The Evolution and Emergence of RNA Viruses

by
Edition: 1st
Format: Paperback
Pub. Date: 2009-08-31
Publisher(s): Oxford University Press
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Summary

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 topublic 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. Thisnovel 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 provides a comprehensive overview of RNA virus evolution, with a particular focus on genomic and phylogenetic approaches. This is the first book to link mechanisms of viral evolution with disease dynamics, using high-profile examples in emergence andevolution such as influenza, HIV, dengue fever, and rabies. It also reveals the underlying evolutionary processes by which emerging viruses cross species boundaries and spread in new hosts.

Author Biography


Edward C. Holmes is Professor of Biology and Eberly College of Science Distinguished Senior Scholar at The Pennsylvania State University. He was authored over 200 scientific publications and in 2003 was awarded the Scientific Medal for 'Achievement in Research by a Zoologist Under the Age of 40' by the Zoological Society of London for his work on evolutionary biology and bioinformatics. He is also co-author of a highly regarded text book in molecular evolution and phylogenetics. His research sits at the interface of four disciplines - evolutionary biology, genomics, infectious disease and bioinformatics - and for the last 20 years he has been involved in the development and use of a variety of computational techniques to reveal the fundamental patterns and processes of evolutionary change in viruses.

Table of Contents

Introductionp. 1
Why study RNA virus evolution?p. 1
Ways to study viral evolutionp. 2
The scope of this bookp. 4
RNA viruses and evolutionary biologyp. 5
The RNA virus worldp. 6
The basics of viral biologyp. 8
A cursory history of virologyp. 8
Virology 101p. 9
Exploring the virospherep. 13
The origins of RNA virusesp. 15
Introductionp. 15
The perils of deep viral phylogenyp. 15
Theories for the origin of RNA virusesp. 16
The regressive origin theoryp. 17
RNA viruses as escaped genesp. 18
RNA viruses and the RNA worldp. 20
EigenÆs paradoxp. 22
The taxonomic distribution of RNA virusesp. 24
Conserved protein structuresp. 25
Deep phylogenetic relationships among RNA virusesp. 28
The æhigher-orderÆ relationships of RNA virusesp. 29
Phylogenies based on genome organizationp. 34
Phylogenies based on protein structurep. 34
RNA viruses and the evolution of the genetic codep. 35
The mechanisms of RNA virus evolutionp. 37
The evolutionary dynamics of RNA virusesp. 37
Mutation rates in RNA viruses and their determinantsp. 37
A comparison of substitution rates in virusesp. 39
Differences in viral generation timep. 42
Slowly evolving RNA viruses?p. 43
Rapidly evolving ssDNA virusesp. 44
What sets the rate of RNA virus evolution?p. 45
Trade-offs and the evolution of mutation ratesp. 46
Mutation rates and mutational loadsp. 47
Are RNA viruses trapped by high mutation rates?p. 48
Recombination and reassortment in RNA virus evolutionp. 48
Recombination frequency in RNA virusesp. 50
Detecting recombination in RNA virusesp. 51
What determines the rate of recombination in RNA viruses?p. 52
Recombination and deleterious mutationp. 53
Natural selection, genetic drift, and the genetics of adaptationp. 55
Effective population sizes in viral evolutionp. 56
Transmission bottlenecksp. 58
The dynamics of allele fixation: estimating selection coefficientsp. 59
The importance of hitch-hikingp. 62
Patterns of synonymous and nonsynonymous evolutionp. 63
Natural selection and transmission modep. 63
Escape from intrinsic immunityp. 65
Strictly neutral evolution in RNA viruses?p. 66
Determinants of codon bias (and nucleotide composition) in RNA virusesp. 68
Deleterious mutation and RNA virus evolutionp. 70
Deleterious mutation and intra-host genetic diversityp. 73
The importance of defective interfering particles and complementationp. 74
Complementation may be commonplace in RNA virusesp. 75
Epistasis in RNA virus evolutionp. 77
Epistasis and robustnessp. 78
The importance of RNA secondary structurep. 80
Convergence and pleiotropyp. 82
The importance of intra-host viral diversityp. 83
The RNA virus quasispeciesp. 87
What is a quasispecies?p. 87
The great quasispecies debatep. 90
WhatÆs in a name: quasispecies or polymorphism?p. 91
Is quasispecies theory different from æclassicalÆ population genetics?p. 92
Does genetic drift destroy the quasispecies?p. 92
The evidence from ædigital organismsÆp. 93
Experimental tests of quasispecies theoryp. 93
Comparative analyses of RNA virus quasispeciesp. 96
Recombination and the quasispeciesp. 99
æMemoryÆ in viral quasispeciesp. 99
Error thresholds, extinction thresholds, and error catastrophesp. 100
Concluding remarksp. 103
Comparative genomics and the macroevolution of RNA virusesp. 104
The evolution of genome architecture in RNA virusesp. 104
The evolution of genome sizep. 104
The exceptions: coronaviruses and ronivirusesp. 107
The evolution of genome organization: an overviewp. 109
The evolution of genome segmentationp. 111
The evolution of genome orientation and dsRNA virusesp. 113
The evolution of overlapping reading framesp. 114
The processes of genome evolutionp. 116
Gene duplication in RNA virus evolutionp. 117
LGT among viruses and hostsp. 118
Modular evolutionp. 119
Patterns and processes of macroevolution in RNA virusesp. 120
Speciation in RNA virusesp. 121
A birth-death model of viral evolutionp. 124
The birth and death of endogenous retrovirusesp. 128
The molecular epidemiology, phylogeography, and emergence of RNA virusesp. 131
Phylodynamics; linking viral evolution at the phylogenetic and epidemiological scalesp. 131
Coalescent approaches to viral epidemiologyp. 133
Cross-species transmission, co-divergence, and emergencep. 135
The RNA/DNA divide againp. 135
Inferring co-divergencep. 137
The evolution of persistence in RNA virusesp. 138
Host phylogeny and viral emergencep. 139
The evolutionary genetics of viral emergencep. 142
Adaptation and emergencep. 142
ÆOff-the-shelf emergencep. 144
The fitness landscapes of emergencep. 146
Recombination, reassortment, and viral emergencep. 147
The phylogeography of human virusesp. 148
Viruses differ in phylogeographic patternp. 149
Major transitions in human ecology and viral evolutionp. 153
The transitionsp. 154
Immunodeficiency and disease emergencep. 155
Case studies in RNA virus evolution and emergencep. 156
The evolutionary biology of influenza virusp. 156
The diversity of influenza virusp. 156
The evolution of avian influenza virusp. 158
Antigenic drift and shiftp. 161
Antigenic cartography and the punctuated evolution of HAp. 162
Genome-wide evolutionary processesp. 165
The emergence and evolution of HIVp. 167
A brief history of HIV/AIDSp. 167
The genetic diversity of HIVp. 169
What and why are subtypes?p. 172
The origins and spread of HIVp. 173
The intra- and inter-host evolutionary dynamics of HIVp. 176
The great obsession moves to HIVp. 177
Epidemiological scale dynamicsp. 178
The evolution of dengue virusp. 180
The origins of DENVp. 182
DENV biodiversityp. 184
Lineage birth-death in DENVp. 186
DENV fitnessp. 187
Comparing dengue and yellow feverp. 188
Why no yellow fever in Asia?p. 190
The phylogeography and evolution of rabies virusp. 191
The world of lyssavirusesp. 192
The spatiotemporal dynamics of RABVp. 195
Epiloguep. 198
Referencesp. 201
Indexp. 209
Table of Contents provided by Ingram. All Rights Reserved.

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