Desk Encyclopedia of General Virology

Front Cover......Page 1
Desk Encyclopedia of General Virology......Page 2
Copyright Page......Page 5
Editors-In-Chief......Page 6
Associate Editors......Page 8
Preface......Page 10
Contributors......Page 12
Contents......Page 16
General Topics......Page 20
Discovery......Page 22
Phage Typing and Ecology......Page 23
Phages as Tools and Products of Molecular Biology......Page 24
Lysogeny......Page 26
Varied and Interesting......Page 27
Applied Research......Page 28
Prehistory......Page 29
The Biological Age......Page 30
The Biochemical/Biophysical Age......Page 31
The Molecular Biology Age......Page 32
Further Reading......Page 33
Yellow Fever Virus......Page 34
The Cultivation of Animal Viruses......Page 35
Tumor Virology......Page 36
The Future......Page 37
The Discovery of Viruses......Page 38
What Is an Organism?......Page 39
The Nature of Viruses......Page 40
Fitness and Viral Evolution......Page 41
Glossary......Page 42
The Classical View of Virus Origin and Its Consequences......Page 43
Viruses Are Ancient......Page 44
The Reduction Hypothesis......Page 45
The Escape Hypothesis......Page 46
Viruses and the Origin of DNA......Page 47
Conclusions......Page 48
Introduction......Page 49
Replication by the Rolling-Circle Mechanism......Page 50
Structure and folding......Page 52
The Hammerhead Ribozyme......Page 53
The Neurospora crassa versus Ribozyme......Page 54
Further Reading......Page 55
Distinguishing between Abstract Classes and Real Objects......Page 56
What Is a Virus Species?......Page 57
Defining Species as a Taxonomic Class Is Not the Same As Demarcating Individual Viral Species......Page 58
Species Names and How to Write Them......Page 59
Further Reading......Page 60
Scientific Context......Page 61
Common Assumptions......Page 62
The error catastrophe......Page 63
High per-base mutation rates......Page 64
Evolutionary parallelisms and convergences......Page 65
Error catastrophe and lethal mutagenesis......Page 66
Further Reading......Page 67
Introduction......Page 68
Data......Page 69
Annotation......Page 72
Access (Searching for Information)......Page 73
Output (Utilizing Information)......Page 74
Errors......Page 75
Major repositories of biological information......Page 76
Nucleotide sequence data......Page 82
Functional motifs and orthologous clusters......Page 83
Further Reading......Page 84
Tree Definitions......Page 85
Phylogenetic Analysis......Page 86
Applications of Phylogeny in Virology......Page 87
Further Reading......Page 88
Introduction......Page 89
Virus Evolution as a Basic Science......Page 90
Error-Prone Replication and Quasispecies......Page 91
Error Catastrophe, Sequence Space......Page 92
Virus-Host Congruence and RNA Stability......Page 93
Tools......Page 94
Patterns of DNA Virus Evolution: Tailed Phage......Page 95
Large Eukaryotic DNA Viruses......Page 96
Endogenous and Autonomous Retroviruses......Page 97
Further Reading......Page 98
Introduction......Page 99
Organization and Structure of ICTV......Page 100
Polythetic Classification and Demarcation Criteria......Page 109
Virus Taxa Descriptions......Page 110
A New Virus Taxon: The Virus Species......Page 111
Species......Page 112
Further Reading......Page 113
Sequence Comparison Methods......Page 114
The Principle of PASC......Page 115
Applications of PASC......Page 116
Advantages of PASC Compared to Other Methods......Page 117
Limitations of PASC......Page 118
Relevant Website......Page 119
Abberant Prion Protein Metabolism Is the Central Feature of Prion Disease......Page 120
Human Prion Diseases Are Biologically Unique......Page 121
Structural Properties of PrPSc......Page 122
Prion Disease Pathogenesis......Page 123
Prion Strains......Page 124
Future Perspective......Page 125
Historical Perspective......Page 126
Viruses as Bioweapons......Page 127
Pandemic Influenza......Page 129
Further Reading......Page 130
Virions......Page 132
Virus Structures......Page 134
Quasi-Equivalent Virus Capsids......Page 135
Picorna-Like Virus Capsids......Page 136
Virus Particle Maturation......Page 138
Concluding Remarks......Page 141
Introduction......Page 142
T=1 Icosahedral Particles......Page 143
Helical Particles......Page 145
T=7 Icosahedral Particles......Page 149
T=25 and Larger Icosahedral Particles: The Double-Barrel Subunit......Page 150
Other Icosahedral Particles with Uncommon Architectures......Page 153
Further Reading......Page 154
Negative Staining......Page 155
Advantages and limitations......Page 158
Metal Shadowing......Page 159
Application: Antibody labeling......Page 160
CEMOVIS: Cryo-EM of vitreous sections......Page 161
Image Analysis......Page 162
Further Reading......Page 163
Cryo-Specimen Preparation......Page 164
Icosahedral Reconstruction......Page 165
Interpreting CryoEM Single-Particle Density Maps......Page 167
Asymmetric Reconstruction of an Icosahedral Particle with a Unique Vertex......Page 168
Low-Dose Cryoelectron Tomographic Imaging of Virus Particles......Page 169
Viral Genome Organization......Page 171
Virus-Antibody and Cell Receptor Complexes......Page 172
Further Reading......Page 174
Architecture of Viruses......Page 175
Atomic Structure of Spherical Viruses......Page 176
Assembly......Page 177
Further Reading......Page 178
Viral Envelope......Page 179
Alphavirus virion structure......Page 180
Alphavirus assembly and budding......Page 181
Flavivirus virion structure......Page 183
Conclusion......Page 184
Further Reading......Page 185
History and Overview......Page 186
Assembly Pathways......Page 188
Assembly and maturation of icosahedral arrays......Page 189
Symmetry disruptions and symmetry mismatches......Page 190
Scaffolds, templates, and jigs......Page 191
Protein cross-linking......Page 192
Further Reading......Page 193
General Considerations......Page 194
dsDNA Packaging......Page 195
Concluding Remarks......Page 199
Introduction......Page 200
Viral Membrane Proteins......Page 201
Viral Fusion......Page 202
Membrane Synthesis and Viral Assembly......Page 205
Further Reading......Page 206
History and Classification......Page 207
Genome Organization......Page 208
Typical NCLDV Core Genes in Mimivirus......Page 210
DNA synthesis......Page 211
Morphology......Page 212
Particle-Associated mRNAs......Page 213
Further Reading......Page 214
Nucleic Acids......Page 216
Recombination in DNA Viruses......Page 218
Recombination in RNA Viruses......Page 221
Defective-Interfering RNAs......Page 224
Summary and Conclusions......Page 225
Glossary......Page 226
Classification......Page 227
Satellite Viruses......Page 228
dsRNA Satellites......Page 231
Subgroup 3: Small, circular ssRNA satellites......Page 232
Satellite DNAs......Page 233
Sequence Variation and Evolution......Page 234
Further Reading......Page 235
History......Page 236
Structure......Page 237
Transposition mechanism......Page 238
SINE structure......Page 239
Origin......Page 240
Retrotransposon Effects on the Genome......Page 241
Retrotransposon Content......Page 242
Effect on Genes......Page 243
Further Reading......Page 244
Generation of DI Genomes......Page 245
Defective Interfering versus Defective Viruses......Page 246
Biological Effects......Page 247
Future Perspectives......Page 248
RNA Interference......Page 249
RNAi Components and Function: Dicers, the Sensors of dsRNA and Initiators of siRNA Production......Page 250
Argonaute Proteins and RNAi......Page 251
Viruses and RNAi......Page 252
Use of RNAi for Disease Control......Page 253
Mosquitoes, RNAi, and Arboviruses......Page 254
Viruses as Vectors in Gene Therapy......Page 255
Introduction......Page 256
Retrovirus Vectors......Page 257
Adeno-Associated Virus Vectors......Page 258
Clinical Trials......Page 259
Further Reading......Page 260
Virus Infection......Page 262
The Identification of Virus Receptors......Page 264
Heparan Sulfate and Other Glycosaminoglycans......Page 265
Immunoglobulin Superfamily Proteins......Page 266
Co-Receptors for Infection......Page 267
Summary......Page 268
Glossary......Page 269
Cell-Wall Penetration......Page 270
Genome Delivery Mechanisms of Phages......Page 271
Icosahedral dsDNA Bacterial Viruses with an Internal Membrane......Page 272
Filamentous ssDNA Bacterial Viruses......Page 273
Further Reading......Page 274
Introduction......Page 275
Biosynthesis of Fusion Proteins......Page 276
Structure of the Low pH-Activated Conformation of Hemagglutinin HA2......Page 277
Class I-Mediated Membrane Fusion......Page 278
Cooperativity of Fusion Proteins......Page 279
Structure of the Native Fusion Protein......Page 280
Class II-Mediated Membrane Fusion......Page 281
Fusion Protein Cooperativity in Membrane Fusion......Page 282
The Fusion Loops......Page 283
Glossary......Page 284
Attachment......Page 285
Entry......Page 286
Group I: Double-Stranded DNA......Page 287
Assembly......Page 288
Release......Page 289
Acute, Persistent, and Latent Infection......Page 290
Pathogenesis of Chronic Infection......Page 292
Immune Control......Page 293
Immune Regulation and Immunopathology......Page 294
Immunomodulation......Page 295
Chronic Disease Manifestations......Page 296
Further Reading......Page 297
Cellular Death Pathways......Page 298
Death Receptor Signaling......Page 299
Viral Caspase Regulators......Page 301
Virus Recognition by Cellular PRRs......Page 304
Yeast Viruses Induce Yeast Programmed Cell Death......Page 305
Entry......Page 306
Spread......Page 307
Shedding and Transmission......Page 308
Viral Genetic Determinants of Virulence......Page 309
Host Determinants of Susceptibility and Resistance......Page 310
The Major Breakthrough......Page 311
Impetus from the Challenge of HIV......Page 314
Definition of Selective Activity Index......Page 315
HIV fusion inhibitors......Page 316
Viral DNA/RNA polymerase inhibitors......Page 317
Antiviral Prodrugs......Page 318
Mechanism of Antiviral Action......Page 319
Virus Latency......Page 320
HCV......Page 321
Further Reading......Page 322
Principles of Serological Assays......Page 323
Neutralizing Antibody Assay......Page 324
Immunoassays......Page 325
Lateral-Flow and Latex Tests......Page 326
Nucleic Acid Detection Assays......Page 327
Motivation for New Diagnostic Methods......Page 330
Microarray Design for Viral Detection......Page 331
Bioinformatics......Page 332
Real-World Applications: Research and Clinical......Page 333
Glossary......Page 334
Notifications......Page 335
Serological Surveillance......Page 336
Completeness......Page 337
Time......Page 338
Interpretation......Page 339
Global and International Surveillance......Page 340
Relevant Websites......Page 341
Immune Responses......Page 342
Cellular Innate Immunity......Page 344
Interferon Induction......Page 345
Type I IFN Signaling......Page 347
Indirect Antiviral Effects of Type I IFNs......Page 348
Further Reading......Page 349
The IFN-alpha/beta System......Page 350
Pathogen-Associated Molecular Patterns and Pattern-Recognition Receptors......Page 351
Signaling Leading to IFN-alpha/beta Production......Page 352
Targeting Components of the PRR Signaling Pathways......Page 353
Viruses Targeting Multiple Aspects of the IFN System......Page 354
Cellular Components of Innate Immunity to Virus Infection......Page 355
Further Reading......Page 356
Antigen-Presenting Cells......Page 357
MHC-I Antigen Presentation......Page 359
MHC-II Antigen Presentation......Page 360
Viral Subversion of Antigen Presentation......Page 361
Glossary......Page 362
Viral Antigenic Sites......Page 363
Continuous and Discontinuous Epitopes......Page 364
Mimotopes......Page 365
Immunogenicity......Page 366
Further Reading......Page 367
Overview of Cytokine Networks......Page 368
IFN-gamma......Page 369
IL-4......Page 370
Chemokines and Chemokine Families......Page 371
Further Reading......Page 372
General Overview......Page 373
T-Cell Receptors......Page 374
Immunodominance......Page 375
Induction of Cell-Mediated Immunity during Viral Infections......Page 376
CD4 T Cells......Page 377
Persistent Viral Infections......Page 378
Immune Evasion......Page 379
Milestones in History......Page 380
Innate Immunity......Page 381
Adaptive Immunity......Page 385
Virus-Neutralizing and Protective Antibodies......Page 388
Antibody-Dependent Enhancement of Viral Diseases......Page 390
Immunoglobulins for Passive Immunization against Human Viruses......Page 391
Veterinary Vaccines......Page 392
Further Reading......Page 394
Influenza A and B Hemagglutinin......Page 395
Influenza C HEF......Page 397
Influenza A Subtype Variation in Antigen Structure......Page 398
Antigenic Variation and Antibody Binding......Page 399
Introduction......Page 400
Types of Vaccines......Page 401
Recombinant Protein Vaccines......Page 402
Rotavirus......Page 403
Viral Vectors......Page 404
Antigenic Variation......Page 405
Influenza Annual Vaccination......Page 406
HIV Approaches......Page 407
Further Reading......Page 408
Introduction......Page 409
Attractiveness of DNA-Based Vaccines......Page 410
Limitations and Clinical Applications of DNA Vaccines......Page 411
Vaccine Delivery......Page 412
Glossary......Page 413
Introduction......Page 414
Manufacture......Page 415
Programmatic Factors, Presentation, and Administration......Page 416
Rates of common, mild vaccine reactions......Page 417
Monitoring and Assessment of Vaccine Safety......Page 418
Surveillance of AEFIs......Page 419
Swine flu......Page 420
HIV Infection......Page 421
Relevant Websites......Page 422
Experimental Measurement......Page 423
Antibody-Antigen Binding and Epitope Occupancy on Virions......Page 424
Kinetics......Page 425
Escape and Resistance......Page 426
Further Reading......Page 428
Introduction......Page 429
Immunopathology......Page 432
Further Reading......Page 434
Description and Molecular Biology of Some Viruses......Page 436
Particle Structure......Page 438
Attachment and Entry......Page 439
DNA Replication......Page 440
Assembly and Release......Page 442
Effects on the Host Cell......Page 443
Further Reading......Page 444
Taxonomy and Classification......Page 445
Genome Organization......Page 447
Gene Expression......Page 449
Inhibitors of Apoptosis......Page 450
Origins of Replication......Page 451
Further Reading......Page 452
Life Cycle......Page 453
Infection Cycle......Page 454
DNA Replication......Page 455
Early Gene Expression......Page 460
Viral Structures - Nucleocapsids......Page 461
Viral Structures - BV and ODV Envelopes......Page 462
Further Reading......Page 463
Introduction......Page 464
Molecular Features of CoVs......Page 465
Replication and Transcription of CoV RNA......Page 467
CoV Accessory Proteins......Page 469
Vaccines and Antiviral Drug Development......Page 470
Introduction......Page 472
Structure and Replication of HBV......Page 473
The Surface Protein, HBsAg......Page 474
Hepatitis B e-Antigen, HBeAg......Page 476
Treatment of Chronic Hepatitis B......Page 477
HBV and HCC......Page 478
The Tegument......Page 479
Transcription and DNA Replication......Page 480
General Properties of Transcripts and Promoters......Page 481
DNA replication proteins......Page 483
Structural proteins......Page 485
Latent Infection......Page 486
Further Reading......Page 487
Properties of the Genome......Page 488
Virion Proteins......Page 489
Characterization of Transcription......Page 491
Cytopathology......Page 492
Introduction......Page 493
Genomic Organization and Replication of HIV......Page 494
Role of Cellular Factors in HIV Replication......Page 496
The Regulator of Expression of Virion Proteins (Rev)......Page 497
The HIV-1-Specific Virus Protein U (Vpu)......Page 498
The Multifunctional Nef Protein......Page 499
Introduction......Page 500
Iridovirus Taxonomy......Page 501
Viral Genome......Page 502
Virus Entry......Page 503
Viral DNA Synthesis and Methylation......Page 504
Virion Assembly......Page 505
Effects of Virus Infection on Host Cell Function and Viability......Page 506
History......Page 507
Evolution......Page 508
Tropism and Cell Entry......Page 509
Latent Persistence and Replication......Page 510
Lytic Replication......Page 511
Inhibition of Apoptosis......Page 512
Multicentric Castleman\'s Disease......Page 513
Taxonomy......Page 514
Promoter Sequences......Page 515
Transcription......Page 519
Nucleocapsid (N) Proteins......Page 520
Viral Glycoprotein(s)......Page 521
Viral Entry......Page 522
Viral Assembly and Budding......Page 523
Taxonomy and Phylogeny......Page 524
Virus Structure......Page 526
The Replicase......Page 528
Structural and Accessory Protein Genes......Page 531
Transcription......Page 532
Effect of Nidovirus Infection on the Host Cell......Page 533
Taxonomy......Page 535
Host Range and Geographic Distribution......Page 536
Alphanodavirus Capsids......Page 537
Virion Assembly and Specific Genome Packaging......Page 538
Genome Structure and Coding Potential......Page 539
Replication Complexes......Page 540
Suppression of RNA Silencing by Protein B2......Page 541
Epidemiology and Pathogenesis......Page 542
Classification and Nomenclature......Page 543
Properties of the Viral Genome and Proteins......Page 544
Virus Attachment and Entry......Page 546
Packaging, Assembly, and Release of Virus......Page 547
Reverse Genetics of Influenza Viruses......Page 548
Manifestations of Antigenic Variation......Page 549
Antigenic Variation in Influenza Viruses......Page 550
Mechanism of Antigenic Drift......Page 551
Mechanisms of Neutralization......Page 553
Antibody and Antigenic Variation in HIV-1 Infection......Page 554
The HIV-1 Replicase and the Generation of Diversity/Variation......Page 555
The HIV-1 Envelope Glycoprotein: Variable Loops and Decoys......Page 556
Env Glycosylation and Antibody Recognition......Page 557
Concluding Remarks......Page 558
Genome......Page 559
Life Cycle......Page 560
Maintenance of the Nonproductive Infectious State......Page 561
The Role of E1......Page 562
The Role of E1^E4......Page 563
The Role of E6......Page 564
The Role of E7......Page 565
The Role of L1 and L2......Page 566
Introduction......Page 567
Genome Organization and Replication......Page 568
Structures of Partitivirus Virions......Page 570
Taxonomic and Phylogenetic Considerations......Page 573
Further Reading......Page 574
Taxonomy and Classification......Page 575
Genomes......Page 577
Virus Replication......Page 580
Additional Chlorella Viruses......Page 581
Ecology......Page 582
Relevant Websites......Page 583
Classification......Page 584
Genome Structure and Features......Page 585
Capsid......Page 586
Translation of Genomic RNA......Page 587
Viral Proteins Involved in RNA Replication......Page 590
Genomic RNA Elements Involved in Picornavirus RNA Replication......Page 592
Synthesis of Positive- and Negative-Strand Viral RNA......Page 594
Further Reading......Page 595
Reovirus Structure......Page 596
Structure of the Genome......Page 598
Inner Capsid Structure......Page 600
Reovirus Replication......Page 601
Further Reading......Page 604
Introduction......Page 605
Vectors, Host Range, and Transmission......Page 606
Virion Properties, Genome, and Replication......Page 607
Antigenic and Phylogenetic Relationships between Seadornaviruses......Page 609
Evolutionary Relationships between BAV and Rotaviruses......Page 610
Structural Features and Relation to Rotaviruses......Page 611
Functional Studies......Page 613
Clinical Features and Diagnostic Assay for Seadornaviruses......Page 614
Relevant Website......Page 615
General Characteristics of Tetravirus Genomic RNAs......Page 616
beta-Like Genome Organization and Replication Model......Page 617
omega-Like Genome Organization and Replication Model......Page 619
High-Resolution Capsid Structure......Page 621
Capsid Maturation, Auto-Proteolysis, and Large-Scale Transitions......Page 623
Application as Biopesticides......Page 624
Glossary......Page 625
Virion Structure and Genome Organization......Page 626
Virus Attachment, Entry, and Uncoating......Page 627
Genome Translation, Transcription, and Replication......Page 628
Infectious Clone Technology......Page 630
Host-Protein Synthesis Shut-Off......Page 631
The Interferon-Mediated Antiviral Response......Page 632
Further Reading......Page 633
Subject Index......Page 634