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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 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.
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
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