RNA viruses provide unique insights into the patterns and processes of evolutionary change in real time. The study of viral evolution is especially topical given the growing awareness that emerging and re-emerging diseases (most of which are caused by RNA viruses) represent a major threat to public health. However, while the study of viral evolution has developed rapidly in the last 30 years, relatively little attention has been directed toward linking work on the mechanisms of viral evolution within cells or individual hosts, to the epidemiological outcomes of these processes. This novel book fills this gap by considering the patterns and processes of viral evolution across their entire range of spatial and temporal scales. The Evolution and Emergence of RNA Viruses provide a comprehensive overview of RNA virus evolution. This is the first book to link mechanisms of viral evolution to epidemiological outcomes, incorporating case studies in RNA virus emergence and evolution using topical examples such as influenza, HIV, dengue fever, and rabies. It reveals the underlying evolutionary processes by which emerging viruses cross species boundaries and spread in new hosts.
Author(s): Edward C. Holmes
Edition: 1
Year: 2009
Language: English
Pages: 288
Contents......Page 10
1.1 Why study RNA virus evolution?......Page 14
1.1.1 Ways to study viral evolution......Page 15
1.1.2 The scope of this book......Page 17
1.2 RNA viruses and evolutionary biology......Page 18
1.2.1 The RNA virus world......Page 19
1.3.1 A cursory history of virology......Page 21
1.3.2 Virology 101......Page 22
1.3.3 Exploring the virosphere......Page 26
2.1.1 The perils of deep viral phylogeny......Page 28
2.2 Theories for the origin of RNA viruses......Page 29
2.2.1 The regressive origin theory......Page 30
2.2.2 RNA viruses as escaped genes......Page 31
2.2.3 RNA viruses and the RNA world......Page 33
2.2.4 Eigen's paradox......Page 35
2.2.5 The taxonomic distribution of RNA viruses......Page 37
2.2.6 Conserved protein structures......Page 38
2.3 Deep phylogenetic relationships among RNA viruses......Page 41
2.3.1 The 'higher-order' relationships of RNA viruses......Page 42
2.3.3 Phylogenies based on protein structure......Page 47
2.4 RNA viruses and the evolution of the genetic code......Page 48
3.1.1 Mutation rates in RNA viruses and their determinants......Page 50
3.1.2 A comparison of substitution rates in viruses......Page 52
3.1.3 Differences in viral generation time......Page 55
3.1.4 Slowly evolving RNA viruses?......Page 56
3.1.5 Rapidly evolving ssDNA viruses......Page 57
3.1.6 What sets the rate of RNA virus evolution?......Page 58
3.1.7 Trade-offs and the evolution of mutation rates......Page 59
3.1.8 Mutation rates and mutational loads......Page 60
3.2 Recombination and reassortment in RNA virus evolution......Page 61
3.2.1 Recombination frequency in RNA viruses......Page 63
3.2.2 Detecting recombination in RNA viruses......Page 64
3.2.3 What determines the rate of recombination in RNA viruses?......Page 65
3.2.4 Recombination and deleterious mutation......Page 66
3.3 Natural selection, genetic drift, and the genetics of adaptation......Page 68
3.3.1 Effective population sizes in viral evolution......Page 69
3.3.2 Transmission bottlenecks......Page 71
3.3.3 The dynamics of allele fixation: estimating selection coefficients......Page 72
3.3.4 The importance of hitch-hiking......Page 75
3.3.6 Natural selection and transmission mode......Page 76
3.3.7 Escape from intrinsic immunity......Page 78
3.3.8 Strictly neutral evolution in RNA viruses?......Page 79
3.3.9 Determinants of codon bias (and nucleotide composition) in RNA viruses......Page 81
3.4 Deleterious mutation and RNA virus evolution......Page 83
3.4.1 Deleterious mutation and intra-host genetic diversity......Page 86
3.4.2 The importance of defective interfering particles and complementation......Page 87
3.4.3 Complementation may be commonplace in RNA viruses......Page 88
3.5 Epistasis in RNA virus evolution......Page 90
3.5.1 Epistasis and robustness......Page 91
3.5.2 The importance of RNA secondary structure......Page 93
3.5.3 Convergence and pleiotropy......Page 95
3.6 The importance of intra-host viral diversity......Page 96
4.1 What is a quasispecies?......Page 100
4.2 The great quasispecies debate......Page 103
4.2.1 What's in a name: quasispecies or polymorphism?......Page 104
4.2.3 Does genetic drift destroy the quasispecies?......Page 105
4.2.5 Experimental tests of quasispecies theory......Page 106
4.2.6 Comparative analyses of RNA virus quasispecies......Page 109
4.2.8 'Memory' in viral quasispecies......Page 112
4.3 Error thresholds, extinction thresholds, and error catastrophes......Page 113
4.4 Concluding remarks......Page 116
5.1.1 The evolution of genome size......Page 117
5.1.2 The exceptions: coronaviruses and roniviruses......Page 120
5.1.3 The evolution of genome organization: an overview......Page 122
5.1.4 The evolution of genome segmentation......Page 124
5.1.5 The evolution of genome orientation and dsRNA viruses......Page 126
5.1.6 The evolution of overlapping reading frames......Page 127
5.2 The processes of genome evolution......Page 129
5.2.1 Gene duplication in RNA virus evolution......Page 130
5.2.2 LGT among viruses and hosts......Page 131
5.2.3 Modular evolution......Page 132
5.3 Patterns and processes of macroevolution in RNA viruses......Page 133
5.3.1 Speciation in RNA viruses......Page 134
5.3.2 A birth-death model of viral evolution......Page 137
5.3.3 The birth and death of endogenous retroviruses......Page 141
6.1 Phylodynamics: linking viral evolution at the phylogenetic and epidemiological scales......Page 144
6.1.1 Coalescent approaches to viral epidemiology......Page 146
6.2.1 The RNA/DNA divide again......Page 148
6.2.2 Inferring co-divergence......Page 150
6.2.3 The evolution of persistence in RNA viruses......Page 151
6.2.4 Host phylogeny and viral emergence......Page 152
6.3.1 Adaptation and emergence......Page 155
6.3.2 'Off-the-shelf' emergence......Page 157
6.3.3 The fitness landscapes of emergence......Page 159
6.3.4 Recombination, reassortment, and viral emergence......Page 160
6.4 The phylogeography of human viruses......Page 161
6.4.1 Viruses differ in phylogeographic pattern......Page 162
6.5 Major transitions in human ecology and viral evolution......Page 166
6.5.1 The transitions......Page 167
6.5.2 Immunodeficiency and disease emergence......Page 168
7.1.1 The diversity of influenza virus......Page 169
7.1.2 The evolution of avian influenza virus......Page 171
7.1.3 Antigenic drift and shift......Page 174
7.1.4 Antigenic cartography and the punctuated evolution of HA......Page 175
7.1.5 Genome-wide evolutionary processes......Page 178
7.2.1 A brief history of HIV/AIDS......Page 180
7.2.2 The genetic diversity of HIV......Page 182
7.2.3 What and why are subtypes?......Page 185
7.2.4 The origins and spread of HIV......Page 186
7.2.5 The intra- and inter-host evolutionary dynamics of HIV......Page 189
7.2.6 The great obsession moves to HIV......Page 190
7.2.7 Epidemiological scale dynamics......Page 191
7.3 The evolution of dengue virus......Page 193
7.3.1 The origins of DENV......Page 195
7.3.2 DENV biodiversity......Page 197
7.3.3 Lineage birth-death in DENV......Page 199
7.3.4 DENV fitness......Page 200
7.3.5 Comparing dengue and yellow fever......Page 201
7.3.6 Why no yellow fever in Asia?......Page 203
7.4 The phylogeography and evolution of rabies virus......Page 204
7.4.1 The world of lyssaviruses......Page 205
7.4.2 The spatiotemporal dynamics of RABV......Page 208
8 Epilogue......Page 211
References......Page 214
C......Page 262
G......Page 263
M......Page 264
P......Page 265
S......Page 266
Y......Page 267
