Basic Virology

The foundational textbook on the study of virology Basic Virology, 4th Edition cements this series’ position as the leading introductory virology textbook in the world. It’s easily read style, outstanding figures, and comprehensive coverage of fundamental topics in virology all account for its immense popularity. This undergraduate-accessible book covers all the foundational topics in virology, including: The basics of virology Virological techniques Molecular biology Pathogenesis of human viral disease The 4th edition includes new information on the SARS, MERS and COVID-19 coronaviruses, hepatitis C virus, influenza virus, as well as HIV and Ebola. New virological techniques including bioinformatics and advances in viral therapies for human disease are also explored in-depth. The book also includes entirely new sections on metapneumoviruses, dengue virus, and the chikungunya virus.

Table of Contents:
Preface Preface to the Second Edition Preface to the Third Edition Preface to the Fourth Edition Acknowledgements [PN]PART I [PT]VIROLOGY AND VIRAL DISEASE [PTOC]INTRODUCTION—THE IMPACT OF VIRUSES ON OUR VIEW OF LIFE AN OUTLINE OF VIRUS REPLICATION AND VIRAL PATHOGENESIS PATHOGENESIS OF VIRAL INFECTION VIRUS DISEASE IN POPULATIONS AND INDIVIDUAL ANIMALS VIRUSES IN POPULATIONS ANIMAL MODELS TO STUDY VIRAL PATHOGENESIS THE DYNAMICS OF VIRUS- HUMAN INTERACTIONS PATTERNS OF SPECIFIC VIRAL DISEASES OF HUMANS ADDITIONAL READING FOR PART I PROBLEMS FOR PART I [CN]CHAPTER 1 [CT]INTRODUCTION—THE IMPACT OF VIRUSES ON OUR VIEW OF LIFE [CTOC] THE SCIENCE OF VIROLOGY The effect of virus infections on the host organism and populations—viral pathogenesis, virulence, and epidemiology The interaction between viruses and their hosts The history of virology  Examples of the impact of viral disease on human history Examples of the evolutionary impact of the virus-host interaction The origin of viruses Viruses have a constructive as well as destructive impact on society Viruses are not the smallest self-replicating pathogens QUESTIONS FOR CHAPTER 1 [CN]CHAPTER 2 [CT]AN OUTLINE OF VIRUS REPLICATION AND VIRAL PATHOGENESIS [CTOC] VIRUS REPLICATION Stages of virus replication in the cell  PATHOGENESIS OF VIRAL INFECTION  Stages of virus-induced pathology Initial stages of infection—entry of the virus into the host The incubation period and spread of virus through the host Multiplication of virus to high levels—occurrence of disease symptoms The later stages of infection—the immune response The later stages of infection—virus spread to the next individual The later stages of infection—fate of the host QUESTIONS FOR CHAPTER 2 [CN]CHAPTER 3 [CT]VIRUS DISEASE IN POPULATIONS AND INDIVIDUAL ANIMALS [CTOC] THE NATURE OF VIRUS RESERVOIRSSome viruses with human reservoirs Some viruses with vertebrate reservoirs VIRUSES IN POPULATIONS Viral epidemiology in small and large populations Factors affecting the control of viral disease in populations ANIMAL MODELS TO STUDY VIRAL PATHOGENESIS A mouse model for studying poxvirus infection and spread Rabies:  where is the virus during its long incubation period? Herpes simplex virus latency Murine models Rabbit models Guinea pig models QUESTIONS FOR CHAPTER 3 [CN]CHAPTER 4 [CT]PATTERNS OF SOME VIRAL DISEASES OF HUMANS [CTOC] THE DYNAMICS OF HUMAN-VIRUS INTERACTIONS The stable association of viruses with their natural host places specific constraints on the nature of viral disease and mode of persistence Classification of human disease-causing viruses according to virus-host dynamics Viral diseases leading to persistence of the virus in the host are generally associated with viruses having long associations with human populations Viral diseases associated with acute, severe infection are suggestive of zoonoses PATTERNS OF SPECIFIC VIRAL DISEASES OF HUMANS  Acute infections followed by virus clearing Colds and respiratory infections Influenza Variola Infection of an “accidental” target tissue leading to permanent damage despite efficient clearing Persistent viral infections Papilloma and polyomavirus infections Herpesvirus infections and latency Other complications arising from persistent infections Viral and subviral diseases with long incubation periods Rabies HIV—AIDS Prion diseases SOME VIRAL INFECTIONS TARGETING SPECIFIC ORGAN SYSTEMS Viral infections of nerve tissue Examples of viral encephalitis with grave prognosis Rabies Herpes encephalitis Viral encephalitis with favorable prognosis for recovery Viral infections of the liver (viral hepatitis) Hepatitis A Hepatitis B Hepatitis C Hepatitis D Hepatitis E QUESTIONS FOR CHAPTER 4 Part I Additional Reading [PN]PART II [PT]BASIC PROPERTIES OF VIRUSES AND VIRUS-CELL INTERACTION [PTOC]VIRUS STRUCTURE AND CLASSIFICATION CLASSIFICATION SCHEMES THE VIROSPHERE THE BEGINNING AND END OF THE VIRUS REPLICATION CYCLE LATE EVENTS IN VIRAL INFECTION: CAPSID ASSEMBLY AND VIRION   RELEASE HOST IMMUNE RESPONSE TO VIRAL INFECTION NATURE OF THE VERTEBRATE IMMUNE RESPONSE LOCAL IMMUNITY PRESENTATION OF ANTIGENS TO IMMUNE REACTIVE CELLS CONTROL AND DYSFUNCTION OF IMMUNITY MEASUREMENT OF THE IMMUNE REACTION STRATEGIES TO PROTECT AGAINST AND COMBAT VIRAL INFECTION VACCINATION—INDUCTION OF IMMUNITY TO PREVENT VIRUS INFECTION EUKARYOTIC CELL–BASED DEFENSES AGAINST VIRAL REPLICATION ANTIVIRAL DRUGS BACTERIAL ANTIVIRAL SYSTEMS—RESTRICTION ENDONUCLEASES ADDITIONAL READING FOR PART II PROBLEMS FOR PART II [CN]CHAPTER 5 [CT]VIRUS STRUCTURE AND CLASSIFICATION [CTOC] THE FEATURES OF A VIRUS Viral genomes Viral capsids Viral envelopes CLASSIFICATION SCHEMES The Baltimore scheme of virus classification Disease-based classification schemes for viruses THE VIROSPHERE QUESTIONS FOR CHAPTER 5 [CN]CHAPTER 6 [CT]THE BEGINNING AND END OF THE VIRUS REPLICATION CYCLE [CTOC] VIRAL ENTRY Animal virus entry into cells—the role of the cellular receptor  Mechanisms of entry of nonenveloped viruses  Entry of enveloped viruses Entry of virus into plant cells Entry of virus into plant cells Nonspecific methods of introducing viral genomes into cells LATE EVENTS IN VIRAL INFECTION: CAPSID ASSEMBLY AND VIRION RELEASE  Assembly of helical capsids Assembly of icosahedral capsids Generation of the virion envelope and egress of the enveloped virion QUESTIONS FOR CHAPTER 6 [CN]CHAPTER 7  [CT] THE INNATE IMMUNE RESPONSE: EARLY DEFENSE AGAINST PATHOGENS HOST CELL–BASED DEFENSES AGAINST VIRUS REPLICATION Toll-like receptors Defensins Interferon Induction of interferon The antiviral state Measurement of interferon activity  Other cellular defenses against viral infection Micro RNAs  THE ADAPTIVE IMMUNE RESPONSE AND THE LYMPHATIC SYSTEM Two pathways of helper T response: the fork in the road  The immunological structure of a protein Role of the antigen-presenting cell in initiation of the immune response Clonal selection of immune reactive lymphocytes Immune memory Complement-mediated cell lysis CONTROL AND DYSFUNCTION OF IMMUNITY Specific viral responses to host immunity Passive evasion of immunity—antigenic drift Passive evasion of immunity—internal sanctuaries for infectious virus Passive evasion of immunity—immune tolerance Active evasion of immunity—immunosuppression Active evasion of immunity—blockage of MHC antigen presentation Consequences of immune suppression to virus infections MEASUREMENT OF THE IMMUNE REACTION Measurement of cell-mediated (T-cell) immunity T-cell proliferation assay Tetramer Assay Measurement of antiviral antibody Enzyme-linked immunosorbent assays (ELISAs) Neutralization tests Inhibition of hemagglutination Complement fixation QUESTIONS FOR CHAPTER 7 [CN]CHAPTER 8 [CT]STRATEGIES TO PROTECT AGAINST AND COMBAT VIRAL INFECTION [CTOC]VACCINATION—INDUCTION OF IMMUNITY TO PREVENT VIRUS INFECTION Antiviral vaccines Smallpox and the history of vaccination How a vaccine is produced Live-virus vaccines Killed-virus vaccines Recombinant virus vaccines  Capsid and Subunit vaccines DNA vaccines Problems with vaccine production and use EUKARYOTIC CELL–BASED DEFENSES AGAINST VIRUS REPLICATION Other cellular defenses against viral infection Small RNA-based defenses Enzymatic modification of viral genomes ANTIVIRAL DRUGS Targeting antiviral drugs to specific features of the virus replication cycle Other approaches BACTERIAL ANTIVIRAL SYSTEMS—RESTRICTION ENDONUCLEASES QUESTIONS FOR CHAPTER 8 [PN]PART III [PT]WORKING WITH VIRUS [PTOC]VISUALIZATION AND ENUMERATION OF VIRUS PARTICLES REPLICATING AND MEASURING BIOLOGICAL ACTIVITY OF VIRUSES THE OUTCOME OF VIRUS INFECTION IN CELLS MEASUREMENT OF THE BIOLOGICAL ACTIVITY OF VIRUSES PHYSICAL AND CHEMICAL MANIPULATION OF THE STRUCTURAL COMPONENTS OF VIRUSES VIRAL STRUCTURAL PROTEINS CHARACTERIZING VIRAL GENOMES 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 VIRUSES USE CELLULAR PROCESSES TO EXPRESS THEIR GENETIC INFORMATION THE MOLECULAR GENETICS OF VIRUSES GENETIC MANIPULATION OF VIRAL GENOMES DELIBERATE AND ACCIDENTAL ALTERATIONS IN VIRAL GENOMES AS A RESULT OF LABORATORY REPLICATION PROBLEMS FOR PART III ADDITIONAL READING FOR PART III [CN]CHAPTER 9 [CT]VISUALIZATION AND ENUMERATION OF VIRUS PARTICLES [CTOC]Using the electron microscope to study and count viruses Counting (enumeration) of virions in the electron microscope 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 [CN]CHAPTER 10 [CT]REPLICATING AND MEASURING BIOLOGICAL ACTIVITY OF VIRUSES [CTOC]Cell culture techniques Maintenance of bacterial cells Plant cell cultures Culture of animal and human cells Maintenance of cells in culture Types of cells  Loss of contact inhibition of growth and immortalization of primary cells THE OUTCOME OF VIRUS INFECTION IN CELLS Fate of the virus Fate of the cell following virus infection Cell-mediated maintenance of the intra- and intercellular environment Virus-mediated Cytopathology—changes in the physical appearance of cells Virus-mediated Cytopathology—changes in the biochemical properties of cells MEASUREMENT OF THE BIOLOGICAL ACTIVITY OF VIRUSES Quantitative measure of infectious centers Plaque assays Generation of transformed cell foci Use of virus titers to quantitatively control infection conditions Examples of plaque assays  Statistical analysis of infection Dilution endpoint methods The relation between dilution endpoint and infectious units of virus QUESTIONS FOR CHAPTER 10 [CN]CHAPTER 11 [CT]PHYSICAL AND CHEMICAL MANIPULATION OF THE STRUCTURAL COMPONENTS OF VIRUSES [CTOC]VIRAL STRUCTURAL PROTEINS Isolation of structural proteins of the virus Size fractionation of viral structural proteins Determining the stoichiometry of capsid proteins The poliovirus capsid—a virion with equimolar capsid proteins Analysis of viral capsids that do not contain equimolar numbers of proteins CHARACTERIZING VIRAL GENOMES Sequence analysis of viral genomes Sanger sequencing High-throughput sequencing (HTS) Measuring the size of viral genomes Direct measure of DNA genome lengths in the electron microscope Rate zonal sedimentation and gel electrophoresis for measuring viral genome size The polymerase chain reaction—detection and characterization of extremely small quantities of viral genomes or transcripts QUESTIONS FOR CHAPTER 11 [CN]CHAPTER 12 [CT]CHARACTERIZATION OF VIRAL PRODUCTS EXPRESSED IN THE INFECTED CELL [CTOC]CHARACTERIZATION OF VIRAL PROTEINS IN THE INFECTED CELL Pulse labeling of viral proteins at different times following infection Use of immune reagents for study of viral proteins Working with antibodies The structure of antibody molecules Monoclonal antibodies Detection of viral proteins using immunofluorescence Related methods for detecting antibodies bound to antigens Use of bacterial staphylococcal A and streptococcal G proteins to detect and isolate antibody-antigen complexes Immunoaffinity chromatography DETECTING AND CHARACTERIZING VIRAL NUCLEIC ACIDS IN INFECTED CELLS Detecting the synthesis of viral genomes Characterization of viral mRNA expressed during infection In situ hybridization Further characterization of specific viral mRNA molecules USE OF MICROARRAY TECHNOLOGY FOR GETTING A COMPLETE PICTURE OF THE EVENTS OCCURRING IN THE INFECTED CELL QUESTIONS FOR CHAPTER 12 [CN]CHAPTER 13 [CT]VIRUSES USE CELLULAR PROCESSES TO EXPRESS THEIR GENETIC INFORMATION [CTOC] Prokaryotic DNA replication is an accurate enzymatic model for the process generally The replication of eukaryotic DNA The replication of viral DNA The effect of virus infection on host DNA replication Expression of mRNA Prokaryotic transcription Prokaryotic RNA polymerase The prokaryotic promoter and the initiation of transcription Control of prokaryotic initiation of transcription Termination of transcription Eukaryotic transcription The promoter and initiation of transcription Control of initiation of eukaryotic transcription Processing of precursor mRNA Posttranscriptional modification of precursor mRNA Visualization and location of splices in eukaryotic transcripts Post-transcriptional Regulation of eukaryotic mRNA function Virus-induced changes in transcription and posttranscriptional processing The mechanism of protein synthesis Eukaryotic translation Prokaryotic translation Virus-induced changes in translation QUESTIONS FOR CHAPTER 13 [PN]PART IV [PT]REPLICATION PATTERNS OF SPECIFIC VIRUSES [PTOC]REPLICATION OF POSITIVE-SENSE RNA VIRUSES 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 BACTERIOPHAGE WITH RNA GENOMES REPLICATION STRATEGIES OF RNA VIRUSES REQUIRING RNA-DIRECTED mRNA TRANSCRIPTION AS THE FIRST STEP IN VIRAL GENE EXPRESSION REPLICATION STRATEGIES OF SINGLE-STRANDED RNA REPLICATION OF NEGATIVE-SENSE RNA VIRUSES WITH A MONOPARTITE GENOME INFLUENZA VIRUSES—NEGATIVE-SENSE RNA VIRUSES WITH A MULTIPARTITE GENOME OTHER NEGATIVE-SENSE RNA VIRUSES WITH MULTIPARTITE GENOMES VIRUSES WITH DOUBLE-STRANDED RNA GENOMES SUBVIRAL PATHOGENS REPLICATION STRATEGIES OF SMALL AND MEDIUM-SIZED DNA VIRUSES PAPOVAVIRUS REPLICATION THE REPLICATION OF ADENOVIRUSES REPLICATION OF SOME SINGLE-STRANDED DNA VIRUSES 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 REPLICATION OF VIRUSES WITH DNA GENOMES THAT ENCODE THEIR OWN TRANSCRIPTION ENZYMES POXVIRUSES—DNA VIRUSES THAT REPLICATE IN THE CYTOPLASM OF EUKARYOTIC CELLS REPLICATION OF “LARGE” DNA-CONTAINING BACTERIOPHAGE A GROUP OF ALGAL VIRUSES SHARES FEATURES OF ITS GENOME STRUCTURE WITH POXVIRUSES AND BACTERIOPHAGES RETROVIRUSES: CONVERTING RNA TO DNA RETROVIRUS FAMILIES AND THEIR STRATEGIES OF REPLICATION MECHANISMS OF RETROVIRUS TRANSFORMATION DESTRUCTION OF THE IMMUNE SYSTEM BY HIV EUKARYOTIC CELLULAR GENETIC ELEMENTS RELATED TO RETROVIRUSES HIV AND OTHER LENTIVIRUSES HEPADNAVIRUSES: VARIATIONS ON THE RETROVIRUS THEME DISCUSSION AND STUDY QUESTIONS FOR PART IV ADDITIONAL READING FOR PART IV   [CN]CHAPTER 14 [CT]REPLICATION OF POSITIVE-SENSE RNA VIRUSES [CTOC] RNA VIRUSES—GENERAL CONSIDERATIONS  A general picture of RNA-directed RNA replication 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 Picornavirus replication The poliovirus genetic map and expression of poliovirus proteins The poliovirus replication cycle Picornavirus cytopathology and disease Flavivirus replication POSITIVE-SENSE RNA VIRUSES ENCODING MORE THAN ONE TRANSLATIONAL READING FRAME Two viral mRNAs are produced in different amounts during togavirus infection The viral genome The virus replication cycle Togavirus cytopathology and disease A somewhat more complex scenario of multiple translational reading frames and subgenomic mRNA expression: coronavirus replication Coronavirus replication Cytopathology and disease caused by coronaviruses REPLICATION OF PLANT VIRUSES WITH RNA GENOMES Viruses with one genome segment Viruses with two genome segments Viruses with three genome segments REPLICATION OF BACTERIOPHAGE WITH RNA GENOMES Regulated translation of bacteriophage mRNA [CS] Case Study QUESTIONS FOR CHAPTER 14 [CN]CHAPTER15 [CT]REPLICATION STRATEGIES OF RNA VIRUSES REQUIRING RNA-DIRECTED mRNA TRANSCRIPTION AS THE FIRST STEP IN VIRAL GENE EXPRESSION [CTOC] REPLICATION OF NEGATIVE-SENSE RNA VIRUSES WITH A MONOPARTITE GENOME The replication of vesicular stomatitis virus—a model for Mononegavirales The vesicular stomatitis virus virion and genome Generation, capping, and polyadenylation of mRNA The generation of new negative-sense virion RNA The mechanism of host shutoff by vesicular stomatitis virus The cytopathology and diseases caused by rhabdoviruses Paramyxoviruses The pathogenesis of paramyxoviruses Filoviruses and their pathogenesis Bornaviruses INFLUENZA VIRUSES—NEGATIVE-SENSE RNA VIRUSES WITH A MULTIPARTITE GENOME Involvement of the nucleus in flu virus replication Generation of new flu nucleocapsids and maturation of the virus Influenza A epidemics OTHER NEGATIVE-SENSE RNA VIRUSES WITH MULTIPARTITE GENOMES Orthobunyaviruses Virus structure and replication Pathogenesis Arenaviruses Virus gene expression Pathogenesis VIRUSES WITH DOUBLE-STRANDED RNA GENOMES Orthoreovirus structure The orthoreovirus replication cycle Pathogenesis SUBVIRAL PATHOGENS Hepatitis delta virus Viroids  Prions [CS] Case Study QUESTIONS FOR CHAPTER15 [CN]CHAPTER 16 [CT]REPLICATION STRATEGIES OF SMALL AND MEDIUM-SIZED DNA VIRUSES [CTOC] DNA VIRUSES EXPRESS GENETIC INFORMATION AND REPLICATE THEIR GENOMES IN SIMILAR, YET DISTINCT, WAYS PAPOVAVIRUS REPLICATION Replication of SV40 virus—the model polyomavirus The SV40 genome and genetic map Productive infection by SV40 Abortive infection of cells nonpermissive for SV40 replication The replication of papillomaviruses The HPV-16 genome Virus replication and cytopathology THE REPLICATION OF ADENOVIRUSES Physical properties of adenovirus Capsid structure The adenovirus genome The adenovirus replication cycle Early events Adenovirus DNA replication Late gene expression VA transcription and cytopathology Transformation of nonpermissive cells by adenovirus REPLICATION OF SOME SINGLE-STRANDED DNA VIRUSES Replication of parvoviruses Dependovirus DNA integrates in a specific site in the host cell genome Parvoviruses have potentially exploitable therapeutic applications  DNA viruses infecting vascular plants Geminiviruses The single-stranded DNA bacteriophage X174 packages its genes very compactly [CS] Case Study QUESTIONS FOR CHAPTER 16 [CN]CHAPTER 17 [CT]REPLICATION OF SOME NUCLEAR-REPLICATING EUKARYOTIC DNA VIRUSES WITH LARGE GENOMES [CTOC]HERPESVIRUS REPLICATION AND LATENCY The herpesviruses as a group Genetic complexity of herpesviruses Common features of herpesvirus replication in the host The replication of the prototypical alphaherpesvirus—HSV The HSV virion The viral genome HSV productive infection HSV latency and the LAT HSV transcription during latency and reactivation How do the LAT and other specific HSV genes function to accommodate reactivation? EBV latent infection of lymphocytes, a different set of problems and answers Pathology of herpesvirus infections  BACULOVIRUS, AN INSECT VIRUS WITH IMPORTANT PRACTICAL USES IN MOLECULAR BIOLOGY Virion structure Viral gene expression and genome replication Pathogenesis Importance of baculoviruses in biotechnology [CS] Case Study QUESTIONS FOR CHAPTER 17 [CN]CHAPTER 18 [CT]REPLICATION OF CYTOPLASMIC DNA VIRUSES AND “LARGE” BACTERIOPHAGES [CTOC]POXVIRUSES—DNA VIRUSES THAT REPLICATE IN THE CYTOPLASM OF EUKARYOTIC CELLS The pox virion is complex and contains virus-coded transcription enzymes The poxvirus replication cycle Early gene expression Genome replication Intermediate and late stages of replication Pathogenesis and history of poxvirus infections Is smallpox virus a potential biological terror weapon? REPLICATION OF “LARGE” DNA-CONTAINING BACTERIOPHAGES Components of large DNA-containing phage virions Replication of phage T7 The genome Phage-controlled transcription The practical value of T7 T4 bacteriophage: the basic model for all DNA viruses The T4 genome Regulated gene expression during T4 replication Capsid maturation and release Replication of phage -- a “simple” model for latency and reactivation The phage  genome Phage  gene expression immediately after infection Biochemistry of the decision between lytic and lysogenic infection in E. coli Factors affecting the lytic/lysogenic “decision” A GROUP OF ALGAL VIRUSES SHARES FEATURES OF ITS GENOME STRUCTURE WITH POXVIRUSES AND BACTERIOPHAGES QUESTIONS FOR CHAPTER 18 [CN]CHAPTER 19 [CT]RETROVIRUSES: CONVERTING RNA TO DNA [CTOC]RETROVIRUS FAMILIES AND THEIR STRATEGIES OF REPLICATION The molecular biology of retrovirus replication Replication of retroviruses: an outline of the replication process Initiation of infection Capsid assembly and maturation Action of reverse transcriptase and RNase H in synthesis of cDNA Integration of the retroviral cDNA into the host genome Transcription and translation of viral mRNA Capsid assembly and morphogenesis MECHANISMS OF RETROVIRUS TRANSFORMATION Transformation through the action of a viral oncogene—a subverted cellular growth control gene Oncornavirus alteration of normal cellular transcriptional control of growth regulation Oncornavirus transformation by growth stimulation of neighboring cells CELLULAR GENETIC ELEMENTS RELATED TO RETROVIRUSES Retrotransposons The relationship between transposable elements and viruses QUESTIONS FOR CHAPTER 19 [CN]Chapter 20 [CT]HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (HIV-1) AND RELATED LENTIVIRUSES [CTOC] 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 [CS] Case Study [CN]CHAPTER 21 [CT]HEPADNAVIRUSES: VARIATIONS ON THE RETROVIRUS THEME [CTOC]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 D virus A plant “hepadnavirus”: cauliflower mosaic virus The evolutionary origin of hepadnaviruses [CS] Case Study QUESTIONS FOR CHAPTER 21 [PN]PART V: [PT]MOLECULAR GENETICS OF VIRUSES [PT]MOLECULAR PATHOGENESIS [PT]VIRAL BIOINFORMATICS AND BEYOND [PT]VIRUSES AND THE FUTURE:  PROBLEMS AND PROMISES DISCUSSION AND STUDY QUESTIONS FOR PART V ADDITIONAL READING FOR PART V [CN]CHAPTER 22 [CT]THE MOLECULAR GENETICS OF VIRUSES [CTOC]Mutations in genes and resulting changes to proteins Analysis of Mutations  Complementation Recombination  Isolation of mutants Selection  HSV thymidine kinase—a portable selectable marker Screening  A TOOL KIT FOR MOLECULAR VIROLOGISTS Viral genomes Locating sites of restriction endonuclease cleavage on the viral genome—restriction mapping Cloning Vectors Cloning of fragments of viral genomes using bacterial plasmids\ Cloning using phage l Cloning single stranded DNA with bacteriophage M13 DNA animal virus vectors RNA virus expression systems Defective virus particles Mutagenesis of viral genes Site directed mutagenesis  Generation of recombinant viruses Bacterial artificial chromosomes CRISPR-Cas QUESTIONS FOR CHAPTER  22 [CN]CHAPTER 23 [CT]MOLECULAR PATHOGENESIS [CTOC] AN INTRODUCTION TO THE STUDY OF VIRAL PATHOGENESIS ANIMAL MODELS Choosing a model: natural host vs. surrogate models Development of new models: transgenic animals Hybrid models: the SCID-hu mouse Considerations regarding the humane use of animals METHODS FOR THE STUDY OF PATHOGENESIS Assays of virulence Analysis of viral spread within the host Resolving the infection to the level of single cells. CHARCTERIZATION OF THE HOST RESPONSE Immunological Assays Use of transgenic mice to dissect critical components of the host immune response that modulate the viral infection QUESTIONS FOR CHAPTER 23 [CN]Chapter 24 [CT]Viral Bioinformatics [CTOC]  Bioinformatics Biological Databases Biological Applications Systems Biology and Viruses Viral Internet Resources Questions for Chapter 24 [CN]CHAPTER 25 [CT]VIRUSES AND THE FUTURE—PROBLEMS AND PROMISES [CTOC]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, viruses as technological tools, the place of viruses in the biosphere. Why study virology?  QUESTIONS FOR CHAPTER 25 Appendix Resource Center Technical Glossary Index

About the Author :
MARTINEZ J. HEWLETT is Professor Emeritus in the Department of Molecular and Cellular Biology at the University of Arizona. DAVID CAMERINI is Assistant Professor in the Department of Molecular Biology and Biochemistry at the University of California Irvine. DAVID C. BLOOM is Associate Professor in the Department of Molecular Genetics and Microbiology at University of Florida.