Basic Virology

Preface

Preface to the Second Edition

Preface to the Third Edition

Preface to the Fourth Edition

Acknowledgements

PART I

VIROLOGY AND VIRAL DISEASE

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

CHAPTER 1

INTRODUCTION—THE IMPACT OF VIRUSES ON OUR VIEW OF LIFE

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

CHAPTER 2

AN OUTLINE OF VIRUS REPLICATION AND VIRAL PATHOGENESIS

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

CHAPTER 3

VIRUS DISEASE IN POPULATIONS AND INDIVIDUAL ANIMALS

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

CHAPTER 4

PATTERNS OF SOME VIRAL DISEASES OF HUMANS

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

PART II

BASIC PROPERTIES OF VIRUSES AND VIRUS-CELL INTERACTION

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

CHAPTER 5

VIRUS STRUCTURE AND CLASSIFICATION

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

CHAPTER 6

THE BEGINNING AND END OF THE VIRUS REPLICATION CYCLE

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

CHAPTER 7

  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

CHAPTER 8

STRATEGIES TO PROTECT AGAINST AND COMBAT VIRAL INFECTION

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

PART III

WORKING WITH VIRUS

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

CHAPTER 9

VISUALIZATION AND ENUMERATION OF VIRUS PARTICLES

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

CHAPTER 10

REPLICATING AND MEASURING BIOLOGICAL ACTIVITY OF VIRUSES

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

CHAPTER 11

PHYSICAL AND CHEMICAL MANIPULATION OF THE STRUCTURAL COMPONENTS OF VIRUSES

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

CHAPTER 12

CHARACTERIZATION OF VIRAL PRODUCTS EXPRESSED IN THE INFECTED CELL

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

CHAPTER 13

VIRUSES USE CELLULAR PROCESSES TO EXPRESS THEIR GENETIC INFORMATION

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

PART IV

REPLICATION PATTERNS OF SPECIFIC VIRUSES

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

 

CHAPTER 14

REPLICATION OF POSITIVE-SENSE RNA VIRUSES

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

CHAPTER15

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

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

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

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

CHAPTER 17

REPLICATION OF SOME NUCLEAR-REPLICATING EUKARYOTIC

DNA VIRUSES WITH LARGE GENOMES

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

CHAPTER 18

REPLICATION OF CYTOPLASMIC DNA VIRUSES AND “LARGE” BACTERIOPHAGES

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

CHAPTER 19

RETROVIRUSES: CONVERTING RNA TO DNA

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

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

[CS] Case Study

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 D virus

A plant “hepadnavirus”: cauliflower mosaic virus

The evolutionary origin of hepadnaviruses

[CS] Case Study

QUESTIONS FOR CHAPTER 21

PART V:

MOLECULAR GENETICS OF VIRUSES

MOLECULAR PATHOGENESIS

VIRAL BIOINFORMATICS AND BEYOND

VIRUSES AND THE FUTURE:  PROBLEMS AND PROMISES

DISCUSSION AND STUDY QUESTIONS FOR PART V

ADDITIONAL READING FOR PART V

CHAPTER 22

THE MOLECULAR GENETICS OF VIRUSES

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

CHAPTER 23

MOLECULAR PATHOGENESIS

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

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, viruses as technological tools, the place of viruses in the biosphere.

Why study virology? 

QUESTIONS FOR CHAPTER 25

Appendix

Resource Center

Technical Glossary

Index

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 4^th 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.