Basic Virology

by
Edition: 2nd
Format: Paperback
Pub. Date: 2003-09-01
Publisher(s): John Wiley & Sons Inc
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Summary

Univ. of California, Irvine. Introductory textbook provides a solid foundation in virology and its relationship to modern biology. Focuses on the fundamentals and stresses the basic concepts of molecular biology and immunology. Provides updated material on HIV treatment, West Nile virus, smallpox, and bioterrorism. Previous edition: c1999. Softcover. DNLM: Virus Diseases--virology.

Author Biography

Edward Wagner is Professor of Molecular Biology and Biochemistry at the University of California, Irvine. He is also a Fellow of the American Association for the Advancement of Science.

Table of Contents

Preface xix
New to the second edition xx
Text organization xx
Specific features of this text designed to aid instructors and students in pursuing topics in greater depth xxiii
Depth of coverage xxiii
Sources for further study xxiii
The Internet xxiii
Chapter outlines xxiv
Review material xxiv
Glossary xxiv
Acknowledgments xxv
PART I VIROLOGY AND VIRAL DISEASE
1(48)
Introduction -- The Impact of Viruses on Our View of Life
3(8)
The effect of virus infections on the host organism and populations --- viral pathogenesis, virulence, and epidemiology
3(2)
The interaction between viruses and their hosts
5(1)
The history of virology
6(1)
Examples of the impact of viral disease on human history
6(1)
Examples of the evolutionary impact of the virus---host interaction
7(1)
The origin of viruses
8(1)
Viruses have a constructive as well as destructive impact on society
9(1)
Viruses are not the smallest self-replicating pathogens
10(1)
Questions for Chapter 1
10(1)
An Outline of Virus Replication and Viral Pathogenesis
11(10)
Virus replication in the cell
13(1)
Pathogenesis of Viral Infection
13(7)
Stages of infection
14(1)
Initial stages of infection --- entry of the virus into the host
15(1)
The incubation period and spread of virus through the host
15(2)
Multiplication of virus to high levels --- occurrence of disease symptoms
17(1)
The later stages of infection --- the immune response
18(1)
The later stages of infection --- virus spread to the next individual
19(1)
The later stages of infection --- fate of the host
19(1)
Questions for Chapter 2
20(1)
Virus Disease in Populations and Individual Animals
21(15)
Some viruses with human reservoirs
21(3)
Some viruses with vertebrate animal reservoirs
24(1)
Viruses in Populations
24(1)
Animal Models to Study Viral Pathogenesis
25(10)
A mouse model for studying poxvirus infection and spread
27(1)
Reovirus infection of mice --- the convenience of a virus with a fragmented genome for identifying genes involved in pathogenesis
28(2)
Rabies: where is the virus during its long incubation period?
30(2)
Herpes simplex virus latency
32(1)
Murine models
33(1)
Rabbit models
33(1)
Guinea pig models
34(1)
Can virus be spread across ``kingdoms''?
34(1)
Questions for Chapter 3
35(1)
Patterns of Some Viral Diseases of Humans
36(13)
Some viral diseases associated with acute infection followed by virus clearing from the host
36(1)
Colds and respiratory infections
37(1)
Influenza
37(1)
Variola
37(1)
Infection of an ``accidental'' target tissue leading to permanent damage despite efficient clearing
37(1)
Persistent viral infections
38(1)
Herpesvirus infections and latency
38(1)
Complications arising from persistent infections
39(1)
Viral and subviral diseases with long incubation periods
39(1)
Rabies
40(1)
HIV --- AIDS
40(1)
Prion diseases
40(1)
Some Viral Infections Targeting Specific Organ Systems
40(4)
Viral infections of nerve tissue
41(1)
Examples of viral encephalitis with grave prognosis
41(1)
Rabies
41(1)
Herpes encephalitis
42(1)
Viral encephalitis with favorable prognosis for recovery
42(1)
Viral infections of the liver (hepatitis)
43(1)
Hepatitis A
43(1)
Hepatitis B
43(1)
Hepatitis C
43(1)
Hepatitis D
44(1)
Hepatitis E
44(1)
Questions for Chapter 4
44(1)
Problems for Part I
45(2)
Additional Reading for Part I
47(2)
PART II BASIC PROPERTIES OF VIRUSES AND VIRUS---CELL INTERACTION
49(68)
Virus Structure and Classification
51(9)
Viral genomes
51(1)
Viral capsids
52(3)
Viral membrane envelopes
55(1)
Classification Schemes
55(4)
The Baltimore scheme of virus classification
57(1)
Disease-based classification schemes for viruses
57(2)
Questions for Chapter 5
59(1)
The Beginning and End of the Virus Replication Cycle
60(17)
Outline of the virus replication cycle
60(1)
Animal virus entry into cells --- the role of the cellular receptor
61(3)
Mechanisms of entry of nonenveloped viruses
64(1)
Entry of enveloped viruses
64(1)
Entry of plant virus into cells
65(2)
The injection of bacteriophage DNA into Escherichia coli
67(2)
Nonspecific methods of introducing viral genomes into cells
69(1)
Late Events in Viral Infection: Capsid Assembly and Virion Release
69(7)
Assembly of helical capsids
69(2)
Assembly of icosahedral capsids
71(4)
Generation of the virion envelope and egress of the enveloped virion
75(1)
Questions for Chapter 6
76(1)
Host Immune Response to Viral Infection: The Nature of the Vertebrate Immune Response
77(19)
The immunological structure of a protein
78(2)
Presentation of Viral Antigens to Immune Reactive Cells
80(6)
Local versus systemic immunity
80(2)
Role of the antigen-presenting cell in initiation of the immune response
82(3)
Clonal selection of immune reactive lymphocytes
85(1)
Immune memory
85(1)
Complement-mediated cell lysis
85(1)
Control and Dysfunction of Immunity
86(4)
Specific viral responses to host immunity
88(1)
Passive evasion of immunity --- antigenic drift
88(1)
Passive evasion of immunity --- internal sanctuaries for infectious virus
88(1)
Passive evasion of immunity --- immune tolerance
89(1)
Active evasion of immunity --- immunosuppression
89(1)
Active evasion of immunity --- blockage of MHC antigen presentation
90(1)
Consequences of immune suppression on virus infections
90(1)
Measurement of the Immune Reaction
90(5)
Measurement of cell-mediated (T cell) immunity
90(1)
Measurement of antiviral antibody
91(1)
Enzyme-linked immunosorbent assays (ELISAs)
91(1)
Neutralization tests
91(1)
Inhibition of hemagglutination
92(1)
Complement fixation
93(2)
Questions for Chapter 7
95(1)
Strategies to Protect Against and Combat Viral Infection
96(21)
Vaccination --- Induction of Immunity to Prevent Virus Infection
97(5)
Antiviral vaccines
97(1)
Smallpox and the history of vaccination
97(1)
How a vaccine is produced
98(1)
Live-virus vaccines
99(1)
Killed-virus vaccines
100(1)
Recombinant virus vaccines
100(1)
Subunit vaccines
101(1)
Future trends in vaccine development and design
101(1)
Problems with vaccine production and use
102(1)
Eukaryotic Cell-based Defenses Against Virus Replication
102(4)
Interferon
102(1)
Induction of interferon
103(1)
The antiviral state
104(1)
Measurement of interferon activity
104(2)
Antiviral Drugs
106(4)
Targeting antiviral drugs to specific features of the virus replication cycle
106(1)
Acyclovir and the herpesviruses
107(1)
Amantadine and influenza A viruses
108(1)
Chemotherapeutic approaches for HIV
109(1)
Multiple drug therapies to reduce or eliminate mutation to drug resistance
109(1)
Other approaches
110(1)
Bacterial Antiviral Systems --- Restriction Endonucleases
110(1)
Questions for Chapter 8
111(1)
Problems for Part II
112(3)
Additional Reading for Part II
115(2)
PART III WORKING WITH VIRUS
117(112)
Visualization and Enumeration of Virus Particles
119(8)
Using the electron microscope to study and count viruses
119(3)
Counting (enumeration) of virions with the electron microscope
122(1)
Atomic Force Microscopy --- a rapid and sensitive method for visualization of viruses and infected cells, potentially in real time
123(2)
Indirect methods for ``counting'' virus particles
125(1)
Questions for Chapter 9
125(2)
Replicating and Measuring Biological Activity of Viruses
127(17)
Cell culture techniques
127(1)
Maintenance of bacterial cells
127(1)
Plant cell cultures
128(1)
Culture of animal and human cells
128(1)
Maintenance of cells in culture
128(1)
Types of cells
128(2)
Loss of contact inhibition of growth and immortalization of primary cells
130(1)
The Outcome of Virus Infection in Cells
131(5)
Fate of the virus
131(2)
Fate of the cell following virus infection
133(1)
Cell-mediated maintenance of the intra- and intercellular environment
133(1)
Virus-mediated cytopathology --- changes in the physical appearance of cells
133(2)
Virus-mediated cytopathology --- changes in the biochemical properties of cells
135(1)
Measurement of the Biological Activity of Viruses
136(6)
Quantitative measure of infectious centers
136(1)
Plaque assays
136(1)
Generation of transformed cell foci
137(1)
Use of virus titers to quantitatively control infection conditions
137(1)
Examples of plaque assays
138(1)
Statistical analysis of infection
139(2)
Dilution endpoint methods
141(1)
The relation between dilution endpoint and infectious units of virus
141(1)
Questions for Chapter 10
142(2)
Physical and Chemical Manipulation of the Structural Components of Viruses
144(21)
Viral Structural Proteins
144(7)
Isolation of structural proteins of the virus
145(2)
Size fractionation of viral structural proteins
147(1)
Determining the stoichiometry of capsid proteins
147(1)
The poliovirus capsid --- a virion with equimolar capsid proteins
148(1)
Analysis of viral capsids that do not contain equimolar numbers of proteins
149(2)
Characterizing Viral Genomes
151(12)
Sequence analysis of viral genomes
151(4)
Measuring the size of viral genomes
155(1)
Direct measure of DNA genome lengths in the electron microscope
156(1)
Rate zonal sedimentation and gel electrophoresis for measuring viral genome size
156(2)
Use of renaturation rates to measure nucleic acid size and complexity
158(2)
The polymerase chain reaction --- detection and characterization of extremely small quantities of viral genomes or transcripts
160(3)
Questions for Chapter 11
163(2)
Characterization of Viral Products Expressed in the Infected Cell
165(20)
Characterization of Viral Proteins in the infected Cell
165(12)
Pulse labeling of viral proteins at different times following infection
165(2)
Use of immune reagents for study of viral proteins
167(1)
Working with antibodies
167(1)
The structure of antibody molecules
167(1)
Monoclonal antibodies
168(2)
Detection of viral proteins using immunofluorescence
170(2)
Related methods for detecting antibodies bound to antigens
172(1)
Use of bacterial staphylococcus A and streptococcus G proteins to detect and isolate antibody-antigen complexes
173(2)
Immunoaffinity chromatography
175(2)
Detecting and Characterizing Viral Nucleic Acids in Infected Cells
177(7)
Detecting the synthesis of viral genomes
177(1)
Characterization of viral mRNA expressed during infection
178(1)
In situ hybridization
179(2)
Further characterization of specific viral mRNA molecules
181(1)
Use of microarray technology for getting a complete picture of the events occurring in the infected cell
182(2)
Questions for Chapter 12
184(1)
Viruses Use Cellular Processes to Express Their Genetic Information
185(22)
Replication of cellular DNA
186(2)
Expression of mRNA
188(1)
Eukaryotic transcription
188(1)
The promoter and initiation of transcription
188(3)
Posttranscriptional modification of precursor mRNA
191(1)
Visualization and location of splices in eukaryotic transcripts
192(4)
Prokaryotic transcription
196(1)
Prokaryotic RNA polymerase
197(1)
The prokaryotic promoter and initiation of transcription
197(1)
Control of prokaryotic initiation of transcription
198(1)
Termination of transcription
199(1)
Virus-induced changes in transcription and posttranscriptional processing
199(2)
The mechanism of protein synthesis
201(1)
Eukaryotic translation
202(2)
Prokaryotic translation
204(1)
Virus-induced changes in translation
205(1)
Questions for Chapter 13
205(2)
The Molecular Genetics of Viruses
207(22)
Viral genomes
208(1)
Locating sites of restriction endonuclease cleavage on the viral genome --- restriction mapping
208(2)
Cloning of fragments of viral genomes using bacterial plasmids
210(4)
Genetic Manipulation of Viral Genomes
214(5)
Mutations in genes and resulting changes to proteins
214(2)
Analysis of mutations
216(1)
Complementation
216(1)
Recombination
216(2)
Isolation of mutants
218(1)
Selection
218(1)
HSV thymidine kinase --- a portable selectable marker
218(1)
Screening
219(1)
Deliberate and Accidental Alterations in Viral Genomes as a Result of Laboratory Replication
219(4)
Virulence and attenuation
219(1)
Generation of recombinant viruses
219(3)
Defective virus particles
222(1)
Questions for Chapter 14
223(1)
Problems for Part III
224(3)
Additional Reading for Part III
227(2)
PART IV REPLICATION PATTERNS OF SPECIFIC VIRUSES
229(175)
Replication of Positive-sense RNA Viruses
231(26)
RNA viruses --- general considerations
231(1)
A general picture of RNA-directed RNA replication
232(2)
Replication of Positive-sense RNA Viruses Whose Genomes Are Translated as the First Step in Gene Expression
234(1)
Positive-sense RNA Viruses Encoding a Single Large Open Reading Frame
234(8)
Picornavirus replication
234(1)
The poliovirus genetic map and expression of poliovirus proteins
235(2)
The poliovirus replication cycle
237(2)
Picornavirus cytopathology and disease
239(2)
Flavivirus replication
241(1)
Positive-sense RNA Viruses Encoding More Than One Translational Reading Frame
242(9)
Two viral mRNAs are produced in different amounts during togavirus infections
243(1)
The viral genome
243(1)
The virus replication cycle
244(1)
Virus entry
244(1)
Early gene expression
244(1)
Viral genome replication and generation of 26s mRNA
244(1)
Generation of structural proteins
244(2)
Togavirus cytopathology and disease
246(2)
A somewhat more complex scenario of multiple translational reading frames and subgenomic mRNA expression: coronavirus replication
248(1)
Coronavirus replication
248(3)
Cytopathology and disease caused by coronaviruses
251(1)
Replication of Plant Viruses with RNA Genomes
251(2)
Viruses with one genome segment
252(1)
Viruses with two genome segments
252(1)
Viruses with three genome segments
252(1)
Replication of Bacteriophages with RNA Genomes
253(2)
Regulated translation of bacteriophage mRNA
253(2)
Questions for Chapter 15
255(2)
Replication Strategies of RNA Viruses Requiring RNA-directed mRNA Transcription as the First Step in Viral Gene Expression
257(29)
Replication of Negative-sense RNA Viruses with a Monopartite Genome
258(9)
The replication of vesicular stomatitis virus --- a model for Mononegavirales
259(1)
The vesicular stomatitis virus virion and genome
259(1)
Generation, capping, and polyadenylation of mRNA
259(1)
The generation of new negative-sense virion RNA
260(3)
The mechanism of host shutoff by vesicular stomatitis virus
263(1)
The cytopathology and diseases caused by rhabdoviruses
264(1)
Paramyxoviruses
264(1)
The pathogenesis of paramyxoviruses
264(1)
Filoviruses and their pathogenesis
265(1)
Bornaviruses
266(1)
Influenza Viruses --- Negative-sense RNA Viruses with a Multipartite Genome
267(5)
Involvement of the nucleus in flu virus replication
267(1)
Generation of new flu nucleocapsids and maturation of the virus
268(2)
Influenza A epidemics
270(2)
Other Negative-sense RNA Viruses with Multipartite Genomes
272(4)
Bunyaviruses
272(1)
Virus structure and replication
272(3)
Pathogenesis
275(1)
Arenaviruses
275(1)
Virus gene expression
275(1)
Pathogenesis
275(1)
Viruses with Double-stranded RNA Genomes
276(3)
Reovirus structure
276(1)
The reovirus replication cycle
276(3)
Pathogenesis
279(1)
Subviral Pathogens
279(5)
Hepatitis delta virus
279(2)
Viroids
281(1)
Prions
282(2)
Questions for Chapter 16
284(2)
Replication Strategies of Small and Medium-sized DNA Viruses
286(25)
DNA viruses express genetic information and replicate their genomes in similar, yet distinct, ways
286(2)
Papovavirus Replication
288(11)
Replication of SV40 virus --- the model polyomavirus
288(3)
The SV40 genome and genetic map
291(1)
The control region
291(1)
The early transcription unit
291(1)
The late transcription unit
292(1)
The polyadenylation region
292(1)
Productive infection by SV40
292(1)
Virus attachment and entry
293(1)
Early gene expression
293(1)
The role of T antigen in viral DNA replication and the early/late transcription switch
293(2)
Abortive infection of cells nonpermissive for SV40 replication
295(1)
The replication of papillomaviruses
296(2)
The HPV-16 genome
298(1)
Virus replication and cytopathology
299(1)
The Replication of Adenoviruses
299(6)
Physical properties of adenovirus
301(1)
Capsid structure
301(1)
The adenovirus replication cycle
301(1)
Early events
301(1)
Adenovirus DNA replication
301(2)
Late gene expression
303(1)
VA transcription and cytopathology
303(1)
Transformation of nonpermissive cells by adenovirus
303(2)
Replication of Some Single-stranded DNA Viruses
305(4)
Replication of parvoviruses
305(1)
Dependovirus DNA integrates in a specific site in the host cell genome
305(1)
Parvoviruses have potentially exploitable therapeutic applications
306(1)
DNA viruses infecting vascular plants
307(1)
Geminiviruses
307(1)
The single-stranded DNA bacteriophage X174 packages its genes very compactly
307(2)
Questions for Chapter 17
309(2)
Replication of Some Nuclear-replicating Eukaryotic DNA Viruses with Large Genomes
311(25)
Herpesvirus Replication and Latency
312(21)
The herpesviruses as a group
312(1)
General features
312(1)
Genetic complexity of herpesviruses
312(1)
Common features of herpesvirus replication in the host
313(1)
The replication of HSV
313(1)
The HSV virion
313(1)
The viral genome
313(6)
HSV productive infection
319(1)
Initial steps in infection: virus entry
319(1)
Immediate-early gene expression
320(3)
Early gene expression
323(1)
Genome replication and late gene expression
323(1)
Virus assembly and release
323(2)
Latent infections with herpesviruses
325(1)
HSV latency and reactivation
326(3)
HSV transcription during latency and reactivation
329(1)
Specific HSV genes whose function may be to accommodate reactivation
329(1)
EBV latent infection, a different set of problems and answers
330(1)
Pathology of herpesvirus infections
331(1)
Herpesviruses as infectious co-carcinogens
332(1)
Baculovirus, an Insect Virus with Important Practical Uses in Molecular Biology
333(1)
Virion structure
333(1)
Viral gene expression and genome replication
333(1)
Pathogenesis
334(1)
Importance of baculoviruses in biotechnology
334(1)
Questions for Chapter 18
334(2)
Replication of Cytoplasmic DNA Viruses and ``Large'' Bacteriophages
336(20)
Poxviruses --- DNA Viruses That Replicate in the Cytoplasm of Eukaryotic Cells
337(5)
The pox virion is complex and contains virus-coded transcription enzymes
337(1)
The poxvirus replication cycle
338(1)
Early events
338(2)
Intermediate stages of replication
340(1)
Late events in the replication cycle
340(1)
Pathogenesis and history of poxvirus infections
340(1)
Is smallpox virus a potential biological terror weapon?
341(1)
Replication of ``Large'' DNA-containing Bacteriophages
342(9)
Components of large DNA-containing phage virions
342(1)
Replication of phage T7
342(1)
The genome
342(1)
Phage-controlled transcription
342(1)
The practical value of T7
343(1)
T4 bacteriophage: the basic model for all DNA viruses
343(1)
The T4 genome
343(2)
Regulated gene expression during T4 replication
345(1)
Capsid maturation and release
346(1)
Replication of phage λ: a ``simple'' model for latency and reactivation
346(2)
The phage λ genome
348(1)
Phage λ gene expression immediately after infection
348(2)
The action of cro: lytic growth
350(1)
Modulating the activity of the N protein: priming the cell for lysogeny
350(1)
Action of cI, cII, and cIII: establishment of lysogeny
350(1)
Integration of λ DNA: generation of the prophage
350(1)
Biochemistry of the decision between lytic and lysogenic infection in E. coli
350(1)
Competition for binding by cro and cI at the operator OR
350(1)
Factors affecting the lytic/lysogenic ``decision''
351(1)
A Group of Algal Viruses Shares Features of Its Genome Structure with Poxviruses and Bacteriophages
351(1)
Questions for Chapter 19
352(4)
Retroviruses: Converting RNA to DNA
356(21)
Retrovirus Families and Their Strategies of Replication
357(18)
The molecular biology of retrovirus
358(1)
Retrovirus structural proteins
358(1)
The retrovirus genome
359(1)
The R:U5:(PB):leader region
360(1)
The gag, gag:prot:pol, and envgenes
360(1)
The 3' end of the genome
360(1)
Genetic maps of representative retroviruses
360(1)
Oncornaviruses
360(2)
Human T-cell leukemia virus (HTLV)
362(1)
Lentiviruses such as human immunodeficiency virus
362(1)
Replication of retroviruses: an outline of the replication process
362(1)
Initiation of infection
362(1)
Generation of cDNA
362(1)
Migration of the cDNA (with integrase) into the nucleus
362(2)
Expression of viral mRNA and RNA genomes
364(1)
Capsid assembly and maturation
364(1)
Action of reverse transcriptase and RNase H in synthesis of cDNA
364(2)
Transcription and translation of viral mRNA
366(1)
Capsid assembly and morphogenesis
366(1)
Mechanisms of Retrovirus Transformation
366(1)
Transformation through the action of a viral oncogene --- a subverted cellular growth control gene
367(1)
Oncornavirus alteration of normal cellular transcriptional control of growth regulation
368(1)
Oncornavirus transformation by growth stimulation of neighboring cells
369(1)
Viruses and cancer --- a reprise
370(1)
Destruction of the Immune System by HIV
371(1)
Cellular Genetic Elements Related to Retroviruses
372(2)
Retrotransposons
374(1)
The relationship between transposable elements and viruses
375(1)
Questions for Chapter 20
375(2)
Hepadnaviruses: Variations on the Retrovirus Theme
377(6)
The virion and the viral genome
377(2)
The viral replication cycle
379(1)
The pathogenesis of hepatitis B virus
379(1)
A plant ``hepadnavirus'': cauliflower mosaic virus
380(1)
Genome structure
380(1)
Viral gene expression and genome replication
380(1)
The evolutionary origin of hepadnaviruses
381(1)
Questions for Chapter 21
382(1)
Viruses and the Future -- Promises and Problems
383(21)
Clouds on the horizon --- emerging disease
383(2)
Sources and causes of emergent virus disease
385(1)
The threat of bioterrorism
386(1)
What are the prospects of using medical technology to eliminate specific viral and other infectious diseases?
387(1)
Silver linings --- viruses as therapeutic agents
388(1)
Viruses for gene delivery
388(2)
Using viruses to destroy other viruses
390(1)
Why study virology?
390(1)
Questions for Chapter 22
391(1)
Discussion and Study Questions for Part IV
392(9)
Additional Reading for Part IV
401(3)
APPENDIX Resource Center
404(5)
Books of historical and basic value
404(1)
Books on virology
405(1)
Molecular biology and biochemistry texts
406(1)
Detailed sources
406(1)
Sources for experimental protocols
406(1)
The Internet
407(2)
Virology sites
407(1)
Important websites for organizations and facilities of interest
408(1)
Technical Glossary 409(19)
Index 428

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