Martinez J. Hewlett - Basic Virology

1 Cover

2 Dedication Page In Memoriam Edward K. Wagner (May 4, 1940 to January 21, 2006) It was one of those telephone calls that you do not want to receive. Each of us, that weekend in late January, heard of the untimely passing of our colleague, co‐author, collaborator, mentor, and friend, Ed Wagner. Ed will be remembered for his many contributions to the teaching of virology and for his research contributing to our understanding of the intricacies of the herpesviruses. From his graduate work at MIT, through his postdoctoral research at the University of Chicago, and on to his professorship at the University of California, Irvine, Ed was a passionate champion for the most rigorous and critical thinking and the most dedicated teaching, setting a standard for the discipline of virology. Beyond the laboratory and the classroom, Ed loved life to the fullest, with his family and friends. The last time we were together as a writing team, in the fall of 2005, we all remember an intense day of work in a conference room at UCI, followed by an evening of touring some of Ed’s favorite haunts in the Southern California coastal towns he called home. It is with those thoughts etched into our memories that we dedicate this edition of Basic Virology to Edward K. Wagner.

3 Title Page

4 Copyright Page

5 Preface to the First Edition

6 Preface to the Second Edition

7 Preface to the Third Edition

8 Preface to the Fourth Edition

9 Acknowledgments

10 PART I: Virology and Viral Disease CHAPTER 1: Introduction – The Impact of Viruses on Our View of Life THE SCIENCE OF VIROLOGY QUESTIONS FOR CHAPTER 1 CHAPTER 2: An Outline of Virus Replication and Viral Pathogenesis VIRUS REPLICATION PATHOGENESIS OF VIRAL INFECTION QUESTIONS FOR CHAPTER 2 CHAPTER 3: Virus Disease in Populations and Individual Animals THE NATURE OF VIRUS RESERVOIRS VIRUSES IN POPULATIONS ANIMAL MODELS TO STUDY VIRAL PATHOGENESIS QUESTIONS FOR CHAPTER 3 CHAPTER 4: Patterns of Some Viral Diseases of Humans THE DYNAMICS OF HUMAN–VIRUS INTERACTIONS PATTERNS OF SPECIFIC VIRAL DISEASES OF HUMANS SOME VIRAL INFECTIONS TARGETING SPECIFIC ORGAN SYSTEMS QUESTIONS FOR CHAPTER 4 Problems PART I Additional Reading for Part I

11 PART II: Basic Properties of Viruses and Virus–Cell Interaction CHAPTER 5: Virus Structure and Classification THE FEATURES OF A VIRUS CLASSIFICATION SCHEMES THE VIROSPHERE THE HUMAN VIROME QUESTIONS FOR CHAPTER 5 CHAPTER 6: The Beginning andEnd of the Virus Replication Cycle OUTLINE OF THE VIRUS REPLICATION CYCLE VIRAL ENTRY LATE EVENTS IN VIRAL INFECTION: CAPSID ASSEMBLY AND VIRION RELEASE QUESTIONS FOR CHAPTER 6 CHAPTER 7: The Innate Immune Response HOST CELL–BASED DEFENSES AGAINST VIRUS REPLICATION THE ADAPTIVE IMMUNE RESPONSE AND THE LYMPHATIC SYSTEM CONTROL AND DYSFUNCTION OF IMMUNITY MEASUREMENT OF THE IMMUNE REACTION QUESTIONS FOR CHAPTER 7 CHAPTER 8: Strategies to Protect Against and Combat Viral Infection VACCINATION – INDUCTION OF IMMUNITY TO PREVENT VIRUS INFECTION EUKARYOTIC CELL‐BASED DEFENSES AGAINST VIRUS REPLICATION ANTIVIRAL DRUGS BACTERIAL ANTIVIRAL SYSTEMS – RESTRICTION ENDONUCLEASES QUESTIONS FOR CHAPTER 8 Problems PART II Additional Reading for Part II

12 PART III: Working with Virus CHAPTER 9: Visualization and Enumeration of Virus Particles USING THE ELECTRON MICROSCOPE TO STUDY AND COUNT VIRUSES ATOMIC FORCE MICROSCOPY – A RAPID AND SENSITIVE METHOD FOR VISUALIZATION OF VIRUSES AND INFECTED CELLS, POTENTIALLY IN REAL TIME INDIRECT METHODS FOR “COUNTING” VIRUS PARTICLES QUESTIONS FOR CHAPTER 9 CHAPTER 10: Replicating and Measuring Biological Activity of Viruses CELL CULTURE TECHNIQUES THE OUTCOME OF VIRUS INFECTION IN CELLS MEASUREMENT OF THE BIOLOGICAL ACTIVITY OF VIRUSES QUESTIONS FOR CHAPTER 10 CHAPTER 11: Physical and Chemical Manipulation of the Structural Components of Viruses VIRAL STRUCTURAL PROTEINS CHARACTERIZING VIRAL GENOMES QUESTIONS FOR CHAPTER 11 CHAPTER 12: Characterization of Viral Products Expressed in the Infected Cell CHARACTERIZATION OF VIRAL PROTEINS IN THE INFECTED CELL DETECTING AND CHARACTERIZING VIRAL NUCLEIC ACIDS IN INFECTED CELLS USE OF MICROARRAY TECHNOLOGY FOR GETTING A COMPLETE PICTURE OF THE EVENTS OCCURRING IN THE INFECTED CELL QUESTIONS FOR CHAPTER 12 CHAPTER 13: Viruses Use Cellular Processes to Express their GeneticInformation PROKARYOTIC DNA REPLICATION IS AN ACCURATE ENZYMATIC MODEL FOR THE PROCESS GENERALLY EXPRESSION OF mRNA PROKARYOTIC TRANSCRIPTION EUKARYOTIC TRANSCRIPTION THE MECHANISM OF PROTEIN SYNTHESIS QUESTIONS FOR CHAPTER 13 Problems PART III Additional Reading for Part III

13 PART IV: Replication Patterns of Specific Viruses CHAPTER 14: Replication of Positive‐Sense RNAViruses RNA VIRUSES – GENERAL CONSIDERATIONS REPLICATION OF POSITIVE‐SENSE RNA VIRUSES WHOSE GENOMES ARE TRANSLATED AS THE FIRST STEP IN GENE EXPRESSION POSITIVE‐SENSE RNA VIRUSES ENCODING A SINGLE LARGE OPEN READING FRAME POSITIVE‐SENSE RNA VIRUSES ENCODING MORE THAN ONE TRANSLATIONAL READING FRAME REPLICATION OF PLANT VIRUSES WITH RNA GENOMES REPLICATION OF BACTERIOPHAGES WITH RNA GENOMES QUESTIONS FOR CHAPTER 14 CHAPTER 15: Replication Strategies of RNA Viruses Requiring RNA‐directed mRNA Transcription as the First Step in Viral Gene Expression REPLICATION OF NEGATIVE‐SENSE RNA VIRUSES WITH A MONOPARTITE GENOME NEGATIVE‐SENSE RNA VIRUSES WITH A MULTIPARTITE GENOME OTHER NEGATIVE‐SENSE RNA VIRUSES WITH MULTIPARTITE GENOMES VIRUSES WITH DOUBLE‐STRANDED RNA GENOMES SUBVIRAL PATHOGENS QUESTIONS FOR CHAPTER 15 CHAPTER 16: Replication Strategies of Small and Medium‐sized DNA Viruses DNA VIRUSES EXPRESS GENETIC INFORMATION AND REPLICATE THEIR GENOMES IN SIMILAR, YET DISTINCT, WAYS PAPOVAVIRUS REPLICATION THE REPLICATION OF ADENOVIRUSES REPLICATION OF SOME SINGLE‐STRANDED DNA VIRUSES QUESTIONS FOR CHAPTER 16 CHAPTER 17: Replication of Some Nuclear‐replicating Eukaryotic DNA Viruses with Large Genomes HERPESVIRUS REPLICATION AND LATENCY BACULOVIRUS: AN INSECT VIRUS WITH IMPORTANT PRACTICAL USES IN MOLECULAR BIOLOGY QUESTIONS FOR CHAPTER 17 CHAPTER 18: Replication of Cytoplasmic DNA Viruses and “Large” Bacteriophages POXVIRUSES – DNA VIRUSES THAT REPLICATE IN THE CYTOPLASM OF EUKARYOTIC CELLS REPLICATION OF “LARGE” DNA‐CONTAINING BACTERIOPHAGES A GROUP OF ALGAL VIRUSES SHARES FEATURES OF ITS GENOME STRUCTURE WITH POXVIRUSES AND BACTERIOPHAGES QUESTIONS FOR CHAPTER 18 CHAPTER 19: Retroviruses RETROVIRUS FAMILIES AND THEIR STRATEGIES OF REPLICATION MECHANISMS OF RETROVIRUS TRANSFORMATION CELLULAR GENETIC ELEMENTS RELATED TO RETROVIRUSES QUESTIONS FOR CHAPTER 19 CHAPTER 20: Human Immunodeficiency Virus Type 1 (HIV‐1) and Related Lentiviruses HIV‐1 AND RELATED LENTIVIRUSES THE ORIGIN OF HIV‐1 AND AIDS HIV‐1 AND LENTIVIRAL REPLICATION DESTRUCTION OF THE IMMUNE SYSTEM BY HIV‐1 QUESTIONS FOR CHAPTER 20 CHAPTER 21: Hepadnaviruses: Variations on the Retrovirus Theme THE VIRION AND THE VIRAL GENOME THE VIRAL REPLICATION CYCLE THE PATHOGENESIS OF HEPATITIS B VIRUS PREVENTION AND TREATMENT OF HEPATITIS B VIRUS INFECTION HEPATITIS DELTA VIRUS A PLANT “HEPADNAVIRUS”: CAULIFLOWER MOSAIC VIRUS THE EVOLUTIONARY ORIGIN OF HEPADNAVIRUSES QUESTIONS FOR CHAPTER 21 Problems PART IV Additional Reading for Part IV VIRUS RESOURCES ON THE INTERNET

14 PART V: Molecular Genetics of Viruses CHAPTER 22: The Molecular Genetics of Viruses MUTATIONS IN GENES AND RESULTING CHANGES TO PROTEINS ANALYSIS OF MUTATIONS ISOLATION OF MUTANTS A TOOL KIT FOR MOLECULAR VIROLOGISTS LOCATING SITES OF RESTRICTION ENDONUCLEASE CLEAVAGE ON THE VIRAL GENOME – RESTRICTION MAPPING CLONING VECTORS DIRECTED MUTAGENESIS OF VIRAL GENES GENERATION OF RECOMBINANT VIRUSES QUESTIONS FOR CHAPTER 22 CHAPTER 23: Molecular Pathogenesis AN INTRODUCTION TO THE STUDY OF VIRAL PATHOGENESIS ANIMAL MODELS METHODS FOR THE STUDY OF PATHOGENESIS CHARACTERIZATION OF THE HOST RESPONSE QUESTIONS FOR CHAPTER 23 CHAPTER 24: Viral Bioinformatics BIOINFORMATICS BIOLOGICAL DATABASES BIOLOGICAL APPLICATIONS SYSTEMS BIOLOGY AND VIRUSES VIRAL INTERNET RESOURCES QUESTIONS FOR CHAPTER 24 CHAPTER 25: Viruses and the Future – Problems and Promises CLOUDS ON THE HORIZON – EMERGING DISEASE WHAT ARE THE PROSPECTS OF USING MEDICAL TECHNOLOGY TO ELIMINATE SPECIFIC VIRAL AND OTHER INFECTIOUS DISEASES? SILVER LININGS – VIRUSES AS THERAPEUTIC AGENTS WHY STUDY VIROLOGY? QUESTIONS FOR CHAPTER 25 Problems PART V Additional Reading for Part V