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    Basic Virology

    Third

    Edition

    Edward K. Wagner

    Department of Molecular Biology and Biochemistry

    University of California Irvine

    Mart inezJ. 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

    Blackwell

    Publishing

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    Brief Contents

    Preface xxi

    Acknowledgments xx ix

    P A R T I V I R O L O G Y A N D V I R A L D IS E A S E 1

    Chapter 1 Intro duct ion Th e Impact of Viruses on O ur View of Life 3

    Chapter 2 An Ou tline of Virus Replication and Viral Pathogenesis 15

    Chapter 3 Virus Disease in Population s and Individual Animals 27

    Chapter 4 Patterns of Some Viral Diseases of H um ans 41 *

    PART I I BASIC PROPE RTIES OF VIRUSES A N D V IR U S -

    CELL INT ER AC TIO N 63

    Chapter 5 Virus Struc ture and Classification 65

    Chapter 6 The Beginning and End of the Virus Replication Cycle 79

    Chapter 7 Ho st Im m une Response to Viral Infection - Th e Na ture of the Vertebrate

    Imm une Response 97

    Chapter 8 Strategies to Protect Against and Co mb at Viral Infection 119

    PART I I I W O R K IN G W IT H V IRUS 145

    Chapter 9 Visualization and Enu me ration of Virus Particles 147

    Chapter 10 Replicating and Me asuring Biological Activity of Viruses 155

    Chapter 11 Physical and Chemical M anipu lation of the Structural Com pon ents of

    Viruses 173

    Chapter 12 Characterization of Viral Products Expressed in the Infected Cell 193

    Chapter 13 Viruses Use Cellular Processes to Express their Genet ic

    Information 213

    P AR T IV R E P L I C A T I O N P A T T E R N S O F S P E C I F I C

    VIRUSES 243

    Chapter 14 Replication of Positive-sense RN A Viruses 245

    Chapter 15 Replication Strategies of RNA Viruses Requ iring RNA -directed m RNA

    Transcriptio n as the First Step in Viral Gene Expression 273

    Chapter 16 Replication Strategies of Small and Medium -sized D N A Viruses 303

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    Contents

    Preface xxi

    Preface to the second edition xxii

    Preface to the third editio n xxii

    Text organization xxiii

    Specific features of this text designed to aid instructors and

    students in pursuin g topics in greater depth xxvi

    Dept h of coverage xxvi

    Sources for further study xxvi

    The Intern et xxvii

    Chap ter outlines xxvii

    Case studies xxvii

    Review mate rial xxvii

    Glossary xxvii

    Acknowledgments xxix

    PART I

    CHAPTER 1

    VIRO LOG Y AN D V IRAL DISEASE 1

    Introduc tion - The Impact of Viruses on Ou r View of Life 3

    Th e science of virology 3

    The effect of virus infections on the host organism and populations

    viral pathogenesis, virulence, and epidemiology 4

    Th e interaction between viruses and their hosts 6

    Th e history of virology 7

    Examples of the impact of viral disease on hum an history 8

    Examples of the evolutionary impact of the virus-host

    interaction 9

    Th e origin of viruses 9

    Viruses have a constructive as well as destructive impact on

    society 12

    Viruses are not the smallest self-replicating path ogen s 13

    Que stions for Cha pter 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

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    VI I I

    CONTENTS

    CHAPTER 3

    CHAPTER 4

    Initial stages of infection - entry of the virus into the host 20

    Th e incuba tion period and spread of virus throug h the host 21

    Multiplication of virus to high levels

    occurrence of disease

    symptoms 23

    The later stages of infection

    the imm une 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

    Virus Disease in Popu lations and Individual Animals 27

    Th e nature of virus reservoirs 27

    Some viruses with huma n reservoirs 28

    Some viruses with verteb rate reservoirs 30

    Viruses in popula tions 30

    Viral epidemiology in small and large popula tions 30

    Factors affecting the control of viral disease in populations 33

    Anim al models to study viral pathogenesis 34

    A mouse model for studying poxvirus infection and spread 35

    Rabies: where is the virus durin g its long incubation period? 37

    Herpes simplex virus latency 37

    Mu rine models 39

    Rabbit models 40

    Guinea pig models 40

    Questions for Chapter 3 40

    Patterns o f Some Viral Diseases of Humans 41

    The dynamics of hum an-viru s 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

    virushost dynam ics 44

    Viral diseases leading to persistence of the virus in the host are

    generally associated with viruses having long associations with

    hum an populations 44

    Viral diseases associated with acute, severe infection are

    suggestive of zoonoses 48

    Patte rns of specific viral diseases of hu m ans 49

    Acu te infections followed by virus clearing 49

    Colds and respiratory infections 49

    Influenza 49

    Variola 49

    Infection of an accidental target tissue leading to permane nt

    dam age despite efficient clearing 50

    Persistent viral infections 50

    Papilloma and polyomavirus infections 50

    Herpesvirus infections and latency 52

    Ot her complications arising from persistent infections 52

    Viral and subviral diseases with long incuba tion periods 53

    Rabies 53

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    CONTENTS IX

    PART II

    CHAPTER 5

    CHAPTER 6

    CHAPTER 7

    HIV-AIDS 53

    Prion diseases 54

    Some viral infections targetin g specific organ systems 54

    Viral infections of nerve tissue 54

    Examples of viral encep halitis with grave progno sis 55

    Rabies 55

    Herpes encephalitis 55

    Viral encepha litis 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

    Que stions for Cha pter 4 58

    Problems for Part I 59

    Add itional Reading for Part I 61

    BASIC PROPERTIES OF VIRUSES A N D

    V I R U S C E L L I N T E R A C T I O N

    63

    Virus Structure and Classification 65

    The features of virus 65

    Viral genomes 69

    Viral capsids 69

    Viral envelopes 72

    Classification schemes 72

    Th e Baltim ore scheme of virus classification 75

    Disease-based classification schemes for viruses 75

    Th e virosphere 77

    Que stions for Chap ter 5 78

    The Beginning and End o f the Virus Replication Cycle 79

    Ou tline of the virus replication cycle 79

    Viral entry 80

    Animal virus entry into cells the role of the cellular receptor 80

    Mech anisms of entry of nonenve loped viruses 83

    En try of enveloped viruses 84

    Entry of virus into plant cells 85

    Injection of bacteriophage DNA into scherichia coli 87

    Nonspecific methods of introd ucing 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

    Question s for Chap ter 6 96

    Host Immune Response to Viral Infection - The Nature of the

    Verteb rate Imm une Response 97

    The innate imm une response - early defense against pathogens 98

    Toll-like receptors 99

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    CONTENTS

    Defensins 99

    Th e adaptive imm un e response and the lymp hatic system 100

    Tw o pathways of helper T response - the fork in the road 101

    The immunological structure of protein 102

    Role of the antigen-presenting cell in initiation of the immune

    response 104

    Clonal selection of im mu ne reactive lympho cytes 107

    Immu ne memory 108

    Co mp lem ent-m ediate d cell lysis 108

    Con trol and dysfunction of imm unity 108

    Specific viral responses to host immu nity 109

    Passive evasion of immunity antigenic drift 110

    Passive evasion of immunity internal sanctuaries for

    infectious virus 110

    Passive evasion of immunity imm une tolerance 110

    Active evasion of imm unity - imm unosuppression 111

    Active evasion of imm unity - blockage of M H C antigen

    presentation 111

    Con sequences of imm un e suppression to virus infections 112

    Measurem ent of the imm une reaction 112

    Measurem ent of cell-mediated (T-cell) imm unity 112

    Measurement of antiviral antibody 112

    Enzym e-linked imm uno sorb ent assays (ELISAs) 113

    Neu tralization tests 114

    Inhibition of hemagg lutination 114

    Complement fixation 115

    Questions for Chap ter 7 ^117

    C H A P T E R 8 Strategies to Protect Against and Com bat Viral Infection 119

    Vaccination

    induction of immunity to prevent virus

    infection 120

    An tiviral vaccines 120

    Smallpox and the history of vaccination 120

    Ho w a vaccine is produced 122

    Live-virus vaccines 122

    Killed-virus vaccines 123

    Reco mb inant virus vaccines 124

    Capsid and subu nit vaccines 124

    DN A vaccines 125

    Edible vaccines 125

    Problem s with vaccine prod uctio n and use 125

    Eu kary otic cell-based defenses against virus replication 126

    Interferon 126

    Ind uctio n of interferon 127

    Th e antiviral state 128

    Me asurem ent of interferon activity 128

    O th er cellular defenses against viral infection 130

    Small RN A-based defenses 130

    Enzym atic modification of viral genom es 131

    Antiviral drugs 131

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    CONTENTS

    X I

    PART

    III

    CHAPTER9

    CHAPTER

    1

    Targeting antiviral drugsto specific featuresof the virus

    replication cycle

    131

    Acyclovir

    and the

    herpesviruses

    132

    Blocking influenza virus entryandvirus maturation 132

    Chemotherapeutic approachesfor HIV 134

    Multiple drug therapies toreduceoreliminate mutationto

    drug resistance

    134

    Other approaches

    135

    Bacterial antiviral systems restriction endonucleases 135

    QuestionsforChapter 8 136

    Problems

    for

    Part

    II 139

    Additional Reading

    for

    Part

    II 143

    WORKING WITH VIRUS 145

    VisualizationandEnumerationofVirus 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 meth od

    for

    visualization

    of

    viruses

    and

    infected cells, potentially

    in

    real

    time

    151

    Indirect methods for coun ting virus particles 152

    Questions forChapter 9 154

    Replicatingand Measuring Biological ActivityofViruses 155

    Cell culture techniques

    156

    Maintenanceof bacterial cells 156

    Plant cell cultures 156

    Culture

    of

    animal

    and

    human cells

    157

    Maintenance

    of

    cells

    in

    culture

    157

    Types

    of

    cells

    157

    Lossof contact inhibition ofgrowth andimmortalizationof

    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 maintenanceof the intra-and intercellular

    environment 162

    Virus-mediated cytopathology changes

    in the

    physical

    appearance

    of

    cells

    163

    Virus-mediated cytopathology changesin thebiochemical

    propertiesofcells 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 titerstoquantitatively control infection conditions 166

    Examples

    of

    plaque assays

    167

    Statistical analysis

    of

    infection

    168

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    X I I CONTENTS

    CHAPTER 11

    CHAPTER 12

    Dilution endpo int methods 169

    The relation between dilution endpoint and infectious units of

    virus 169

    Ques tions for Chap ter 10 170

    Physical and Chemical Manipulation of the Structural

    Com ponents of Viruses 173

    Viral structural proteins 173

    Isolation of structural proteins of the virus 174

    Size fractionation of viral structu ral prote ins 176

    Det erm ining 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

    Sequen ce analysis of viral genom es 180

    Mea suring 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 geno me 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

    PC R as an epidemiological tool 190

    Que stions for Chap ter 11 191

    Characterization of Viral Products Expressed in the Infected

    Cell 193

    Cha racteri zation of viral prote ins in the infected cell 193

    Pulse labeling of viral proteins at different times following

    infection 194

    Use of imm une reagents for study of viral proteins 195

    Work ing with antibodies 196

    Dete ction of viral proteins using immuno fluorescence 198

    Related methods for detecting antibodies bound to

    antigens 201

    Detecting and characterizing viral nucleic acids in infected

    cells 205

    Dete cting the synthesis of viral genomes 205

    Characterization of viral mR NA expressed durin g 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 Chap ter 12 212

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    CONTENTS

    XIII

    CHAPTER 13

    PART IV

    CHAPTER 14

    Viruses Use Cellular Processes to Express Their Genetic

    Information 213

    Prokaryotic DNA replication is an accurate enzymatic model for

    the process generally 21 5

    Th e replication of eukaryotic DN A 216

    Th e replication of viral DN A 21 7

    Th e effect of virus infection on host D N A replication 217

    Expression of mR NA 217

    Prokaryotic transcription 219

    Prokaryotic RNA polymerase 219

    The prokaryotic promoter and initiation of

    transcription 220

    Con trol of prokaryotic initiation of transcription 220

    Term ination of prokaryotic transcription 221

    Eukaryotic transcription 221

    Th e promo ter and initiation of transcription 221

    Con trol of initiation of eukaryotic transcription 223

    Processing of precursor mR NA 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

    Th e mechanism of protein synthesis 232

    Euk aryotic translation 233

    Prokaryotic translation 234

    Virus-ind uced changes in translation 236

    Questions for Chap ter 13 236

    Problems for Part III 239

    Additional Reading for Part III 241

    R E P L I C A T I O N

    VIRUSES 243

    PATTERNS OF SPECIF IC

    245

    eplication of Positive-sense RNA Viruses

    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

    Th e poliovirus replication cycle 252

    Picornavirus cytopatholog y and disease 254

    Flavivirus replicatio n 25 6

    Positive-sense RNA viruses encoding more than one translational

    reading frame 257

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    XIV CONTENTS

    Two viral mRNAs are produced in different amounts during

    togavirus infections 258

    Th e viral genome 258

    Th e virus replication cycle 258

    Togavirus cytopatholog y and disease 262

    A somewhat more complex scenario of multiple translational

    reading frames and subgenomic mRNA expression: coronavirus

    replication 263

    Coron avirus replication 264

    Cyto patho logy and disease caused by coronaviruses 266

    Replication of plant viruses with RNA genomes 267

    Viruses with one genome segment 268

    Viruses with two genom e segments 268

    Viruses with three genom e segments 269

    Replication of bacteriophage with RNA genomes 269

    Regulated translation of bacteriophage mR NA 269

    Questions for Chap ter 14 272

    C H A PT

    R 1 5 Replication Strategies o f 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 genom e 275

    Generation, capping, and polyadenylation of mR NA 276

    Gen eration of new negative-sense virion RNA 278

    Mech anism of host shutoff by vesicular stomatitis virus 279

    Cyto patho logy and diseases caused by rhabdoviruses 280

    Paramyxoviruses 280

    Pathogenesis of paramyxoviruses 280

    Filoviruses and their pathogenesis 28 2

    Bornaviruses 282

    Influenza viruses - negative-sense RN A viruses with a

    multipartite genome 283

    Involvem ent 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

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    CONTENTS

    XV

    CHAPTER 16

    CHAPTER 17

    Reovirus structu re 292

    Reovirus replication cycle 294

    Pathogenesis 295

    Subviral pathog ens 29 5

    Hep atitis delta virus 296

    Viroids 297

    Prions 298

    Que stions for Ch apter' 15 301

    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 30 5

    Replication of SV40 virus - the model polyomavirus 305

    Th e SV40 genome and genetic map 309

    Productive infection by SV40 310

    Abortive infection of cells nonpermissive for SV40

    replication 312

    Replication of papillomaviruses 31 4

    The HPV -16 genome 316

    Virus replication and cytopatholog y 316

    Replication of adenoviruses 319

    Physical properties of adenovirus 319

    Capsid structure 319

    Th e adenovirus genome 319

    Th e adenovirus replication cycle 319

    Early events 31 9

    Adenovirus DN A replication 321

    Late gene expression 321

    VA transcription and cytopathology 321

    Transfo rmation of nonperm issive cells by adenovirus 323

    Replication of some single-stranded D N A viruses 32 3

    Replication of parvoviruses 323

    Dependovirus DNA integrates in a specific site in the host cell

    genome 324

    Parvoviruses have potentially exploitable therapeutic

    applications 325

    DN A viruses infecting vascular plants 325

    Geminiviruses 325

    Single-stranded DNA bacteriophage OX174 packages its genes

    very comp actly 326

    Questions for Chapter 16 328

    Replication of Some Nuclear-Replicating Eukaryotic DNA Viruses

    wi th Large Genomes 331

    Herpesvirus replication and latency 332

    Th e herpesviruses as a group 332

    Gen etic complexity of herpesviruses 33 3

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    XVI CONTENTS

    Co mm on features of herpesvirus replication in the host 33 3

    Th e replication of the prototypical alpha-herpesvirus -

    HSV 334

    The HSV virion 334

    Th e viral genome 334

    HS V productive infection 338

    HS V latency and LAT 347

    HS V transcription during latency and reactivation 348

    Ho w do LA T and other specific HS V genes function - may be

    to accom mo date 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 genom e replication 356

    Pathogenesis 356

    Imp ortance of baculoviruses in biotechnolo gy 356

    Questions for Chapter 17 357

    C H A P T E R 1 8 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

    T he poxvirus replication cycle 361

    Early gene expression 363

    Geno me replication 363

    Interm ediate and late stages of replication 363

    Pathogenesis and history of poxvirus infections 36 4

    Is smallpox virus a poten tial biological terror weapon? 364

    Replication of large DN A-con taining bacteriophages 365

    Co mp onen ts of large DN A-co ntaining phage virions 365

    Replication of phage T7 367

    The genome 367

    Phage-controlled transcription 367

    Th e practical value of T 7 367

    T4 bacterioph age: the basic mod el for all DN A viruses 367

    The T4 genome 368

    Regulated gene expression dur ing T 4 replication 369

    Capsid ma turatio n and release 370

    Replication of phage

    X:

    a simple model for latency and

    reactivation 370

    The phage Xgenome 372

    Phage

    X

    gene expression imm ediately after infection 37 2

    Biochemistry of the decision between lytic and lysogenic

    infection in

    E. coli

    375

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    CONTENTS

    XVII

    CHAPTER 19

    CHAPTER 20

    CHAPTER 21

    A group of algal viruses shares features of its genome structure with

    poxviruses and bacteriophages 376

    Que stions for Cha pter 18 377

    Retroviruses: Conv erting RNA to DNA 381

    Retrovirus families and their strategies of replication 382

    Th e molecular biology of retrovirus 383

    Retrovirus structural proteins 383

    Th e retrovirus genom e 384

    Gene tic maps of representative retroviruses 386

    Replication of retroviruses: an outline of the replication

    process 386

    Initiation of infection 386

    Capsid assembly and ma turation 389

    Action of reverse transcriptase and RNase-H in synthesis of

    cDNA 389

    Virus gene expression, assembly, and ma turatio n 391

    Transcription and translation of viral mRN A 391

    Capsid assembly and morphog enesis 391

    Mechan isms of retrovirus transformation 392

    Transformation through the action of

    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

    Th e relationship between transposable elements and viruses 397

    Qu estions for Cha pter 19 397

    Human Immunodeficiency Virus Type 1 (HIV-1) and Related

    Lentiviruses 399

    HI V- 1 and related lentiviruses 399

    The origin of HIV -1 and AIDS 399

    HI V- 1 and lentiviral replication 400

    Destruction of the imm une system by HIV-1 406

    Questions for Chapter 20 411

    Hepadnaviruses: Variations on the Retrovirus Theme 413

    Th e virion and the viral genom e 413

    Th e viral replication cycle 41 5

    The pathogenesis of hepatitis B virus 415

    A plant hepadna virus : cauliflower mosaic virus 416

    Geno me structure 416

    Viral gene expression and genom e replication 416

    Th e evolutionary origin of hepadnaviruses 417

    Questions for Chapter 21 419

    Problems for Part IV 421

    Add itional Reading for Part IV 429

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    XVII I

    CONTENTS

    PART V

    CHAPTER 22

    CHAPTER 23

    CHAPTER 24

    V I R U S E S : N E W A P P R O A C H E S A N D N E W

    PROBLEMS 433

    The Mo lecular Genetics of Viruses 435

    M utatio ns in genes and resulting changes to proteins 437

    Analysis of mu tation s 43 8

    Complementation 438

    Recombination 439

    Isolation of mutan ts 440

    Selection 440

    HS V thymidine kinase - a portable selectable marker 440

    Screening

    441

    441 tool kit for molecular virologists

    Viral genomes 441

    Locating sites of restriction endonuclease cleavage on the viral

    genome - restriction mapp ing 442

    Clon ing vectors 44 3

    Cloning of fragments of viral genomes using bacterial

    plasmids 444

    Cloning using phage X 449

    Clonin g single-stranded DN A with bacteriophage M 13 451

    DN A animal virus vectors 451

    RN A virus expression systems 45 3

    Defective virus particles 45 4

    Directed mutagenesis of viral genes

    Site-directed mutagenesis 45 6

    Generation of recombinant viruses

    Bacterial artificial chromosomes

    Questions for Chapter 22 461

    454

    456

    458

    Molecu lar Pathogenesis 463

    An introd uctio n to the study of viral pathogenesis 46 3

    Animal models 464

    Choo sing a model: natural host vs. surrogate models 464

    Dev elopm ent of new models: transgenic animals 464

    Hyb rid models: the SC ID-h u mouse 464

    Considerations regarding the hum ane use of animals 465

    Meth ods for the study of pathogenesis 466

    Assays of virulenc e 46 6

    Analysis of viral spread within the host 46 7

    Resolving the infection to the level of single cells 47 0

    Characterization of the host response 470

    Imm unolog ical assays 470

    Use of transgenic mice to dissect critical components of the host

    im mu ne response that mo dulate the viral infection 471

    Question for Chap ter 23 471

    Viral Bioinformatics and Beyond

    Bioinformatics 473

    Bioinformatics and virology 47 3

    Biological databases 47 4

    473

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    CONTENTS X IX

    CHAPTER 25

    APPENDIX

    Primary databases 47 4

    Secondary databases 475

    Com posite databases 475

    Oth er databases 476

    Biological applications 47 6

    Similarity searching tools 476

    Protein functional analysis 478

    Sequ ence analysis ,478

    Structural modeling 478

    Structural analysis 47 8

    Systems biology and viruses 479

    Viral internet resources 481

    Questions for Chap ter 24 484

    Viruses and the Future - Problems and Promises 485

    Clouds on the horizon emerging disease 48 5

    Sources and causes of emergen t virus disease 488

    Th e threat of bioterrorism 489

    What are the prospects of using medical technology to eliminate

    specific viral and othe r infectious diseases? 49 0

    Silver linings viruses as therape utic agents 49 0

    Viruses for gene delivery 49 1

    Using viruses to destroy other viruses 49 3

    Viruses and nanotechnology 49 3

    Th e place of viruses in the biosphere 49 4

    W hy study virology? 494

    Questions for Chap ter 25 495

    Problems for Part V 49 7

    Additional Reading for Part V 499

    Resource Center 501

    Books of historical and basic value 501

    Books on virology 501

    Mo lecular biology and biochem istry texts 503

    Detailed sources 50 3

    Sources for experimental protocols 503

    Th e Internet 504

    Virology sites 504

    Important websites for organizations and facilities of

    interest 505

    Technical Glossary 507

    Index 533