S. Jane Flint - Principles of Virology, Volume 2

1 Cover

2 Preface Preface The enduring goal of scientific endeavor, as of all human enterprise, I imagine, is to achieve an intelligible view of the universe. One of the great discoveries of modern science is that its goal cannot be achieved piecemeal, certainly not by the accumulation of facts. To understand a phenomenon is to understand a category of phenomena or it is nothing. Understanding is reached through creative acts. A. D. HERSHEY Carnegie Institution Yearbook 65 All five editions of this textbook have been written according to the authors’ philosophy that the best approach to teaching introductory virology is by emphasizing shared principles. Studying the common steps of the viral reproductive cycle, illustrated with a set of representative viruses, and considering mechanisms by which these viruses can cause disease provides an integrated overview of the biology of these infectious agents. Such knowledge cannot be acquired by learning a collection of facts about individual viruses. Consequently, the major goal of this book is to define and illustrate the basic principles of virus biology. In this information-rich age, the quantity of data describing any given virus can be overwhelming, if not indigestible, for student and expert alike. The urge to write more and more about less and less is the curse of reductionist science and the bane of those who write textbooks meant to be used by students. In the fifth edition, we continue to distill information with the intent of extracting essential principles, while providing descriptions of how the information was acquired and tools to encourage our readers’ exploration of the primary literature. Boxes are used to emphasize major principles and to provide supplementary material of relevance, from explanations of terminology to descriptions of trailblazing experiments. Our goal is to illuminate process and strategy as opposed to listing facts and figures. In an effort to make the book readable, we have been selective in our choice of viruses that are used as examples. The encyclopedic Fields’ Virology [Knipe DM, Howley PM (ed). 2020. Fields Virology , 7th ed. Lippincott Williams & Wilkins, Philadelphia, PA] is recommended as a resource for detailed reviews of specific virus families.

3 Acknowledgments

4 About the Authors

5 Key of Repetitive Elements

6 1 Infections of Populations: History and Epidemiology Introduction to Viral Pathogenesis A Brief History of Viral Pathogenesis Viral Epidemics in History Epidemiology Parameters That Govern the Ability of a Virus to Infect a Population Perspectives References

7 2 Barriers to Infection Introduction An Overview of Infection and Immunity Successful Infections Must Modulate or Bypass Host Defenses Viral Tropism Spread throughout the Host Organ Invasion Shedding of Virus Particles Perspectives References

8 3 The Early Host Response: Cell Autonomous and Innate Immunity Introduction The First Critical Moments: How Do Individual Cells Detect a Virus Infection? Cell-Intrinsic Defenses Secreted Mediators of the Innate Immune Response The Innate Immune Response Perspectives References

9 4 Adaptive Immunity and Establishment of Memory Introduction Attributes of the Host Response Lymphocyte Development, Diversity, and Activation Events at the Site of Infection Set the Stage for the Adaptive Response Antigen Processing and Presentation The CTL (Cell-Mediated) Response The Humoral (Antibody) Response Immunological Memory Perspectives References

10 5 Patterns and Pathogenesis Introduction Animal Models of Human Diseases Patterns of Infection Viral Virulence Pathogenesis Perspectives References

11 6 Cellular Transformation and Oncogenesis Introduction Oncogenic Viruses Activation of Cellular Signal Transduction Pathways by Viral Transforming Proteins Disruption of Cell Cycle Control Pathways by Viral Transforming Proteins Transformed Cells Increase in Size and Survive Tumorigenesis Requires Additional Changes in the Properties of Transformed Cells Other Mechanisms of Transformation and Oncogenesis by Human Tumor Viruses Perspectives References

12 7 Vaccines Introduction The Origins of Vaccination Vaccine Basics The Science and Art of Making Vaccines Vaccine Technology: Delivery and Improving Antigenicity The Ongoing Quest for an AIDS Vaccine Perspectives References

13 8 Antiviral Drugs Introduction Discovering Antiviral Compounds Drug Resistance Examples of Antiviral Drugs Expanding Targets for Antiviral Drug Development Two Stories of Antiviral Success Perspectives References

14 9 Therapeutic Viruses Introduction Phage Therapy Oncolytic Animal Viruses Gene Therapy Vaccine Vectors Perspectives References

15 10 Virus Evolution Virus Evolution How Do Virus Populations Evolve? The Origin of Viruses Host-Virus Relationships Drive Evolution Lessons from Paleovirology Perspectives References

16 11 Emergence The Spectrum of Host-Virus Interactions Encountering New Hosts: Humans Constantly Provide New Venues for Infection Common Sources for Animal-to-Human Transmission Viral Diseases That Illustrate the Drivers of Emergence The Contribution to Emergence of Mutation, Recombination, or Reassortment New Technologies Uncover Previously Unrecognized Viruses Perceptions and Possibilities Perspectives References

17 12 Human Immunodeficiency Virus Type I Pathogenesis Introduction HIV-1 Is a Lentivirus Entry and Transmission The Course of Infection Virus Reproduction Immune Responses to HIV-1 HIV-1 and Cancer Prospects for Treatment and Prevention Perspectives References

18 13 Unusual Infectious Agents Introduction Viroids Satellite Viruses and RNAs Prions and Transmissible Spongiform Encephalopathies Perspectives References

19 APPENDIX: Epidemiology and Pathogenesis of Selected Human Viruses Adenoviruses Arenaviruses Bunyaviruses Caliciviruses Coronaviruses Filoviruses Flaviviruses Flaviviruses Flaviviruses Hepadnaviruses Herpesviruses Herpesviruses Herpesviruses Orthomyxoviruses Papillomaviruses Paramyxoviruses Paramyxoviruses Picornaviruses Picornaviruses Picornaviruses Polyomaviruses Poxviruses Reoviruses Reoviruses Retroviruses Retroviruses Rhabdoviruses Togaviruses Togaviruses

20 Glossary

21 Index

22 End User License Agreement

1 Chapter 1 Table 1.1 Reproductive numbers for selected viruses

2 Chapter 3Table 3.1 Some viral modulators of the interferon responseTable 3.2 Some chemokine receptors and their ligands

3 Chapter 5Table 5.1 Incubation periods of some common virusesTable 5.2 Some persistent viral infections of humansTable 5.3 Epstein-Barr latency programs

4 Chapter 6Table 6.1 Oncogenic viruses and cancerTable 6.2 Some transforming gene products of adenoviruses, papillomaviruses,...

5 Chapter 7Table 7.1 Viral vaccines licensed in the United StatesTable 7.2 When can we expect an HIV vaccine?

6 Chapter 8Table 8.1 Approved drugs targeted against human immunodeficiency virus

7 Chapter 10Table 10.1 Fitness decline compared to initial virus clone after passage thr...

8 Chapter 13Table 13.1 Viroids and satellitesTable 13.2 Some transmissible spongiform encephalopathies

1 Chapter 1 Figure 1.1 Conquerors of yellow fever. This painting by Dean Cornwell (1939) d... Figure 1.2 The pace of discovery of new infectious agents in the dawn of virol... Figure 1.3 Consequences of the 1918 influenza pandemic. (A) The 1918–19 influe... Figure 1.4 Deaths caused by the yellow fever epidemic in Philadelphia, 1793. T... Figure 1.5 Spread of West Nile virus in the United States. The maps show the s... Figure 1.6 Fruit bat geographic range in Southeast Asia, and prevalence of Nip... Figure 1.7 Ebola outbreak. Health care workers in areas of the Ebola virus out... Figure 1.8 Zika spread in Brazil. (A) In three short years, from 2014 to 2016,... Figure 1.9 Twitter as a tool in viral epidemiology. Between May 1 and December... Figure 1.10 Seasonal variation in disease caused by three human pathogens in t...