okvet [Viral Pathogenesis, 3rd Edition

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Viral Pathogenesis: From Basics to Systems Biology, Third Edition, has been thoroughly updated to cover topical advances in the evolving field of viral pathogenesis, while also providing the requisite classic foundational information for which it is recognized.

The book provides key coverage of the newfound ability to profile molecular events on a system-wide scale, which has led to a deeper understanding of virus-host interactions, host signaling and molecular-interaction networks, and the role of host genetics in determining disease outcome.

In addition, the content has been augmented with short chapters on seminal breakthroughs and profiles of their progenitors, as well as short commentaries on important or controversial issues in the field. Thus, the reader will be given a view of virology research with perspectives on issues such as biomedical ethics, public health policy, and human health. In summary, the third edition will give the student a sense of the exciting new perspectives on viral pathogenesis that have been provided by recent developments in genomics, computation, modeling, and systems biology.

Covers all aspects of viral infection, including viral entry, replication, and release, as well as innate and adaptive

Provides a fresh perspective on the approaches used to understand how viruses cause disease

Features molecular profiling techniques, whole genome sequencing, and innovative computational methods

Highlights the use of contemporary approaches and the insights they provide to the field

Table of Contents

Preface

Part I. History and Essentials of Viral Pathogenesis

Introduction
Chapter 1. The Human Toll of Viral Diseases: Past Plagues and Pending Pandemics
- 1. Introduction
- 2. The Human Toll of Specific Viral Diseases
- 3. Epidemics and Society
- 4. Viruses, Prions, and Chronic Disease
- 5. Lessons Learned: The Root Causes of Significant Viral Diseases of Humans
- 6. Viral Infections of Animals
- 7. Score Card: Are We Controlling Major Viral Diseases?
- 8. Pandemics Yet to Come: What Does the Future Hold?
- 9. Final Comments
Chapter 2. Historical Roots: The Family Tree of Viral Pathogenesis
- 1. From Cells and Viruses to Diseases
- 2. The Cellular Pathology of Virchow
- 3. Pasteur and Microbes
- 4. Cytopathology: Return to Pathogenesis
- 5. Host Responses as Pathologies
- 6. Reprise
Chapter 3. Basic Concepts: A Step-by-Step Guide to Viral Infection
- 1. Virus–Cell Interactions
- 2. Routes of Viral Transmission
- 3. Viral Dissemination and Movement
- 4. Virus Shedding and Transmission
- 5. Patterns of Virus Infection
- 6. Major Disease Mechanisms
- 7. Reprise
Chapter 4. Innate Immunity: Recognizing and Responding to Foreign Invaders—No Training Needed
- 1. Introduction
- 2. Interferons
- 3. Sensors of Infection
- 4. Innate Immune Cells
- 5. Defensins
- 6. Complement and “Natural” Antibodies
- 7. Relationship between Innate and Adaptive Immune Responses
- 8. Innate Functions in Sustained or Subsequent Viral Infection
- 9. Individual Variation
- 10. Reprise
Chapter 5. Adaptive Immunity: Neutralizing, Eliminating, and Remembering for the Next Time
- 1. Overview of the Immune System
- 2. Antibody
- 3. Cellular Immunity
- 4. Mucosal Immune Responses
- 5. Immunity as a Host Defense
- 6. Reprise
Chapter 6. Aberrant Immunity: The Consequences of Overreacting or Underperforming
- 1. Introduction
- 2. Virus-Initiated Immunopathology
- 3. Virus-Induced Immunosuppression
- 4. Viral Proteins that Perturb the Immune Response
- 5. Reprise
Chapter 7. Patterns of Infection: Unwanted Guests—Quick Visits and Extended Stays
- 1. Virulence Defined
- 2. How Can Virulence Be Altered? Classical Methods
- 3. How Can Virulence Be Altered? Genetics to the Fore
- 4. Enter the Host: How Virulent and Attenuated Viruses Differ in Their Pathogenesis
- 5. How Do Viruses Persist?
- 6. Reprise
Chapter 8. Viral Oncogenesis: Infections that Can Lead to Cancer
- 1. Introduction
- 2. Oncogenic RNA Viruses
- 3. Oncogenic DNA Viruses
- 4. Reprise
Chapter 9. HIV and AIDS: Science Wrestles with 10,000 Nucleotides—Points but No Pin
- 1. Introduction
- 2. Virology
- 3. Virus–Cell Interactions
- 4. Sequence of Events in HIV Infection
- 5. Immune Response to HIV
- 6. Pathogenesis
- 7. Genetic Determinants of Host Susceptibility to HIV
- 8. Vaccines
- 9. HIV Reservoir and Cure
- 10. Reprise
Chapter 10. Animal Models: No Model Is Perfect, but Many Are Useful
- 1. Introduction
- 2. Commonly Used Species
- 3. Considerations When Using Animal Models
- 4. Examples to Illustrate the Selection of Animal Models
- 5. Genetic Interventions in the Mouse: The Future of Animal Models
- 6. Other New Methodologies
- 7. Animal Models for Emerging Viruses
- 8. Vaccine Development
- 9. Reprise

Part II. Systems-Level Approaches to Viral Pathogenesis

Introduction
Chapter 11. Systems Virology: Why everybody wants to measure everything
- 1. Introduction
- 2. Using Genomics to Study Viral Pathogenesis
- 3. Diagnostics and Prognostics
- 4. Host-Response Networks
- 5. Drug Repurposing
- 6. New Views of the Transcriptional Landscape: Long Noncoding RNAs and Viral Infection
- 7. Concluding Remarks
Chapter 12. The Virus–Host Interactome: Knowing the Players to Understand the Game
- 1. Introduction
- 2. Genetic Functional Screens
- 3. Physical Protein Interaction Screens
- 4. Data Integration and Network Analysis
- 5. Reprise
Chapter 13. Host Genetics: It Is Not Just the Virus, Stupid
- 1. Introduction
- 2. Complex and Polymorphic Genetic Interactions
- 3. Biomedical Advances in Viral Diseases
- 4. Genetic Mapping to Identify Variants Affecting Complex Traits
- 5. Recombinant Inbred Panels
- 6. Reprise
Chapter 14. Metabolomics and Lipidomics: Yet More Ways Your Health Is Influenced by Fat
- 1. Introduction
- 2. Defining the Role of the Lipidome in Virus–Host Interactions
- 3. Lipids in Viral Replication and Pathogenesis
- 4. Concluding Remarks: Exploitation of Viral Dependence on Host Lipids as a Selective Antiviral Strategy
Chapter 15. Mathematical Modeling: Solving Equations to Measure Viral Diseases—Math Rules
- 1. HIV Modeling
- 2. Hepatitis C Virus
- 3. Drug Resistance
- 4. Concluding Remarks

Part III. Emergence and Control of Viral Infections

Introduction
Chapter 16. Emerging Viral Diseases: Why We Need to Worry about Bats, Camels, and Airplanes
- 1. How Do New Viral Diseases Emerge?
- 2. Zoonotic Infections as a Source of Emerging Viral Diseases
- 3. Why Viral Diseases Are Emerging at an Increasing Frequency
- 4. How Are Emergent Viruses Identified?
- 5. Reprise
Chapter 17. Viral Evolution: It Is All About Mutations
- 1. Introduction
- 2. Mutation and Substitution Rates in Viruses
- 3. Multiplicity of Infection
- 4. Phylodynamics: Evolution in a Host Population
- 5. Summary and Challenges Ahead
Chapter 18. Viral Epidemiology: Tracking Viruses with Smartphones and Social Media
- 1. History
- 2. Surveillance
- 3. Viral Infections in Space and Time
- 4. Population Movement
- 5. Transmission Networks
- 6. Molecular Epidemiology
- 7. Phylodynamics
- 8. Mathematical Models of Transmission Dynamics
- 9. Synthesis
Chapter 19. Viral Vaccines: Fighting Viruses with Vaccines
- 1. Introduction
- 2. Vaccine Modalities
- 3. Mechanisms of Protection by Established Vaccines
- 4. Vaccines Much Needed and Yet to Come
- 5. Systems Approaches to Vaccinology
- 6. Vaccines and Public Health
- 7. Reprise
Chapter 20. Antiviral Therapy
- 1. Principles of Antiviral Therapy
- 2. Examples of Antiviral Therapy
- 3. The Future of Drug Development

Part IV. Prizes and Predictions for Viral Pathogenesis

Introduction
Chapter 21. Breakthrough: Nobel Prize Discoveries in Viral Pathogenesis
- 1. Introduction
- Chapter 21.1. Yellow Fever Vaccine
- Chapter 21.2. Cultivation of Polioviruses
- Chapter 21.3. Discovery of Prions
- Chapter 21.4. Tumor-Inducing Viruses
- Chapter 21.5. Cellular Origin of Retroviral Oncogenes
- Chapter 21.6. Cell-Mediated Immune Defense
- Chapter 21.7. Innate Immunity
- Chapter 21.8. Discovery of the Dendritic Cell
Chapter 22. What Lies Ahead?: Scientists Look into Their Crystal Balls
- 1. Introduction
- 2. What Lies Ahead: Individual Visions
- Chapter 22.1. Systems Analysis of Host–Virus Interactions
- Chapter 22.2. New Cellular Assays
- Chapter 22.3. The Virome: Our Viral Commensals
- Chapter 22.4. Forward Genetics and Viral Pathogenesis
- Chapter 22.5. The Future of Synthetic Virology
- Chapter 22.6. Precision Medicine: Applications of Genetics to Pathogenesis and Treatment of Viral Diseases
- Chapter 22.7. Oncolytic Viruses
- Chapter 22.8. Prions and Chronic Diseases
- Chapter 22.9. Pathogenesis Research and the HIV/AIDS Pandemic
- Chapter 22.10. The Future of Viral Vaccines
- Chapter 22.11. Emerging Viruses
- Chapter 22.12. Pandemics: What Everyone Needs to Know
- Chapter 22.13. One Health
- Chapter 22.14. Controversial Policy Issues

Glossary and Abbreviations

Index

Author Information

Dr. Katze is Professor of Microbiology at the University of Washington and Associate Director for Molecular Sciences and Core Staff Scientist at the Washington National Primate Research Center. He has studied virus-host interactions for 35 years and is an international leader in applying systems biology approaches to infectious disease research. He is an author of over 300 papers and reviews, the majority of which are related to the use of high-throughput and computational methods. He has received the Milstein Award from the International Society of Interferon and Cytokine Research, the Dozor Scholar Award from the Israeli Microbiology Society, and is a Fellow of the American Academy of Microbiology.

Marcus Korth

Dr. Korth is a Senior Research Scientist in the Department of Microbiology at the University of Washington. He specializes in technical and medical writing and the effective communication of scientific concepts in grants, contracts, and the professional literature. He is a member of the American Medical Writers Association and holds a BA in psychology from the University of Wisconsin-Eau Claire, a BS in microbiology and BSMT in medical technology from the University of Montana, and a PhD in microbiology from the University of Washington. His research interests are in the use of systems biology approaches to study viral pathogenesis.

G. Lynn Law

Dr. Law is a Senior Research Scientist in the Department of Microbiology at the University of Washington. Her research interests are in the use of high-throughput and computational approaches to study virus-host interactions. She has managed several large programs that utilize different animal models, high-throughput technologies such as microarray and RNS-seq assays, and computational approaches to define the host response to a variety of viruses including influenza, SARS, MERS, and SIV. The overarching goal of these studies is to identify host targets for therapeutic interventions. She holds a BA in chemistry from the University of Colorado and a PhD in biochemistry from Washington State University.

Neal Nathanson

Neal Nathanson is emeritus Professor of Microbiology at the University of Pennsylvania. He has spent most of his 50-year career working on the pathogenesis of a wide variety of viral infections, using animal models to investigate the viral and host determinants of disease. He edited the prior two editions of Viral Pathogenesis.