovine Leukemia Virus (Retroviridae) Glossary Classification Epidemiology and Clinical Features Diagnosis Prevention and Treatment Life Cycle Virion Structure Genome Organization and Expression Pathogenesis Acknowledgments References Bovine Viral Diarrhea, Border Disease, and Classical Swine Fever Viruses (Flaviviridae) Classification Genome Structure and Polyprotein Processing Virion Structure Pestiviral Nonstructural Proteins and the Regulation of RNA Replication and Virion Morphogenesis Npro p7 NS2 NS3 NS2-3 NS4A NS4B NS5A NS5B Life Cycle Epidemiology Classical Swine Fever Bovine Viral Diarrhea and Border Disease Clinical Features and Pathogenesis Classical Swine Fever Acute CSF Chronic CSF Late Onset CSF Bovine Viral Diarrhea and Mucosal Disease Acute BVDV infection Fetal infection with BVDV Persistent BVDV infection Mucosal disease Border Disease Prevention and Control Diagnosis Vaccines Vaccines against classical swine fever Vaccines against bovine viral diarrhea Control of Classical Swine Fever in Domestic Pigs Control of Classical Swine Fever in Wild Boar Control of Bovine Virus Diarrhea Control of Border Disease of Sheep Further Reading Capripoxviruses, Parapoxviruses, and Other Poxviruses of Ruminants (Poxviridae) Introduction Classification Virion Structure Genome Life Cycle Sheeppox and Goatpox Virus Epidemiology Clinical features and pathology Histopathology Pathogenesis Diagnosis Treatment Prevention Lumpy Skin Disease Virus Epidemiology Clinical features Pathology Pathogenesis Diagnosis Treatment Prevention Orf Virus Epidemiology Clinical features and gross pathology Histopathology Pathogenesis Diagnosis Treatment Prevention Bovine Papular Stomatitis Virus Pseudocowpoxvirus Parapoxvirus of Red Deer in NZ Vaccinia Virus Cervidpoxvirus Further Reading Chikungunya Virus (Togaviridae) Glossary Classification Virion Structure Genome Organization and Features Protein-Coding Regions Non-Coding Elements CHIKV 3prime UTR Life Cycle Attachment and Entry Non-Structural Protein Expression and Viral Replication Structural Protein Expression and Virion Assembly Epidemiology Clinical Features Pathogenesis Diagnosis, Treatment, and Prevention Further Reading Circoviruses (Circoviridae) Glossary Classification Virion Structure Genome Life Cycle Epidemiology Clinical Features Pathogenesis Diagnosis Disease Control Conclusions Further Reading Relevant Website Coronaviruses: General Features (Coronaviridae) Glossary Introduction Taxonomy and Classification Virion Properties Virion Structure and Composition Genome Organization and Expression Replication Cycle Genome Replication and Recombination Diseases and Host Range See also Further Reading Coronaviruses: Molecular Biology (Coronaviridae) Glossary Introduction Molecular Features of CoVs Replication and Transcription of CoV RNA CoV Accessory Proteins Manipulating CoV Genomes Using RNA Recombination and Reverse Genetics Vaccines and Antiviral Drug Development Future Perspectives See also Further Reading Relevant Websites Crimean-Congo Hemorrhagic Fever Virus and Nairoviruses of Medical Importance (Nairoviridae) Introduction Virion Structure, Genome and Life Cycle The S Segment The M Segment The L Segment Virus Life Cycle Epidemiology Clinical Features Pathogenesis Diagnosis Prevention DNA Vaccines Inactivated Vaccines Modified Vaccinia Virus Ankara (MVA) Adenovirus Vaccine Treatment Further Reading Dengue Viruses (Flaviviridae) Glossary History Taxonomy and Classification Geographic and Seasonal Distribution Host Range and Virus Propagation Genetics Evolution Serologic Relationships and Variability Epidemiology Transmission and Tissue Tropism Pathogenesis Clinical Features of Infection Pathology and Histopathology Immune Response Prevention and Control of Dengue Vaccines Future Further Reading Ebola Virus (Filoviridae) Classification Epidemiology Genome Virion Structure Replication Cycle Virus Attachment and Fusion Primary Transcription & Translation Replication Assembly & Budding Immune Evasion Clinical Features Early Disease Peak Disease Recovery Virus Persistence Pathogenesis Diagnosis Treatment Monoclonal Antibody Therapy Small Interfering RNAs (siRNAs) Small-Molecule Compounds Prevention Adenovirus 26 (Ad26) & Modified Vaccinia Ankara (MVA) Vesicular Stomatitis Virus Acknowledgments Further Reading Relevant Website Enteroviruses (Picornaviridae) Glossary Classification (Compact) Virion Structure Genome Life Cycle Epidemiology Clinical Features Pathogenesis Diagnosis Treatment Prevention Further Reading Relevant Websites Enveloped, Positive-Strand RNA Viruses (Nidovirales) Glossary Taxonomy and Phylogeny Diseases Associated with Nidoviruses Virus Structure Genome Organization The Replicase Structural and Accessory Protein Genes Replication Transcription Origin of Nidoviruses Effect of Nidovirus Infection on the Host Cell See also Further Reading Epstein-Barr Virus (Herpesviridae) Classification Virion and Genome Structure History Epidemiology and Natural History of Infection EBV Strain Variation Immune Response EBV-Associated Diseases Infectious Mononucleosis Multiple Sclerosis Lymphomas in Immunosuppressed Individuals Diffuse Large B-Cell Lymphomas Burkitt’s Lymphoma Hodgkin’s Lymphoma EBV-Associated T Cell and NK Cell Lymphomas Nasopharyngeal Carcinoma Gastric Carcinoma and Other Epithelial Tumors Control and Prevention of EBV Infection Future Perspectives Further Reading Equine Herpesviruses (Herpesviridae) Introduction Classification Virion Structure Genomes Life Cycle Latency Epidemiology Pathogenesis and Immune Response Clinical Features and Pathology Control Future Perspectives Further Reading Equine, Canine, and Swine Influenza (Orthomyxoviridae) Glossary Classification (Compact) Virion Structure Genome Life Cycle Epidemiology Pathogenesis Clinical Features Diagnosis Treatment Prevention Concluding Remarks Further Reading Feline Calicivirus (Caliciviridae) Classification Virus Characteristics Genome Organisation and Viral Proteins Non-structural proteins Life Cycle Epidemiology Pathogenesis Control and Prevention Disease Control Vaccination Further Reading Relevant Websites Feline Leukemia and Sarcoma Viruses (Retroviridae) History Taxonomy and Classification Virion and Genome Structure Replication Geographic Distribution Epidemiology FeLV Subgroups and Host Range Clinical Features and Pathology Envelope Gene Variation and Pathogenicity FeLV Oncogenesis: Virus Evolution and Mutagenesis of Cellular Oncogenes Immune Response Transmission Prevention and Control Future Perspectives Further Reading Fish and Amphibian Alloherpesviruses (Herpesviridae) Glossary Introduction and Classification Virion Structure Genome Life Cycle Epidemiology Fish Alloherpesviruses Amphibian Alloherpesviruses Pathogenesis Fish Alloherpesviruses Amphibian Alloherpesviruses Clinical Features Fish Alloherpesviruses Amphibian Alloherpesviruses Diagnosis Management and Treatment Prevention Further Reading Fish Retroviruses (Retroviridae) Glossary Introduction Retroviruses and their Life Cycle Skin Tumors in Walleye and Their Associated Retroviruses Isolation and Sequencing of Retroviruses from WDS and WEH Lesions Roles of the WDSV Accessory Proteins in Pathogenesis Control of the Seasonal Cycle of Disease Snakehead Retrovirus Salmon Swimbladder Sarcoma-Associated Retrovirus Isolation of a Retrovirus from Salmon Swimbladder Sarcoma Sequence Comparisons of SSSV with Other Retroviruses Prevalence, Seasonality, and Transmission of SSSV Pathogenesis of SSSV Zebrafish Endogenous Retrovirus Phylogeny of Fish Retroviruses Acknowledgment See also Further Reading Fish Rhabdoviruses (Rhabdoviridae) Glossary Classification Virus Structure Genome Genetic Diversity Life Cycle Epidemiology Clinical Features Pathogenesis and Immune Response Diagnosis Prevention Conclusions Further Reading Relevant Websites Foot-and-Mouth Disease Viruses (Picornaviridae) History Classification Virion Structure Genome Protein Products Leader protein P1 region P2 region P3 region Life Cycle Cell Attachment and Entry RNA Replication Translation Post-Translation Processing Virus Assembly and Release Epidemiology Host Range Genetics and Evolution Serological Relationships and Variability Pathogenesis and Clinical Features Immune Response Diagnosis Prevention and Control Future Perspectives Further Reading Relevant Website Fowlpox Virus and Other Avipoxviruses (Poxviridae) Glossary Introduction Classification Virion Structure Genome Life Cycle Epidemiology Pathogenesis Host range Immunomodulation Control & treatment Use of APV as recombinant vaccine vectors Further Reading Relevant Websites Hantaviruses (Hantaviridae) Glossary Historical Introduction Virology Ecology and Epidemiology Clinical Picture and Pathogenesis Diagnostics and Prevention Further Reading Henipaviruses (Paramyxoviridae) Glossary Introduction Classification Virion Structure Genome Life Cycle Epidemiology Clinical Features Pathogenesis Diagnosis Treatment Prevention Further Reading Relevant Websites Hepatitis A Virus (Picornaviridae) Glossary History Taxonomy and Evolutionary Origin Morphology and Physicochemical Properties Genome Organization and Expression, Replication, Morphogenesis Host Range, Transmission and Tissue Tropism Cell Culture and Growth Characteristics Clinical Features and Pathology Common Course of Infection Prolonged Hepatitis A Relapsing Hepatitis A Fulminant Hepatitis A Extrahepatic Manifestations Pathology Innate and Adaptive Immune Response Innate Immune Response Adaptive Immune Response Diagnosis Epidemiology Prevention and Control Further Reading Hepatitis B Virus (Hepadnaviridae) Glossary Introduction Classification Virion Structure Genome Transcription and Translation Surface proteins Core and polymerase X protein Life Cycle Attachment Penetration and Uncoating Transcription/Translation Encapsidation Maturation Egress Epidemiology Genotypes Subtypes Variants Clinical Features Acute HBV Infection Chronic HBV Infection Course of Chronic Infection Mutant Viruses and Chronic Infection Pathogenesis Diagnosis Treatment Resistance Prevention Further Reading Relevant Websites Hepatitis C Virus (Flaviviridae) Glossary Classification Virion Structure and Properties Genome Organization and Viral Proteins Life Cycle Formation of the HCV Replication Organelle Host Cell Factors Contributing to Various Steps of the HCV Replication Cycle Host Cell Lipids of Relevance to the HCV Replication Cycle Activation and Inhibition of Innate and Adaptive Immunity by HCV Epidemiology Clinical Features Pathogenesis Diagnosis Treatment Prevention Acknowledgments Further Reading Relevant Websites Hepeviruses (Hepeviridae) Glossary Classification Virion Structure Genome Life Cycle Epidemiology Clinical Features Pathogenesis Diagnosis Treatment Prevention Further Reading Relevant Websites Herpes Simplex Virus 1 and 2 (Herpesviridae) Glossary Classification Virion Structure Genome Life Cycle Lytic Infection Epigenetic Regulation Host Factors Latent Infection Epidemiology Clinical Features Mucocutaneous Infections Gingivostomatitis Genital herpes Herpetic keratitis Other skin manifestations Neonatal Herpes Simplex Virus Infection Herpes Simplex Encephalitis Herpes Simplex Virus Infections in the Immunocompromised Host Pathogenesis Diagnosis Treatment Prevention Further Reading Relevant Websites History of Virology: Vertebrate Viruses Introduction The Word Virus Early Investigations Foot-and-Mouth Disease Virus Yellow Fever Virus Physical Studies of Viruses The Chemical Composition of Viruses The Cultivation of Animal Viruses Biochemistry Structure of the Virion Tumor Virology Impact on Immunology Vaccines and Disease Control Recognition of HIV-AIDS Arthropod-Borne Viruses of Vertebrates Taxonomy and Nomenclature The Future See also Further Reading Human Boca- and Protoparvoviruses (Parvoviridae) Glossary Introduction Classification Virion Structure Genome Life Cycle Epidemiology Human Bocaviruses Human Protoparvoviruses Clinical Features Human Bocaviruses Human Protoparvoviruses Pathogenesis Diagnosis Prevention Further Reading Relevant Websites Human Coronavirus-229E, -OC43, -NL63, and -HKU1 (Coronaviridae) Glossary Background Classification Virion Structure Genome Non-Structural Proteins Accessory Proteins Life Cycle Attachment Viral Entry and Uncoating Formation of the Replication-Transcription Complex Viral RNA Synthesis Assembly and Release of Virion HCoV-Host Interactions Translational Control ER Stress Response MAP Kinase Pathway Autophagy Apoptosis Pathogenesis Epidemiology and Clinical features HCoV-229E HCoV-OC43 HCoV-NL63 HCoV-HKU1 Diagnosis Treatment Prevention Acknowledgment Conflict of Interest Further Reading Relevant Websites Human Cytomegalovirus (Herpesviridae) Glossary Classification Virion Structure Genome Structure Evolution Life Cycle Host Range Replication Steps Epidemiology Patterns of Infection Virus Propagation Clinical Features Congenital Disease Immunocompromised Host Pathogenesis Transmission Persistence and Latency Immunity Modulation of the Host Response to Infection Modulation of cell autonomous response to infection Modulation of the innate immune response to infection Modulation of adaptive immune response to infection Diagnosis Prophylaxis and Treatment Prevention Future Perspectives Further Reading Relevant Website Human Immunodeficiency Virus (Retroviridae) Glossary Classification The Origin of HIV-1 Organization of the Genome Expression of Viral Genes Virion Proteins The Other Viral Proteins Work Intracellularly Life Cycle Early Phase Attachment and Entry Uncoating, Reverse Transcription, Nuclear Localization, and Integration Late Phase Gene Expression and Assembly Budding and Maturation Epidemiology Modes of Transmission and Risk Factors Prevalence Diagnosis Clinical Features Pathogenesis Coreceptor Switch Macrophage-Tropic HIV-1 and Infection of the CNS Evolution of Drug Resistance Latency Treatment Entry Inhibitors Reverse Transcriptase Inhibitors Protease Inhibitors Integrase Inhibitors Prevention Biomedical Prevention What is PrEP? Social and Educational Prevention Further Reading Relevant Websites Human Metapneumovirus (Pneumoviridae) Glossary Classification Virion Structure and Virus Proteins Genome Life Cycle The Entry of hMPV Viral RNA Synthesis Viral Particle Assembly and Spread Epidemiology and Clinical Features Pathogenesis Cellular Responses Pattern Recognition Receptors (PRRs) and Antagonism of Immune Responses Diagnosis Treatment Prevention Further Reading Human Norovirus and Sapovirus (Caliciviridae) Introduction Norovirus Viral Classification Genome Virion Structure Life Cycle Epidemiology Clinical Features Pathogenesis Immunity Diagnosis Treatment Prevention Sapovirus Classification Virion Structure Genome Life Cycle Epidemiology Clinical Features Pathogenesis Cell Culture Immunity Diagnosis Prevention Further Reading Relevant Website Human Papillomaviruses (Papillomaviridae) Taxonomy, Classification, and Evolutionary Relationships Virion Structure Genome Host Range and Tissue Tropism Life Cycle Entry Early Stages of Infection Maintenance Phase of Infection Late Stages of Infection Functions of Individual Viral Genes The E1 Protein The E2 Protein The E8circE2 Protein The E1circE4 Protein The E5 Protein The E6 Protein The E7 Protein The L1 Protein The L2 Protein Natural History, Transmission and Epidemiology Clinical features, Pathogenesis and Histopathology of HPV Infection Oncogenic HPVs HPV-associated Cancers Immune Response Diagnosis Treatment Prevention Acknowledgments Further Reading Relevant Websites Human Parainfluenza Viruses (Paramyxoviridae) Classification Virion Structure Genome Life Cycle Epidemiology Clinical Features Pathogenesis Diagnosis Treatment and Prevention Further Reading Human Pathogenic Arenaviruses (Arenaviridae) History and Classification Mammarenavirus Virion Structure Mammarenavirus Genome Organization and Proteins Mammarenavirus Life Cycle Cell Attachment and Entry Expression and Replication of the Viral Genome Assembly and Budding Epidemiology of Human Pathogenic Mammarenaviruses Lassa Fever (LF) Lujo Hemorrhagic Fever (LHF) Lymphocytic Choriomeningitis (LCM) Argentinian Hemorrhagic Fever (AHF) Bolivian Hemorrhagic Fever (BHF) Venezuelan Hemorrhagic Fever (VeHF) Pathogenesis and Pathology Clinical Features LF and LHF LCM NW Mammarenaviral HFs Diagnosis LF LCM NW Mammarenaviral HFs Prevention and Control Medical Management Antiviral Drugs Antibody Therapy Vaccines Perspective Disclaimer Further Reading Human Polyomaviruses (Papillomaviridae) Glossary Introduction Virion Structure Genome Infectious Cycle BKPyV BKPyV Clinical Features BKPyV Infectious Cycle JCPyV JCPyV Clinical Features JCPyV Infectious Cycle MCPyV MCPyV Clinical Features MCPyV Infectious Cycle Other HPyVs Polyomaviruses of the Skin Polyomaviruses of the Other Tissues Perspectives Further Reading Relevant Websites Human T-Cell Leukemia Virus-1 and -2 (Retroviridae) Glossary Classification Virion Structure Viral Entry Genome Life Cycle Viral Gene Transcription Viral Translation Assembly, Budding, and Maturation Epidemiology Transmission Clinical Features ATL HAM/TSP HTLV-2-Associated Symptoms Pathogenesis Tax Hbz Viral Clonality In Vivo Animal Models Immune Response Diagnosis and Prevention Treatment Further Reading Relevant Websites Infectious Bursal Disease Virus (Birnaviridae) Glossary Introduction and Classification Virion Structure and Genome Pathogenesis and Clinical Features Diagnosis and Control Further Reading Relevant Websites Infectious Pancreatic Necrosis Virus (Birnaviridae) Glossary Introduction Classification Virion Structure and Genomic Organization Life Cycle Epidemiology Pathogenesis and Clinical Features Molecular Determinants of Virulence Control Further Reading Influenza A Viruses (Orthomyxoviridae) Glossary Classification of Influenza A Viruses Virion Structure Genome Genomic Organization Reassortment and Mutagenesis Life Cycle Attachment and Entry Transcription and Translation Genome Replication Viral Assembly Budding of New Virions Immunological Responses and Immune Evasion Innate Immune Responses Adaptive Immune Responses Immune Evasion Strategies of IAV Evolution and Epidemiology Evolution of IAV IAV Epidemics and Pandemics Clinical Features Pathogenesis Diagnosis Treatment and Prevention Antivirals Vaccines See also Further Reading Relevant Websites Influenza B, C and D Viruses (Orthomyxoviridae) Glossary Classification (Compact) Influenza B virus Virion Structure Genome Life Cycle and Functions of Viral Proteins Virus Entry and Genome Expression and Replication by Polymerase Proteins Hemagglutinin (HA) Neuraminidase (NA) NB Matrix protein (M1) BM2 Non-structural protein 1 (NS1) NEP Epidemiology Clinical Features Pathogenesis Diagnosis Treatment Prevention Influenza C and D viruses Virion Structure and Genome Functions of the HEF Glycoprotein During the Life Cycle Epidemiology Clinical Features and Pathogenesis Diagnosis Treatment and Prevention Further Reading Relevant Websites Jaagsiekte Sheep Retrovirus (Retroviridae) History Classification Genetic Organization and Virion Proteins Replication Cycle enJSRVs Ovine Pulmonary Adenocarcinoma Mechanisms of Virus-Induced Cell Transformation Enzootic Nasal Tumor Virus Future Perspectives Further Reading Japanese Encephalitis Virus (Flaviviridae) Classification Virion Structure The Extracellular Mature Virion The Intracellular Immature Virion Genome Genome Structure Gene Expression Structural proteins Nonstructural proteins Life Cycle Viral Entry Viral Translation and RNA Replication Viral Morphogenesis Epidemiology Geographic Distribution and Epidemiologic Patterns Genetic Diversity Transmission Vector-Borne Transmission Non-Vector-Borne Transmission Clinical Features Pathogenesis Diagnosis Clinical Diagnosis Laboratory Diagnosis Treatment Prevention Further Reading Relevant Websites Kaposi’s Sarcoma-Associated Herpesvirus (Herpesviridae) Glossary Classification Virion Structure Genome Life Cycle Binding and Entry of the Virus to the Host Cell Transport of the Virus in the Host Cytoplasm and Entry of Viral DNA Into the Nucleus Latency Replication of the Latent KSHV Episome Genome Segregation Lytic Activation Interaction of KSHV With the Host Immune System Epidemiology Clinical Features Kaposi’s Sarcoma Primary Effusion Lymphoma Multicentric Castleman’s Disease Pathogenesis Kaposi’s Sarcoma Primary Effusion Lymphoma Multicentric Castleman’s Disease KSHV Inflammatory Cytokine Syndrome Diagnosis Kaposi’s Sarcoma Primary Effusion Lymphoma Multicentric Castleman’s Disease Treatment Kaposi’s Sarcoma Classical Kaposi’s sarcoma Post-transplantation or iatrogenic Kaposi’s sarcoma HIV associated Kaposi’s sarcoma Primary Effusion Lymphoma Multicentric Castleman’s Disease Prevention No Vaccination Against KSHV is Available Today Further Reading Marburg and Ravn Viruses (Filoviridae) Epidemiology Classification Virion Structure Genome NP VP35 VP40 GP VP30 VP24 L Life Cycle Clinical Features Pathogenesis Diagnosis Treatment Prevention Further Reading Relevant Websites Measles Virus (Paramyxoviridae) Glossary Classification Virion Structure Genome Replicative Complex Transcription and Replication Envelope Complex Life Cycle Epidemiology Clinical Features Complications Immunosuppression Immune Responses Persistent Infections Pathogenesis Diagnosis Treatment Prevention MeV-Based Vaccines and Cancer Therapeutics Further Reading Relevant Websites Molluscum Contagiosum Virus (Poxviridae) Glossary Virion Structure History Genome Life Cycle Epidemiology Clinical Features Pathogenesis Diagnosis Treatment Prevention Further Reading Relevant Websites Mumps Virus (Paramyxoviridae) History Taxonomy and Classification Properties of the Virion Properties of the Genome Properties of the MuV Proteins Physical Properties Replication Serologic Relationships and Variability Evolution and Genetics Epidemiology Geographic and Seasonal Distribution Transmission and Tissue Tropism Clinical Features of Primary Infection Systemic Manifestations Parotid Glands Neurological Disease Pancreas Genitourinary Tract Cardiac Symptoms Musculoskeletal System Other Symptoms Pathogenesis Immune Response Differential Diagnosis Laboratory Diagnosis Detection of Mumps Virus Antibody Response Neutralisation Tests Utilization of Assays Primary Infection and Primary Vaccine Failure Secondary Infection and Secondary Vaccine Failure Prevention and Control Future Perspectives Further Reading Murine Leukemia and Sarcoma Viruses (Retroviridae) Glossary Classification History Genome and Structure Replication Host-Virus Interactions Pathology: Murine Leukemia Viruses Pathology: Murine Sarcoma Viruses MLV Vectors Endogenous MLVs See also Further Reading Newcastle Disease Virus (Paramyxoviridae) Glossary Classification Virion Structure Genome Life Cycle Epidemiology Pathogenesis Clinical Features Diagnosis Prevention Further Reading Relevant Websites Orthobunyaviruses (Peribunyaviridae) Glossary Classification Serological Classification Phylogenetic Analysis by Sequencing Genome Genome and Encoded Proteins Life Cycle Transmission Vector Vertebrate Hosts Reassortment Evidence of Reassortment Effects of Reassortment Epidemiology Viral Discovery Surveying Viral Endemic Ranges and Tracking Viral Spread Orthobunyavirus Outbreaks and Tracking Host and Viral Determinants of Disease-Species Barriers Clinical Features and Pathogenesis Anopheles A Bunyamwera Bwamba California Simbu Diagnosis Serological Assays Polymerase Chain Reaction (PCR) Detection of Viral RNA Treatment and Prevention Acknowledgments References Further Reading Relevant Websites Parapoxviruses (Poxviridae) Introduction Taxonomy and Classification Host Range, Epidemiology, and Virus Propagation Serologic Relationships Clinical Features Orf, Scabby Mouth, Contagious Pustular Dermatitis (CPD), Ecthyma Contagiosum Milker’s Nodule, Paravaccinia, Pseudocowpox Bovine Papular Stomatitis (BPS) Parapox of Red Deer Physical Properties Virion Properties PPV Genomes Viral Replication Viral Proteins Known or Putative Genes Involved in Pathogenesis and Virulence VEGF-E - ORF 132 Viral Interferon Resistance Protein - ORF 020 Viral dUTPase - ORF 007 Viral IL-10 - ORF127 Viral GM-CSF Inhibitory Factor (GIF) - ORF 117 Chemokine Binding Protein (vCBP) - ORF112 NF-κB Inhibitors - ORF 002, 024, 073, 119, 121 Poxvirus APC/C Regulator (PACR) - ORF 014 Ankyrin Repeat (ANK)/F-box Genes - ORFs 008, 123, 126, 128, 129 Inhibitor of Apoptosis - ORF 125 Pathogenesis and the Host Immune Response to Infection Immune Response to Infection Diagnosis ORFV Vector Vaccines Oncolytic Potency Prevention and Control Further Reading Parechoviruses (Picornaviridae) Glossary Classification Virion Structure Genome Life Cycle Epidemiology Seroprevalence Outbreaks Japan Australia Parechovirus Species B-D Clinical Features Virus Genetics and Association to Disease Pathogenesis Diagnosis Treatment and Prevention Further Reading Relevant Websites Parvoviruses of Carnivores, and the Emergence of Canine Parvovirus (Parvoviridae) Glossary Classification (Compact) Virion Structure and Genome Life Cycle Epidemiology Host Range Variation, Its Control, and the Emergence of CPV Pathogenesis and Clinical Features Diagnosis Treatment Prevention Further Reading Polioviruses (Picornaviridae) Introduction The Virus Genome The Virus Particle The Poliovirus Receptor Classification of Picornaviridae Pathogenesis and Disease Vaccines Attenuation of the Sabin Vaccine Strains The Global Polio Eradication Program Vaccine-Derived Poliovirus Cessation of Vaccination Further Reading Relevant Website Porcine Reproductive and Respiratory Syndrome Virus and Equine Arteritis Virus (Arteriviridae) Glossary Classification Virion Structure Genome Organization Life Cycle Epidemiology Clinical Features PRRSV EAV Pathogenesis and Immunity PRRSV Pathogenesis PRRSV Immunity EAV Pathogenesis EAV Immunity Diagnosis PRRSV EAV Prevention and Control Further Reading Relevant Websites Prions of Vertebrates Glossary Introduction Aberant Prion Protein Metabolism is the Central Feature of Prion Disease Human Prion Diseases are Biologically Unique The Protein-Only Hypothesis of Prion Propagation Structure and Putative Function of PrPC Structural Properties of PrPSc Prion Disease Pathogenesis Prion Strains Neuronal Cell Death in Prion Disease Future Perspectives See also Further Reading Pseudorabies Virus (Herpesviridae) History Classification Virion Structure Genome Capsid Tegument Envelope Replication Cycle Clinical Features and Pathogenesis Immunity Latency Epidemiology and Prevention Pseudorabies Virus as a Tool in Neurobiology Future Perspectives Acknowledgments Further Reading Rabbit Hemorrhagic Disease Virus and European Brown Hare Syndrome Virus (Caliciviridae) Classification Virion Structure Genome Epidemiology Clinical Features Pathogenesis and Host Immunity Diagnosis Prevention and Control Treatment Further Reading Rabbit Myxoma Virus and the Fibroma Viruses (Poxviridae) Glossary Myxoma Virus and the Fibroma Viruses Classification Virion Structure Genome Life Cycle Epidemiology Myxoma Virus Californian Myxoma Virus Myxomatosis in European Rabbits Clinical Disease in European Rabbits Pathogenesis of Myxomatosis in European Rabbits Diagnosis Treatment Prevention of Myxomatosis Rabbit Fibroma Virus Squirrel Fibroma Virus Hare Fibroma Virus Further Reading Relevant Website Rabies and Other Lyssaviruses (Rhabdoviridae) Glossary Classification (Compact) Virion Structure Genome Life Cycle Epidemiology Clinical Features Pathogenesis Diagnosis Treatment Prevention Conclusions Further Reading Relevant Websites Respiratory Syncytial Virus (Pneumoviridae) Glossary History RSV Disease Classification Virus Entry The Virion The F Glycoprotein The G Glycoprotein Genome Transcription and Replication Non-Structural Viral Proteins The Third Viral Glycoprotein Animal Models of RSV Protection From RSV Disease Vaccination - The First Attempt Passive Immunity and Prophylactic Therapy Maternal Vaccination Live Attenuated Vaccines Vectored RSV Vaccines Treatment of RSV: Antiviral Agents References Further Reading Relevant Websites Rhinoviruses (Picornaviridae) Glossary Classification Virion Structure Genome Life Cycle Receptor Entry Uncoating Translation Replication Assembly Epidemiology Pathogenesis Clinical Features Asymptomatic Infections Common Cold Acute Otitis Media (AOM) Bronchiolitis and Recurrent Wheezing Asthma Pneumonia Chronic Obstructive Pulmonary Disease (COPD) Diagnosis Sampling Nucleic Acid Detection Culture Typing Treatment Prevention Further Reading Relevant Websites Rift Valley Fever Virus and Other Phleboviruses (Phenuiviridae) Glossary Introduction Virion Structure, Genome, and Strategy of Replication Functions of Nonstructural Proteins The Viruses Rift Valley Fever Virus Sandfly Fever Naples and Sandfly Fever Sicilian viruses Toscana Virus Punta Toro and Cocle Viruses Phleboviruses in the Candiru Antigenic Complex Chagres Virus Huaiyangshan Banyangvirus (Formerly Severe Fever With Thrombocytopenia Syndrome Virus: SFTSV) Heartland Banyangvirus (HRTV) Bhanja Virus Other Phleboviruses Further Reading Roseoloviruses: Human Herpesviruses 6A, 6B and 7 (Herpesviridae) Glossary Introduction Biology of the Viruses Viral Genomics HHV-6A and HHV-6B HHV-7 Virus Structure and Replication Roseolovirus Cell Tropism HHV-6A and HHV-6B HHV-7 Chromosomal Integration of HHV-6A and HHV-6B Mechanism of chromosomal integration Viral Latency State of viral genome during latency Reactivation from latency CIHHV-6 and the possibility of reactivation Epidemiology Occurrence HHV-6B and HHV-7 primary infections HHV-6A Chromosomal integration Tissue Distribution Transmission Horizontal transmission of HHV-6 and HHV-7 Vertical transmission of HHV-6A and HHV-6B Transmission of HHV-6 by organ donation Immune Responses HHV-6, HHV-7 and Immunomodulation HHV-6A, HHV-6B and HHV-7 Disease Associations CIHHV-6 and Disease CIHHV-6 and potential for disease in the immunocompetent CIHHV-6 and potential for disease in the immunocompromised HHV-6B and HHV-7 Primary Infection and Disease Exanthem subitum Encephalitis FSE and temporal lobe epilepsy HHV-6 and HHV-7 Disease in Older Children and Adults Delayed primary infection HHV-6 and HHV-7 and the possibility of encephalitis HHV-6B and DRESS (drug rash with eosinophilia and systemic symptoms) HHV-6 and multiple sclerosis Alzheimer’s disease HHV-6B and Disease After Organ Transplant HHV-6B encephalitis after HSCT HHV-7 and Disease after Organ Transplant HHV-6 and HIV HHV-6 and HHV-7 Laboratory Tests and Diagnosis of Infection Antibody Detection - HHV-6 and HHV-7 Primary HHV-6B Primary HHV-7 Virus detection - HHV-6A, HHV-6B and HHV-7 CIHHV-6 and Misdiagnosis of Active Infection Diagnosis of CIHHV-6 HHV-6 and HHV-7 and Antiviral Therapy Concluding Remarks Further Reading Rotaviruses (Reoviridae) Glossary Classification Virion Structure Genome Life Cycle Epidemiology Clinical Features Pathogenesis Diagnosis Treatment Immune Response and Prevention Further Reading Relevant Websites Rubella Virus (Picornaviridae) Glossary Introduction Classification Host Range and Virus Propagation Properties of the Virion Genomic Organization Intracellular Replication Cycle Genetics and Evolution Serologic Relationships and Variability Epidemiology Transmission and Tissue Tropism Clinical Features of Infection Pathogenesis, Pathology, and Histopathology Immune Response and Serodiagnosis Diagnosis Prevention and Control of Rubella Future Further Reading Saint Louis Encephalitis Virus (Flaviviridae) Glossary History Virion Structure/Genome Classification/Genetic Characterization Life Cycle Host Range Epidemiology Pathogenesis/Clinical Features Diagnosis Prevention Further Reading Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) (Coronaviridae) Glossary History Emergence of SARS Virology SARS- and MERS-CoVs SARS- and MERS-CoV Genomes Phylogeny Virus Receptors Epidemiology Ecology, Animal Reservoir and Zoonotic Transmission SARS MERS-CoV Human-to-Human Transmission Clinical Features Laboratory Diagnosis Animal Infection Models SARS MERS Pathogenesis SARS MERS-CoV Treatment SARS MERS Vaccines and Immunity SARS MERS Conclusion Further Reading Relevant Website Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) (Coronaviridae) Glossary Further Reading Simian Immunodeficiency Virus (SIV) and HIV-2 (Retroviridae) Glossary Introduction SIV and HIV-2-Taxonomy and Classification SIV and HIV-2-Virion Structure SIV and HIV-2-Genome SIV and HIV-2 Lifecycle SIV Epidemiology SIV Clinical Features Immunity to SIV Epidemiology of HIV-2 Risk and Transmission of HIV-2 Diagnosis of HIV-2 HIV-2 Clinical Features Pathogenesis of HIV-2 Immunity to HIV-2 HIV-2 Humoral Immunity HIV-2 Cellular Immunity Treatment of HIV-2 Prevention of HIV-2 Interactions of HIV-2 and HIV-1 in Vivo HIV-2 Protection From HIV-1 In vitro evidence for HIV-2 protection from HIV-1 Further Reading Relevant Websites Sindbis Virus (Togaviridae) Classification Virion Structure Genome Life Cycle Epidemiology Clinical Features Pathogenesis Diagnosis Treatment Prevention Further Reading Relevant Website Tick-Borne Encephalitis Virus (Flaviviridae) Classification Virion Structure TBEV Life Cycle Viral Proteins Epidemiology Clinical Features Pathogenesis Diagnosis Treatment Prevention Further Reading Relevant Website Transmissible Gastroenteritis Virus of Pigs and Porcine Epidemic Diarrhea Virus (Coronaviridae) Classification Virion Structure Genome Life Cycle Epidemiology Clinical Features Pathogenesis Diagnosis Treatment Prevention Further Reading Vaccinia Virus (Poxviridae) The Origin of Vaccinia Virus Classification Virion Structure Genome Life Cycle Entry Transcription and Translation Genome Replication Assembly Host Range Virulence Immunomodulators VACV: The Smallpox Vaccine VACV: The Vaccine Vectors Antiviral Drugs Further Reading Relevant Website Varicella-Zoster Virus (Herpesviridae) Glossary Classification Virion Structure Genome Life Cycle Epidemiology Clinical Features Pathogenesis Diagnosis Treatment Prevention Further Reading Variola and Monkeypox Viruses (Poxviridae) Glossary History Classification and Structural Morphology Viral Life Cycle Pathogenesis Clinical Features Epidemiology Smallpox Monkeypox Diagnosis Prevention Treatment Disclaimer Further Reading Relevant Websites Vesicular Stomatitis Virus and Bovine Ephemeral Fever Virus (Rhabdoviridae) Glossary Classification Virus Structure Genomes and Proteins Life Cycle Attachment, Entry and Uncoating Gene Expression and Replication Assembly and Budding Inhibition and Modification of Host Cell Functions Epidemiology Pathogenesis and Clinical Features Control and Treatment Further Reading Relevant Websites West Nile Virus (Flaviviridae) Glossary Classification Virion Structure Genome and Viral Proteins C Protein prM/M E Protein NS1 NS2A and NS2B NS3 NS4A and NS4B NS5 Life Cycle Epidemiology Clinical Manifestations Pathogenesis Diagnosis Treatment and Prevention Acknowledgment Further Reading Yellow Fever Virus (Flaviviridae) Glossary Classification (Compact) Virion Structure Genome Life Cycle Epidemiology Clinical Features Diagnosis Treatment (When Applicable) Prevention Further Reading Relevant Websites Zika Virus (Flaviviridae) Glossary Introduction Classification Virion Structure and Genome Organization Life Cycle Ecology and Transmission Cycles Virus Replication Cycle Epidemiology Brief History ZIKV Lineages and Disease Association Potential Factors Contributing to ZIKV Emergence Clinical Features Pathogenesis Diagnosis Treatment Prevention and Control Further Reading Relevant Websites e9780128145159v3_WEB Cover ENCYCLOPEDIA OF VIROLOGY FOURTH EDITION EDITORS IN CHIEF EDITORIAL BOARD SECTION EDITORS FOREWORD PREFACE HOW TO USE THE ENCYCLOPEDIA LIST OF CONTRIBUTORS CONTENT OF ALL VOLUMES PLANT VIRUSES An Introduction to Plant Viruses Introduction Prehistory Recognition of Viral Entity The Biological Age The Biochemical/Biophysical Age The Molecular Biology Age See also Further Reading Emerging and Re-Emerging Plant Viruses Glossary Introduction Vegetable Viruses Tobamoviruses Cucumber Green Mottle Mosaic Virus Geographical distribution Causal agent and classification Disease symptoms and yield losses Epidemiology Control Tomato Brown Rugose Fruit Virus Geographical distribution Causal agent and classification Disease symptoms and yield losses Epidemiology Control Orthotospoviruses Tomato Spotted Wilt Virus Geographical distribution Causal agent and classification Disease symptoms and yield losses Epidemiology Control Resistance breaking strains Begomoviruses Squash Leaf Curl Virus Geographical distribution Causal agent and classification Disease symptoms and yield losses Epidemiology Control Grapevines Viruses Grapevine Roditis Leaf Discoloration-Associated Virus Geographical distribution Disease symptoms and yield losses Causal agent and classification Epidemiology Control Grapevine Pinot Gris Virus Geographical distribution Disease symptoms and yield losses Causal agent and classification Epidemiology Control Staple Crops: Cassava Brown Steak Disease Geographical distribution Causal agent and classification Disease symptoms and yield losses Epidemiology Control Ornamental Viruses: Rose Rosette Virus Geographical distribution Disease symptoms and yield losses Causal agent and classification Epidemiology Control Further Reading Relevant Websites Emerging Geminiviruses (Geminiviridae) Glossary Introduction The Tomato Yellow Leaf Curl Disease Geographical Distribution The Disease Symptoms, Host Range and Yield Losses Causal Agent and Taxonomy Epidemiology Control The Tomato Leaf Curl New Delhi Disease Geographical Distribution The Disease Symptoms and Yield Losses Epidemiology Component Capturing and Exchange of Helper Components Control The African Cassava Mosaic Disease Geographical Distribution The Disease Symptoms and Yield Losses Classification of Cassava Mosaic Begomoviruses Epidemiology Recent Outbreak of CMD in South East Asia Control The Cotton Leaf Curl Disease in the Indian Sub-Continent Geographical Distribution The Disease Symptoms and Yield Losses Causal Agent and Disease Classification Epidemiology Control Conclusion Further Reading Movement of Viruses in Plants Glossary Introduction Intracellular Movement Intercellular Transport Systemic Transport Virus Movement and Plant Defense Responses Further Reading Plant Antiviral Defense: Gene-Silencing Pathways Glossary Introduction Diverse Gene-Silencing Pathways in Plants Antiviral RNA Silencing Viral and Plant RNA-Silencing Suppressors Antiviral Silencing in Crops Viral siRNA-Mediated Antiviral RNAi in Mammalian Cells View of Applications of av-RNAi Further Reading Relevant Websites Plant Resistance to Viruses: Engineered Resistance Glossary Introduction A Historical Perspective on Engineered Resistance Against Plant Viruses Molecular Underpinnings of Engineered Resistant to Plant Viruses Field Resistance and Commercial Adoption Benefits of Virus-Resistant Transgenic Plants to Agriculture Environmental and Human Health Safety Issues Conclusions Further Reading Relevant Websites Plant Resistance to Viruses: Natural Resistance Associated With Dominant Genes Glossary Introduction R Gene Products R Gene Responses to Viruses Mechanisms of Recognition Signaling Mechanisms Resistosome Non-NB-lRR Resistance Outlook Further Reading Plant Resistance to Viruses: Natural Resistance Associated With Recessive Genes Glossary Introduction Overview of Naturally Occurring Recessive Resistance Cloned Recessive Resistance Genes Characteristics of eIF4E-Mediated Recessive Resistance Molecular Mechanisms of eIF4E-Mediated Recessive Resistance New Recessive Resistance Genes Found in Natural Diversity Toward the Application of Recessive Resistance in Agriculture Conclusions Further Reading Plant Viral Diseases: Economic Implications Glossary Introduction Cereal Viral Diseases Root and Tuber Crops Viral Diseases Cassava Viral Diseases Potato Viral Diseases Sweet Potato Viral Diseases Vegetable Viral Diseases Chilli Viral Diseases Cucurbit Viral Diseases Okra Viral Diseases Tomato Viral Diseases Fruit Virus Diseases Banana Viral Diseases Cacao Swollen Shoot Disease Citrus Tristeza Virus Papaya Ring Spot Virus Plum Pox Virus (Sharka) Disease of Stone Fruits Legume Viral Diseases Cash Crops Viral Diseases Sugarcane Viral Diseases Ornamentals and Orchids Viral Diseases Further Reading Relevant Websites Retrotransposons of Plants Glossary Introduction and General Classification The Life Cycle of LTR Retrotransposons High Similarities with Intracellular Steps of the Retroviral Cycle Evolution as Quasispecies-Like Populations The Different Genera of LTR Retrotransposons The Family Pseudoviridae (Ty1/copia Retrotransposons) The Family Metaviridae (Ty3/gypsy Retrotransposons) Unclassified LTR Retrotransposons Env-Like Functions in Plants? The Nomenclature Issue See also Further Reading Relevant Websites Vector Transmission of Plant Viruses Glossary Introduction Plant Virus Vectors Transmission of Plant Viruses by Insects History of the Typology of the Transmission Modes Circulative Transmission Circulative Non-Propagative Transmission Case of Aphid-Transmitted Luteovirids Case of Leafhopper-Transmitted Mastreviruses Case of Whitefly-Transmitted Begomoviruses Circulative Propagative Transmission Non-Circulative Transmission Capsid Strategy Case of Aphid-Transmitted Cucumoviruses Helper Strategy Case of Aphid-Transmitted Potyviruses Case of Aphid-Transmitted Caulimoviruses Transmission by Beetles Transmission by Non-Insect Vectors Transmission by Mites Transmission by Nematodes Transmission by Fungi and Protists Host and Vector ‘Manipulation’ by Plant Viruses Future Prospects See also Further Reading Viral Suppressors of Gene Silencing Glossary Introduction Antiviral Gene Silencing Pathway Small Interfering RNAs Direct Antiviral Immunity Viral Suppressors of Gene Silencing Promote Infection Mechanisms of Gene Silencing Suppression Small RNA Binding Inhibition of siRNA Biogenesis Homeostasis of Gene Silencing Components Inhibition of Assembly or Activity of RNA-Induced Silencing Complexes Inhibition of Silencing Amplification Interference With DNA Methylation Activation of Cellular Transcription Assays to Identify and Characterize Gene Silencing Suppressors Viral Suppressors of Gene Silencing Need Cellular Factors Evolution of Viral Suppressors of Gene Silencing Effect of Gene Silencing Suppressors on Plant Development Silencing Suppressors Mediate Viral Synergism Viral Suppressors in Support of Biotechnology Further Reading Virus-Induced Gene Silencing (VIGS) Glossary Introduction PTGS and VIGS Establishment of a VIGS System VIGS Vectors VIGS Application Advantages and Limitations Conclusion and Prospects Further Reading Relevant Websites Alfalfa Mosaic Virus (Bromoviridae) Glossary History Taxonomy and Classification Particle Structure and Composition Genome Structure Interaction Between Viral RNA and Coat Protein Translation of Viral RNA Replication of Viral RNA Virus Encapsidation and Movement Role of Coat Protein in the AMV Replication Cycle Virus-Host Relationships Host Range and Economic Significance Transmission Epidemiology and Control See also Further Reading Alphaflexiviruses (Alphaflexiviridae) Glossary Introduction Taxonomy, Phylogeny of Family Members, and Evolution Virion Structure Genome Organization Properties and Functions of Gene Products Replication and Propagation Transmission, Host Range Epidemiology and Control Virus-Host Relationships Diagnosis Satellite RNAs Associated With Infections of Alphaflexiviridae Further Reading Alphasatellites (Alphasatellitidae) Glossary Introduction Classification Structure of Alphasatellites Likely Origins of Alphasatellites Life Cycle/Epidemiology Pathogenesis See also Further Reading Amalgaviruses (Amalgaviridae) Glossary Classification Virion Structure Genome Life Cycle Epidemiology Pathogenesis Diagnosis Treatment Prevention See also Further Reading Relevant Websites Badnaviruses (Caulimoviridae) Glossary Introduction Classification Virion Structure Genome Life Cycle Epidemiology Clinical Features Pathogenesis Diagnosis Prevention Further Reading Relevant Websites Banana Bunchy Top Virus (Nanoviridae) Glossary Introduction Taxonomy, Phylogeny, and Evolution Virion Structure Genome Organization and Functions of Gene Products Host Range and Transmission Virus-Host Relationships Diagnosis Geographical Distribution Historical Records and Possible Origins Epidemiology and Control of BBTV See also Further Reading Outline placeholder Glossary Introduction Taxonomy and Classification Virion Properties and Composition Genome Organization and Expression Host Range and Transmission Replication Virus-Host Relationships Epidemiology Diagnosis Control See also Further Reading Bean Common Mosaic Virus and Bean Common Mosaic Necrosis Virus (Potyviridae) Glossary History Taxonomy and Classification Geographic Distribution Host Range and Transmission Properties of the Virion and Genome Properties of particles Serological relationships Properties of the genome and replication Pathogenicity, Pathology, and Resistance Genes Recombination and Variability Diagnosis Host range and symptomatology Serological techniques Reverse transcription-polymerase chain reaction Prevention and Control See also Further Reading Bean Golden Mosaic Virus and Bean Golden Yellow Mosaic Virus (Geminiviridae) Glossary Introduction Taxonomy, Phylogeny, and Evolution Virion Structure, Genome Organization, Properties and Functions of Gene Products, Replication and Propagation Transmission, Host Range, and Epidemiology Virus-Host Relationships Diagnosis Management Further Reading Beet Curly Top Virus (Geminiviridae) Glossary Introduction History Classification and Nomenclature The Origin of BCTV and the Beet Leafhopper Vector: An Early Example of Global Transport of a Plant Pathogen and its Vector Geographic and Seasonal Distribution Changes in BCTV Strain Prevalence Genome Organization and Gene Expression Replication Virus Movement Host Range and Pathogenesis Transmission of BCTV by the Beet Leafhopper Vector Experimental Systems for Infection of Plants by BCTV Management of Curly Top Disease Caused by BCTV Resistant Varieties Cultural Practices Management of the Leafhopper Vector With Insecticides Sanitation IPM for Curly Top Disease Further Reading Beet Necrotic Yellow Vein Virus (Benyviridae) Glossary Classification Virion Structure Genome Organization and Functions of Gene Products Transmission Epidemiology Disease Symptoms Virus-host Relationships Diagnosis Prevention See also Further Reading Benyviruses (Benyviridae) Glossary History Virion Structure, Particle Properties and Associations of Viral Particles With Cellular Structures Organization of the Genome and Properties of the Encoded Proteins Disease, Host Range, and Epidemiology Transmission Diagnosis Control Similarities and Dissimilarities With Other Taxa Further Reading Relevant Websites Betaflexiviruses (Betaflexiviridae) Glossary Introduction Taxonomy and Phylogeny Members of the Family Virion Structure Genome Organization Properties and Functions of Gene Products Replication and Propagation Transmission and Host Range Geographical Distribution See also Further Reading Betasatellites and Deltasatelliles (Tolecusatellitidae) Glossary Introduction Classification and Nomenclature Genome Organization Genetic Diversity and Center of Origin for Betasatellites Life Cycle, Epidemiology Replication of Betasatellites Functional Role of betaC1 in Disease Development Resistance Against Betasatellites Deltasatellites Introduction Genome Organization of Deltasatellites Trans-Replication of Deltasatellites See also Further Reading Bluner-, Cile-, and Higreviruses (Kitaviridae) Glossary Introduction Taxonomy, Phylogeny, and Evolution Members of the Family Virion Structure Genome Organization and Gene Product Function Replication and Propagation Transmission and Host Range Diseases, Epidemiology, and Control Diagnosis Concluding Remarks Further Reading Brome Mosaic Virus (Bromoviridae) Glossary Introduction Virion Structure and RNA Encapsidation Genome Organization Genome Structure, Gene Expression and Sequences Noncoding Regions, Cis Signals, and Sub-Genomic Promoter Replication and Propagation In Vitro and In Vivo Replication Studies Sub-Genomic mRNA Synthesis RNA Recombination Properties and Functions of Viral Gene Products BMV 1a and Viral Replication Compartments Host Factors in RNA Replication Host Genes That Regulate Lipid Metabolism and Membrane Composition Host Genes That Induce/Stabilize Spherules Host Genes That Regulate Translation of Viral Proteins and 1a Targeting Host Genes Required for Viral Replication Activity Transmission and Host Range BMV Application in Biotechnology Future Perspectives See also Further Reading Bromoviruses (Bromoviridae) Glossary Introduction Phylogeny and Biodiversity of the Family Bromoviridae Virion Properties and Structure Genome Organization and Expression Genomic RNA Replication and Recombination Biology Further Reading Bymoviruses (Potyviridae) Glossary Classification Member Species Virion Structure, Serological- and Cytological Properties Nucleic Acid Properties and Differentiation of Bymoviruses Organization of the Genome and Properties of the Encoded Proteins Virus Transmission and Movement Symptoms, Epidemiology and Host Range Diagnosis Control Further Reading Relevant Websites Cacao Swollen Shoot Virus (Caulimoviridae) Glossary Introduction Taxonomy Host Range and Symptomatology Transmission Virion Structure Genome Organization Phylogeny Epidemiology: Geographical Distribution of Viral Molecular Diversity Diagnosis Serological Diagnostics PCR Diagnosis Control of the Disease See also Further Reading Carmo-Like Viruses (Tombusviridae) Glossary Introduction Taxonomy, Classification, and Evolutionary Relationships Distribution, Host Range, Transmission, and Economic Significance Virion Structure and Assembly Genome Structure and Protein Functions Replication and Gene Expression Satellites, Defective-Interfering RNAs Virus-Host Interaction Further Reading Relevant Websites Cassava Brown Streak Viruses (Potyviridae) Glossary Introduction Aetiology, Host Range and Transmission Current Status of CBSD in Africa Genome Organization and Gene Functions Evolution, Diversity and Distribution of Viruses Involved in CBSD Management and Control of CBSD Sources of CBSD Resistance and Their Introgression Engineering CBSD Resistance Cross Reading With Other Chapters See also Further Reading Relevant Websites Cassava Mosaic Viruses (Geminiviridae) Glossary Taxonomy Intraspecific Diversity History Virion Structure Genome Replication Transmission Pathogenesis and Symptoms Epidemiology Diversity and Distribution Distribution of the African CMGs Distribution of CMGs in Asia Recombination and the CMD pandemic Field-Level Epidemiology Regional Epidemiology Diagnosis Economic Importance Control Host Plant Resistance Cultural Methods Virus Resistance by Engineering Biosafety considerations See also Further Reading Relevant Websites Caulimoviruses (Caulimoviridae) Glossary Introduction Taxonomy, Phylogeny, and Evolution Virion Structure Genome Organization Properties and Functions of CaMV Gene Products Movement Protein (MP) Aphid Transmission Factor (P2) Virion-Associated Protein (P3) Capsid Protein (P4) Protease/Reverse Transcriptase (P5) Transactivator/Viroplasmin (P6) Replication and Propagation Transmission, Host Range Virus-Host Relationships Further Reading Cheraviruses, Sadwaviruses and Torradoviruses (Secoviridae) Glossary Classification Virion Structure Genome Organization Life Cycle and Epidemiology Host Range Geographic Distribution Transmission Clinical Features and Pathogenesis Diagnosis Treatment Prevention References Further Reading Relevant Websites Citrus Tristeza Virus (Closteroviridae) Glossary Introduction History Taxonomy and Classification Geographic Distribution Economic Costs of CTV Host Range and Cytopathology The CTV Virions The CTV Genome The Untranslated Regions (UTRs) Gene Functions The CTV Sub-Genomic RNAs Defective RNAs Virus-Virus Interactions Transmission CTV Control Measures CTV Diagnosis Attempts to Apply Transgenic Resistance to CTV Epilogue See also Further Reading Closteroviruses (Closteroviridae) Glossary Introduction Classification Genome Organization Infectious Cycle Epidemiology Disease Symptoms Pathogenesis Diagnosis Treatment Prevention Further Reading Relevant Websites Comoviruses and Fabaviruses (Secoviridae) Glossary Introduction Taxonomy and Classification Physical Properties of Viral Particles Viral Structure Genome Structure Expression of the Viral Genome Functions of the Viral Proteins Relationships With Other Viruses Use in Biotechnology Geographic Distribution Host Range Transmission Epidemiology Symptomatology and Cytopathology Economic Importance Further Reading Relevant Websites Cotton Leaf Curl Disease (Geminiviridae) Glossary Introduction History of CLCuD CLCuD in Africa CLCuD in Southern Asia Etiology of CLCuD Elucidation of the Etiology of CLCuD Components of the CLCuD Complex Begomoviruses Associated With CLCuD CLCuD in Africa CLCuD in the Indian subcontinent CLCuD-Associated Alphasatellite Components CLCuD-Associated Betasatellite Control of CLCuD Strategies to Control the CLCuD Complex Short Term Strategies Long Term Strategies Genetics of host plant resistance to CLCuD Engineered Resistance to the CLCuD Complex Pathogen Derived Resistance (PDR) Antisense RNA technology RNAi technology Non-Pathogen Derived Resistance Genome Editing Strategy: CRISPR/Cas9 Approach to Control CLCuD See also Further Reading Cowpea Mosaic Virus (Secoviridae) Glossary Introduction Taxonomy and Classification Biology Physical Properties of Viral Particles Viral Structure Genome Structure Expression of the Viral Genome Functions of the Viral Proteins Replication Use in Biotechnology See also Further Reading Relevant Websites Cucumber Mosaic Virus (Bromoviridae) Glossary Introduction Taxonomy and Phylogeny Geographic Distribution Host Range Symptoms and Diagnosis Cytopathology Virion Structure Genome Organization Properties and Functions of Gene Products The CMV Infection Cycle Replication Cell-to-Cell and Long-Distance Movement Transmission Variation and Evolution Epidemiology and Control See also Further Reading Dianthovirus (Tombusviridae) Glossary Introduction Taxonomy and Classification Genome Organization Virions, Transmission, and Epidemiology Gene Expression RNA Replication Host Factors in Dianthovirus RNA Replication Cell-to-Cell and Systemic Movement RNA Silencing Suppression Further Reading Endornaviruses (Endornaviridae) Glossary Introduction Plant Endornaviruses Fungal Endornaviruses Endornaviruses From Other Eukaryotic Kingdoms Genome Organization Gene Products Replication (RdRp Activity) Vertical Transmission Horizontal Transmission Regulation of Copy Number Pathogenesis Virus-Host Relationship (Host RNA Silencing Against Endornaviruses) Further Reading Fimoviruses (Fimoviridae) Glossary Introduction Classification Virion Structure Genome Life Cycle (Replication) Epidemiology Symptomatology and Economic Impact Diagnosis Treatment and Prevention Further Reading Furoviruses (Virgaviridae) Glossary Classification Virion Structure Nucleic Acid Properties and Differentiation of Furoviruses Organization of the Genome and Properties of the Encoded Proteins Virus Transmission and Movement Symptoms, Epidemiology and Host Range Diagnosis Control Similarities and Dissimilarities with Other Taxa Further Reading Relevant Websites Geminiviruses (Geminiviridae) Glossary Introduction Taxonomy, Phylogeny, and Evolution Becurtovirus Begomovirus Capulavirus Curtovirus Eragrovirus Grablovirus Mastrevirus Topocuvirus Turncurtovirus Virion Structure Genome and Viral Proteins DNA Satellites Associated With Geminiviruses Diagnosis Life Cycle Pathogenicity Control Further Reading Relevant Websites Hordeiviruses (Virgaviridae) Glossary Introduction Taxonomy and Characteristic Virus Particle Structure Genome Structure and Expression Function and Relatedness of the Hordeivirus Proteins Replicase Proteins (alphaa and gammaa) Coat Protein TGB Movement Proteins TGB1 TGB2 protein TGB3 protein Pathogenesis Protein (gammab) Cytopathology and Replication Pathogenesis Hordeivirus-Host Interactions gammab Interference With Host Defenses RNA silencing pathways Autophagy responses ROS bursts Post-Translational Modifications of BSMV Proteins Hordeivirus Applications to Cereal Genomic Analyses Future Perspectives Further Reading Relevant Websites Idaeoviruses (Mayoviridae) Glossary Introduction Geographical Distribution Natural and Experimental Transmission Disease Symptoms and Effects Naturally Infected Plants Experimentally Infected Plants Virion Structure Genome Viral Proteins The Coat Protein The Movement Protein The Replicase Protein Diagnosis and Detection Serological Testing Reverse Transcriptase - PCR (RT-PCR) Therapy Prevention and Control Relationships With Other Viruses Further Reading Ilarviruses (Bromoviridae) Glossary Introduction Classification Virion Structure Genome Infection Cycle Replication Transmission Control Symptoms and Pathogenesis Diagnosis Further Reading Luteoviruses (Luteoviridae) Glossary Introduction Taxonomy and Classification Virion Properties Virion Structure and Composition Genome Organization and Expression Evolutionary Relationships Host Range and Transmission Replication Virus-Host Relationships Epidemiology Diagnosis Control Further Reading Machlomovirus and Panicoviruses (Tombusviridae) Glossary Classification Virion Structure Genomes Hosts and Distribution Life Cycle Epidemiology Pathogenesis Diagnosis Prevention Further Reading Maize Streak Virus (Geminiviridae) Glossary Introduction History and Taxonomy Host Range and Symptoms Diversity and Evolution Transmission Particle Structure Genome Organization The Long Intergenic Region The Short Intergenic Region The Complementary Sense Genes (Rep and RepA) The Virion Sense Genes (MP and CP) Molecular Biology of MSV Replication Particle Assembly and Movement Control of MSD MSD Epidemiology Leafhopper Vectors Plant Hosts The Virus Future Threat See also Further Reading Relevant Websites Nanoviruses (Nanoviridae) Glossary Introduction Classification and Taxonomy Particle Properties Genome Organization Properties and Functions of Nanovirid Proteins Nanovirid Replication Taxonomy and Phylogeny Nanovirid Evolution Nanovirid-Associated Alphasatellites Transmission and Host Range Tissue Tropism and Means of Transmission Transmission by Aphids Host Range Epidemiology and Control Diagnosis Concluding Remarks Further Reading Necro-Like Viruses (Tombusviridae) Glossary Taxonomy and Classification Virion Properties, Structure and Composition Genome Organization and Expression Intraspecific Relationships Satellites Transmission and Host Range Cytopathology Further Reading Relevant Websites Nepoviruses (Secoviridae) Glossary Introduction and Historical Perspective Taxonomy, Phylogeny, and Evolution Virion Structure Genome Organization and Function of Viral Proteins Production of Viral Proteins: Translation and Polyprotein Processing Viral RNA Replication Cell-to-Cell and Systemic Movement in the Plant Host Range, Symptom Determinants and Interaction With Plant Defense Responses Transmission Population Structures: Quasi-Species, Satellite RNAs and Defective-Interfering RNAs Diseases, Economic Considerations and Control Concluding Remarks Further Reading Ophioviruses (Aspiviridae) Glossary Introduction Taxonomy, Phylogeny and Evolution Virion Structure Genome Organization and Replication Properties and Functions of Gene Products Pathogenicity and Geographic Distribution Diagnosis Transmission, Experimental Host-Range and Control Cytopathology Concluding Remarks Further Reading Relevant Websites Orthotospoviruses (Tospoviridae) Glossary History Taxonomy and Classification Geographic Distribution Host-Range and Virus Propagation Virion Properties Genome Properties Protein Properties Replication Pathogenicity and Cytopathology Transmission and Epidemiology Genetics and Evolution Detection and Diagnosis Prevention and Control Future Perspectives Further Reading Ourmiaviruses (Botourmiaviridae) Glossary Introduction Taxonomy, Phylogeny and Evolution Virion Structure Genome Organization Properties and Functions of Gene Products Replication and Propagation Transmission, Host Range Epidemiology and Control Virus-Host Relationships Diagnosis Concluding Remarks Further Reading Papaya Ringspot Virus (Potyviridae) Glossary History and Taxonomy Classification and Relationship With Other Potyviruses: The “PRSV Cluster” Host Range, Symptomatology, and Geographic Distribution Transmission and Epidemiology General Properties and Genome of PRSV Sequence Diversity and Evolution; Molecular Clock Analyzes Molecular Determinants for Biological Properties Diagnostics Virus Control Cultural Practices: Prophylactic Measures Cross-Protection Breeding for Resistance Pathogen-Derived Resistance for Controlling PRSV: The Hawaii Case Transgenic Resistance Summary Remarks Cross Check With Other Chapters See also Further Reading Pecluviruses (Virgaviridae) Glossary History Taxonomy and Classification Geographic and Seasonal Distribution Host Range and Symptoms Transmission Seed and Sap Transmission Soil-Borne Vector Transmission Virion Morphology Physical Properties Molecular Properties Genome Structure and Expression Strategies Coding Sequences 5 prime and 3prime Noncoding Sequences Sequence Comparisons and Phylogeny Assembly of Virus Particles Detection and Diagnosis Immunoassays Molecular Assays Vector Epidemiology and Disease Cycle Disease Development Cycle Disease Control Cultural Practices Host Plant Genetic Resistance Future Perspectives Further Reading Pepino Mosaic Virus (Alphaflexiviridae) Glossary Introduction Taxonomy and Classification Virion Properties Genome Organization and Expression Host Range and Symptomatology Virus Isolates and Strains Virus Transmission and Epidemiology Diagnostic Virus Damage and Control See also Further Reading Relevant Websites Plant Reoviruses (Reoviridae) Glossary Introduction Taxonomy and Classification Virion Structure and Genome Organization Fijivirus Oryzavirus Phytoreovirus Replication and Gene Expression Distribution Host Range and Virus Transmission Fijiviruses Oryzaviruses Phytoreoviruses Pathogenicity Diagnosis and Control Future Further Reading Relevant Websites Plant Resistance to Geminiviruses Glossary Introduction An Overview of Natural Resistance to Viruses in Plants Resistance to Cassava Mosaic Geminiviruses Geminivirus Resistance in Tomato The Case of Resistance to Tomato Yellow Leaf Curl Virus Breeding for TYLCV Resistance Characterization of Ty Genes Genetic Engineering for TYLCV Resistance Resistance to Beet Curly Top Virus Geminivirus Resistance in Beans Resistance to Mungbean Yellow Mosaic Viruses Resistance to Cotton Leaf Curl Virus in Cotton Resistance to Maize Streak Virus Conclusion Further Reading Plant Rhabdoviruses (Rhabdoviridae) Glossary Introduction Taxonomy and Classification Particle Morphology and Composition Genome Structure and Organization Properties of Viral Proteins The Nucleocapsid Protein (N) The Phosphoprotein (P) The P3 Movement Protein The Matrix Protein (M) The Glycoprotein (G) The Polymerase Protein (L) Other Accessory Proteins Cytopathology and Replication Entry Transcription and Genome Replication Morphogenesis Cell-To-Cell Movement Vector Relationships, Distribution and Evolution Further Reading Relevant Websites Plant Satellite Viruses (Albetovirus, Aumaivirus, Papanivirus, Virtovirus) Glossary Introduction Albetoviruses: Viruses Related to Satellite Tobacco Necrosis Virus Aumaivirus: Satellite Maize White Line Mosaic Virus Papaniviruses: Viruses Related to Satellite Panicum Mosaic Virus Virtovirus: Satellite Tobacco Mosaic Virus Effect of Mixed Infections on the Host and the Helper Viruses Common Ancestry of Plant Satellite Viruses? Concluding Remarks Further Reading Plum Pox Virus (Potyviridae) Glossary Introduction Economical Importance History and Geographical Distribution Host Range and Symptomatology Virion Structure and Genome Properties Strains/Molecular Groups Detection Virus Spread Ecology and Control Further Reading Relevant Websites Poleroviruses (Luteoviridae) Glossary Introduction Polerovirus Physical Properties Polerovirus Genome Organization and Gene Expression Polerovirus Phylogenetic Diversity Polerovirus Transmission Virus-Virus Interactions Silencing Suppression by Poleroviruses Potato Leafroll Virus Sugarcane Yellow Leaf Virus Beet Poleroviruses Diagnosis Disease Management Further Reading Pomoviruses (Virgaviridae) Glossary Introduction Taxonomy and Classification Physical Properties of Particles Genome Properties and Functions of the Encoded Proteins Virus-Host Interactions and Movement Host Range, Geographical Distribution, Transmission by Vector and Variability Serological Relationships, Diagnosis, and Control Further Reading Relevant Websites Potato Virus Y (Potyviridae) Glossary Introduction Viral Particle, Genome and Cytopathology Host Range Transmission Serology Phylogeny and Evolution PVY in Potato Control Methods PVY in Pepper PVY in Tomato PVY in Tobacco Prospects See also Further Reading Potexviruses (Alphaflexiviridae) Glossary Introduction Taxonomy, Phylogeny, and Evolution Virion Structure Genome Organization Properties and Functions of Gene Products Replication and Propagation Transmission, Host Range Epidemiology and Control Diagnosis Concluding Remarks Further Reading Potyviruses (Potyviridae) Glossary Introduction Taxonomy, Phylogeny and Evolution Virion Structure Properties of the Genome Properties and Functions of Gene Products Derived From the Polyprotein Expression of Overlapping Gene Products Replication and Propagation Pathogenicity Epidemiology and Control Diagnosis Concluding Remarks Further Reading Relevant Websites Quinviruses (Betaflexiviridae) Glossary Introduction Taxonomy and Phylogeny Virion Structure Genome Organization Properties and Functions of Gene Products Replication and Propagation Transmission and Host Range Epidemiology and Control Diagnosis Concluding Remarks Further Reading Reverse-Transcribing Viruses (Belpaoviridae, Metaviridae, and Pseudoviridae) Glossary Introduction: The Paradigm of LTR Retrotransposons and Reverse-Transcribing Viruses Genome Organization and Functions of Gene Products and Other Structural Features Taxonomy, Phylogeny and Members of the Families Life Cycle and Replication Host Range and Evolutionary Dynamics Impact and Relationships of LTR retrotransposons and Retroviruses With Their Hosts Concluding Remarks Further Reading Relevant Websites Rice Tungro Disease (Secoviridae, Caulimoviridae) Glossary Introduction Rice Tungro Disease Rice Tungro Bacilliform Virus Taxonomy Transmission and Host Range Structure Genome Functions of Proteins Genome Variability Virus-Host Relationships Control Biotechnological Applications Rice Tungro Spherical Virus Taxonomy Transmission and Host Range Structure Gene Functions Genome Diversity Genome Virus-Host Relationships Control Concluding Remarks See also Further Reading Rice Yellow Mottle Virus (Solemoviridae) Introduction Virion Properties Organization of the Genome Relationships of the Species With Other Taxa Biological Properties Diagnostic and Identification Epidemiological Aspects Diversity and Evolution Further Reading Satellite Nucleic Acids and Viruses Glossary Introduction History Geographical Distribution Classification General Properties and Effects of Satellites Satellite Viruses Satellite Nucleic Acids and Satellite-Related Nucleic Acids Replication and Structure Satellite RNAs Satellite DNAs Sequence Variation and Evolution Expression of Foreign Sequences From Satellite Vectors Satellite-Mediated Control of Viruses See also Further Reading Secoviruses (Secoviridae) Glossary Introduction Taxonomy, Phylogeny, and Evolution Members of the Family Virion Structure Genome Organization Properties and Functions of Gene Products Replication and Propagation Transmission, Host Range Epidemiology and Control Biotechnological Applications Diagnosis Concluding Remarks Further Reading Relevant Websites Sequiviruses and Waikaviruses (Secoviridae) Glossary Introduction Classification: Taxonomy, Phylogeny, and Evolution Variation of Isolates and Strains Properties of Virions Genome Organization Properties of Viral Proteins Transmission Diseases and Management Concluding Remarks Further Reading Relevant Websites Solemoviruses (Solemoviridae) Glossary Introduction Virion Structure Genome Phylogenetic Relationships Replication and Movement Host Range and Transmission Pathological and Epidemiological Aspects Further Reading Tenuiviruses (Phenuiviridae) Glossary Introduction Taxonomy Classification Virion Structure Morphology Physical and Physicochemical Properties Components Genome Organization Replication and Transcription Biological Properties Host Range and Geographic Distribution Cytopathology Disease Symptoms and Control Insect Vector and Type of Transmission Relation to Other Taxa Further Reading Tobacco Mosaic Virus (Virgaviridae) Glossary The Beginnings of Virology Physical and Chemical Properties of TMV Self-Assembly of TMV Particles Virus Disassembly Antigenicity of TMV Taxonomy and Classification Replication and Cell-to-Cell Movement of TMV Biotechnology Applications of TMV Bionanotechnology Applications of TMV See also Further Reading Tobamoviruses (Virgaviridae) Glossary History of Tobamovirus Research Taxonomy and Classification Evolution Virus Structure and Composition Genome Organization Viral Proteins Interactions Between Viral and Host Proteins Virus Replication The Cis-Acting Sequences Satellite Tobacco Mosaic Virus Host Range and Symptomology Transmission Further Reading Tobraviruses (Virgaviridae) Glossary Taxonomy and Characteristics Virus Particle Production and Structure M-Type and NM-Type Infections Genome Structure and Expression RNA Sequences Expression of Virus Genes Recombination and Sequence Deletions in Tobravirus RNAs Viral Proteins RNA1 RNA2 Tobraviruses as Gene Expression/Silencing Vectors Diseases Caused by Tobraviruses Further Reading Tomato Leaf Curl New Delhi Virus (Geminiviridae) Glossary Introduction Tomato Leaf Curl Disease and Virus Biodiversity on Tomato in the Indian Subcontinent Phylogeny and Molecular Diversity Genome Organization and Function of Gene Products Synergism and Genetic Changes Leading to Begomovirus Emergence and Evolution Host Range of ToLCNDV Transmission and Epidemiology Virus-Host Interactions Small Non-Coding RNAs Counter Defense RNA Silencing Basal Level of Defense Resistance Gene or R-Gene Mediated Defense Diagnosis and Management See also Further Reading Tomato Spotted Wilt Virus (Tospoviridae) Glossary Classification Virion Structure Genome Transmission Epidemiology Pathogenesis Diagnosis Prevention Plant Resistance Further Reading Relevant Websites Tomato Yellow Leaf Curl Viruses (Geminiviridae) Glossary Introduction Classification and Taxonomy Virion Structure Genome Monopartite TYLCVs Bipartite TYLCVs Satellite DNAs Associated With TYLCVs TYLCV Genome Evolution Life Cycle Hosts Epidemiology Geographical Distribution and Spread TYLCV-Whitefly Vector Relationship Path of the virus in the insect Retention of the virus in the insect vector Replication of the virus in the insect vector Effects of TYLCV on life expectancy and fertility of the whitefly vector Pathogenesis Diagnosis Symptom observation Microscopy Immunodetection Nucleic acid hybridization Nucleic acid amplification Sequencing Treatment Prevention Planting in whitefly-free period, eradication of inoculum Cultures under cover Chemical control of whiteflies Biological control of whiteflies Breeding for Resistance Genetic Engineering Expression of viral genes RNAi CRISPR/Cas9 TYLCV Transmission to Tomato and Host Response Transmission by whiteflies Response of plants to TYLCV infection RNAi Aggregates Transcriptome and metabolome Involvement of heat shock and quality control proteins in the establishment of TYLCV infection Further Reading Relevant Websites Tombusvirus-Like Viruses (Tombusviridae) Glossary Introduction Taxonomy, Phylogeny, and Evolution Virion Structure, Assembly, and Disassembly Genome Structure Gene Function Gene Expression Genome Replication Subviral RNAs Symptoms and Transmission Host Range and Geographic Distribution Applied Aspects Concluding Remarks Further Reading Relevant Websites Tombusviruses (Tombusviridae) Glossary Classification Taxonomy, Phylogeny and Evolution Virion Structure Genome Organization and Replication Strategy Life Cycle Cytopathology Subviral Molecules Pathogenesis Further Reading Relevant Websites Tritimoviruses and Rymoviruses (Potyviridae) Glossary Introduction Taxonomy and Classification Virion Structure Genome Organization Functions of Viral Proteins Life Cycle and Epidemiology Host Range Vector Transmission Seed Transmission Disease Cycle Pathogenicity Diagnosis Disease Management Cultural Practice Genetic Resistance Biotechnological Application Concluding Remarks Further Reading Relevant Websites Triviruses (Betaflexiviridae) Glossary Introduction Classification Virion Structure Genomic Organization and Properties of Encoded Proteins Phylogenetic Relationships of the Different Triviruses Cellular Localization of Trivirus Particles and Viral Replication Host Range and Distribution of Triviruses Symptomology, Impact and Vectors Diagnosis Prevention and Treatment Further Reading Relevant Websites Tymoviruses (Tymoviridae) Glossary The Family and Its Distinguishing Features Tymoviruses Properties and Distinguishing Characteristics Capsid Structure Genome Organization Replication Cycle Infection and Transmission Phylogenetic Relationships and Species Demarcation Marafiviruses Properties and Distinguishing Characteristics Virion Structure, Genome Organization, Replication Cycle, and Phylogenetic Relationships Infection and Transmission Maculaviruses Properties and Distinguishing Characteristics Poinsettia Mosaic Virus Properties and Distinguishing Characteristics Bombyx Mori Latent Virus Properties and Distinguishing Characteristics Further Reading Relevant Websites Umbraviruses (Tombusviridae) Glossary Introduction Classification Virion Structure Genome Organization and Expression Similarity With Other Taxa Replication Satellite RNA Cell-to-Cell Movement Function Phloem-Dependent Long-Distance Movement Function Involvement of Nucleolus in Umbravirus Systemic Infection Interaction With Assistor Virus Host Range Transmission Prevention and Control Further Reading Varicosaviruses (Rhabdoviridae) Glossary Introduction Taxonomy and Classification Genetics and Evolution L Protein Encoded on RNA1 Proteins Encoded on RNA2 Transcription Termination/Initiation Strategy Host Range and Geographic Distribution Transmission and Vectors Further Reading Virgaviruses (Virgaviridae) Glossary Introduction Taxonomy, Phylogeny and Evolution Virion Structure Genome Organization Replication Infectious Cycle Diagnosis Pathogenicity Epidemiology and Control Unassigned Virgaviruses Further Reading Relevant Websites Viroids (Pospiviroidae and Avsunviroidae) Glossary Taxonomy Introduction Genome Structure Classification Host Range and Transmission Symptomatology Geographic Distribution Epidemiology and Control Molecular Biology Replication Movement Pathogenicity Implications for Host Range Origin and Evolution References Further Reading Watermelon Mosaic Virus and Zucchini Yellow Mosaic Virus (Potyviridae) Glossary History and Taxonomy Watermelon Mosaic Virus Zucchini Yellow Mosaic Virus Classification Symptomatology Watermelon Mosaic Virus Zucchini Yellow Mosaic Virus Synergism and Antagonism Geographic Distribution Host Range Diagnostic Methods Vector Relationships Epidemiology Virus Sources Efficient Vectors Pattern of Spread Control Methods Prophylactic Measures Cross-Protection Resistant Cultivars Variability Genetics and Evolution Biotechnological Application Further Reading e9780128145159v4_WEB Cover ENCYCLOPEDIA OF VIROLOGY FOURTH EDITION EDITORS IN CHIEF EDITORIAL BOARD SECTION EDITORS FOREWORD PREFACE HOW TO USE THE ENCYCLOPEDIA LIST OF CONTRIBUTORS CONTENT OF ALL VOLUMES BACTERIAL VIRUSES History of Virology: Bacteriophages Discovery of Phages Phage Therapy Phage Typing Phage Genetics Phage Biochemistry Phage and Biotechnology Phage Ecology and Evolution Conclusion Further Reading Icosahedral Phages – Single-Stranded DNA (φX174) Glossary History Virion Morphology and Genome Content Host Cell Recognition, Attachment, Eclipse and Penetration DNA Replication Gene Expression Morphogenesis DNA Packaging and the DNA Binding Protein Lysis Evolution and Evolutionary Studies Evolution of a Two Scaffolding Protein System φX174-Like Viruses as a Model System for Experimental Evolution Further Reading Single-Stranded RNA Bacterial Viruses Glossary Icosahedral ssRNA Bacterial Viruses Background Phage lifecycle Phage Structure and Assembly Biotechnological Applications Further Reading Enveloped Icosahedral Phages – Double-Stranded RNA (phiv6) Glossary Introduction The Cystoviridae Family Classification and Host Range Virion Structure and Properties Physico-Chemical Properties Architecture of the Polymerase Complex and the Nucleocapsid The Protein Components of the Cystovirus Portal Complex and Nucleocapsid P1 P2 P4 P7 P8 Membrane Envelope Host Cell Attachment Complex Genome Organization and Sequence Similarity Replication Cycle Plasma Membrane Penetration and NC Entrance into the Cytoplasm Transcription PC Assembly and Packaging NC maturation Membrane acquisition and host cell lysis Recombination and Reassortment Carrier State Reverse Genetics and Self Assembly Applications and Intellectual Property Further Reading Relevant Websites Membrane-Containing Icosahedral DNA Bacteriophages Glossary Introduction Virion Structure and Properties Overall Structure Membrane and DNA Life Cycle Receptor Recognition and DNA Delivery Genome Replication Particle Assembly Cell Lysis Genomes and Genomics Acknowledgment Further Reading Relevant Websites Tailed Double-Stranded DNA Phages Glossary Introduction The Structure of Tailed dsDNA Bacteriophages Bacteriophage Structure and Function Capsids Tails and Tail Fibers Temperate Versus Virulent Bacteriophages Injection DNA Injection Protein Injection Host Interactions and Regulation of Gene Expression Classes of Genes Early Genes Late Genes Virion Assembly Assembly Pathways Tail Assembly Capsid Assembly Lysis Genomes and Genomics Chromosome Diversity and Replication Diversity in Genome Size and Organization Common Themes in Genome Structure Horizontal Exchange of Genes is Widespread Common Ancestry Further Reading Relevant Websites Helical and Filamentous Phages Glossary Introduction Biotopes: Prolific, Temperate and Pathogenic Structure of Filamentous Phages Infection Process Replication by the Rolling Circle Mechanism Biosynthesis of M13 (fd, f1) The Coat Proteins The Major Coat Protein gp8 The Minor Coat Proteins gp7 and gp9 The Minor Coat Proteins gp3 and gp6 Assembly and Secretion Biotechnological Applications of Filamentous Phage Further Reading Replication of Bacillus Double-Stranded DNA Bacteriophages Glossary Introduction DNA Replication of SPO1-Like Viruses DNA Replication of SPP1-Like Viruses DNA Replication of phi29-Like Viruses References Relevant Websites Lytic Transcription Glossary Introduction Transcription Initiation and Elongation by Host RNA Polymerase Developmental Pathways and Transcription Control by T7, T4, and N4 T4 T7 Early transcription Phage RNAP and late gene transcription The transcription cycle Elongation Termination N4 Inhibition of Host RNAP by T4, T7, and N4, and Other Members of Those Families Summary Further Reading Lysogeny Glossary Introduction Why Lysogeny? Persistence of DNA Integration Into the Chromosome Extrachromosomal Persistence of DNA Maintenance of the Lysogenic State Bacteriophage λ Bacteriophage 186 Integration-Dependent Bacteriophage Immunity Use of a Host Protein as an Immunity Repressor RNA to Maintain Lysogeny Prophage Induction Evolutionary and Phenotypical Effects of Lysogeny Lysogenic Conversion Gene Disruption Genomic Rearrangement Conclusion Acknowledgments Further Reading Relevant Websites Decision Making by Temperate Phages Glossary Introduction The Post-Infection Decision of Phage Lambda Counting by Infecting Phages The View From the Single Cell The Decision to Remain Dormant Conclusion Acknowledgments Further Reading Mobilization of Phage Satellites Glossary Introduction Genetic Organization Integration and Excision, Gene Induction, and Replication Packaging and Horizontal Transmission Strategies PICIs Use to Interfere With Their Helper Phages Prevalence of Phage Satellites Counter-Evolution by Phages to Avoid Parasitism by Satellites Consequences of Phage Satellites in Human Health and Disease Conclusion Further Reading Portal Vertex Glossary Introduction Formation of a Prohead DNA Packaging into the Prohead Virion Maturation The Structural Features of the Portal Proteins Functions of the Portal Proteins The Viral Portal Protein as a Nucleator in the Assembly of the Prohead With Proper Morphology Portal Proteins Provide Binding Sites for Terminases Portal Proteins Bound With Adapter Proteins Facilitates Tail Attachment Portal Proteins Help to Spool Condensed Genomic DNA in the Capsid to Form a Highly Ordered Structure Portal Proteins as a Check-Valve Preventing DNA From Slipping Out Portal Proteins as a Sensor to Control the DNA Packaging The Portal Proteins Actively Assists DNA Packaging Coupling With ATP Hydrolysis The terminase-driven mechanism plays a key role at the initial stage of DNA packaging The portal proteins actively assists DNA packaging at the late stage of DNA packaging The portal directly-mediated packaging mode Rotation of the portal protein may apply forces to DNA Lengthwise channel expansion and contraction in the portal protein may apply forces to DNA Sequential movement of tunnel loops may apply force to DNA The portal indirectly-mediated packaging mode DNA translocation driven by the energy from the DNA deformation in the portal protein DNA translocation driven by a brownian motor inherent in the portal protein Main Techniques Used to Study Protal Protein Structure and Function Biochemical methods Techniques for structural analysis The optical tweezers: a technique to observe DNA packaging in real time Molecular dynamics simulation Planar bilayer membrane (BLM) technology Concluding Remarks Further Reading Outline placeholder Glossary Introduction Major Capsid Protein Before Capsid Assembly Prohead Assembly Scaffolding Protein Accelerating assembly Promote correct geometry Delay MCP transformation Exclude host factors Scaffold involvement in portal incorporation The Portal Structure of the Prohead Stability of the Prohead Assembly Parasites Further Reading Enzymology of Viral DNA Packaging Machines Glossary Introduction Unit Length Versus Headful Packaging Mechanisms The Viral Terminase Enzymes The TerS Subunits The TerL Subunits The Terminase Holoenzymes The Lambda System The Terminase Enzyme of Phage Lambda The lambda TerS Subunit The TerL DNA Packaging Domain The lambda TerL Maturation Domain Escherichia Coli Integration Host Factor The Genome Maturation Complex The Lambda Cohesive End Site and Assembly of the Genome Maturation Complex Model for the Assembly of the Genome Maturation Complex Genome Maturation: The cos-Cleavage Reaction Genome Maturation Summary The Genome Packaging Complex Assembly of the Packaging Motor cos-Clearance: Transition to a Translocating Motor A Nucleotide Switch for cos-Clearance? The Translocating Motor Structure of the Translocating Motors Coordinated ATP Hydrolysis by the Terminase Motors Mechanochemical Coupling and DNA Translocation Termination of Packaging Unit Length Packaging Motors Terminase Ejection and Virion Completion Conclusion Further Reading DNA Packaging: DNA Recognition Glossary Introduction Genome Replication and Selection Mechanisms Monomeric replication products Concatemeric replication products The Shape of DNA Protein-DNA Binding A Question of Fidelity: Sequence Specific and Non-Specific Binding DNA Binding Domains Strength in Numbers: Multiple Binding Events Regulate Complex Assembly Recognition of Viral Genomic DNA Monomeric Genomes and Terminal Proteins Concatemeric DNA and Terminase Proteins Direct terminal repeats: T3 and T7 Cohesive ends: λ-like Genome recognition in headful bacteriophages DNA Wrapping/Bending is a Common Feature in Selective Packaging Further Reading Relevant Websites DNA Packaging: The Translocation Motor Glossary Introduction Terminase and Phi29 Motors are Branches Within the ASCE Family of ATPases Phi29 Motors Terminase Motors The “Inchworm” Translocation Model The “Lever” Translocation Model The DNA “Crunching” or “Compression” Translocation Model Termination of Packaging Outlook and Future Studies Further Reading Biophysics of DNA Packaging Glossary Introduction Molecular Structure DNA Packaging Characteristics Packaging Speed Force Generation Pausing and Slipping DNA Packaging Mechanisms Mechanochemical Coupling Motor-substrate Interactions Force Generation Motor Coordination Further Reading Energetics of the DNA-Filled Head Glossary Introduction Equilibrium Energy and Structure of Intracapsid DNA Metastability of Intra-Capsid DNA Facilitating or Inhibiting Viral DNA Ejection The Mobility of Packaged Genome Controls Ejection Dynamics Pressure-Driven Release of Viral Genome Into a Host Cell is a Mechanism Leading to Infection Concluding Remarks Further Reading Bacteriophage Receptor Proteins of Gram-Negative Bacteria Glossary History and Overview Techniques and Methods for Studying Phage Receptors Properties of Receptor Proteins Ecology and Evolution of Phage-Host Interactions Relevance of Phage-Receptor Interactions to Phage Therapy Summary Appendix: Methods for Receptor Identification or Characterization Acknowledgments Further Reading Relevant Websites Tail Structure and Dynamics Glossary Introduction Caudovirales Organization and Assembly of Long Tails The Tube The Sheath Baseplates of Long Contractile Tails Tail Tip Complex of Long Non-Contractile Tails Short Non-Contractile Tails: Tube-Like Tail Structure The Tailspikes, Tail Fibers and Phage-Host Interaction Acknowledgments Further Reading Relevant Website Bacteriophage Tail Fibres, Tailspikes, and Bacterial Receptor Interaction Glossary Introduction Structures of Bacteriophage Tail Fibers Structures of Bacteriophage Tailspikes and Other Receptor-Binding Proteins Host Cell Recognition Conclusion and Perspectives Acknowledgments Further Reading Phage Genome and Protein Ejection In Vivo Glossary Protein Ejection and Trans-Envelope Channel Formation Proteins are Ejected into the Host Cell at the Initiation of Infection Tail-Less Phages Short-Tailed Phages (Podoviridae) Non-Contractile Long-Tailed Phages (Siphoviridae) Contractile Long-Tailed Phages Factors Affecting Phage Genome Translocation Transcription-Mediated Genome Internalization In Vivo Non-Transcriptional Genome Internalization In Vivo Models of Phage Genome Ejection In Vivo Acknowledgments See also Further Reading Dealing With the Whole Head: Diversity and Function of Capsid Ejection Proteins in Tailed Phages Glossary Introduction Tailed Phage Capsids With Low Numbers of E Proteins in Specific Locales Low copy number E proteins with specific locales in the capsid Podoviral E proteins Capsids With Large Numbers of E Proteins Distributed Throughout the DNA Capsids With Large Numbers of Co-Localized E Proteins The Enigmas of E Proteins Phages with yet to be identified E proteins What mechanisms ensure encapsidation of E proteins? Impacts of E proteins on capsid DNA packaging and ejection Impacts of E proteins on DNA ejection Potential of E protein delivery from capsid derived nanocontainers Conclusions References Jumbo Phages Glossary Introduction History Isolation and Characterization Virion Structure Morphotypes Icosahedral Geometries Virion DNA Density Head and Tail Fibers Genome Features Terminal Redundancies Genome Nucleotide Composition Nucleotide Modifications and Substitutions ORFan Genes Transfer RNA Genes Advanced Capabilities RNA Polymerases DNA Repair Enzymes NADplus Salvage Pathway LPS Biosynthesis Phage Nucleus Evolution Concluding Remarks Further Reading CRISPR-Cas Systems and Anti-CRISPR Proteins: Adaptive Defense and Counter-Defense in Prokaryotes and Their Viruses Glossary The Phage-Host Arms Race CRISPR-Cas, A Brief History CRISPR-Cas Diversity and Classification Mechanisms of CRISPR-Cas Immunity Adaptation Defense Anti-CRISPR Proteins Prophage-Dependent Functional Approach Guilt-By Association Bioinformatic Approach Self-Targeting Bioinformatic Approach Lytic Phage Dependent Functional Approach Concluding Thoughts Further Reading Relevant Website Bacteriophage: Therapeutics and Diagnostics Development Glossary Introduction The Development of Phage as Therapeutics for Bacterial Infections The Development of Phage as Diagnostics for Bacterial Infections Major Advantages of Phage Technology Specificity Self-Replication Major Limitations of Phage Technology Narrow Host Range Phage Resistance Additional Challenges for Phage Therapy Preclinical Data Translation Safety and Efficacy Dosing Strategies Chemistry, Manufacturing, and Controls (CMC) Regulatory Pathway Environmental Impact Additional Challenges for Phage Diagnostics Phage Manipulation Multiplex Testing Intracellular Bacteria Sample Interference Market Acceptance Conclusions Further Reading Bacteriophage Vaccines Introduction Architecture of Phage T4 Phage T4 as a Vaccine Platform In Vivo VLP Assembly In Vitro VLP Assembly Phage T4 VLP Vaccines Other Phage Vaccine Platforms Conclusion Statement Acknowledgments Further Reading Relevant Website Bacteriophage Diversity Glossary Introduction Understanding the Nature of Tailed Phage Diversity and Phage Classification Strategies for Studying Phage Diversity Examples of Phage Diversity Top Down Studies Human phageome Marine phageome Bottom Up Studies Two large diversity studies The Enterobacteriales tailed phage example Contribution of Prophages to Phage Diversity Phage Diversity and Horizontal Exchange of Genetic Information The Nature of Horizontally Exchangeable Mosaic Section Alleles How did Genome Mosaicism Arise? Genetic Exchange Among Superclusters Phage-host Relationships and Phage Diversity Phage Cluster-Host Species Relationships With the Enterobacteriales Narrow and Wide Host Range Phages Summary Further Reading Relevant Websites Genetic Mosaicism in the Tailed Double-Stranded DNA Phages Glossary Introduction Evidence for Genome Mosaicism Before the Advent of DNA Sequencing DNA Sequencing Illuminates Properties of Bacteriophage Genomes Comparative Genomics of Complete Bacteriophage Sequences Shows Diversity and Mosaicism Mosaicism in the Siphoviridae Mosaicism in the Myoviridae Mosaicism in the Podoviridae Clusters and Superclusters: Large Scale Comparative Genome Analysis Different Phage Clusters Acquire New Genes at Different Rates Mosaicism, Hybrids, and Single Gene Surveys Further Reading Relevant Websites Bacteriophages of the Human Microbiome Glossary Introduction Human Phageome Distribution and Composition Dynamics and Implications of the Human Phage Community Clinical Utility of Bacteriophages of the Human Microbiome Concluding Remarks Further Reading Bacteriophage: Red Recombination System and the Development of Recombineering Technologies Glossary Introduction Bacteriophage Homologous Recombination Systems in E. coli and λ Phage Biological Roles of the λ Red System Role in DNA Replication Genetic Exchange Among Similar Phages – Generating Genetic Diversity DNA Repair Classical Models of λ Recombination Development of Recombineering Recombineering With dsDNA Markerless Gene Deletions and Counterselection Schemes Recombineering With ssDNA In vivo Cloning Mechanism of Oligo-Mediated Recombineering Mechanism of dsDNA Recombineering Recombineering in Pathogenic Bacteria Combining Recombineering With Other Gene Modification Technologies Recombinase-Independent Recombination Final Thoughts Further Reading Nanotechnology Application of Bacteriophage DNA Packaging Nanomotors Glossary Introduction The Revolving Mechanism of Biomotors in Bacteriophages The Revolution Mechanism Without Rotation Common to the dsDNA Packaging Motors of all the dsDNA Bacteriophages Revolving Mechanisms Determined by Motor Channel Sizes Revolving Motors Distinguished by Chirality Special Aspects of Revolving Motor Actions The Application of Bacteriophage DNA Packaging Motors in Single Pore Sensing of DNA, RNA, Chemicals, and Proteins Phi29 Connector SPP1 Connector T7 Connector The Mechanism of Single Pore Sensing Applications of the Biological Nanopore Channel as a Conduit for Single Pore Sensing Summary Acknowledgments Further Reading General Ecology of Bacteriophages Glossary Introduction Phage Existence Within Environments Overview Phage Isolation and Host Range Microscopic Determination Phage Ecology Overview Phage Organismal Ecology Bacteria-like versus virion-emphasizing modes of existence Phage Population Ecology Phage Community Ecology Phage Ecosystem Ecology Further Reading Relevant Websites Marine Bacteriophages Glossary A Short Introduction in Marine Phages Morphological Diversity of Marine Phages Genomic Diversity of Marine Phages and How do we Study it Phage Marker Genes Viral Metagenomics (Viromics) Viral Contigs From Fosmid Libraries Single Virus Genomics Long Read Viromics Metagenome Assembled Viral Genomes (MAVGs) Linking Phage Genomes With Host Identity ssDNA Phages in the Marine Environment Cultivated Phages Infecting Main Groups of Marine Bacteria Phages of Marine Cyanobacteria - Cyanophages Phages of unicellular cyanobacteria Phages of filamentous cyanobacteria Phages of Marine Alphaproteobacteria Phages of marine Pelagibacterales SAR116 phages Phages of marine Rhodobacteraceae - Roseophages Phages of Marine Gammaproteobacteria Vibriophages Pseudoalteromonas phages Phages of Marine Bacteroidetes Marine Phage Ecology Phage Micro- and Macro-diversity in the Marine Environment Marine Phages as Factors Driving Bacterial Mortality and Diversity Diel Rhythms of Phage Infections in the Marine Environment Auxiliary Metabolic Genes in Marine Phages Transfer RNAs (tRNAs) in Phages and Their Role in Phage-Host Interactions Conclusions References Further Reading Ecology of Phages in Extreme Environments Glossary Introduction Phages in Hypersaline Environments Phages in Thermal Environments Terrestrial Hot Springs Deep-Sea Hydrothermal Vents Hot Deserts Phages in Polar and Other Cold Environments Polar Oceans Glaciers Polar Lakes Sea Ice Permafrost Other Cold Environments Atmosphere Conclusions Further Reading Diversity of Hyperthermophilic Archaeal Viruses Glossary Introduction Morphology and Structure Viruses with particular morphologies Family Ampullaviridae (from Latin ampulla for “bottle”) Family Bicaudaviridae (from Latin bi, “two”, and cauda for “tail”) Family Clavaviridae (from Latin clava for “club”, “stick”) Family Fuselloviridae (from Latin fusello for “little spindle”) Family Guttaviridae (from Latin gutta for “droplet”) Family Spiraviridae (from Latin spira for “coil”) Spherical viruses Family Globuloviridae (from Latin globulus for “small ball”) Family Ovaliviridae (from Latin ovalis for “oval”) Family Portogloboviridae (from Latin porto for “to bear”, and globus for “ball”) Family Turriviridae (from Latin turris for “tower”) Filamentous viruses Proposed class Tokiviricetes: order Ligamenvirales: family Rudiviridae (from the Latin rudis for “small rod”) order... General comments Genomes Family Fuselloviridae Order Ligamenvirales Evolutionary relationships Further Reading ARCHAEAL VIRUSES Euryarchaeal Viruses Glossary Introduction Icosahedral Tailed Viruses Icosahedral Tailed Viruses of Halophilic Euryarchaea Tailed Viruses of Methanogenic Euryarchaea Icosahedral Internal Membrane-Containing Viruses Pleomorphic, Spindle-Shaped, and Spherical Viruses Pleomorphic Viruses Spindle-Shaped Viruses Spherical Virus Metsv Culture-Independent Studies Conclusions Further Reading Relevant Websites Vesicle-Like Archaeal Viruses Glossary Introduction An Overview of the Virion Structure and Viral Life Cycle Genomic Characteristics Gene Content and Conserved Genes Family Pleolipoviridae: Related Viruses With Different Genome Types New Isolates and Haloarchaeal Genomic Regions Stability of Pleolipovirus Infectivity Salinity Temperature and Other Significant Factors Structural Proteins The Spike Protein Further Reading Relevant Website Virus-Host Interactions in Archaea Glossary Introduction Virus Entry Interaction With Cellular Appendages Interaction With Cell-Surface Kinetics of Virus Entry Genome Replication Genome Integration Transcription Transcription Regulators Transcriptional Control Virion Egress Cell Membrane Disruption Viral Release Without Membrane Disruption Antiviral Defense and Viral Counterdefense Mechanisms Antiviral Defense Mechanisms CRISPR-Cas systems Toxin-antitoxin system Counterdefense Mechanisms Conclusions Further Reading Antiviral Defense Mechanisms in Archaea Glossary Introduction CRISPR-Cas: The Prokaryotic Adaptive Immune System Spacer Acquisition and its Regulation in Archaea Expression of CRISPR Loci and crRNA Biogenesis Archaeal Type I CRISPR-Cas Systems Archaeal Type III CRISPR-Cas Systems Novel Archaeal CRISPR-Cas Systems Anti-CRISPR Proteins of Archaeal Viruses Archaeal Innate Antiviral Systems Future Perspectives Further Readings Discovery of Archaeal Viruses in Hot Spring Environments Using Viral Metagenomics Introduction Sample Collection and Processing Next Generation Sequencing of Samples Post Sequence Analysis What Have we Learned? Looking Forward Further Reading Metagenomes of Archaeal Viruses in Hypersaline Environments Glossary Introduction How can Archaeal Viruses be Studied Using Viral Metagenomes? What Viral Metagenomes are Available From Hypersaline Environments and What are Their General Characteristics? Viruses of Haloquadratum Walsbyi Viruses of the Nanohaloarchaea Concluding Remarks Further Reading Extreme Environments as a Model System to Study How Virus–Host Interactions Evolve Along the Symbiosis Continuum Glossary Aspects of Viral Fitness Environment Impact on Host-Virus Interaction Viruses of Acidic Hot Springs Complexity of Host Virus-Interactions How do Ecology and Evolution Shape Archaeal Viruses? How do Virus Interactions Impact Ecology and Evolution? Acknowledgments References Further Reading FUNGAL VIRUSES An Introduction to Fungal Viruses Glossary Introduction Biological Properties Host Range Symptom Expression Transmission Mixed Infections Fungal Virus Taxonomy dsRNA Mycoviruses Single-Stranded RNA Viruses Unassigned ssRNA Viruses Replication and Gene Expression Strategy Recent Technical Advances in Fungal Virology Future Perspectives Cross-Kingdom Infection by Viruses and Viroids Yeast as a (Model) Host to Study Viral Replication Virus Neo-Lifestyles Host Defense Against Mycoviruses and Their Counter-Defense Role of Mycoviruses in Plant-Fungal Mutualistic Associations Mycovirus as Biocontrol Agents and as Tools for Fundamental Studies Further Reading Relevant Websites Cross-Kingdom Virus Infection Introduction Viruses That Replicate in Both Plants and Insects Closely Related Viruses Independently Infect Plants and Fungi Artificially Established Viral Cross Infections Between Plants and Fungi Evidence of the Natural Transmission of a Plant Virus to a Fungus A Fungal DNA Virus That Replicates in an Insect and Uses It as a Vector The Contribution of Cross-Kingdom Viral Infection to Virus Evolution Concluding Remarks Further Reading Diversity of Mycoviruses in Aspergilli Glossary Introduction Prevalence Transmission Genomes The Aspergillus foetidus Mycovirus Complex Partitiviruses Chrysoviruses Narnaviruses and Mitoviruses Polymycoviruses Phenotypes Further Reading Evolution of Mycoviruses Glossary Introduction Evolutionary History and Drivers of Evolution Effects of Host Divergence in the Evolution Coinfection and Evolution Structural Evolution of Mycoviruses Further Readings Relevant Website Mixed Infections of Mycoviruses in Phytopathogenic Fungus Sclerotinia sclerotiorum Glossary Introduction Strain Ep-1PN Harbors Two Positive-Single Stranded RNA Mycoviruses Strain SX247 is Co-Infected With Two plusssRNA Mycoviruses Strain AH98 is a Mix-Infection by Two Unrelated Single-Stranded RNA Mycoviruses The Hypovirulent Strain SZ-150 Contains Three Mycoviruses and a Satellite RNA Four Mycoviruses Co-Infect a Hypovirulent Strain SCH941 Megabirnavirus Infects the Hypovirulent Strain SX466 With a Mitovirus and a Partitivirus Strain Sunf-M is Coinfected With Two Unrelated dsRNA Mycoviruses Mitoviruses Widely Exist in and Co-Infect S. sclerotiorum Three Strains of S. sclerotiorum Harbor Multiple Unassigned Mycoviruses or dsRNA Elements The Possible Reasons for the Co-Infections of Mycoviruses in S. sclerotiorum References Further Reading Mycovirus-Mediated Biological Control Glossary Introduction Disease Cycle of Plant Pathogenic Fungi Basic Concepts for Mycovirus-Mediated Biological Control General Procedure for Developing a Mycovirus-Mediated Biological Control System Virus Detection and Characterization Testing for Phenotypic Effects of the Mycovirus Transmission Properties Biocontrol Testing in the Field Biosafety Issues Molecular Approaches to Improve the Use of Mycoviruses as Biological Control Agents Selected Examples for Mycovirus-Mediated Biological Control Hypovirulence in Cryphonectria parasitica The “exclusive transmissible hypovirulence” Artificial application of hypovirulence Hypovirulence in Ophiostoma novo-ulmi Hypovirulence in Sclerotinia sclerotiorum Hypovirulence in Botrytis cinerea Hypovirulence in Rosellinia necatrix Hypovirulence in Helminthosporium victoriae Hypovirulence in Fusarium graminearum Future Perspectives Further Reading Mycoviruses With Filamentous Particles Glossary Introduction Botrytis virus F (BotV-F) Family - Gammaflexiviridae Genus - Mycoflexivirus Genome Structure Biological Properties Virion Morphology Phylogenetic Relationships Botrytis Virus X (BotV-X) Family - Alfaflexiviridae Genus - Botrexvirus Genome Structure Biological Properties Virion Morphology Phylogenetic Relationships Sclerotinia Sclerotimonavirus Family - Mymonaviridae Genus - Sclerotimonavirus Genome Structure Biological Properties Virion Morphology Phylogenetic Relationships Fusarium Graminearum Negative-Stranded RNA virus 1 Family - Mymonaviridae (?) Genus - Unclassified Genome Structure Biological Properties Particle Morphology Phylogenetic Relationships Colletotrichum Camelliae Filamentous Virus 1 Family - Unclassified Genus - Unclassified Genome Structure Biological Properties Virion Morphology Phylogenetic Relationships Relationships Between Filamentous Viruses From Fungi and Plants Further Reading Prions of Yeast and Fungi Glossary Introduction and History Genetic Signature of a Prion Self-Propagating Amyloid as the Basis for Most Yeast Prions Shuffling Prion Domains and Amyloid Structure Shuffleable Prion Domains Suggests Parallel In-Register beta-Sheet Structure Infectious Prion Amyloids Have In-Register Parallel Folded beta-sheet Architecture Prion Variants and the Species Barrier Prion Variant Information Templating Mechanism Chaperones and Prions Prion Generation, and [PIN]: A Prion That Gives Rise to Prions Biological Roles of Prions: A Help or a Hindrance? Anti-Prion Systems Inositol Polyphosphates and Prion Propagation Enzyme as Prion Conclusions Acknowledgment See also Further Reading Single-Stranded DNA Mycoviruses Glossary Introduction The Host of the DNA Mycovirus Discovery of DNA Mycoviruses The Genome and Proteins of SsHADV-1 Host Range of SsHADV-1 Extracellular Entry of SsHADV-1 Mutualistic Interaction Between SsHADV 1 and Mushroom Sciarid Fly Transmission of SsHADV-1 Distribution of SsHADV-1 The Taxonomy of SsHADV-1 Explore SsHADV-1 to Control Fungal Disease Further Reading Structure of Double-Stranded RNA Mycoviruses Introduction Structure of dsRNA Virus Capsids Totiviruses Chrysoviruses Quadriviruses Partitiviruses Megabirnaviruses Evolutionary Relationships Based on Structural Comparisons RdRp and dsRNA Organization Within Mycovirus Capsids Concluding Remarks and Future Perspectives See also Further Reading Ustilago maydis Viruses and Their Killer Toxins The Totiviruses The Killer Phenomena KP4 Effects of KP4 on U. maydis Cells KP4 Blocks L-type Voltage Gated Ca2+ Channels Effect of KP4 on Plants Possible Application of KP4: Fungal Resistance in Plants Evolutionary Origin of KP4 KP6 The Atomic Structure of KP6 KP1 Comparison of the Killer Proteins Further Reading Vegetative Incompatibility in Filamentous Fungi Glossary Introduction Characteristics of the Vegetative Incompatibility Reaction Microscopic and Macroscopic Analyses of Hyphal Fusion Identification of VCGs Barrage assay Microscopy Visualization of labeled proteins during co-culture Auxotrophic complementation Detecting the PCD of fused cells The Genetics of Vegetative Incompatibility The Signaling Pathways of Vegetative Incompatibility HET Protein Involved in NLR-Mediated Innate Immunity in Fungi Mycovirus Transmission Mycoviruses can be Horizontally Transmitted Among VCGs Potential Approaches to Enhance Mycovirus Transmission Between VCGs Further Reading Viral Diseases of Agaricus bisporus, the Button Mushroom Glossary Introduction La France Disease - Agaricus Bisporus Virus 1 (AbV1) Genome Organization Virion Structure and Composition Taxonomy and Classification Biological Properties (Virus Host Relationships) Epidemiology Diagnostics and Identification Control Brown Cap Mushroom Disease - Agaricus Bisporus Virus 16 (AbV16) Genome and Virion Structure Classification Viral Expression and Disease Development Epidemiology Diagnosis Further Reading Viral Killer Toxins Glossary Introduction DsRNA Viruses and Killer Phenotype Expression in S. Cerevisiae Viral Replication Cycle Viral Preprotoxin Processing and Toxin Maturation Endocytosis and Intracellular Transport of the K28 Virus Toxin ER Exit and Nuclear Entry of the K28 Virus Toxin K28 Affects DNA Synthesis, Cell-Cycle Progression, and Induces Apoptosis Lethality of Membrane Damaging Viral Killer Toxins Self-Protection in Killer Virus-Infected Yeast - Toxin Immunity Further Reading Alternaviruses (Unassigned) Glossary Introduction Genome Organization Virion Properties Biological Effects of Alternavirus on Their Host Proteins Encoded by Alternaviruses 3prime Poly (A) Structure of Alternaviruses Evolutionary Relationships Among Chrysoviruses Reference Further Reading Barnaviruses (Barnaviridae) Glossary Introduction MBV Virion Properties MBV Virion Structure and Composition MBV Genome Organization and Expression MBV Evolutionary Relationships MBV Transmission and Host Range Further Reading Botybirnaviruses (Botybirnavirus) Glossary Introduction Virion Properties Genome Organization and Replication Taxonomy and Similarity With Other Viruses Transmission and Distribution Biology Further Reading Chrysoviruses (Chrysoviridae) - General Features and Chrysovirus-Related Viruses Glossary Introduction Virion Properties Virion structure and composition Genome Organization Genome Expression and Replication Chrysovirus RdRps Chrysovirus CPs Alphachryso-P3 Shares a ‘Phytoreo S7 Domain’ With Core Proteins of Phytoreoviruses Chryso-P4 is a Putative Protease and Virion Associated as a Minor Protein Replication of Chrysoviruses Taxonomy and Phylogenetic Analysis Biology and Effects of Chrysoviruses on Fungal Hosts Acknowledgment Further Reading Fungal Partitiviruses (Partitiviridae) Glossary Introduction Classification Virion Structure Genome Life Cycle Epidemiology Pathogenesis Taxonomic and Phylogenetic Considerations Further Reading Relevant Websites Fusariviruses (Unassigned) Glossary Introduction Taxonomy and Classification Virion Property Genome Organization Gene Expression Virus Transmissions Virus-Host Interactions Summary and Future Prospective Further Reading Relevant Website Giardiavirus (Totiviridae) History Taxonomy, Classification and Evolution Host Range and Geographic Distribution Physical and Biochemical Characteristics Organization and Molecular Biology of GLV and GCV dsRNA Genomes Infection and Replication References Hypoviruses (Hypoviridae) Glossary Introduction Taxonomy and Genetic Organization Hypovirus Gene Expression Strategy Hypovirus Functional Domains Anti-Hypovirus Defense Mechanisms Further Reading Megabirnaviruses (Megabirnaviridae) Glossary Introduction Virion Properties Genome Organization Genome Expression and Replication Virion Structure Biological Properties Taxonomic and Phylogenetic Considerations Future Perspectives Functions of Megabirna-P3 and -P4 Further Reading Mitoviruses (Mitoviridae) Glossary Genome Structure Accessory RNAs Associated With Mitovirus Infections Phenotypic Effects of Mitovirus Infection Phylogenetic Relationships Taxonomy and Nomenclature Transmission Engineering Mitoviruses for Infectivity Host Defense Codon Usage and Implications for Mitovirus Biology and Evolution Origin and Evolution Plant Mitoviruses Further Reading Mycoreoviruses (Reoviridae) Glossary Structure-Function Relationships Taxonomy and Nomenclature Genome Structures, Organizations, and Relationships Mycoreovirus 1 Expression of MyRV1 Gene Products Mycoreovirus 2 Mycoreovirus 3 Sclerotinia Sclerotiorum Reoviruses Mycoreovirus 4 Sclerotinia Sclerotiorum Reovirus 1 Effects of Mycoreoviruses on Fungal Gene Expression Coinfections of Mycoreovirus and Other Viruses Mycoreovirus Genome Rearrangements Further Reading Mymonaviruses (Mymonaviridae) Glossary Introduction Phylogenetic Status of Mymonoviridae and its Related Families Species and Tentative Species in the Family Mymonoviridae Virion The Genomic Structure The Impact on the Host Host and Distribution Further Reading Narnaviruses (Narnaviridae) Glossary Introduction Historical Background Viral Genomes Ribonucleoprotein Complexes as a Viral Entity Replication Intermediates Generation of Narnaviruses in Vivo Cis-Acting Signals for Replication Cis-Signals for Formation of Ribonucleoprotein Complexes Narnavirus Persistence in the Host Further Reading Phlegiviruses (Unassigned) Introduction Virion Properties Genome Organization Biological Properties Evolutionary Relationships among Phlegiviruses Future Perspectives Further Reading Plant and Protozoal Partitiviruses (Partitiviridae) Glossary Introduction Current Taxonomy of the Partitiviridae Virion Properties Alphapartitivirus Betapartitivirus Cryspovirus Deltapartitivirus Genome Organization and Replication Strategy Genome Organization 5prime and 3primeUTRs RNA1& 2 Replication Strategy Transmission Virus-Host-Interaction Further Reading Relevant Websites Quadriviruses (Quadriviridae) Glossary Introduction Virion Structure and Composition Genome Organization and Expression Molecular and Biological Properties Phylogenetic and Evolutionary Relationships of RnQV1 to Other dsRNA Mycoviruses See also Further Reading Relevant Website Totiviruses (Totiviridae) Glossary Introduction Taxonomy of and Evolutionary Relationships Among Totivirids Virion Properties Virion Structure and Composition Genome Organization and Expression Virus Replication Cycle Biological Properties Virus-Host Relationships Conclusions Further Reading Yado-kari Virus 1 and Yado-nushi Virus 1 (Unassigned) Glossary Introduction Virion Morphology Genome Characteristics of YnV1 Genome Characteristics of YkV1 Phylogenetic Placements of YnV1 and YkV1 Proposed Replication Model for YnV1 and YkV1 Molecular Entities Sharing Similar YkV1/YnV1-Like Interactions YkV1/YnV1-Like Virus Combinations in Other Fungi Predicted Past and Future of YkV1 Concluding Remarks and Future Directions Further Reading Yeast L-A Virus (Totiviridae) Glossary Introduction History Virion Structure Genome Organization Replication Cycle Transcription RNA Packaging RNA Replication Viral Translation L-A Genetics Other RNA Replicons in Yeast: L-BC, 20S RNA, 23S RNA See also Further Reading ALGAL VIRUSES Algal Marnaviruses (Marnaviridae) RNA Viruses Infecting Marine Protists Development of a Taxonomic Framework and Resulting Changes in Taxonomy Marine RNA Virus Quasispecies Importance of RNA Viruses in Marine Microbial Ecology Summary Further Reading Algal Mimiviruses (Mimiviridae) Glossary History General Properties Proposed Subfamily Mesomimivirinae Unclassified Algae-Infecting Members in the Family Mimiviridae Further Reading Miscellaneous Algal Viruses (Alvernaviridae, Bacilladnaviridae, Dinodnavirus, Reoviridae) Introduction Algal single-stranded RNA Viruses Genus Dinornavirus Algal double-stranded RNA Viruses Genus Mimoreovirus Algal single-stranded DNA Viruses Genus Bacilladnavirus Algal double-stranded DNA Viruses (not Belonging to Either of the Families: Phycodnaviridae or Mimiviridae) Genus Dinodnavirus Reference Further Reading Phycodnaviruses (Phycodnaviridae) History Taxonomy and Classification Virion Structure and Composition Morphology Physicochemical and Physical Properties Nucleic Acids Proteins Lipids Carbohydrates Genomes Virus Replication Virus Transcription Ecology Resistance to Phycodnavirus Infections Phycodnavirus Genes Encode Some Interesting and Unexpected Proteins Perspectives Acknowledgments Further Reading INVERTEBRATE VIRUSES An Introduction to Viruses of Invertebrates Glossary Introduction Artoviridae Ascoviridae Baculoviridae Bidnaviridae Birnaviruses of Invertebrates (Entomobirnavirus) Dicistroviridae Hytrosaviridae Iflaviridae Iridoviruses of Invertebrates (Betairidovirinae) Malacoherpesviridae Mesoniviridae Nimaviridae Nodaviridae Nudiviridae Nyamiviridae Parvoviruses of Insects (Densovirinae and Hamaparvovirinae) Polydnaviridae Poxviruses of Invertebrates (Entomopoxvirinae) Reoviruses of Invertebrates (Sedoreovirinae and Spinaviridae) Rhabdoviruses of Invertebrates (Rhabdoviridae, Almendravirus, Alphanemrhavirus, Caligrhavirus, Sigmavirus) Roniviridae Sarthroviridae Solinviviridae Tetraviruses (Families, Alphatetraviridae, Carmotetraviridae, Permutotetraviridae) Taxa of Other Viruses of Invertebrates Arboviruses in Their Invertebrate Vectors Plant Viruses in Their Invertebrate Vectors Retrotransposons Associated With Invertebrates Acknowledgments See also Further Reading Relevant Websites Ascoviruses (Ascoviridae) Glossary Introduction History Distribution and Taxonomy Virion Structure and Composition Transmission and Ecology Host Range Pathology and Pathogenesis Signs of Disease Cytopathology and Cell Biology Tissue Tropism Replication and Virion Assembly Origin and Evolution Future Perspectives Further Reading Baculovirus–Host Interactions: Repurposing Host-Acquired Genes (Baculoviridae) Glossary Introduction Viruses Acquiring Genes From Their Hosts Hosts Acquiring Genes From Infecting Viruses Baculovirus Replication Baculovirus Acquisition of Genes Baculovirus Host Range Genes Virus Defense and Resistance to Baculoviruses Concluding Remarks Classification (Compact) Virion Structure Genome Replication Cycle Epidemiology Pathogenesis Diagnosis Further Reading Baculoviruses: General Features (Baculoviridae) Glossary Historical Perspective Nomenclature, Taxonomy, and Classification Morphology Genomes, Gene Content, Organization Evolution Infection Cycle Baculovirus Transmission and Host Behavioral Manipulation Baculovirus Expression Technology Baculoviral Insecticides Further Reading Relevant Website Baculoviruses: Molecular Biology and Replication (Baculoviridae) Glossary Introduction Infection Cycle Two Virion Phenotypes Oral and Systemic Infection Dissemination of OBs Genome Organization and Content Baculovirus Gene Expression Temporal Regulation of Transcription Early gene expression Late and very late gene expression Viral DNA Replication Virion Morphogenesis and Protein Composition Nucleocapsids BV Morphogenesis GP64 glycoprotein characteristics F protein properties ODV Assembly and ODV Envelopes Tegument Proteins Appendix A Supplementary Material See also Further Reading Bidensoviruses (Bidnaviridae) Classification Genome Organization and Expression Strategy Pathology of Silkworm Associated With BmBDV Viral Non-Structural Proteins Viral Structural Protein Viral Replication Virus Evolution Further Reading Bunyaviruses of Arthropods (Mypoviridae, Nairoviridae, Peribunyaviridae, Phasmaviridae, Phunuiviridae, Wupedeviridae) Glossary Introduction Virion Structure Genome and Coding Strategies of the Viral Genomes Viral Replication Cycle Host Associations, Virus Maintenance Cycles and Pathogenicity Further Reading Dicistroviruses (Dicistroviridae) Glossary Introduction Taxonomy and Classification Biophysical Properties Organization of the Dicistrovirus Genome Virus Replication and Genome Expression Host Range Pathology and Transmission Geographic and Strain Variation Relationships Within the Family Similarity With Other Taxa Acknowledgments Further Reading Entomobirnaviruses (Birnaviridae) Glossary Classification (Compact) Virion Structure Genome Life Cycle Epidemiology Clinical Features Pathogenesis Further Reading Relevant Website Hytrosaviruses (Hytrosaviridae) Glossary Introduction Taxonomy and Classification Similarities With Other Virus Taxa Virion Structure Genome Organization Modes of Infection and Gene Expression Major Structural Proteins Host Range Pathogenesis and Tissue Tropism Pathogenesis in the Salivary Glands Pathogenesis in Other Host Tissues Viral Latency Transmission and Epidemiology GpSGHV Transmission Dynamics in the Tsetse Fly MdSGHV Transmission Dynamics in the Housefly Diagnosis and Management of SGHV Infections Diagnosis Management Conclusions Further Reading Relevant Website Iflaviruses (Iflaviridae) Glossary Classification Virion Structure Genome Life Cycle Epidemiology Clinical Signs Pathogenesis Diagnosis/Detection Methods Prevention Further Reading Relevant Websites Iridoviruses of Invertebrates (Iridoviridae) Glossary Introduction Classification of Iridovirids Morphology and Composition IIV-6 Persistence and Sensitivity to External Factors Host Range and Pathology Genome Organization and Codon Usage Virion Proteins Viral Entry, Replication, and Release Strategy Transcriptional Regulation Promoter Elements and Transcriptional Regulation Induction/Inhibition of Apoptosis in Infections Concluding Remarks Further Reading Relevant Website Mesoniviruses (Mesoniviridae) Classification Virion Structure Genome ORF1a/ORF1b Structural Proteins Life Cycle Reference Further Reading Nimaviruses (Nimaviridae) Glossary Introduction Taxonomy Virion Structure and Composition Genome and Phylogeny Life Cycle Apoptosis Hemocyte Responses to WSSV Infection Epidemiology Clinical Features and Pathology Protection of Shrimp Against WSSV Infection Using Vaccination and RNAi Strategies Further Reading Relevant Website Nodaviruses of Invertebrates and Fish (Nodaviridae) Classification (Compact): Family Nodaviridae, genera Alphanodavirus and Betanodavirus Provisional Nodaviruses Proposed Six Clade Taxonomic Structure Virion Structure Genome Proteins RNA-Dependent RNA Polymerase (RdRp) Capsid Proteins Proteins B1 and B2 Physical Properties Life Cycle Epidemiology Clinical Features VNN WTD VCMD Pathogenesis Immune Responses to Nodavirus Infection Innate Immune Responses Adaptive Immune Responses in Nodavirus Infection Diagnosis VNN WTD VCMD Treatment Prevention VNN WTD VCMD Further Reading Nudiviruses (Nudiviridae) Glossary Classification History Criteria for Classification Members of the Nudiviridae Phylogeny (Evolution of Nudiviridae and Other dsDNA Arthropod Viruses) Virion Structure Transmission and Pathogenesis Virus Life Cycle Genome General Features Gene Content Gene Regulation for Switching Productive and Latent Infections Negative Impacts and Potential Applications Further Reading Parvoviruses of Invertebrates (Parvoviridae) Glossary Introduction Discovery, Taxonomy and Evolution of Densoviruses; of Polyphyly, Paraphyly and its Tangled Relationship With... Biology, Pathology and Host Range General Features Shrimp Densoviruses Penaeus stylirostris penstyldensovirus 1 (PstDV1) Fenneropenaeus chinensis hepandensovirus (FcHDV) New invertebrate DVs Biochemical Properties and Purification of Densoviruses Structural Features of Virions Biophysical Features and Functions Associated With the Densovirus Capsid Densovirus Genome Structure and Replication Expression Strategies Conclusions Acknowledgments Reference Further Reading Relevant Websites Polydnaviruses (Polydnaviridae) Glossary Classification (Compact) Life Cycle of PDVs Virion Structure Morphogenesis of PDV Particles The PDV Packaged Genome Function of the Genes Encoded by PDV Packaged Genome Fate of the PDV Packaged Genome in the Parasitized Insect The Proviral Genome Maintained in the Wasp Genome Organization of PDV Proviral Segments in the Wasp Genome The PDV Viral Machineries Concluding Remarks Further Reading Poxviruses of Insects (Poxviridae) Glossary Introduction Classification Virus/Midgut Interactions Replication in Larvae Genomics Conserved and Shared Genes Gene Families Entomopoxvirus Phylogeny Acknowledgment Further Reading Reoviruses of Invertebrates (Reoviridae) Glossary Taxonomy Introduction Spinareovirinae Historical Overview Host Range, Diseases, Transmission, and Distribution Cypoviruses Idnoreoviruses Dinovernavirus Aquareovirus Fijivirus Orthoreovirus Virion Properties, Genome, and Replication Cypoviruses Idnoreoviruses Dinovernavirus Antigenic and Genetic Relationships Cypoviruses Idnoreoviruses Dinovernaviruses Sedoreovirinae Cardoreovirus Phytoreovirus Seadornavirus See also Further Reading Rhabdoviruses of Insects (Rhabdoviridae) Classification Virion Structure Genome Sigmavirus Genome Almendraviruses Genome Other Insect Rhabdovirus Genomes Life Cycle Integration Into the Host Genome Epidemiology Distribution, Spatial and Temporal Transmission Prevalence Population Dynamics Clinical Features Pathogenesis Diagnosis Further Reading Relevant Websites Sarthroviruses (Sarthroviridae) Glossary Introduction Geographical Distribution Clinical Signs of WTD and Histopathology Morphology of Virus Genome Organization Taxonomic Position Pathogenicity and Transmission of Disease Host Range Susceptibility of Cell Line to XSV Diagnostic Tools Control Measures Acknowledgment References Relevant Website Solinviviruses (Solinviviridae) Glossary Introduction Classification (Compact) Virion Structure Genome Life Cycle Epidemiology (Host Specificity/Prevalence/Transmission) Clinical Features Pathogenesis Diagnosis (Detection) Prevention (Biocontrol) Further Reading Relevant Websites Tetraviruses (Alphatetraviridae, Carmotetraviridae, Permutotetraviridae) Introduction Genome Organization Alphatetraviridae Permutotetraviridae Carmotetraviridae Viral Replication The Tetravirus Capsid Capsid Structure Capsid Maturation, Auto-Proteolysis and Dynamics Pathology Symptoms and Transmission Host Range Persistent Infections Concluding Remarks Reference Further Reading e9780128145159v5_WEB Cover ENCYCLOPEDIA OF VIROLOGY FOURTH EDITION EDITORS IN CHIEF EDITORIAL BOARD SECTION EDITORS FOREWORD PREFACE HOW TO USE THE ENCYCLOPEDIA LIST OF CONTRIBUTORS CONTENT OF ALL VOLUMES DIAGNOSIS Introduction to Virus Diagnosis and Treatment References Electron Microscopy for Viral Diagnosis Glossary Introduction to Virus Diagnosis by Electron Microscopy Diagnostic Transmission Electron Microscopy Biological EM Challenges and Sample Preparation General Protocol for the Study of Viruses by Negative Staining Negative Staining for Diagnosis of Fecal Samples Preparation of Agarose Slides Limitations of Traditional Processing Techniques and Advanced Protocols Cryo Electron Microscopy Advances in Scanning Electron Microscopy Conclusion Further Reading Relevant Websites Serological Approaches for Viral Diagnosis Introduction Principles of Serological Assays IgG Avidity General Considerations and Sources of Error Restrictions and Limitations Principles of Widely Used Serological Tests Immunoassays Solid-phase microwell immunoassays Immunoblotting Immunofluorescence microscopy Lateral-flow immunoassays Homogenous wash-free immunoassays Neutralizing Antibody Assay Latex Agglutination Hemagglutination Inhibition Complement Fixation Sequencing Analysis of Antibody Repertoire Point-of-Care Serodiagnostics Future Perspectives Further Reading A Brief History of the Development of Diagnostic Molecular-Based Assays Isothermal Amplification Non-Isothermal PCR Based Technologies References Sequencing Strategies Glossary General Overview First Generation Sequencing Technology Second Generation or Parallel Sequencing Technologies Application of NGS in Virology Third Generation Sequencing Technologies Sample Preparation Strategies for Sequencing Viruses Nucleic Acid Sequence Dependent Strategies for Known Viruses Nucleic Acid Sequence Independent Strategies for Sequencing Virus Databases Further Reading Relevant Websites Validating Real-Time Polymerase Chain Reaction (PCR) Assays Introduction The Need for Validation In-House Assays Commercial Assays The Validation Process: Consultation Stage Preliminary Considerations The Validation plan Analytical Verification Stage Reference Materials and Sample Numbers Template, Primers and Probes: In-Silico Design Choice of the Quantification Standards Reaction Controls Reverse Transcription PCR Westgard Rules Experimental Optimization Normalization Analytical Specificity and Sensitivity Inhibition Study PCR Efficiency Linear Dynamic Range or Reportable Range Clinical Validation Stage Precision, Accuracy and Trueness The Gold Standard Comparative Study The Study Without a Gold Standard Inter-Laboratory Testing Maintaining the Validated Status and Re-Validation Acknowledgment References Further Reading Relevant Websites Rapid Point-of-Care Assays Introduction PoC Technologies PoC Strategy and Implementation Point-of-Care Laboratory Grade 1A Point-of-Care Laboratory Grade 1B Point-of-Care Laboratory Grade 2A Point-of-Care Laboratory Grade 2B Point-of-Care Laboratory Grade 3 PoC Menus PoC Clinical Impact Conclusion References Relevant Websites Standardization of Diagnostic Assays Glossary Introduction Physical Standards (Reference Materials) Preparation and Evaluation of Standards Written Standards and Guidelines Quality Assurance The Use of Controls Batch Testing External Quality Assessment/Proficiency Testing Laboratory Accreditation Commercial and Laboratory-Developed tests Virus Isolation The Use of International Standards in Clinical Practice Conclusions Further Reading Relevant Websites Quality Assurance in the Clinical Virology Laboratory Glossary The Principles of Quality Assurance and Quality Management Quality Management System (QMS) Quality Management Documentation Document Control Specimen Management Transportation and Storage of Specimens Laboratory Specimen Retention Times Personnel Training, Competency, and Continuous Professional Development (CPD) Laboratory Facilities and Equipment Equipment Qualification, Calibration, Maintenance and Monitoring Equipment Qualification Equipment Calibration Equipment Maintenance and Monitoring Internal and External Audits Assay Verification and Validation Accuracy Precision Reportable range and limit of detection (LoD) Linearity/analytical measurement range (AMR) Sensitivity, Specificity, and Clinical Utility Internal Quality Assessment (IQA) Internal Quality Control Procedures and Monitoring Assay Performance Over Time Suitable Standards, Reference Materials and Controls to Support Quality Assurance in Virology External Quality Assessment and Performance Criteria EQA Design and Objectives Summary and Future Aspects of QA to Virology Laboratory Further Reading Relevant Websites Biosafety and Biosecurity in Diagnostic Laboratories Introduction Biosafety and Biosecurity Diagnostic Laboratories Laboratory Biosafety Biological Agents Laboratory Biosafety Levels Risk Assessment Routes of Transmission and Infective Dose Personal Protective Equipment (PPE) Biosafety Cabinets Decontamination and Waste Management Laboratory Accidents Occupational Health and Special Groups Shipment of Clinical Specimens Laboratory Biosecurity Biorisk Management System and Legislation Further Reading Relevant Websites Screening for Viral Infections Introduction Pathology Culture Nucleic Acid Tests Polymerase Chain Reaction Assays Multiplex PCR DNA Microarrays High Throughput Sequencing VirCapSeq-VERT Clustered Regularly Interspaced Short Palindromic Repeats (CRISPER) Platforms Serology Hemagglutination Inhibition Assays Plaque Reduction Neutralization (PRNT) Assays Immunofluorescent Assays (IFA), Enzyme-Linked Immunosorbent Assays (ELISA) and Immunoblot Assays Lateral Flow Assays (LFA) Multiplex Platforms for High Throughput Serology Discussion/Summary References Clinical Diagnostic Virology Glossary Introduction Respiratory Tract Infections Background Assays Clinical Impact Gastrointestinal Infections Background Assays Clinical Impact Central Nervous System Infections Background Assays Clinical Impact Hepatitis E Virus Infection References Further Reading Virus Diagnosis in Immunosuppressed Individuals Introduction Viral Diagnostic Tests Human Cytomegalovirus (HCMV) Epstein-Barr Virus (EBV) Polyomaviruses (PyV) Adenoviruses (AdVs) Other Viruses Herpes Simplex Virus (HSV) Varicella-Zoster Virus (VZV) Hepatitis E Virus Conclusion Further Reading Diagnosis; Future Prospects on Direct Diagnosis PCR and Its Evolution Next-Generation Sequencing (NGS) CRISPR-Cas MALDI-TOF Mass Spectrometry Multiplex and POCT Microfluidics Conclusions and Future Perspectives References Further Reading TREATMENT Antiviral Classification Glossary Introduction Human Immunodeficiency Virus (HIV) HIV Reverse Transcriptase HIV Protease HIV Integrase HIV GP41 HIV GP120 Hepatitis C Virus (HCV) HCV NS3/4A Protease HCV NS5A Phosphoprotein HCV NS5B Polymerase Respiratory Syncytial Virus (RSV) RSV RNA Polymerase RSV Fusion Glycoprotein Herpes Simplex Virus (HSV) HSV DNA Polymerase UL30 HSV Envelope Protein Human Cytomegalovirus (HCMV) HCMV DNA Polymerase UL54 HCMV Terminase UL56 Human Influenza Virus Viral RNA Polymerase Neuraminidase Matrix Protein 2 Variola Virus (Human Smallpox) VP37 Envelope Wrapping Protein Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) SARS-CoV-2 Polymerase Varicella Zoster Virus (VZV) VZV DNA Polymerase Hepatitis B Virus (HBV) HBV DNA Polymerase Conclusion References Antiretroviral Therapy - Nucleoside/Nucleotide and Non-Nucleoside Reverse Transcriptase Inhibitors Retroviruses and Reverse Transcription Reverse Transcriptase Structure and Functions The Process of Reverse Transcription A tRNA primer binds to the primer binding site on the HIV-1 RNA Reverse transcriptase (RT) starts at this binding site and copies RNA into a single strand of complementary DNA RNase H degrades the section of the RNA which has been copied Nucleoside/nucleotide Reverse-Transcriptase Inhibitors (NRTIs) NRTIs and Their Mechanism of Action Clinical Uses of NRTIs NRTI Toxicities Drug-Drug Interactions With NRTIs Mechanisms of NRTI Resistance New Drugs Non-Nucleoside Reverse-Transcriptase Inhibitors (NNRTIs) NNRTIs and Their Mechanism of Action Clinical Uses of NNRTIs NNRTI Toxicities Drug-Drug Interactions With NNRTIs Mechanisms of NNRTI Resistance References Relevant Websites Protease Inhibitors Glossary Protease Inhibitors Introduction Mechanism of Action Pharmacodynamics and Pharmacokinetics in PIs PIs in Combination With Other ART Classes Protease Inhibitor-Based Regimens Triple therapy: Boosted PI plus 2 NRTI Dual therapy: boosted PI plus 1 NRTI or 1 INSTI Darunavir Atazanavir Lopinavir New PIs Tolerability of PIs Side effects Hepatotoxicity Gastrointestinal Dyslipidemia, lipodystrophy and insulin resistance Cardiovascular Kidney stones Drug-Drug Interactions Resistance to PIs Protease Inhibitors in Low Resource Settings Sub-Saharan Africa Protease Inhibitors in Clinical Practice References Further Reading Relevant Websites HIV Integrase Inhibitors and Entry Inhibitors Glossary Integrase Strand Transfer Inhibitors Virology First Generation INSTI Raltegravir Resistance Clinical trials in cART naïve individuals Clinical trials in cART-experienced patients Elvitegravir Clinical trials Resistance Second Generation INSTI Dolutegravir Clinical trials: Therapy-naïve with 2 NRTI Clinical trials: Treatment-experienced Clinical trials: Dual therapy Resistance Bictegravir Phase 3 randomized controlled trials Resistance Cabotegravir Entry Inhibitors Maraviroc Enfuvirtide Ibalizumab-Uiyk Fostemsavir Pregnancy Children and Adolescents Post-Exposure and Pre-Exposure Prophylaxis (PEP and PrEP) HIV-2 Further Reading Management of Respiratory Syncytial Virus Infections (Pneumoviridae) Introduction and Epidemiology Pathogenesis and Immunity Clinical Features Treatment Strategies Prophylaxis RSV Vaccination Conclusion References Further Reading Management of Influenza Virus Infections (Orthomyxoviridae) Introduction Seasonal Influenza Pandemic Influenza Zoonotic Influenza Antiviral Drugs Available Adamantanes or M2 Blockers (Fig. 1) Neuraminidase Inhibitors (Fig. 1) Polymerase Inhibitors (Fig. 1) Ribavirine (Ribavirinreg) Baloxavir Marboxil (Xofluzareg) Pimodivir Favipiravir (Aviganreg) Drugs Under Development With Other Mechanisms of Action HA processing blockers (Fig. 1) HA attachment blockers (Fig. 1) Perspectives at Short and Medium Term Host Target Molecules (i.e., Diltiazem) Macrolides Other Immunomodulators Sirolimus Combined Treatments (Double, Triple) NAI combinations Triple therapy (amantadine, ribavirine oseltamivir) Combined oseltamivir plus monoclonal antibodies Combined oseltamivir plus favipiravir Combined baloxavir plus oseltamivir Pimodivir and oseltamivir Complementary Treatments for Disease Management ECMO (Extracorporeal Membrane Oxygenation) Conclusion References Further Reading Management of Herpes Simplex Virus Infections (Herpesviridae) Brief Overview of Available Antiviral Agents for HSV Infections Management of Infections Beyond the Neonatal Period Orolabial Infections Cutaneous Infections Ocular Infections CNS Infections Genital Herpes Neonatal Herpes Simplex Virus Infection Immunocompromised Hosts Immunoprophylaxis Further Reading Management of Varicella-Zoster Virus Infections (Herpesviridae) Glossary Laboratory Diagnosis Submission of Samples Direct Detection of Virus Detection of Antibodies Antiviral Treatment Antiviral Agents in Clinical Use Acyclovir Valaciclovir Famciclovir Foscarnet (trisodium phosphonoformate) Brivudine ((E)-5-(2-bromovinyl)-2 prime-deoxyuridine) Development of Resistance Thymidine kinase gene DNA polymerase gene Resistance Testing Phenotyping Genotyping Prevention Prevention of Varicella by Vaccination Passive Immunoprophylaxis of Varicella Prevention of Zoster by Vaccination Further Reading Treatment and Prevention of Herpesvirus Infections in the Immunocompromised Host Introduction Cytomegalovirus (Human Herpesvirus 5) Pre-Transplant Risk Stratification Prevention Strategies of CMV Disease After Transplantation Diagnosis of CMV Disease and Treatment Antiviral Drug Resistance HSV (Herpes Simplex Virus, Human Herpesvirus 1 and 2) Varicella Zoster Virus (VZV, Human Herpesvirus 3) Human Herpes Virus - 6 and 7 Epstein-Barr Virus (Human Herpesvirus 4) Human Herpes Virus-8 Further Reading Management of Adenovirus Infections (Adenoviridae) Glossary Taxonomy Family and Genus Types and Subtypes Structure Epidemiology Clinical Description of Infection Incubation Period Upper Respiratory Tract Infections Lower Respiratory Tract Infections Ocular Infections Gastroenteritis Genitourinary Diseases Diseases Infrequently Associated With Human Adenoviruses Infections Adenovirus Infections of Immunocompromised Patients Animal Adenoviruses Diagnosis Polymerase Chain Reaction (PCR) for Human Adenoviruses DNA Detection Quantitative Human Adenoviruses PCRs and Screening of High-Risk Patients Other Diagnostic Methods Adenovirus Differentiation and Typing Treatment and Prevention Antivirals Vaccines Germicides Further Reading Relevant Websites Management of Hepatitis A and E Virus Infection Introduction Taxonomy Hepatitis A Virus Hepatitis E Virus Epidemiology and Transmission Epidemiology Hepatitis A virus Very high and high endemicity pattern Low endemicity pattern Intermediate endemicity pattern Hepatitis E virus HEV genotypes 1 and 2 HEV genotypes 3 and 4 Transmission Hepatitis A virus Water- and food-borne transmission Person-to-person transmission Other modes of transmission Hepatitis E virus Clinical Presentation and Course Hepatitis A virus Hepatitis E Virus Diagnosis Antigen Detection Hepatitis A virus Hepatitis E virus Nucleic Acid Detection Hepatitis A virus Hepatitis E virus Serological Tests Hepatitis A virus Hepatitis E virus Vaccines and Antiviral Agents Hepatitis A Virus Immunoglobulin Vaccine Treatment Hepatitis E Virus Prophylaxis Vaccine Management of acute hepatitis E Management of chronic infections Conclusion Further Reading Relevant Websites Management of Patients With Chronic Hepatitis B (Hepadnaviridae) and Chronic Hepatitis D Infection (Deltavirus) Glossary Management of Chronic Hepatitis B and Hepatitis D Chronic Hepatitis B Introduction Treatment Indications Treatment Goals in CHB Treatment Options Nucleo(s)tide Analogs Safety Choosing the Appropriate First-Line Agent Management of Patients With NA Failure Finite NA Therapy Pegylated Interferon Alfa Efficacy in HBeAg-Positive Patients Efficacy in HBeAg-Negative Patients Safety of PEG-IFN in CHB Selection of Patients for PEG-IFN Therapy HBeAg-Positive Patients HBeAg-Negative Patients On-Treatment Prediction of Response HBeAg-Positive Patients HBeAg-Negative Patients Optimizing Response Rates: Treatment Prolongation and Combination Therapy Optimizing Response to NA With PEG-IFN Management of CHB in Special Populations Pregnancy Immunosuppression Chronic Hepatitis Delta Introduction Screening Treatment Indication and Goals Treatment Options Interferon Alpha Nucleo(s)tide Analogs Future References Further Reading Relevant Websites Studying Population Genetic Processes in Viruses: From Drug-Resistance Evolution to Patient Infection Dynamics Glossary The Population Dynamics of Infection Direct Selection and Linked Selection Effects Other Key Aspects of the Population Genetic Environment An Outlook on Evolutionarily Informed Treatment Strategies See also References Further Reading Virus-Based Cancer Therapeutics Glossary Definition Introduction and Historic Notes Re-engineered Viruses: The Beginnings Three Classes of Modifications Retargeting Virus Tropism Cell Entry Targeting of Enveloped Viruses Cell Entry Targeting of Non-Enveloped Viruses Cell Entry Targeting by Protease Activation Transcriptional Regulation of Replication Post-Transcriptional Regulation of Replication Preferential Tumor Spread Combination of Targeting Modalities Shielding From the Host Immune Response Virus Engineering Chemical Shielding and Cell Carriers Arming Viruses Prodrug Convertases Radiosensitizers for Therapy and Imaging Immunomodulators Combination Therapies Perspectives Further Reading Relevant Websites PREVENTION Surveillance of Infectious Diseases Glossary Introduction Essential Characteristics of Surveillance Collection of Data: Sources of Data in Surveillance of Viruses Death Certification Notifications Other Sources of Data Laboratory Data Surveillance of Outbreaks Hospital Admissions Serological Surveillance Surveillance of Viruses in Nonhuman and Environmental Sources Other Sources of Data Newer Types of Surveillance System Syndromic Surveillance Sentinel Surveillance Enhanced Surveillance Active Surveillance Surveillance of HIV/AIDS Attributes of Surveillance Systems Completeness Timeliness Accuracy Representativeness Consistency Analysis of Data Time Person Place Interpretation Feedback Evaluation of Surveillance Global and International Surveillance Further Reading Relevant Websites Preparing for Emerging Zoonotic Viruses Drivers of (Emerging) Zoonotic Diseases Disease X Emerging Disease Detection and the One Health Concept Developing Targeted, Risk Based Sampling Sample Collection The Value of Non-Invasive and Bulk Samples Catch-All Detection Methods From Genotype to Phenotype: Deriving Meaningful Information From Genomic Data Conclusion Note Added in Proof: December 2020 SARS-CoV-2 One Health and Animal Reservoirs Emerging Disease Detection, Full Genome Sequencing and Rapid Data Sharing Population Surveys and Sero-epidemiological Studies Concluding Remarks References Relevant Websites Use of Immunoglobulins in the Prevention of Viral Infections Introduction Polyclonal Immunoglobulins Used in the Prevention of Infectious Diseases Hepatitis A Measles Hyperimmune Immunoglobulins Used in the Prevention of Infectious Diseases Hepatitis B Hyperimmune Globulin Cytomegalovirus Hyperimmune Immunoglobulin Rabies Hyperimmune Immunoglobulin Vaccinia Hyperimmune Globulin Varicella Hyperimmune Immunoglobulin Monoclonal Antibodies Approved by the Food and Drug Administration Respiratory Syncytial Virus Human Immunodeficiency Virus Experimental Immunoglobulin Therapies Seasonal Influenza Avian Influenza Mers-Cov Ebola and Other Hemorrhagic Fevers Other Experimental Infections References Further Reading Relevant Websites Vaccine Production, Safety, and Efficacy Glossary Introduction The History of Vaccination What has Happened When Vaccine Reaches the Market? The Development of Shingrix Phases and Timelines in Vaccine Development: From Discovery to Product Preclinical Studies In Human Studies Costs and Duration of Vaccine Development Vaccine Production More About Vaccine Development The Licensing of Influenza Vaccines Follows a Different Procedure The Vaccine Industry Taking Stock The Challenge of Emerging Viral Diseases Looking Forward The Development of COVID-19 Vaccines References Relevant Websites Vaccines Against Viral Gastroenteritis Glossary Introduction Rotavirus Vaccines Licensed Rotavirus Vaccines Vaccine Effectiveness and Impact Rotavirus Vaccines in Development Rotavirus Vaccine Safety Monitoring Norovirus Norovirus Vaccine Development Norovirus Vaccines in Human Clinical Trials Norovirus Vaccines in Pre-Clinical Development Future Considerations for Norovirus Vaccines CDC Disclaimer Further Reading Human Papillomavirus (HPV) Vaccines and Their Impact Glossary HPV and HPV-Related Diseases HPV Vaccines Vaccine Immunogenicity HPV Vaccine Impact Impact on HPV Infection and Precancerous Lesions Impact on HPV-Related Cancer Impact on Anogenital Warts Current Status and Future Directions Vaccine Safety and Confidence Models on Impact and Cost-Effectiveness of HPV Vaccination References Relevant Websites Influenza Vaccination Introduction Influenza as a Disease Epidemiology of Influenza Brief History of Influenza Vaccines Production of Influenza Vaccines Timeline of the Production Process Production Steps Influenza Vaccine Composition Valency Dosage Formulations of Seasonal Influenza Vaccines Traditional Inactivated Vaccines Recombinant and Cell-Based Influenza Vaccines Live Attenuated Influenza Vaccines Adjuvanted Vaccines High-Dose Influenza Vaccines Intradermal Vaccines The Future of Influenza Vaccines Vaccination in Practice Administration Routes Timing of Programs Vaccine Uptake Duration of Protection Safety and Contraindications Overview Local and Systemic Inflammatory Reactions Allergic Reactions Rare Adverse Events: Neurological Syndromes Evaluating the Impact of Influenza Vaccines Immunogenicity Vaccine Efficacy Vaccine Effectiveness Understanding Vaccine Efficacy and Effectiveness Vaccination of Specific Population Groups Elderly Underlying Conditions Pregnancy Healthy Children Healthy Adults Pandemic Influenza Vaccines Further Reading Relevant Websites Polio Eradication Background Vaccines Poliovirus Surveillance Status of Eradication New Vaccines Antivirals Containment Transition of Global Polio Eradication Initiative Assets Post-Eradication Further Reading Relevant Websites Subject Index
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