Anti Viral Treatment for COVID Discussion

BASIC VIROLOGYIn Memoriam
Edward K. Wagner
(May 4, 1940 to January 21, 2006)
It was one of those telephone calls that you do not want to receive. Each of us, that weekend
in late January, heard of the untimely passing of our colleague, co-author, collaborator, mentor,
and friend, Ed Wagner. Ed will be remembered for his many contributions to the teaching of
virology and for his research contributing to our understanding of the intricacies of the
herpesviruses. From his graduate work at MIT, through his postdoctoral research at the
University of Chicago, and on to his professorship at the University of California, Irvine,
Ed was a passionate champion for the most rigorous and critical thinking and the most
dedicated teaching, setting a standard for the discipline of virology. Beyond the laboratory
and the classroom, Ed loved life to the fullest, with his family and friends. The last time we
were together as a writing team, in the fall of 2005, we all remember an intense day of work
in a conference room at UCI, followed by an evening of touring some of Ed’s favorite haunts
in the Southern California coastal towns he called home. It is with those thoughts etched
into our memories that we dedicate this edition of Basic Virology to Edward K. Wagner.
Basic Virology
Third
Edition
Edward K. Wagner
Department of Molecular Biology and Biochemistry
University of California, Irvine
Martinez J. Hewlett
Department of Molecular and Cellular Biology
University of Arizona
David C. Bloom
Department of Molecular Genetics and Microbiology
University of Florida
David Camerini
Department of Molecular Biology and Biochemistry
University of California, Irvine
© 1999, 2004, 2008 by Blackwell Publishing
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First edition published 1999
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1 2008
Library of Congress Cataloging-in-Publication Data
Basic virology / Edward K. Wagner . . . [et al.]. – 3rd ed.
p. ; cm.
Rev. ed. of: Basic virology / Edward K. Wagner, Martinez J. Hewlett. 2nd ed. 2004.
Includes bibliographical references and index.
ISBN-13: 978-1-4051-4715-6 (pbk. : alk. paper)
ISBN-10: 1-4051-4715-6 (pbk. : alk. paper)
1. Viruses. 2. Virus diseases. 3. Virology. 4. Medical virology. I. Wagner, Edward K.
II. Wagner, Edward K. Basic virology.
[DNLM: 1. Virus Diseases–virology. 2. Genome, Viral. 3. Virus Replication.
4. Viruses–pathogenicity. WC 500 B311 2008]
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Brief Contents
Preface xxi
Acknowledgments
xxix
PART I
VIROLOGY AND VIRAL DISEASE
Chapter
Chapter
Chapter
Chapter
Introduction – The Impact of Viruses on Our View of Life 3
An Outline of Virus Replication and Viral Pathogenesis 15
Virus Disease in Populations and Individual Animals 27
Patterns of Some Viral Diseases of Humans 41
1
2
3
4
1
PART II BASIC PROPERTIES OF VIRUSES AND VIRUS–
CELL INTERACTION 63
Chapter 5
Chapter 6
Chapter 7
Chapter 8
PART III
Chapter 9
Chapter 10
Chapter 11
Chapter 12
Chapter 13
Virus Structure and Classification 65
The Beginning and End of the Virus Replication Cycle 79
Host Immune Response to Viral Infection – The Nature of the Vertebrate
Immune Response 97
Strategies to Protect Against and Combat Viral Infection 119
WORKING WITH VIRUS
145
Visualization and Enumeration of Virus Particles 147
Replicating and Measuring Biological Activity of Viruses 155
Physical and Chemical Manipulation of the Structural Components of
Viruses 173
Characterization of Viral Products Expressed in the Infected Cell 193
Viruses Use Cellular Processes to Express their Genetic
Information 213
PART IV REPLICATION PATTERNS OF SPECIFIC
VIRUSES 243
Chapter 14 Replication of Positive-sense RNA Viruses 245
Chapter 15 Replication Strategies of RNA Viruses Requiring RNA-directed mRNA
Transcription as the First Step in Viral Gene Expression 273
Chapter 16 Replication Strategies of Small and Medium-sized DNA Viruses 303
vi
BRIEF CONTENTS
Chapter 17 Replication of Some Nuclear-replicating Eukaryotic DNA Viruses with
Large Genomes 331
Chapter 18 Replication of Cytoplasmic DNA Viruses and “Large” Bacteriophages 359
Chapter 19 Retroviruses: Converting RNA to DNA 381
Chapter 20 Human Immunodeficiency Virus Type 1 (HIV-1) and Related
Lentiviruses 399
Chapter 21 Hepadnaviruses: Variations on the Retrovirus Theme 413
PART V VIRUSES: NEW APPROACHES AND NEW
PROBLEMS 433
Chapter
Chapter
Chapter
Chapter
22
23
24
25
The Molecular Genetics of Viruses 435
Molecular Pathogenesis 463
Viral Bioinformatics and Beyond 473
Viruses and the Future – Problems and Promises
Appendix
Resource Center
Technical Glossary 507
Index 533
501
485
Contents
Preface xxi
Preface to the second edition xxii
Preface to the third edition xxii
Text organization xxiii
Specific features of this text designed to aid instructors and
students in pursuing topics in greater depth xxvi
Depth of coverage xxvi
Sources for further study xxvi
The Internet xxvii
Chapter outlines xxvii
Case studies xxvii
Review material xxvii
Glossary xxvii
Acknowledgments xxix
PART I
VIROLOGY AND VIRAL DISEASE
1
CHAPTER 1
Introduction – The Impact of Viruses on Our View of Life 3
The science of virology 3
The effect of virus infections on the host organism and populations
– viral pathogenesis, virulence, and epidemiology 4
The interaction between viruses and their hosts 6
The history of virology 7
Examples of the impact of viral disease on human history 8
Examples of the evolutionary impact of the virus–host
interaction 9
The origin of viruses 9
Viruses have a constructive as well as destructive impact on
society 12
Viruses are not the smallest self-replicating pathogens 13
Questions for Chapter 1 14
CHAPTER 2
An Outline of Virus Replication and Viral Pathogenesis
Virus replication 15
Stages of virus replication in the cell 17
Pathogenesis of viral infection 19
Stages of virus-induced pathology 19
15
viii
CONTENTS
Initial stages of infection – entry of the virus into the host 20
The incubation period and spread of virus through the host 21
Multiplication of virus to high levels – occurrence of disease
symptoms 23
The later stages of infection – the immune response 24
The later stages of infection – virus spread to the next
individual 24
The later stages of infection – fate of the host 24
Questions for Chapter 2 25
CHAPTER 3
Virus Disease in Populations and Individual Animals 27
The nature of virus reservoirs 27
Some viruses with human reservoirs 28
Some viruses with vertebrate reservoirs 30
Viruses in populations 30
Viral epidemiology in small and large populations 30
Factors affecting the control of viral disease in populations 33
Animal models to study viral pathogenesis 34
A mouse model for studying poxvirus infection and spread 35
Rabies: where is the virus during its long incubation period? 37
Herpes simplex virus latency 37
Murine models 39
Rabbit models 40
Guinea pig models 40
Questions for Chapter 3 40
CHAPTER 4
Patterns of Some Viral Diseases of Humans 41
The dynamics of human–virus interactions 42
The stable association of viruses with their natural host places
specific constraints on the nature of viral disease and mode of
persistence 42
Classification of human disease-causing viruses according to
virus–host dynamics 44
Viral diseases leading to persistence of the virus in the host are
generally associated with viruses having long associations with
human populations 44
Viral diseases associated with acute, severe infection are
suggestive of zoonoses 48
Patterns of specific viral diseases of humans 49
Acute infections followed by virus clearing 49
Colds and respiratory infections 49
Influenza 49
Variola 49
Infection of an “accidental” target tissue leading to permanent
damage despite efficient clearing 50
Persistent viral infections 50
Papilloma and polyomavirus infections 50
Herpesvirus infections and latency 52
Other complications arising from persistent infections 52
Viral and subviral diseases with long incubation periods 53
Rabies 53
CONTENTS
HIV–AIDS 53
Prion diseases 54
Some viral infections targeting specific organ systems 54
Viral infections of nerve tissue 54
Examples of viral encephalitis with grave prognosis 55
Rabies 55
Herpes encephalitis 55
Viral encephalitis with favorable prognosis for recovery 56
Viral infections of the liver (viral hepatitis) 56
Hepatitis A 57
Hepatitis B 57
Hepatitis C 57
Hepatitis D 57
Hepatitis E 58
Questions for Chapter 4 58
Problems for Part I 59
Additional Reading for Part I 61
PART II
BASIC PROPERTIES OF VIRUSES AND
VIRUS–CELL INTERACTION 63
CHAPTER 5
Virus Structure and Classification 65
The features of a virus 65
Viral genomes 69
Viral capsids 69
Viral envelopes 72
Classification schemes 72
The Baltimore scheme of virus classification 75
Disease-based classification schemes for viruses 75
The virosphere 77
Questions for Chapter 5 78
CHAPTER 6
The Beginning and End of the Virus Replication Cycle 79
Outline of the virus replication cycle 79
Viral entry 80
Animal virus entry into cells – the role of the cellular receptor 80
Mechanisms of entry of nonenveloped viruses 83
Entry of enveloped viruses 84
Entry of virus into plant cells 85
Injection of bacteriophage DNA into Escherichia coli 87
Nonspecific methods of introducing viral genomes into cells 89
Late events in viral infection: capsid assembly and virion release 89
Assembly of helical capsids 89
Assembly of icosahedral capsids 92
Generation of the virion envelope and egress of the enveloped
virion 93
Questions for Chapter 6 96
CHAPTER 7
Host Immune Response to Viral Infection – The Nature of the
Vertebrate Immune Response 97
The innate immune response – early defense against pathogens 98
Toll-like receptors 99
ix
x
CONTENTS
Defensins 99
The adaptive immune response and the lymphatic system 100
Two pathways of helper T response – the fork in the road 101
The immunological structure of a protein 102
Role of the antigen-presenting cell in initiation of the immune
response 104
Clonal selection of immune reactive lymphocytes 107
Immune memory 108
Complement-mediated cell lysis 108
Control and dysfunction of immunity 108
Specific viral responses to host immunity 109
Passive evasion of immunity – antigenic drift 110
Passive evasion of immunity – internal sanctuaries for
infectious virus 110
Passive evasion of immunity – immune tolerance 110
Active evasion of immunity – immunosuppression 111
Active evasion of immunity – blockage of MHC antigen
presentation 111
Consequences of immune suppression to virus infections 112
Measurement of the immune reaction 112
Measurement of cell-mediated (T-cell) immunity 112
Measurement of antiviral antibody 112
Enzyme-linked immunosorbent assays (ELISAs) 113
Neutralization tests 114
Inhibition of hemagglutination 114
Complement fixation 115
Questions for Chapter 7 117
CHAPTER 8
Strategies to Protect Against and Combat Viral Infection 119
Vaccination – induction of immunity to prevent virus
infection 120
Antiviral vaccines 120
Smallpox and the history of vaccination 120
How a vaccine is produced 122
Live-virus vaccines 122
Killed-virus vaccines 123
Recombinant virus vaccines 124
Capsid and subunit vaccines 124
DNA vaccines 125
Edible vaccines 125
Problems with vaccine production and use 125
Eukaryotic cell-based defenses against virus replication 126
Interferon 126
Induction of interferon 127
The antiviral state 128
Measurement of interferon activity 128
Other cellular defenses against viral infection 130
Small RNA-based defenses 130
Enzymatic modification of viral genomes 131
Antiviral drugs 131
CONTENTS
Targeting antiviral drugs to specific features of the virus
replication cycle 131
Acyclovir and the herpesviruses 132
Blocking influenza virus entry and virus maturation 132
Chemotherapeutic approaches for HIV 134
Multiple drug therapies to reduce or eliminate mutation to
drug resistance 134
Other approaches 135
Bacterial antiviral systems – restriction endonucleases 135
Questions for Chapter 8 136
Problems for Part II 139
Additional Reading for Part II 143
PART III
WORKING WITH VIRUS
145
CHAPTER 9
Visualization and Enumeration of Virus Particles 147
Using the electron microscope to study and count viruses 147
Counting (enumeration) of virions with the electron
microscope 149
Atomic force microscopy – a rapid and sensitive method for
visualization of viruses and infected cells, potentially in real
time 151
Indirect methods for “counting” virus particles 152
Questions for Chapter 9 154
CHAPTER 10 Replicating and Measuring Biological Activity of Viruses 155
Cell culture techniques 156
Maintenance of bacterial cells 156
Plant cell cultures 156
Culture of animal and human cells 157
Maintenance of cells in culture 157
Types of cells 157
Loss of contact inhibition of growth and immortalization of
primary cells 159
The outcome of virus infection in cells 160
Fate of the virus 160
Fate of the cell following virus infection 162
Cell-mediated maintenance of the intra- and intercellular
environment 162
Virus-mediated cytopathology – changes in the physical
appearance of cells 163
Virus-mediated cytopathology – changes in the biochemical
properties of cells 163
Measurement of the biological activity of viruses 164
Quantitative measure of infectious centers 164
Plaque assays 164
Generation of transformed cell foci 165
Use of virus titers to quantitatively control infection conditions 166
Examples of plaque assays 167
Statistical analysis of infection 168
xi
xii
CONTENTS
Dilution endpoint methods 169
The relation between dilution endpoint and infectious units of
virus 169
Questions for Chapter 10 170
CHAPTER 11 Physical and Chemical Manipulation of the Structural
Components of Viruses 173
Viral structural proteins 173
Isolation of structural proteins of the virus 174
Size fractionation of viral structural proteins 176
Determining the stoichiometry of capsid proteins 177
The poliovirus capsid – a virion with equimolar capsid
proteins 178
Analysis of viral capsids that do not contain equimolar numbers
of proteins 179
Characterizing viral genomes 179
Sequence analysis of viral genomes 180
Measuring the size of viral genomes 184
Direct measure of DNA genome lengths in the electron
microscope 185
Rate zonal sedimentation and gel electrophoresis for measuring
viral genome size 185
The polymerase chain reaction – detection and characterization of
extremely small quantities of viral genomes or transcripts 187
Real time PCR for precise quantitative measures of viral
DNA 189
PCR detection of RNA 190
PCR as an epidemiological tool 190
Questions for Chapter 11 191
CHAPTER 12 Characterization of Viral Products Expressed in the Infected
Cell 193
Characterization of viral proteins in the infected cell 193
Pulse labeling of viral proteins at different times following
infection 194
Use of immune reagents for study of viral proteins 195
Working with antibodies 196
Detection of viral proteins using immunofluorescence 198
Related methods for detecting antibodies bound to
antigens 201
Detecting and characterizing viral nucleic acids in infected
cells 205
Detecting the synthesis of viral genomes 205
Characterization of viral mRNA expressed during infection 205
In situ hybridization 207
Further characterization of specific viral mRNA
molecules 209
Use of microarray technology for getting a complete picture of the
events occurring in the infected cell 210
Questions for Chapter 12 212
CONTENTS
CHAPTER 13 Viruses Use Cellular Processes to Express Their Genetic
Information 213
Prokaryotic DNA replication is an accurate enzymatic model for
the process generally 215
The replication of eukaryotic DNA 216
The replication of viral DNA 217
The effect of virus infection on host DNA replication 217
Expression of mRNA 217
Prokaryotic transcription 219
Prokaryotic RNA polymerase 219
The prokaryotic promoter and initiation of
transcription 220
Control of prokaryotic initiation of transcription 220
Termination of prokaryotic transcription 221
Eukaryotic transcription 221
The promoter and initiation of transcription 221
Control of initiation of eukaryotic transcription 223
Processing of precursor mRNA 224
Visualization and location of splices in eukaryotic
transcripts 226
Posttranscriptional regulation of eukaryotic mRNA
function 231
Virus-induced changes in transcription and posttranscriptional
processing 232
The mechanism of protein synthesis 232
Eukaryotic translation 233
Prokaryotic translation 234
Virus-induced changes in translation 236
Questions for Chapter 13 236
Problems for Part III 239
Additional Reading for Part III 241
PART IV
REPLICATION PATTERNS OF SPECIFIC
VIRUSES 243
CHAPTER 14 Replication of Positive-sense RNA Viruses 245
RNA viruses – general considerations 246
A general picture of RNA-directed RNA replication 246
Replication of positive-sense RNA viruses whose genomes are
translated as the first step in gene expression 248
Positive-sense RNA viruses encoding a single large open reading
frame 249
Picornavirus replication 249
The poliovirus genetic map and expression of poliovirus
proteins 249
The poliovirus replication cycle 252
Picornavirus cytopathology and disease 254
Flavivirus replication 256
Positive-sense RNA viruses encoding more than one translational
reading frame 257
xiii
xiv
CONTENTS
Two viral mRNAs are produced in different amounts during
togavirus infections 258
The viral genome 258
The virus replication cycle 258
Togavirus cytopathology and disease 262
A somewhat more complex scenario of multiple translational
reading frames and subgenomic mRNA expression: coronavirus
replication 263
Coronavirus replication 264
Cytopathology and disease caused by coronaviruses 266
Replication of plant viruses with RNA genomes 267
Viruses with one genome segment 268
Viruses with two genome segments 268
Viruses with three genome segments 269
Replication of bacteriophage with RNA genomes 269
Regulated translation of bacteriophage mRNA 269
Questions for Chapter 14 272
CHAPTER 15 Replication Strategies of RNA Viruses Requiring RNA-directed
mRNA Transcription as the First Step in Viral Gene
Expression 273
Replication of negative-sense RNA viruses with a monopartite
genome 275
Replication of vesicular stomatitis virus – a model for
Mononegavirales 275
Vesicular stomatitis virus virion and genome 275
Generation, capping, and polyadenylation of mRNA 276
Generation of new negative-sense virion RNA 278
Mechanism of host shutoff by vesicular stomatitis virus 279
Cytopathology and diseases caused by rhabdoviruses 280
Paramyxoviruses 280
Pathogenesis of paramyxoviruses 280
Filoviruses and their pathogenesis 282
Bornaviruses 282
Influenza viruses – negative-sense RNA viruses with a
multipartite genome 283
Involvement of the nucleus in flu virus replication 284
Generation of new flu nucleocapsids and maturation of the
virus 285
Influenza A epidemics 285
Other negative-sense RNA viruses with multipartite
genomes 288
Bunyaviruses 288
Virus structure and replication 288
Pathogenesis 291
Arenaviruses 291
Virus gene expression 292
Pathogenesis 292
Viruses with double-stranded RNA genomes 292
CONTENTS
Reovirus structure 292
Reovirus replication cycle 294
Pathogenesis 295
Subviral pathogens 295
Hepatitis delta virus 296
Viroids 297
Prions 298
Questions for Chapter 15 301
CHAPTER 16 Replication Strategies of Small and Medium-Sized DNA
Viruses 303
DNA viruses express genetic information and replicate their
genomes in similar, yet distinct, ways 304
Papovavirus replication 305
Replication of SV40 virus – the model polyomavirus 305
The SV40 genome and genetic map 309
Productive infection by SV40 310
Abortive infection of cells nonpermissive for SV40
replication 312
Replication of papillomaviruses 314
The HPV-16 genome 316
Virus replication and cytopathology 316
Replication of adenoviruses 319
Physical properties of adenovirus 319
Capsid structure 319
The adenovirus genome 319
The adenovirus replication cycle 319
Early events 319
Adenovirus DNA replication 321
Late gene expression 321
VA transcription and cytopathology 321
Transformation of nonpermissive cells by adenovirus 323
Replication of some single-stranded DNA viruses 323
Replication of parvoviruses 323
Dependovirus DNA integrates in a specific site in the host cell
genome 324
Parvoviruses have potentially exploitable therapeutic
applications 325
DNA viruses infecting vascular plants 325
Geminiviruses 325
Single-stranded DNA bacteriophage ΦX174 packages its genes
very compactly 326
Questions for Chapter 16 328
CHAPTER 17 Replication of Some Nuclear-Replicating Eukaryotic DNA Viruses
with Large Genomes 331
Herpesvirus replication and latency 332
The herpesviruses as a group 332
Genetic complexity of herpesviruses 333
xv
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CONTENTS
Common features of herpesvirus replication in the host 333
The replication of the prototypical alpha-herpesvirus –
HSV 334
The HSV virion 334
The viral genome 334
HSV productive infection 338
HSV latency and LAT 347
HSV transcription during latency and reactivation 348
How do LAT and other specific HSV genes function – may be
to accommodate reactivation? 350
EBV latent infection of lymphocytes, a different set of problems
and answers 351
Pathology of herpesvirus infections 354
Herpesviruses as infectious co-carcinogens 354
Baculovirus, an insect virus with important practical uses in
molecular biology 355
Virion structure 355
Viral gene expression and genome replication 356
Pathogenesis 356
Importance of baculoviruses in biotechnology 356
Questions for Chapter 17 357
CHAPTER 18 Replication of Cytoplasmic DNA Viruses and “Large”
Bacteriophages 359
Poxviruses – DNA viruses that replicate in the cytoplasm of
eukaryotic cells 360
The pox virion is complex and contains virus-coded transcription
enzymes 360
The poxvirus replication cycle 361
Early gene expression 363
Genome replication 363
Intermediate and late stages of replication 363
Pathogenesis and history of poxvirus infections 364
Is smallpox virus a potential biological terror weapon? 364
Replication of “large” DNA-containing bacteriophages 365
Components of large DNA-containing phage virions 365
Replication of phage T7 367
The genome 367
Phage-controlled transcription 367
The practical value of T7 367
T4 bacteriophage: the basic model for all DNA viruses 367
The T4 genome 368
Regulated gene expression during T4 replication 369
Capsid maturation and release 370
Replication of phage λ: a “simple” model for latency and
reactivation 370
The phage λ genome 372
Phage λ gene expression immediately after infection 372
Biochemistry of the decision between lytic and lysogenic
infection in E. coli 375
CONTENTS
A group of algal viruses shares features of its genome structure with
poxviruses and bacteriophages 376
Questions for Chapter 18 377
CHAPTER 19 Retroviruses: Converting RNA to DNA 381
Retrovirus families and their strategies of replication 382
The molecular biology of retrovirus 383
Retrovirus structural proteins 383
The retrovirus genome 384
Genetic maps of representative retroviruses 386
Replication of retroviruses: an outline of the replication
process 386
Initiation of infection 386
Capsid assembly and maturation 389
Action of reverse transcriptase and RNase-H in synthesis of
cDNA 389
Virus gene expression, assembly, and maturation 391
Transcription and translation of viral mRNA 391
Capsid assembly and morphogenesis 391
Mechanisms of retrovirus transformation 392
Transformation through the action of a viral oncogene – a
subverted cellular growth control gene 392
Oncornavirus alteration of normal cellular transcriptional control
of growth regulation 393
Oncornavirus transformation by growth stimulation of
neighboring cells 395
Cellular genetic elements related to retroviruses 395
Retrotransposons 396
The relationship between transposable elements and viruses 397
Questions for Chapter 19 397
CHAPTER 20 Human Immunodeficiency Virus Type 1 (HIV-1) and Related
Lentiviruses 399
HIV-1 and related lentiviruses 399
The origin of HIV-1 and AIDS 399
HIV-1 and lentiviral replication 400
Destruction of the immune system by HIV-1 406
Questions for Chapter 20 411
CHAPTER 21 Hepadnaviruses: Variations on the Retrovirus Theme 413
The virion and the viral genome 413
The viral replication cycle 415
The pathogenesis of hepatitis B virus 415
A plant “hepadnavirus”: cauliflower mosaic virus 416
Genome structure 416
Viral gene expression and genome replication 416
The evolutionary origin of hepadnaviruses 417
Questions for Chapter 21 419
Problems for Part IV 421
Additional Reading for Part IV 429
xvii
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CONTENTS
PART V
VIRUSES: NEW APPROACHES AND NEW
PROBLEMS 433
CHAPTER 22 The Molecular Genetics of Viruses 435
Mutations in genes and resulting changes to proteins 437
Analysis of mutations 438
Complementation 438
Recombination 439
Isolation of mutants 440
Selection 440
HSV thymidine kinase – a portable selectable marker 440
Screening 441
A tool kit for molecular virologists 441
Viral genomes 441
Locating sites of restriction endonuclease cleavage on the viral
genome – restriction mapping 442
Cloning vectors 443
Cloning of fragments of viral genomes using bacterial
plasmids 444
Cloning using phage λ 449
Cloning single-stranded DNA with bacteriophage M13 451
DNA animal virus vectors 451
RNA virus expression systems 453
Defective virus particles 454
Directed mutagenesis of viral genes 454
Site-directed mutagenesis 456
Generation of recombinant viruses 456
Bacterial artificial chromosomes 458
Questions for Chapter 22 461
CHAPTER 23 Molecular Pathogenesis 463
An introduction to the study of viral pathogenesis 463
Animal models 464
Choosing a model: natural host vs. surrogate models 464
Development of new models: transgenic animals 464
Hybrid models: the SCID-hu mouse 464
Considerations regarding the humane use of animals 465
Methods for the study of pathogenesis 466
Assays of virulence 466
Analysis of viral spread within the host 467
Resolving the infection to the level of single cells 470
Characterization of the host response 470
Immunological assays 470
Use of transgenic mice to dissect critical components of the host
immune response that modulate the viral infection 471
Question for Chapter 23 471
CHAPTER 24 Viral Bioinformatics and Beyond 473
Bioinformatics 473
Bioinformatics and virology 473
Biological databases 474
CONTENTS
Primary databases 474
Secondary databases 475
Composite databases 475
Other databases 476
Biological applications 476
Similarity searching tools 476
Protein functional analysis 478
Sequence analysis 478
Structural modeling 478
Structural analysis 478
Systems biology and viruses 479
Viral internet resources 481
Questions for Chapter 24 484
CHAPTER 25 Viruses and the Future – Problems and Promises 485
Clouds on the horizon – emerging disease 485
Sources and causes of emergent virus disease 488
The threat of bioterrorism 489
What are the prospects of using medical technology to eliminate
specific viral and other infectious diseases? 490
Silver linings – viruses as therapeutic agents 490
Viruses for gene delivery 491
Using viruses to destroy other viruses 493
Viruses and nanotechnology 493
The place of viruses in the biosphere 494
Why study virology? 494
Questions for Chapter 25 495
Problems for Part V 497
Additional Reading for Part V 499
APPENDIX
Resource Center 501
Books of historical and basic value 501
Books on virology 501
Molecular biology and biochemistry texts 503
Detailed sources 503
Sources for experimental protocols 503
The Internet 504
Virology sites 504
Important websites for organizations and facilities of
interest 505
Technical Glossary 507
Index 533
xix
Preface
Viruses have historically flickered in and out of the public consciousness. In the eight years
since we finished the first edition of Basic Virology much has happened, both in the world and
in virology, to fan the flames of this awareness.
In this period we have seen the development of a vaccine to protect women against human
papilloma virus type 16. This major advance could well lead to a drastic reduction in the occurrence of cervical cancer. In addition, viruses as gene delivery vectors have increased the prospect
of targeted treatments for a number of genetic diseases. The heightened awareness and importance of the epidemiological potential of viruses, both in natural and man-caused outbreaks,
has stimulated the search for both prophylactic and curative treatments.
However, the events of September 11, 2001 dramatically and tragically altered our perceptions. A new understanding of threat now pervades our public and private actions. In this new
arena, viruses have taken center stage as the world prepares for the use of infectious agents such
as smallpox in acts of bioterrorism.
Naturally occurring virological issues also continue to capture our attention. West Nile virus,
originally limited to areas of North Africa and the Middle East, has utilized the modern transportation network to arrive in North America. Its rapid spread to virtually every state in the
union has been both a public health nightmare and a vivid demonstration of the opportunism
of infectious diseases. The continuing AIDS pandemic reminds us of the terrible cost of this
opportunism. In addition, we are now faced with the very real prospect of the next pandemic
strain of influenzas, perhaps derived from the avain H5N1 virus now circulating in wild and
domestic birds.
It is against this backdrop of hope and concern that we have revised Basic Virology.
This book is based on more than 40 years in aggregate of undergraduate lectures on virology
commencing in 1970 given by the coauthors (Wagner, Hewlett, Bloom, and Camerini) at the
University of California, Irvine (UCI), the University of Arizona, Arizona State University, and
the University of Florida. The field of virology has matured and grown immensely during this
time, but one of the major joys of teaching this subject continues to be the solid foundation
it provides in topics running the gamut of the biological sciences. Concepts range from population dynamics and population ecology, through evolutionary biology and theory, to the most
fundamental and detailed analyses of the biochemistry and molecular biology of gene expression
and biological structures. Thus, teaching virology has been a learning tool for us as much, or
more, than it has been for our students.
Our courses are consistently heavily subscribed, and we credit that to the subject material,
certainly not to any special performance tricks or instructional techniques. Participants have
been mainly premedical students, but we have enjoyed the presence of other students bound
xxii
PREFACE
for postgraduate studies, as well as a good number of those who are just trying to get their
degree and get out of the “mill” and into the “grind.”
At UCI, in particular, the course had a tremendous enrollment (approximately 250
students per year) in the past 5–8 years, and it has become very clear that the material is
very challenging for a sizable minority studying it. While this is good, the course was
expanded in time to five hours per week for a 10-week quarter to accommodate only those
students truly interested in being challenged. Simply put, there is a lot of material to
master, and mastery requires a solid working knowledge of basic biology, but most importantly,
the desire to learn. This “experiment” has been very successful, and student satisfaction
with the expanded course is, frankly, gratifying. To help students acquire such working
knowledge, we have encouraged further reading. We have also included a good deal of reinforcement material to help students learn the basic skills of molecular biology and rudimentary
aspects of immunology, pathology, and disease. Further, we have incorporated numerous study
and discussion questions at the end of chapters and sections to aid in discussion of salient
points.
It is our hope that this book will serve as a useful text and source for many undergraduates
interested in acquiring a solid foundation in virology and its relationship to modern biology.
It is also hoped that the book may be of use to more advanced workers who want to make a
quick foray into virology but who do not want to wade through the details present in more
advanced works.
Preface to the second edition
The text retains our organizational format. As before, Part I concerns the interactions of viruses
and host populations, Part II is about the experimental details of virus infection, Part III discusses the tools used in the study of viruses, and Part IV is a detailed examination of families
and groupings of viruses. We have found, in our own teaching and in comments from colleagues, that this has been a useful approach. We have also kept our emphasis on problem
solving and on the provision of key references for further study.
What is new in the second edition has been driven by changes in virology and in the tools
used to study viruses. Some of these changes and additions include:
• a discussion of bioterrorism and the threat of viruses as weapons;
• updated information on emerging viruses such as West Nile, and their spread;
• current state of HIV antiviral therapies;
• discussions of viral genomics in cases where sequencing has been completed;
• discussion of cutting-edge technologies, such as atomic force microscopy and DNA microarray analysis;
• updated glossary and reference lists.
We have, throughout the revision, tried to give the most current understanding of the state of
knowledge for a particular virus or viral process. We have been guided by a sense of what our
students need in order to appreciate the complexity of the virological world and to come away
from the experience with some practical tools for the next stages in their careers.
Preface to the third edition
It is with a true sense of our loss that the three of us sit in Irvine, California, Gainesville, Florida,
and Taos, New Mexico, working towards completion of this edition. The absence of our friend
and colleague, Ed Wagner, is all the more apparent as we write the preface to this latest edition
of Basic Virology. In his spirit, we offer our colleagues and students this book that is our latest
view of the field that Ed pursued with such passion and dedication.
PREFACE
In this new edition, we have attempted to bring the current state of our discipline into focus
for students at the introductory and intermediate levels. To this end, we have done the job of
providing the most current information, at this writing, for each of the subjects covered. We
have also done some reorganization of the material. We have added three new chapters, in
recognition of the importance of these areas to the study of viruses.
The book now includes a chapter devoted completely to HIV and the lentiviruses (Chapter
20), previously covered along with the retroviruses in general. Given that we continue to face
the worldwide challenge of AIDS, we feel that this is an important emphasis.
You will also notice that this version now includes a Part V (Viruses: New Approaches and
New Problems). This section begins with a consideration of the molecular tools used to study
and manipulate viruses (Chapter 22), follows with coverage of viral pathogenesis at the molecular level (Chapter 23), and continues with a chapter dealing with viral genomics and bioinformatics (Chapter 24). We intend that these three will give our students insight into the current
threads of molecular and virological thinking. Part V concludes with our chapter on Viruses
and the Future (Chapter 25), containing updated material on emerging viruses, including
influenza, as well as viruses and nanotechnology.
A major change in this edition is the use of full-color illustrations. We welcome this effort
from our publisher, Blackwell Publishing, and hope that you find this adds value and utility
to our presentation.
In conjunction with the expanded coverage, the Glossary has been revised. In addition, all
of the references, both text and web-based, have been reviewed and made current, as of this
writing. To augment the basic material on individual viruses in Part IV, we have included case
studies which provide a clinical perspective of the viral diseases.
Most of these changes were either finished or discussed in detail before Ed’s untimely passing.
As a result, we are proud to say that Basic Virology, third edition, bears the welcome imprint
of the scientist/teacher who inspired the first one. We hope you agree and enjoy the fruits of
this effort.
Marty Hewlett, Taos New Mexico
Dave Bloom, Gainesville Florida
David Camerini, Irvine, California
Text organization
Virology is a huge subject, and can be studied from many points of view. We believe that
coverage from the most general aspects to more specific examples with corresponding details is
a logical way to present an overview, and we have organized this text accordingly. Many of our
students are eagerly pursuing careers in medicine and related areas, and our organization has
the added advantage that their major interests are addressed at the outset. Further development
of material is intended to encourage the start of a sophisticated understanding of the biological
basis of medical problems, and to introduce sophistication as general mastery matures. We are
fully aware that the organization reflects our prejudices and backgrounds as molecular biologists,
but hopefully it will not deter those with a more population-based bias from finding some value
in the material.
Following this plan, the book is divided into five sections, each discussing aspects of virology
in molecular detail. General principles of viral disease and its spread, the nature of viral pathogenesis, and the mechanistic basis for these principles are repeatedly refined and applied to
more detailed examples as the book unfolds.
Part I covers the interactions between viruses and populations and the impact of viral disease
and its study on our ever-expanding understanding of the molecular details behind the biological behavior of populations. A very basic discussion of theories of viral origins is presented, but
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PREFACE
not stressed. This was an editorial decision based on our opinion that a satisfactory molecular
understanding of the relationship between biological entities will require an appreciation and
mastery of the masses of comparative sequence data being generated now and into the next
several decades.
The major material covered in this introductory section is concerned with presenting a
generally consistent and experimentally defensible picture of viral pathogenesis and how this
relates to specific viral diseases – especially human disease. The use of animal models for the
study of disease, which is a requisite for any careful analysis, is presented in terms of several
well-established systems that provide general approaches applicable to any disease. Finally, the
section concludes with a description of some important viral diseases organized by organ system
affected.
Part II introduces experimental studies of how viruses interact with their hosts. It begins
with some basic descriptions of the structural and molecular basis of virus classification schemes.
While such schemes and studies of virus structure are important aspects of virology, we have
not gone into much detail in our discussion. We believe that such structural studies are best
covered in detail after a basic understanding of virus replication and infection is mastered; then
further detailed study of any one virus or virus group can be digested in the context of the
complete picture. Accordingly, more detailed descriptions of some virus structures are covered
in later chapters in the context of the techniques they illustrate.
This elementary excursion into structural virology is followed by an in-depth general discussion of the basic principles of how viruses recognize and enter cells and how they assemble and
exit the infected cell. This chapter includes an introduction to the interaction between animal
and bacterial viruses and the cellular receptors that they utilize in entry. It concludes with a
description of virus maturation and egress. While it can be argued that these two aspects of virus
infection are the “soup and nuts” of the process and do not belong together, we would argue that
many of the same basic principles and approaches for the study of the one are utilized in understanding the other. Further, by having the beginnings and ends of infection in one integrated
unit, the student can readily begin to picture the fact that virus infection cannot take place
without the cell, and that the cell is a vital part of the process from beginning to end.
Part II concludes with two chapters describing how the host responds to viral infections.
The first of these chapters is a basic outline of the vertebrate immune response. We believe that
any understanding of virus replication must be based on the realization that virus replication
in its host evokes a large number of complex and highly evolved responses. It just makes no
sense to attempt to teach virology without making sure that students understand this fact.
While the immune system is (to a large degree) a vertebrate response to viral infection, understanding it is vital to understanding the experimental basis of much of what we know of disease
and the effects of viral infections on cells. The last chapter in this section deals with the use of
immunity and other tools in combating viral infection. While “natural” cell-based defenses
such as interferon responses and restriction endonucleases are described, the emphasis is on the
understanding of virus replication and host responses in countering and preventing virusinduced disease. It seems logical to conclude this section with a description of vaccines and
antiviral drug therapy since these, too, are important host responses to virus infection and
disease.
Experimental descriptions of some of the tools scientists use to study virus infections, and
the basic molecular biological and genetic principles underlying these tools are described in
Part III. We emphasize the quantitative nature of many of these tools, and the use that such
quantitative information can be put to. This organization ensures that a student who is willing
to keep current with the material covered in preceding chapters will be able to visualize the use
of these tools against a background understanding of some basic concepts of pathology and
disease.
The section begins with the use of the electron microscope in the study of virus infection
PREFACE
and virus structure, and, perhaps as importantly, in counting viruses. While some of our colleagues would argue that such material is “old-fashioned” and detracts from discussion of
modern methodology, we would argue that the fundamental quantitative nature of virology
really requires a full understanding of the experimental basis of such quantitation. Accordingly,
we have included a fairly complete description of virus assay techniques, and the statistical
interpretation of such information. This includes a thorough discussion of cell culture technology and the nature of cultured cells.
The next two chapters introduce a number of experimental methods for the study and
analysis of virus infection and viral properties. Again, while we attempt to bring in important
modern technology, we base much of our description on the understanding of some of the
most basic methods in molecular biology and biochemistry. These include the use of differential
centrifugation, incorporation of radioactive tracers into viral products, and the use of immune
reagents in detecting and characterizing viral products in the infected cell. We have also
included basic descriptions of the methodology of cloning recombinant DNA and sequencing
viral genomes. We are well aware that there are now multitudes of novel technical approaches,
many using solid-state devices, but all such devices and approaches are based on fundamental
experimental principles and are best understood by a description of the original technology
developed to exploit them.
Since virology can only be understood in the context of molecular processes occurring inside
the cell, we include in Part III a chapter describing (essentially reviewing) the molecular biology
of cellular gene expression and protein synthesis.
Part IV, which essentially comprises the book’s second half, deals with the replication
processes of individual groups of viruses. We emphasize the replication strategies of viruses
infecting vertebrate hosts, but include discussions of some important bacterial and plant
viruses to provide scope. The presentation is roughly organized according to increasing complexity of viral gene expression mechanisms. Thus, it follows a modified “Baltimore”-type
classification. The expression of viral proteins is implicitly taken as the fundamental step in
virus gene expression, and accordingly, those viruses that do not need to transcribe their
genomes prior to translation of viral proteins (the “simple” positive-sense RNA viruses) are
described first.
The description of viruses that use RNA genomes but that must transcribe this RNA into
messenger RNA (mRNA) prior to viral gene expression follows. We logically include the replication of viruses using double-stranded RNA and “subviral” pathogens in this chapter. Somewhat less logically, we include a short discussion of the nature of prions here. This is not because
we wish to imply that these pathogens utilize an RNA genome (they almost certainly do not),
but rather because the techniques for their study are based in the virologist’s “tool kit.” Also,
the problems engendered by prion pathogenesis are similar in scope and potential for future
concern to those posed by numerous “true” viruses.
Organization of DNA viruses generally follows the complexity of encoded genetic information, which is roughly inversely proportional to the amount of unmodified cellular processes
utilized in gene expression. According to this scheme, the poxviruses and the large DNA-containing bacteriophages rather naturally fall into a single group, as all require the expression of
their own or highly modified transcription machinery in the infected cell.
We complete the description of virus replication strategies with three chapters covering retroviruses and their relatives. We depart from a more usual practice of placing a discussion of
retrovirus replication as a “bridge” between discussions of replication strategies of viruses with
RNA or DNA genomes, respectively, for a very good reason. We believe that the subtle manner
by which retroviruses utilize cellular transcription and other unique aspects in their mode of
replication is best understood by beginning students in the context of a solid background of
DNA-mediated gene expression illustrated by DNA viruses. Because of the continuing importance of HIV and the related lentiviruses, we have decided to devote a single chapter to their
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PREFACE
consideration. We end this section with the hepadnaviruses, another take on the reverse transcriptase mode of viral replication.
Part V begins with a brief overview of some of the principles of molecular and classic genetics that have special application to the study of viruses. The basic processes of using genetics
to characterize important mutations and to produce recombinant genomes are an appropriate
ending point for our general description of the basics of virology.
We follow this with two new chapters: one on molecular pathogenesis and another on viral
genomics and bioinformatics. The first of these focuses our attention on the rich area of investigation that deals with the mechanisms used by disease-causing viruses at the molecular level
in their hosts. The second is an introduction to the cutting-edge field of genomics and bioinformatics, with an emphasis on the analysis of viruses. We pay particular attention to the use
of database analysis tools available on the Internet.
The final chapter in this section is included for balance and closure. We use it to highlight
areas of interest for the future, including emerging viruses, viruses as therapeutic tools, and
viruses and nanotechnology. Clearly, some of the students taking this course will be continuing
their studies in much greater depth, but many students may not. It is important to try to remind
both groups of the general lessons that can be learned and (perhaps) remembered by their first
(and possibly only) excursion into virology.
Specific features of this text designed to aid instructors and students in
pursuing topics in greater depth
Depth of coverage
This book is intended as a basic text for a course that can be covered fully in a single semester.
Clearly, the coverage is not deep, nor is such depth necessary for such an introduction. While
the first solid virology text emphasizing molecular biology, General Virology by S. E. Luria and
(later) by J. E. Darnell, was only about half the length of this present text, it covered much of
what was known in virology to a high level of completion. The present wealth of our detailed
mechanistic knowledge of biological processes (one of the glories of modern biology) cannot
be condensed in any meaningful way. More detailed information on individual virus groups
or topics covered in this text can be found in their own dedicated books. For similar reasons,
we have generally eschewed citing contributions by individual scientists by name. This is certainly not to denigrate such contributions, but is in recognition of the fact that a listing of the
names and efforts of all who have participated in the discoveries leading to modern molecular
biology and medicine would fill several books the size of this one.
Sources for further study
We have provided the means of increasing the depth of coverage so that instructors or students
can pursue their own specific interests in two ways. First, we suggest appropriate further reading
at the end of each section. Second, we include a rather extensive survey of sources on virology
and the techniques for the study of viruses in an appendix following the body of the text. We
hope that these sources will be used because we are convinced that students must be presented
with source material and encouraged to explore on their own at the start of this study. Mastery
of the literature (if it is ever really possible) comes only by experience and ease of use of primary
sources. This comes, in turn, by undergraduate, graduate, and postgraduate students assimilating the appreciation of those sources. Therefore, the detailed foundations of this very brief
survey of the efforts of innumerable scientists and physicians carried out over a number of
centuries are given the prominence they deserve.
PREFACE
The Internet
The Internet is providing a continually expanding source of up-to-date information concerning
a vast number of topics. We have carried out an opinionated but reasonably thorough survey
of Web sites that should be of use to both students and instructors in developing topics indepth. This survey is included in the appendix. To maximize flexibility and timeliness of our
coverage of individual viruses in Part IV, we include as many sites on the Web dedicated to
specific viruses as we could locate that we found to be useful. One word of caution, however:
While some Web sites are carefully reviewed, and frequently updated, others may not be. Caveat
emptor !
Chapter outlines
We include an outline of the material covered in each section and each chapter at their respective beginnings. This is to provide a quick reference that students can skim and use for more
detailed chapter study. These outlines also provide a ready list of the topics covered for the
instructor.
Case studies
We have included a number of “Case Studies” dealing with specific viruses covered in the
chapters of Part IV. These case studies appear at the end of the chapters and take the form of
a clinical case presentation where symptoms of a disease caused by a given virus are given, followed by medical test results and a diagnosis. Treatment information and additional material
relevant to the pathobiology of the disease are also discussed. It is hoped that these case studies
will be useful in augmenting the material in the chapters with a clinical perspective.
Review material
Each chapter is followed with a series of relatively straightforward review questions. These are
approximately the level and complexity that we use in our midterm and final exams. They
should be of some value in discussion sections and informal meetings among groups of students
and instructors. Rather more integrative questions are included at the end of each major section
of the book. These are designed to be useful in integrating the various concepts covered in the
individual chapters.
Glossary
Because a major component of learning basic science is mastery of the vocabulary of science,
we include a glossary of terms at the end of the text. Each term is highlighted at its first usage
in the body of the text.
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Acknowledgments
Even the most basic text cannot be solely the work of its author or authors; this is especially
true for this one. We are extremely grateful to a large number of colleagues, students, and
friends. They provided critical reading, essential information, experimental data, and figures,
as well as other important help. This group includes the following scholars from other research
centers: J. Brown, University of Virginia; R. Condit, University of Florida; J. Conway, National
Institutes of Health; K. Fish and J. Nelson, Oregon Health Sciences University; D.W. Gibson,
Johns Hopkins University; P. Ghazal, University of Edinburgh; H. Granzow, Friedrich-Loeffler-Institute – Insel Riems; C. Grose, University of Iowa; J. Hill, Louisiana State University
Eye Center – New Orleans; J. Langland, Arizona State University; D. Leib, Washington
University; F. Murphy, University of California, Davis; S. Rabkin, Harvard University; S. Rice,
University of Alberta–Edmonton; S. Silverstein, Columbia University; B. Sugden, University
of Wisconsin; Gail Wertz, University of Alabama–Birmingham; and J.G. Stevens, University
of California, Los Angeles. Colleagues at University of California, Irvine who provided aid
include R. Davis, S. Larson, A. McPherson, T. Osborne, R. Sandri-Goldin, D. Senear, B.
Semler, S. Stewart, W.E. Robinson, I. Ruf; and L. Villarreal. Both current and former workers
in Edward Wagner’s laboratory did many experiments that aided in a number of illustrations;
these people include J.S. Aguilar, K. Anderson, R. Costa, G.B. Devi-Rao, R. Frink, S. Goodart,
J. Guzowski, L.E. Holland, P. Lieu, N. Pande, M. Petroski, M. Rice, J. Singh, J. Stringer, and
Y-F. Zhang.
We were aided in the writing of the second edition by comments from Robert Nevins
(Milsap College), Sofie Foley (Napier University), David Glick (King’s College), and David
Fulford (Edinboro University of Pennsylvania).
Many people contributed to the physical process of putting this book together. R. Spaete
of the Aviron Corp carefully read every page of the manuscript and suggested many important
minor and a couple of major changes. This was done purely in the spirit of friendship and
collegiality. K. Christensen used her considerable expertise and incredible skill in working with
us to generate the art. Not only did she do the drawings, but also she researched many of them
to help provide missing details. Two undergraduates were invaluable to us. A. Azarian at University of California, Irvine made many useful suggestions on reading the manuscript from a
student’s perspective, and D. Natan, an MIT student who spent a summer in Edward Wagner’s
laboratory, did most of the Internet site searching, which was a great relief and time saver.
Finally, J. Wagner carried out the very difficult task of copyediting the manuscript.
A number of people at Blackwell Publishing represented by Publisher N. Hill-Whilton
demonstrated a commitment to a quality product. We especially thank Elizabeth Frank,
Caroline Milton, and Rosie Hayden who made great efforts to maintain effective communications and to expedite many of the very tedious aspects of this project. Blackwell Publising
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ACKNOWLEDGMENTS
directly contacted a number of virologists who also read and suggested useful modifications to
this manuscript, including Michael R. Roner, University of Texas, Arlington; Lyndon Larcom,
Clemson University; Michael Lockhart, Truman State University; Lloyd Turtinen, University
of Wisconsin, Eau Claire; and Paul Wanda, Southern Illinois University.
All of these colleagues and friends represent the background of assistance we have received,
leading to the preparation of this third edition. We would especially like to acknowledge Dr.
Luis Villareal and the Center for Virus Research at the University of California, Irvine, for
supporting our efforts in bringing this book to a timely completion.
Virology and
Viral Disease
✷
✷
✷
✷
✷
✷
Introduction – the Impact of Viruses on Our View of Life
✷ The Science of Virology
An Outline of Virus Replication and Viral Pathogenesis
✷ Virus Replication
✷ Pathogenesis of Viral Infection
Virus Disease in Populations and Individual Animals
✷ The Nature of Virus Reservoirs
✷ Viruses in Populations
✷ Animal Models to Study Viral Pathogenesis
Patterns of Some Viral Diseases of Humans
✷ The Dynamics of Human–Virus Interactions
✷ Patterns of Specific Viral Diseases of Humans
✷ Some Viral Infections Targeting Specific Organ Systems
Problems for Part I
Additional Reading for Part I
P A R T
I
Introduction – The
Impact of Viruses on
Our View of Life
CHAPTER
✷ 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
THE SCIENCE OF VIROLOGY
The study of viruses has historically provided and continues to provide the basis for much of
our most fundamental understanding of modern biology, genetics, and medicine. Virology has
had an impact on the study of biological macromolecules, processes of cellular gene expression,
mechanisms for generating genetic diversity, processes involved in the control of cell growth
and development, aspects of molecular evolution, the mechanism of disease and response of
the host to it, and the spread of disease in populations.
In essence, viruses are collections of genetic information directed toward one end: their own
replication. They are the ultimate and prototypical example of “selfish genes.” The viral
genome contains the “blueprints” for virus replication enciphered in the genetic code, and
must be decoded by the molecular machinery of the cell that it infects to gain this end. Viruses
are; thus, obligate intracellular parasites dependent on the metabolic and genetic functions of
living cells.
Given the essential simplicity of virus organization – a genome containing genes dedicated
to self replication surrounded by a protective protein shell – it has been argued that viruses are
nonliving collections of biochemicals whose functions are derivative and separable from
the cell. Yet this generalization does not stand up to the increasingly detailed information
accumulating describing the nature of viral genes, the role of viral infections on evolutionary
change, and the evolution of cellular function. A view of viruses as constituting a major
1
4
BASIC VIROLOGY PART I VIROLOGY AND VIRAL DISEASE
subdivision of the biosphere as ancient as and fully interactive and integrated with the three
great branches of cellular life becomes more strongly established with each investigational
advance.
It is a major problem in the study of biology at a detailed molecular and functional level
that almost no generalization is sacred, and the concept of viruses as simple parasitic collections
of genes functioning to replicate themselves at the expense of the cell they attack does not hold
up. Many generalizations will be made in the survey of the world of viruses introduced in this
book, most if not all will be ultimately classified as being useful, but unreliable tools for the
full understanding and organization of information.
Even the size range of viral genomes, generalized to range from one or two genes to a few
hundred at most (significantly less than those contained in the simplest free living cells), cannot
be supported by a close analysis of data. While it is true that the vast majority of viruses studied
range in size from smaller than the smallest organelle to just smaller than the simplest cells
capable of energy metabolism and protein synthesis, the mycoplasma and simple unicellular
algae, the recently discovered Mimivirus (distantly related to poxviruses such as smallpox or
variola) contains nearly 1000 genes and is significantly larger than the smallest cells. With such
caveats in mind it is still appropriate to note that despite their limited size, viruses have evolved
and appropriated a means of propagation and replication that ensures their survival in freeliving organisms that are generally between 10 and 10,000,000 times their size and genetic
complexity.
The effect of virus infections on the host organism and populations –
viral pathogenesis, virulence, and epidemiology
Since a major motivating factor for the study of virology is that viruses cause disease of varying
levels of severity in human populations and in the populations of plants and animals which
support such populations, it is not particularly surprising that virus infections have historically
been considered episodic interruptions of the well being of a normally healthy host. This view
was supported in some of the earliest studies on bacterial viruses, which were seen to cause the
destruction of the host cell and general disruption of healthy, growing populations of the host
bacteria. Despite this, it was seen with another type of bacterial virus that a persistent, lysogenic,
infection could ensue in the host population. In this case, stress to the lysogenic bacteria could
release infectious virus long after the establishment of the initial infection.
These two modes of infection of host populations by viruses, which can be accurately
modeled by mathematical methods developed for studying predator–prey relationships
in animal and plant populations, are now understood to be general for virus–host interactions.
Indeed, persistent infections with low or no levels of viral disease are universal in virus–host
ecosystems that have evolved together for extended periods – it is only upon the introduction
of a virus into a novel population that widespread disease and host morbidity occurs.
While we can, thus, consider severe virus-induced disease to be evidence of a recent introduction of the virus into the population in question, the accommodation of the one to the
other is a very slow process requiring genetic changes in both virus and host, and it is by no
means certain that the accommodation can occur without severe disruption of the host population – even its extinction. For this reason, the study of the replication and propagation of a
given virus in a population is of critical importance to the body politic, especially in terms of
formulating and implementing health policy. This is, of course, in addition to its importance
to the scientific and medical communities.
The study of effects of viral infection on the host is broadly defined as the study of viral
pathogenesis. The sum total of the virus-encoded functions that contribute to virus propaga-
CHAPTER 1 INTRODUCTION
– THE IMPACT OF VIRUSES ON OUR VIEW OF LIFE
tion in the infected cell, in the host organism, and in the population is defined as pathogenicity
of that virus. This term essentially describes the genetic ability of members of a given specific
virus population (which can be considered to be genetically more or less equivalent) to cause
a disease and spread through (propagate in) a population. Thus, a major factor in the pathogenicity of a given virus is its genetic makeup or genotype.
The basis for severity of the symptoms of a viral disease in an organism or a population is
complex. It results from an intricate combination of expression of the viral genes controlling
pathogenicity, physiological response of the infected individual to these pathogenic determinants, and response of the population to the presence of the virus propagating in it. Taken
together, these factors determine or define the virulence of the virus and the disease it
causes.
A basic factor contributing to virulence is the interaction among specific viral genes and the
genetically encoded defenses of the infected individual. It is important to understand, however,
that virulence is also affected by the general health and genetic makeup of the infected population, and in humans, by the societal and economic factors that affect the nature and extent of
the response to the infection.
The distinction and gradation of meanings between the terms pathogenesis and virulence can
be understood by considering the manifold factors involved in disease severity and spread
exhibited in a human population subjected to infection with a disease-causing virus. Consider
a virus whose genotype makes it highly efficient in causing a disease, the symptoms of which
are important in the spread between individuals – perhaps a respiratory infection with accompanying sneezing, coughing, and so on. This ideal or optimal virus will incorporate numerous,
random genetic changes during its replication cycles as it spreads in an individual and in the
population. Some viruses generated during the course of a disease may, then, contain genes
that are not optimally efficient in causing symptoms. Such a virus is of reduced virulence, and
in the extreme case, it might be a virus that has accumulated so many mutations in pathogenic
genes that it can cause no disease at all (i.e., has mutated to an avirulent or apathogenic strain).
While an avirulent virus may not cause a disease, its infection may well lead to complete or
partial immunity against the most virulent genotypes in an infected individual. This is the
basis of vaccination, which is described in Chapter 8, Part II. But the capacity to generate an
immune response and the resulting generation of herd immunity also means that as a virus
infection proceeds in a population, its virulence either must change or the virus must genetically
adapt to the changing host.
Other factors not fully correlated with the genetic makeup of a virus also contribute to
variations in virulence of a pathogenic genotype. The same virus genotype infecting two immunologically naive individuals (i.e., individuals who have never been exposed to any form of
the virus leading to an immune response) can cause very different outcomes. One individual
might only have the mildest symptoms because of exposure to a small amount of virus, or
infection via a suboptimal route, or a robust set of immune and other defense factors inherent
in his or her genetic makeup. Another individual might have a very severe set of symptoms or
even death if he or she receives a large inoculum, or has impaired immune defenses, or happens
to be physically stressed due to malnutrition or other diseases.
Also, the same virus genotype might cause significantly different levels of disease within two
more or less genetically equivalent populations that differ in economic and technological
resources. This could happen because of differences in the ability of one society’s support net
to provide for effective medical treatment, or to provide for isolation of infected individuals,
or to have available the most effective treatment protocols.
Taken in whole, the study of human infectious disease caused by viruses and other pathogens
defines the field of epidemiology (in animals it is termed epizoology). This field requires a
good understanding of the nature of the disease under study and the types of medical and other
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BASIC VIROLOGY PART I VIROLOGY AND VIRAL DISEASE
remedies available to treat it and counter its spread, and some appreciation for the dynamics
and particular nuances and peculiarities of the society or population in which the disease
occurs.
The interaction between viruses and their hosts
The interaction between viruses (and other infectious agents) and their hosts is a dynamic one.
As effective physiological responses to infectious disease have evolved in the organism and (more
recently) have developed in society through application of biomedical research, viruses themselves respond by exploiting their naturally occurring genetic variation to accumulate and select
mutations to become wholly or partially resistant to these responses. In extreme cases, such
resistance will lead to periodic or episodic reemergence of a previously controlled disease – the
most obvious example of this process is the periodic appearance of human influenza viruses
caused disease.
The accelerating rate of human exploitation of the physical environment and the accelerating
increase in agricultural populations afford some viruses new opportunities to “break out” and
spread both old and novel diseases. Evidence of this is the ongoing acquired immune deficiency syndrome (AIDS) epidemic, as well as sporadic occurrences of viral diseases, such as
hemorrhagic fevers in Asia, Africa, and southwestern United States. Investigation of the course
of a viral disease, as well as societal responses to it, provides a ready means to study the role of
social policies and social behavior of disease in general.
The recent worldwide spread of AIDS is an excellent example of the role played by economic
factors and other aspects of human behavior in the origin of a disease. There is strong evidence
to support the view that the causative agent, human immunodeficiency virus (HIV), was
introduced into the human population by an event fostered by agricultural encroachment of
animal habitats in equatorial Africa. This is an example of how economic need has accentuated risk.
HIV is not an efficient pathogen; it requires direct inoculation of infected blood or body
fluids for spread. In the Euro-American world, the urban concentration of homosexual males
with sexual habits favoring a high risk for venereal disease had a major role in spreading
HIV and resulting in AIDS throughout the male homosexual community. A partial overlap of
this population with intravenous drug users and participants in the commercial sex industry
resulted in spread of the virus and disease to other portions of urban populations. The result
is that in Western Europe and North America, AIDS has been a double-edged sword threatening two disparate urban populations: the relatively affluent homosexual community and the
impoverished heterosexual world of drug abusers – both highly concentrated urban populations.
In the latter population, the use of commercial sex as a way of obtaining money resulted in
further spread to other heterosexual communities, especially those of young, single men and
women.
An additional factor is that the relatively solid medical and financial resources of a large
subset of the “economic first world” resulted in wide use of whole blood transfusion, and more
significantly, pooled blood fractions for therapeutic use. This led to the sudden appearance of
AIDS in hemophiliacs and sporadically in recipients of massive transfusions due to intensive
surgery. Luckily, the incidence of disease in these last risk populations has been reduced owing
to effective measures for screening blood products.
Different societal factors resulted in a different distribution of HIV and AIDS in equatorial
Africa and Southeast Asia. In these areas of the world, the disease is almost exclusively found
in heterosexual populations. This distribution of AIDS occurred because a relatively small
concentration of urban commercial sex workers acted as the source of infection of working men
CHAPTER 1 INTRODUCTION
– THE IMPACT OF VIRUSES ON OUR VIEW OF LIFE
living apart from their families. The periodic travel by men to their isolated village homes
resulted in the virus being found with increasing frequency in isolated family units. Further
spread resulted from infected women leaving brothels and prostitution to return to their villages
to take up family life.
Another overweening factor in the spread of AIDS is technology. HIV could not have spread
and posed the threat it now does in the world of a century ago. Generally lower population
densities and lower concentrations of individuals at risk at that time would have precluded HIV
from gaining a foothold in the population. Slower rates of communication and much more
restricted travel and migration would have precluded rapid spread; also the transmission of
blood and blood products as therapeutic tools was unknown a century ago.
Of course, this dynamic interaction between pathogen and host is not confined to viruses;
any pathogen exhibits it. The study and characterization of the genetic accommodations viruses
make, both to natural resistance generated in a population of susceptible hosts and to humandirected efforts at controlling the spread of viral disease, provide much insight into evolutionary
processes and population dynamics. Indeed, many of the methodologies developed for the study
of interactions between organisms and their environment can be applied to the interaction
between pathogen and host.
The history of virology
The historic reason for the discovery and characterization of viruses, and a continuing major
reason for their detailed study, involves the desire to understand and control the diseases and
attending degrees of economic and individual distress caused by them. As studies progressed,
it became clear that there were many other important reasons for the study of viruses and their
replication.
Since viruses are parasitic on the molecular processes of gene expression and its regulation
in the host cell, an understanding of viral genomes and virus replication provides basic information concerning cellular processes in general.
The whole development of molecular biology and molecular genetics is largely based on the
deliberate choice of some insightful pioneers of “pure” biological research to study the replication and genetics of viruses that replicate in bacteria: the bacteriophages. (Such researchers
include Max Delbrück, Salvadore Luria, Joshua Lederberg, Gunther Stent, Seymour Benzer,
Andre Lwoff, François Jacob, Jacques Monod, and many others.)
The bacterial viruses (bacteriophage) were discovered through their ability to destroy human
enteric bacteria such as Escherichia coli, but they had no clear relevance to human disease. It is
only in retrospect that the grand unity of biological processes from the most simple to the most
complex can be seen as mirrored in replication of viruses and the cells they infect.
The biological insights offered by the study of viruses have led to important developments
in biomedical technology and promise to lead to even more dramatic developments and tools.
For example, when infecting an individual, viruses target specific tissues. The resulting
specific symptoms, as already noted, define their pathogenicity. The normal human, like all
vertebrates, can mount a defined and profound response to virus infections. This response often
leads to partial or complete immunity to reinfection. The study of these processes was instrumental to gaining an increasingly clear understanding of the immune response and the precise
molecular nature of cell–cell signaling pathways. It also provided therapeutic and preventive
strategies against specific virus-caused disease. The study of virology has and will continue to
provide strategies for the palliative treatment of metabolic and genetic diseases not only
in humans, but also in other economically and aesthetically important animal and plant
populations.
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BASIC VIROLOGY PART I VIROLOGY AND VIRAL DISEASE
Examples of the impact of viral disease on human history
There is archeological evidence in Egyptian mummies and medical texts of readily identifiable
viral infections, including genital papillomas (warts) and poliomyelitis. There are also somewhat
imperfect historical records of viral disease affecting human populations in classical and
medieval times. While the recent campaign to eradicate smallpox has been successful and it no
longer exists in the human population (owing to the effectiveness of vaccines against it, the
genetic stability of the virus, and a well-orchestrated political and social effort to carry out the
eradication), the disease periodically wreaked havoc and had profound effects on human history
over thousands of years. Smallpox epidemics during the Middle Ages and later in Europe
resulted in significant population losses as well as major changes in the economic, religious,
political, and social life of individuals. Although the effectiveness of vaccination strategies
gradually led to decline of the disease in Europe and North America, smallpox continued to
cause massive mortality and disruption in other parts of the world until after World War II.
Despite its being eradicated from the environment, the attack of September 11, 2001 on the
World Trade Center in New York has lead some government officials to be concerned that the
high virulence of the virus and its mode of spread might make it an attractive agent for
bioterrorism.
Other virus-mediated epidemics had equally major roles in human history. Much of the
social, economic, and political chaos in native populations resulting from European conquests
and expansion from the fifteenth through nineteenth centuries was mediated by introduction
of infectious viral diseases such as measles. Significant fractions of the indigenous population
of the western hemisphere died as a result of these diseases.
Potential for major social and political disruption of everyday life continues to this day. As
discussed in later chapters of this book, the “Spanish” influenza (H1N1) epidemic of 1918–19
killed tens of millions worldwide and, in conjunction with the effects of World War I, came
very close to causing a major disruption of world civilization. Remarkable medical detective
work using virus isolated from cadavers of victims of this disease frozen in Alaskan permafrost
has lead to recovery of the complete genomic sequence of the virus and reconstruction of the
virus itself (some of the methods used will be outlined in Part V). While we may never know
all the factors that caused it to be so deadly, it is clear that the virus was derived from birds
passing it directly to humans. Further, a number of viral proteins have a role in its virulence.
Ominously, there is no reason why another strain of influenza could not arise with a
similar or more devastating aftermath or sequela – indeed as of the spring/summer of 2005
there is legitimate cause for concern because a new strain of avian influenza (H5N1) has been
transmitted to humans. At the present time, human transmission of H5N1 influenza has not
been confirmed, but further adaptation of this new virus to humans could lead to its establishing itself as a major killer in the near future.
A number of infectious diseases could become established in the general population as a
consequence of their becoming drug resistant, human disruption of natural ecosystems, or
introduced as weapons of bioterrorism. As will be discussed in later chapters, a number of different viruses exhibiting different details of replication and spread could, potentially, be causative agents of such diseases.
Animal and plant pathogens are other potential sources of disruptive viral infections. Sporadic outbreaks of viral disease in domestic animals, for example, vesicular stomatitis virus in
cattle and avian influenza in chickens, result in significant economic and personal losses. Rabies
in wild animal populations in the eastern United States has spread continually during the past
half-century. The presence of this disease poses real threats to domestic animals and through
them occasionally, to humans. An example of an agricultural infection leading to severe economic disruption is the growing spread of the Cadang-cadang viroid in coconut palms of the
CHAPTER 1 INTRODUCTION
– THE IMPACT OF VIRUSES ON OUR VIEW OF LIFE
Philippine Islands and elsewhere in Oceania. The loss of coconut palms led to serious financial
hardship in local populations.
Examples of the evolutionary impact of the virus–host interaction
There is ample genetic evidence that the interaction between viruses and their hosts
had a measurable impact on evolution of the host. Viruses provide environmental stresses
to which organisms evolve responses. Also, it is possible that the ability of viruses to
acquire and move genes between organisms provides a mechanism of gene transfer between
lineages.
Development of the immune system, the cellular-based antiviral interferon (IFN) response,
and many of the inflammatory and other responses that multicellular organisms can mount to
ward off infection is the result of successful genetic adaptation to infection. More than this,
virus infection may provide an important (and as yet underappreciated) basic mechanism to
affect the evolutionary process in a direct way.
There is good circumstantial evidence that the specific origin of placental mammals is the
result of an ancestral species being infected with an immunosuppressive proto-retrovirus. It is
suggested that this immunosuppression permitted an immunological accommodation in the
mother to the development of a genetically distinct individual in the placenta during a prolonged period of gestation!
Two current examples provide very strong evidence for the continued role of viruses in
the evolution of animals and plants. Certain parasitic wasps lay their eggs in the caterpillars
of other insects. As the wasp larvae develop, they devour the host, leaving the vital parts
for last to ensure that the food supply stays fresh! Naturally, the host does not appreciate
this attack and mounts an immune defense against the invader – especially at the earliest
stages of the wasp’s embryonic development. The wasps uninfected with a polydnavirus do
not have a high success rate for their parasitism and their larvae are often destroyed. The case
is different when the same species of wasp is infected with a polydnavirus that is then
maintained as a persistent genetic passenger in the ovaries and egg cells of the wasps. The
polydnavirus inserted into the caterpillar along with the wasp egg induces a systemic, immunosuppressive infection so that the caterpillar cannot eliminate the embryonic tissue at an early
stage of development! The virus maintains itself by persisting in the ovaries of the developing
female wasps.
A further example of a virus’s role in development of a symbiotic relationship between its
host and another organism can be seen in replication of the Chlorella viruses. These viruses
are found at concentrations as high as 4 × 104 infectious units/ml in freshwater throughout the
United States, China, and probably elsewhere in the world. Such levels demonstrate that the
virus is a very successful pathogen. Despite this success, the viruses can only infect free algae;
they cannot infect the same algae when the algae exist semi-symbiotically with a species of
paramecium. Thus, the algae cells that remain within their symbiotes are protected from infection, and it is a good guess that existence of the virus is a strong selective pressure toward
establishing or stabilizing the symbiotic relationship.
The origin of viruses
In the last decade or so, molecular biologists have developed a number of powerful techniques
to amplify and sequence the genome of any organism or virus of interest. The correlation
between sequence data, classical physiological, biochemical and morphological analyses and the
geological record has provided one of the triumphs of modern biology. We now know that the
biosphere is made up of three major superkingdoms, the eubacteria, the eukaryotes (nucleated
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BASIC VIROLOGY PART I VIROLOGY AND VIRAL DISEASE
cells), and the archaebacteria – the latter only discovered through the ribosomal RNA (rRNA)
sequence studies of Woese and his colleagues in the past 15 years or so. Further, analysis of
genetic changes in conserved sequences of critical proteins as well as ribosomal RNA confirm
that eukaryotes are more closely related to and, thus, derived from the ancestors of archaea than
they are eubacteria.
Carefully controlled statistical analysis of the frequency and numbers of base changes in
genes encoding conserved enzymes and proteins mediating essential metabolic and other cellular
processes can be used to both measure the degree of relatedness between greatly divergent
organisms, and provide a sense of when in the evolutionary time scale they diverged from a
common ancestor. This information can be used to generate a phylogenetic tree, which graphically displays such relationships. An example of such a tree showing the degree of divergence
of some index species in the three superkingdoms is shown in Fig. 1.1.
Although there is no geological record of viruses (they do not form fossils in any currently
useful sense), the analysis of the relationship between the amino acid sequences of viral and
cellular proteins and that of the nucleotide sequences of the genes encoding them provide ample
genetic evidence that the association between viruses and their hosts is as ancient as the origin
of the hosts themselves. Some viruses (e.g., retroviruses) integrate their genetic material into
the cell they infect, and if this cell happens to be germ line, the viral genome (or its relict) can
be maintained essentially forever. Analysis of the sequence relationship between various retroviruses found in mammalian genomes demonstrates integration of some types before major
groups of mammals diverged.
While the geological record cannot provide evidence of when or how viruses originated,
genetics offers some important clues. First, the vast majority of viruses do not encode genes for
ribosomal proteins or genetic evidence of relicts of such genes. Second, this same vast majority
mimi/pox viruses
Eukaryotes
Human
Yeast
Archaea
Arabidopsis
E. coli
B. subtilis
Eubacteria
Fig. 1.1 A phylogenetic tree of selected species from the three superkingdoms of life,
Eukaryotes, Eubacteria, and Archaea. The tree is based upon statistical analysis of
sequence variation in seven universally conserved protein sequences: arginyl-t-RNA
synthetase, methionyl-t-RNA synthetase, tyrosyl-t-RNA synthetase, RNA pol II
largest subunit, RNA pol II second largest subunit, PCNA, and 5′–3′
exonuclease.(Figure based upon Raoult et al. The 1.2-megabase genome sequence of
mimivirus. Science 2004;306:1344–1350.)
CHAPTER 1 INTRODUCTION
– THE IMPACT OF VIRUSES ON OUR VIEW OF LIFE
of viruses does not contain genetic evidence of ever having encoded enzymes involved in energy
metabolism. This is convincing evidence that the viruses currently investigated did not evolve
from free-living organisms. This finding distinctly contrasts with two eukaryotic organelles, the
mitochondrion and the chloroplast, which are known to be derived from free-living
organisms.
Genetics also demonstrates that a large number of virus-encoded enzymes and proteins have
a common origin with cellular ones of similar or related function. For example, many viruses
containing DNA as their genetic material have viral-encoded DNA polymerases that are related
to all other DNA polyisomerases isolated from plants, animals, and archaea.
Statistical analysis of the divergence in three highly conserved regions of eukaryotic
DNA polymerases suggests that the viral enzymes including both those from herpesviruses,
and poxviruses and relatives (including mimiviruses) have existed as long as have the three
superkingdoms themselves. Indeed, convincing arguments exist that the viral enzymes are more
similar to the ancestral form. This, in turn, implies that viruses or virus-like self-replicating
entities (replicons) had a major role, if not the major role, in the origin of DNA-based genetics. The phylogenetic tree of relationships between two forms of eukaryotic DNA polymerase
(alpha and delta), and two forms of the enzyme found in archaebacteria as well as those of
three groups of large DNA viruses and some other DNA viruses infecting algae and protests is
shown Fig. 1.2.
Another example of the close genetic interweaving of early cellular and early viral life forms
is seen in the sequence analysis of the reverse transcriptase enzyme encoded by retroviruses,
which is absolutely required for converting retroviral genetic information contained in RNA
to DNA. This enzyme is related to an important eukaryotic enzyme involved in reduplicating
the telomeres of chromosomes upon cell division – an enzyme basic to the eukaryotic mode of
genome replication. Reverse transcriptase is also found in cellular transposable genetic elements
(retrotransposons), which are circular genetic elements that can move from one chromosomal
location to another. Thus, the relationship between certain portions of the replication cycle of
retroviruses and mechanisms of gene transposition and chromosome maintenance in cells are
so intimately involved that it is impossible to say which occurred first.
A major complication to a complete and satisfying scheme for the origin of viruses is
that a large proportion of viral genes have no known cellular counterparts, and viruses themselves may be a source of much of the genetic variation seen between different free-living
organisms. In an extensive analysis of the relationship between groups of viral and cellular genes,
L.P. Villarreal points out that the deduced size of the Last Universal Common Ancestor
(LUCA) to eukaryotic and prokaryotic cells is on the order of 300 genes – no bigger than a
large virus – and provides some very compelling arguments for viruses having provided some
of the distinctive genetic elements that distinguish cells of the eukaryotic and prokaryotic
kingdoms. In such a scheme, precursors to both viruses and cells originated in pre-biotic
environment hypothesized to provide the chemical origin of biochemical reactions leading to
cellular life.
At the level explored here, it is probably not that useful to expend great efforts to be more
definitive about virus origins beyond their functional relationship to the cell and organism they
infect. The necessarily close mechanistic relationship between cellular machinery and the
genetic manifestations of viruses infecting them makes viruses important biological entities, but
it does not make them organisms. They do not grow, they do not metabolize small molecules
for energy, and they only “live” when in the active process of infecting a cell and replicating
in that cell. The study of these processes, then, must tell as much about the cell and the organism as it does about the virus. This makes the study of viruses of particular interest to biologists
of every sort.
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BASIC VIROLOGY PART I VIROLOGY AND VIRAL DISEASE
DNA Pol delta
Human
Drosophila
Yeast
DNA Pol
alpha
Algae/protist/plasmodium
lower eukaryotes
and their viruses
Protists/lower
eukaryotes
Mouse
HHV-6
HHV-7
Archaea
Pol II (b)
Rice
Yeast
Mouse
Human
Herpesviruses
HCMV
EBV
phage T4
VZV
HHV-8
E.coli
Pol II
Plasmodium
HSV-2
HSV-1
Vaccinia
Archaea
Pol ll (a)
Variola
Poxviruses
Baculoviruses
Fig. 1.2 A phylogenetic tree of selected eukaryotic and archaeal species along with specific large DNA-containing viruses based upon sequence
divergence in conserved regions of DNA polymerase genes. (Figure based upon Villarreal and DeFilippis. A hypothesis for DNA viruses as the origin
of eukaryotic replication proteins. Journal of Virology 2000;74:7079–7084.)
Viruses have a constructive as well as destructive impact on society
Often the media and some politicians would have us believe that infectious diseases and viruses
are unremitting evils, but to quote Sportin’ Life in Gershwin’s Porgy and Bess, this “ain’t necessarily so.” Without the impact of infectious disease, it is unlikely that our increasingly profound
understanding of biology would have progressed as it has. As already noted, much of our
understanding of the mechanisms of biological processes is based in part or in whole on research
carried out on viruses. It is true that unvarnished human curiosity has provided an understanding of many of the basic patterns used to classify organisms and fostered Darwin’s intellectual
triumph in describing the basis for modern evolutionary theory in his Origin of Species. Still,
focused investigation on the microscopic world of pathogens needed the spur of medical necessity. The great names of European microbiology of the nineteenth and early twentieth centuries
– Pasteur, Koch, Ehrlich, Fleming, and their associates (who did much of the work with which
their mentors are credited) – were all medical microbiologists. Most of the justification
for today’s burgeoning biotechnology industry and research establishment is medical or
economic.
Today, we see the promise of adapting many of the basic biochemical processes encoded by
viruses to our own ends. Exploitation of viral diseases of animal and plant pests may provide
CHAPTER 1 INTRODUCTION
– THE IMPACT OF VIRUSES ON OUR VIEW OF LIFE
a useful and regulated means of controlling such pests. While the effect was only temporary
and had some disastrous consequences in Europe, the introduction of myxoma virus – a
pathogen of South American lagomorphs (rabbits and their relatives) – had a positive role in
limiting the predations of European rabbits in Australia. Study of the adaptation dynamics of
this disease to the rabbit population in Australia taught much about the coadaptation of host
and parasite.
The exquisite cellular specificity of virus infection is being adapted to generate biological
tools for moving therapeutic and palliative genes into cells and organs of individuals with
genetic and degenerative diseases. Modifications of virus-encoded proteins and the genetic
manipulation of viral genomes are being exploited to provide new and (hopefully) highly specific prophylactic vaccines as well as other therapeutic agents. The list increases monthly.
Viruses are not the smallest self-replicating pathogens
Viruses are not the smallest or the simplest pathogens able to control their self-replication in a
host cell – that distinction goes to prions. Despite this, the methodology for the study of viruses
and the diseases they cause provides the basic methodology for the study of all subcellular
pathogens.
By the most basic definition, viruses are composed of a genome and one or more proteins
coating that genome. The genetic information for such a protein coat and other information
required for the replication of the genome are encoded in that genome. There are genetic variants of viruses that have lost information either for one or more coat proteins or for replication
of the genome. Such virus-derived entities are clearly related to a parental form with complete
genetic information, and thus, the mutant forms are often termed defective virus particles.
Defective viruses require the coinfection of a helper virus for their replication; thus, they
are parasitic on viruses. A prime example is hepatitis delta virus, which is completely dependent
on coinfection with hepatitis B virus for its transmission.
The hepatitis delta virus has some properties in common with a group of RNA pathogens
that infect plants and can replicate in them by, as yet, obscure mechanisms. Such RNA molecules, called viroids, do not encode any protein, but can be transmitted between plants by
mechanical means and can be pathogens of great economic impact.
Some pathogens appear to be entirely composed of protein. These entities, called prions,
appear to be cellular proteins with an unusual folding pattern. When they interact with normally folded proteins of the same sort in neural tissue, they appear to be able to induce abnormal
refolding of the normal protein. This abnormally folded protein interferes with neuronal cell
function and leads to disease. While much research needs to be done on prions, it is clear that
they can be transmitted with some degree of efficiency among hosts, and they are extremely
difficult to inactivate. Prion diseases of sheep and cattle (scrapie and “mad cow” disease)
recently had major economic impacts on British agriculture, and several prion diseases (kuru
and Creutzfeldt–Jacob disease [CJD]) affect humans. Disturbingly, passage of sheep scrapie
through cattle in England has apparently led to the generation of a new form of human disease
similar to, but distinct from, CJD.
The existence of such pathogens provides further circumstantial evidence for the idea that
viruses are ultimately derived from cells. I…

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