Origin and evolution of viruses

cover.jpg......Page 1
Contributors......Page 2
Preface to the Second Edition......Page 6
Preface to the First Edition......Page 8
What is a replicon?......Page 9
Simple replicons and the origin of replication......Page 13
RNA catalysis and the RNA world (Figure 1.3)......Page 15
Replication and coupling to environment......Page 19
Replication in open systems......Page 21
Replication in lipid aggregates......Page 24
Parabolic and exponential growth......Page 25
Hyperbolic growth......Page 27
Molecular evolution experiments......Page 29
Fitness landscapes......Page 31
Quasispecies and error propagation......Page 32
Evolution of phenotypes and computer simulation......Page 38
Concluding remarks......Page 42
Acknowledgments......Page 44
References......Page 45
Abstract......Page 50
The origin of viroids: molecular fossils from the RNA world......Page 51
Taxonomic relationships among viroids and their relationship with other RNAs......Page 53
Mechanisms of genetic variability......Page 55
Viroid quasispecies......Page 62
Has RNA silencing shaped viroid structure and evolution?......Page 66
Viroid epidemiology......Page 67
References......Page 68
Introduction......Page 72
The experimental system......Page 73
The mechanism of RNA replication......Page 75
Selection of RNA species......Page 77
Mutation in replicating RNA......Page 80
Mutant spectra......Page 82
Recombination among RNA molecules......Page 85
Creating biological information from scratch......Page 86
Structural signals for replication......Page 88
References......Page 89
Abstract......Page 93
Error-prone replication necessitates limited genetic complexity to protect against error catastrophe......Page 94
Intra-population complementation and interference in viral quasispecies: mutant distributions as the units of selection......Page 98
Fitness and its modulation by viral population size......Page 102
Fitness variations in changing environments......Page 106
Overview......Page 113
References......Page 115
Introduction......Page 125
Phylogenetic analyses of RNA viruses......Page 126
Measuring recombination......Page 129
The analysis of evolutionary rates and times to common ancestry......Page 131
Natural selection on RNA viruses......Page 133
The population dynamics of RNA viruses......Page 136
References......Page 137
Introduction......Page 141
Polymerase five-step kinetic mechanism and fidelity......Page 145
Biochemical analysis of polymerase function......Page 147
Kinetics and thermodynamics of polymerase fidelity......Page 148
Structural perspectives on the single-nucleotide addition cycle and fidelity......Page 152
Polymerase fidelity influences viral population fitness......Page 155
Conclusions and future directions......Page 160
References......Page 163
Introduction......Page 167
RNA-silencing mechanisms......Page 168
Antiviral function of RNA silencing......Page 170
Virus-encoded miRNAs......Page 174
Cellular miRNAs and viruses......Page 175
Evolutionary implications of RNAi......Page 176
References......Page 182
Introduction......Page 188
Retroviruses and cytidine deaminases......Page 189
Mechanisms of A3G antiviral action......Page 196
HIV-1 evolutionary dynamics......Page 199
References......Page 204
Introduction......Page 211
Basic model......Page 212
Deleterious mutations......Page 213
Graphical visualization of the extinction threshold......Page 215
Extinction is thwarted by an error catastrophe......Page 217
Beneficial mutations......Page 218
Estimating the parameters of lethal mutagenesis......Page 219
An alternative model of mutation......Page 220
Future directions......Page 221
References......Page 222
Natural populations, abundance and turnover......Page 223
Genome comparisons and evolutionary mechanisms......Page 224
Population structure, metagenomics......Page 227
Deep evolutionary connections......Page 229
References......Page 230
Abstract......Page 232
Plants, virus hosts from a different universe......Page 233
Symbiotic and commensal relationships and virus synergies......Page 236
Genetic diversity of plant virus populations and the evolutionary processes that produce and control that diversity......Page 237
The comparative phylogenetics of plant viruses......Page 242
Origins of plant virus families......Page 246
Postscript......Page 247
References......Page 248
Introduction......Page 254
Mutation rates and frequencies......Page 255
Genetic bottlenecks......Page 257
Evolutionary implications of mutant swarms and bottlenecks......Page 259
References......Page 260
Introduction......Page 262
Genome organization as a starting point......Page 263
Error and recombination......Page 265
Retroviral fixation rates vary hugely......Page 269
How far can variation go for a retrovirus?......Page 270
Phylogeny......Page 271
Genome design impacts the tempo of evolution......Page 272
Endogenous retroviruses and multiple introductions......Page 273
Back to the futureor recovering retroviral ancestors......Page 274
How good is the retroviral tree?......Page 275
The future of retroviral evolution?......Page 278
References......Page 279
Abstract......Page 281
Within-host population dynamics of HIV infection......Page 282
Effective population size......Page 291
Recombination......Page 294
References......Page 298
Hepatitis A virus......Page 304
Hepatitis B virus......Page 306
Hepatitis C virus......Page 317
Hepatitis delta virus......Page 329
Hepatitis E virus......Page 331
References......Page 333
Transmission cycles, evolutionary history and systematics of the arboviruses......Page 351
Inferences on arbovirus evolution from phylogenetic studies......Page 354
Recombination and reassortment in arbovirus evolution......Page 363
Emergence mechanisms of zoonotic arboviral diseases......Page 364
Geographic range expansion of arboviruses......Page 369
Effects of arbovirus transmission cycles on their evolution......Page 371
Other impacts of vector and host biology on arbovirus evolution......Page 373
Quasispecies diversity in arboviruses......Page 375
Challenges to the control of arboviral diseases......Page 380
References......Page 382
Parvoviruses and their properties......Page 392
Gene structure and replication......Page 393
Viral gene functions......Page 394
Non-structural proteins......Page 395
Structure and variation of the viral capsid......Page 396
Mechanisms of transmission......Page 397
Human B19 and related erythroviruses......Page 398
CPV and related viruses......Page 400
Aleutian mink disease virus (AMDV)......Page 401
Rodent parvoviruses......Page 402
Genetic variation and replication error rate......Page 403
Intra-host diversity during natural infections......Page 405
Spatial heterogeneity of CPV and related viruses......Page 407
Temporal variation......Page 408
Conclusions......Page 409
References......Page 410
Introduction......Page 416
The biology and pathogenesis of papillomaviruses......Page 417
The phylogeny-based taxonomy of papillomaviruses......Page 418
Recent evolutionary changes: Alpha-papillomaviruses and their variants......Page 420
Genetic and biological diversity of alpha-papillomaviruses from humans, apes, and monkeys......Page 421
Deeper branching of the phylogenetic tree of mammalian and bird papillomaviruses......Page 422
The interpretation of host-linked evolution......Page 423
The relevance of papillomavirus phylogeny for medical research......Page 424
The origin of papillomaviruses and the relationship of papillomaviridae with other families of viruses......Page 425
References......Page 426
Introduction......Page 429
Entomopoxvirinae......Page 430
Chordopoxvirinae......Page 434
Evolution of immune evasion......Page 439
Poxvirus tropism and host range......Page 440
Studies in evolution at the host species level......Page 441
Conclusions......Page 442
References......Page 443
Abstract......Page 445
Introduction......Page 446
Comparative herpesvirus genomics......Page 447
Phylogeny of herpesviruses......Page 454
Evolution of herpesvirus gene systems......Page 460
Frontiers in herpesvirus genomic evolution......Page 464
Evolutionary relationships of the order Herpesvirales......Page 467
Conclusions......Page 468
References......Page 469
Abstract......Page 474
Introduction......Page 475
Exemplars of virus evolution......Page 479
Fitness, consortia, and persistence......Page 480
The real world of viral RNA in human disease......Page 488
The analytical problem of quasispecies: group selection, reticulation, and recombination......Page 490
The big bang of biology......Page 492
Genomic stability: persistence and temperate lifestyle......Page 493
Episomal stability: the P1 exemplar of persistence......Page 494
Prokaryotes and their viruses as one evolutionary pool......Page 495
The transition to eukaryotic DNA viruses......Page 496
Herpesvirus; mostly persisting and co-speciation......Page 498
Real-time virushost evolution: koala bear exemplar......Page 503
References......Page 504
Index......Page 514