Front Cover

Advances in Virus Research

Copyright

Contents

Contributors

Preface to Volume 100: History and Looking Forward

1. Discovery of Viruses: The First “Golden Age” of Virology

2. The World’s Oldest Review Series in Virology: Advances in Virus Research

3. Virology Today: Another Golden Age in Virus Research

Acknowledgments

References

Further Reading

Chapter One: The Species Problem in Virology

1. Introduction

2. The Logic of Hierarchical Virus Classification

3. Definitions of Virus Species

4. Diagnostic Markers Useful for Virus Identification Are Not Species-Defining Properties

5. Only Viruses But Not Their Genome Sequences Can Be Classified Into Species and Genus Classes

5.1. The Phenotypic Properties of a Virus Cannot Be Inferred From Its Genome Sequence

6. The Current Debate on Non-Latinized Binomial Names of Virus Species

Acknowledgments

References

Further Reading

Chapter Two: The Role of Immune Responses in HIV Mother-to-Child Transmission

1. Introduction

2. Epidemiology of HIV MTCT

3. Modes and Mechanisms of Transmission

4. Current Approaches to Prevention of MTCT

5. Harnessing the Immune Response for Prevention of MTCT: Humoral Immune Correlates of HIV MTCT

5.1. Passive Transfer of Antibodies

5.2. Neutralizing Antibodies

5.3. Antibody-Dependent Cellular Cytotoxicity

5.4. Identification of Protective Antibody Epitopes

6. The Role of Cellular and Innate Immunity in HIV MTCT

6.1. T Cells in MTCT

6.2. Innate Immune Factors

7. The Way Forward: The Future of Prevention of HIV MTCT

7.1. Preventative and Therapeutic Passive Immunization

7.2. Active Vaccination to Prevent HIV MTCT

7.3. The HIV Reservoir and Potential for a Cure

8. Conclusions

Acknowledgments

References

Chapter Three: African Swine Fever Virus Biology and Vaccine Approaches

1. Emergence and Host Range of African Swine Fever Virus

2. Virus Transmission and Spread

3. Molecular Biology of the Virus

4. Virus Entry, Intracellular Traffic, and Viral Machinery of Translation

4.1. African Swine Fever Virus Entry and Traffic

4.2. African Swine Fever Virus Control of Cellular Protein Synthesis

5. African Swine Fever Virus Genes Modulating Host Responses

6. African Swine Fever Virus Vaccines

6.1. Modulation of the Host Immune System by African Swine Fever Virus

6.2. Cells Susceptible to African Swine Fever Virus Infection

6.3. Live-Attenuated African Swine Fever Virus Vaccines

6.4. Subunit Vaccines

6.5. The Future of African Swine Fever Virus Vaccinology

Acknowledgments

References

Chapter Four: Morbillivirus Pathogenesis and Virus-Host Interactions

1. Introduction

2. History

3. Genome Organization

4. Infection Cycle

5. Similarities and Differences in Morbillivirus Disease Manifestation

6. Morbillivirus-Associated Neurological Complications

7. Morbillivirus-Host Interactions

7.1. Host Factors Involved in RNA Synthesis and Particle Assembly

7.2. Host Factors Involved in IFN Response

8. Conclusions

References

Further Reading

Chapter Five: Viruses of Plant-Interacting Fungi

1. Introduction

2. Types of Virus/Host Interactions

2.1. Beneficial Interactions With Host Fungi

2.2. Harmful Interactions With Host Fungi

3. Types of Virus/Virus Interactions

3.1. Synergistic Interactions Between Viruses

3.2. Mutualistic Interactions Between Viruses

3.3. Antagonistic Interactions Between Viruses

3.4. Genome Rearrangements During Coinfection

3.5. Implication of Coinfections by Multiple Mito- and Mito-Like Viruses

4. Conclusions and Prospects

Acknowledgments

References

Chapter Six: Protein Localization and Interaction Studies in Plants: Toward Defining Complete Proteomes by Visualization

1. Introduction

2. The Perfect Image

3. Getting Started: What Is the Question That Needs to Be Addressed?

4. A Startling Array of Imaging Technologies and Instrumentation

5. Validating Expression

6. Points of Reference

7. Avoiding Cross Talk

8. Colocalization: What It Is, and What It Is Not

9. Does the Localization Pattern Make Biological Sense?

10. What Supporting Data Are Needed?

11. The Published Micrograph Is the Localization Pattern

12. The Case for a Protein Atlas for Plant Proteins

13. The Nucleus in Virus-Host Interactions

14. Brief Protocol for Expression of Proteins in Plant Cells Using Agroinfiltration

Acknowledgments

References

Chapter Seven: So What Have Plant Viruses Ever Done for Virology and Molecular Biology?

1. Introduction

2. Biochemical Characterization

3. Structural Studies

4. Life Created in a Test-Tube

5. Molecular Genetics

6. Genomic Sequences

7. Reverse Genetics of RNA Viruses

8. Gene Silencing

9. Bio- and Nanotechnology

10. Conclusion

Acknowledgments

References

Chapter Eight: Hosts and Sources of Endemic Human Coronaviruses

1. Introduction

1.1. Endemic Human Coronavirus Disease

1.2. Definitions and Concepts

1.2.1. Virus Species

1.2.2. Application of Niche- vs Genetic Distance Criteria in Species Classification

1.2.3. Natural Hosts

1.2.4. Zoonotic Sources

1.2.5. Tropism Changes During Emergence

1.3. Natural Hosts and Zoonotic Sources of Human Coronaviruses

2. HCoV-NL63

3. HCoV-229E

4. HCoV-OC43

5. HCoV-HKU1

5.1. Perspectives

Acknowledgment

References

Chapter Nine: Filoviruses: Ecology, Molecular Biology, and Evolution

1. Introduction

2. Taxonomy

3. Virus Ecology

3.1. Ebolaviruses

3.2. Marburgviruses

3.3. Cuevaviruses

4. Filoviral Particles

4.1. Morphology

4.2. Genome Structure

4.3. Protein Structure and Function

4.3.1. Nucleoprotein Complex

4.3.2. Polymerase Complex

4.3.3. Matrix Protein

4.3.4. Viral Surface Spike

4.3.5. Nonstructural Glycoproteins

4.3.6. Interferon Antagonists

5. Viral Life Cycle

5.1. Entry and Uncoating

5.2. Transcription and Replication

5.3. Virion Assembly

5.4. Budding

6. Evolution

7. Future Perspectives

Acknowledgments

References

Chapter Ten: An Orchestra of Reovirus Receptors: Still Searching for the Conductor

1. Introduction

2. Reovirus Background

3. Sialic Acid Is a Serotype-Specific Reovirus Attachment Factor

4. Junctional Adhesion Molecule A Is Required for Hematogenous Dissemination of Reovirus

5. Nogo-66 Receptor 1 Is a Neural Receptor for Reovirus

6. Concluding Thoughts

Acknowledgments

References

Chapter Eleven: Antiviral Immune Response and the Route of Infection in Drosophila melanogaster

1. Introduction

2. Routes of Infection

2.1. Through the Cuticle

2.2. Through the Trachea

2.3. Through the Gut

2.4. Through the Genital Organ

3. Drosophila: Most Common Modes of Infection

4. Infection Outcomes and Immune Responses

5. Drosophila Antiviral Immune Responses Upon Different Routes and Modes of Infection

5.1. RNA Interference

5.2. Inducible Responses

5.2.1. Jak-STAT Pathway

5.2.2. IMD Pathway

5.2.3. Toll Pathway

5.3. Cellular Responses

5.3.1. Phagocytosis

5.3.2. Apoptosis

5.3.3. Autophagy

5.4. Other Factors Involved in Antiviral Immunity

5.4.1. Vago

5.4.2. dFOXO

5.4.3. Heat Shock Pathway

5.4.4. Polymorphisms and Virus Sensitivity

6. Virus-Bacteria Interactions

7. The Most Studied Drosophila Virus: DCV

8. DCV Tropism and the Infection Mode

9. Conclusions and Future Perspectives

Acknowledgments

References

Chapter Twelve: Changing Role of Wild Birds in the Epidemiology of Avian Influenza A Viruses

1. Introduction

2. Circulation of LPAIV Among Wild Birds

3. Transmission of LPAIV From Wild Birds to Poultry

4. The Emergence of HPAIV H5N1 in 1997, and Its Spillover to Wild Birds From 2002 to 2005

5. Continued Detection of HPAIV H5N1 in Wild Birds, 2006-11

6. Global Spread of HPAIV Clade 2.3.4.4 H5N8, 2014-16

7. Routes of Spread of HPAIV From Poultry to Wild Birds

8. Wild Waterbirds as a Long-Distance Vector of HPAIV

9. Wild Birds as a Maintenance Reservoir of HPAIV?

10. Discussion

References

Chapter Thirteen: Intracellular Antiviral Immunity

1. Pattern Recognition Receptors in Antiviral Defense

1.1. Toll-Like Receptors

1.2. C-Type Lectin Receptors

1.3. NOD-Like Receptors

1.4. RIG-I-Like Receptors

1.5. AIM-Like Receptors

1.6. OAS-Like Receptors

2. TRIM Proteins in Innate Immunity

2.1. Structure of TRIM Proteins

2.2. Functions of TRIM Proteins in Viral Restriction

2.3. Functions of TRIM Proteins in Innate Immune Regulation

2.4. The Role of TRIM21 in Innate Immunity

2.5. TRIM21 Effector Mechanism

2.6. The Role of TRIM21 in Innate Immune Regulation and Autoimmunity

Acknowledgments

References

Chapter Fourteen: How Does Vaccinia Virus Interfere With Interferon?

1. Introduction to Vaccinia Virus

1.1. Origin of Vaccinia Virus

1.2. Vaccinia Virus Replication Cycle

1.3. Vaccinia Virus Genes

2. Interferons

2.1. Induction of IFNβ Expression

2.2. IFN-Induced Signaling

2.3. IFN-Stimulated Genes

3. Preventing Production of IFN

3.1. Inhibition of Protein Synthesis in Virus-Infected Cells

3.2. Limiting the Formation or Availability of Virus Nucleic Acid PAMPs

3.2.1. Limiting dsRNA Formation by Gene Arrangement

3.2.2. Expression of a dsRNA Binding Protein E3

3.2.3. Targeting DNA-PK by Protein C16

3.3. Inhibition of Signaling Pathways Leading to Expression of IFNβ

3.3.1. Inhibition of IRF3 Activation

3.3.2. Inhibition of NF-κB Activation

3.3.3. Modulation of AP-1 Activation

4. Blocking Binding of IFNs to IFN Receptors

5. Blocking IFN-Induced Signaling Pathways

6. Blocking the Antiviral Action of ISGs

7. Summary

Acknowledgments

References

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