The Evolution and Emergence of RNA Viruses
by Holmes, Edward C.-
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Summary
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
| Introduction | p. 1 |
| Why study RNA virus evolution? | p. 1 |
| Ways to study viral evolution | p. 2 |
| The scope of this book | p. 4 |
| RNA viruses and evolutionary biology | p. 5 |
| The RNA virus world | p. 6 |
| The basics of viral biology | p. 8 |
| A cursory history of virology | p. 8 |
| Virology 101 | p. 9 |
| Exploring the virosphere | p. 13 |
| The origins of RNA viruses | p. 15 |
| Introduction | p. 15 |
| The perils of deep viral phylogeny | p. 15 |
| Theories for the origin of RNA viruses | p. 16 |
| The regressive origin theory | p. 17 |
| RNA viruses as escaped genes | p. 18 |
| RNA viruses and the RNA world | p. 20 |
| EigenÆs paradox | p. 22 |
| The taxonomic distribution of RNA viruses | p. 24 |
| Conserved protein structures | p. 25 |
| Deep phylogenetic relationships among RNA viruses | p. 28 |
| The æhigher-orderÆ relationships of RNA viruses | p. 29 |
| Phylogenies based on genome organization | p. 34 |
| Phylogenies based on protein structure | p. 34 |
| RNA viruses and the evolution of the genetic code | p. 35 |
| The mechanisms of RNA virus evolution | p. 37 |
| The evolutionary dynamics of RNA viruses | p. 37 |
| Mutation rates in RNA viruses and their determinants | p. 37 |
| A comparison of substitution rates in viruses | p. 39 |
| Differences in viral generation time | p. 42 |
| Slowly evolving RNA viruses? | p. 43 |
| Rapidly evolving ssDNA viruses | p. 44 |
| What sets the rate of RNA virus evolution? | p. 45 |
| Trade-offs and the evolution of mutation rates | p. 46 |
| Mutation rates and mutational loads | p. 47 |
| Are RNA viruses trapped by high mutation rates? | p. 48 |
| Recombination and reassortment in RNA virus evolution | p. 48 |
| Recombination frequency in RNA viruses | p. 50 |
| Detecting recombination in RNA viruses | p. 51 |
| What determines the rate of recombination in RNA viruses? | p. 52 |
| Recombination and deleterious mutation | p. 53 |
| Natural selection, genetic drift, and the genetics of adaptation | p. 55 |
| Effective population sizes in viral evolution | p. 56 |
| Transmission bottlenecks | p. 58 |
| The dynamics of allele fixation: estimating selection coefficients | p. 59 |
| The importance of hitch-hiking | p. 62 |
| Patterns of synonymous and nonsynonymous evolution | p. 63 |
| Natural selection and transmission mode | p. 63 |
| Escape from intrinsic immunity | p. 65 |
| Strictly neutral evolution in RNA viruses? | p. 66 |
| Determinants of codon bias (and nucleotide composition) in RNA viruses | p. 68 |
| Deleterious mutation and RNA virus evolution | p. 70 |
| Deleterious mutation and intra-host genetic diversity | p. 73 |
| The importance of defective interfering particles and complementation | p. 74 |
| Complementation may be commonplace in RNA viruses | p. 75 |
| Epistasis in RNA virus evolution | p. 77 |
| Epistasis and robustness | p. 78 |
| The importance of RNA secondary structure | p. 80 |
| Convergence and pleiotropy | p. 82 |
| The importance of intra-host viral diversity | p. 83 |
| The RNA virus quasispecies | p. 87 |
| What is a quasispecies? | p. 87 |
| The great quasispecies debate | p. 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 organismsÆ | p. 93 |
| Experimental tests of quasispecies theory | p. 93 |
| Comparative analyses of RNA virus quasispecies | p. 96 |
| Recombination and the quasispecies | p. 99 |
| æMemoryÆ in viral quasispecies | p. 99 |
| Error thresholds, extinction thresholds, and error catastrophes | p. 100 |
| Concluding remarks | p. 103 |
| Comparative genomics and the macroevolution of RNA viruses | p. 104 |
| The evolution of genome architecture in RNA viruses | p. 104 |
| The evolution of genome size | p. 104 |
| The exceptions: coronaviruses and roniviruses | p. 107 |
| The evolution of genome organization: an overview | p. 109 |
| The evolution of genome segmentation | p. 111 |
| The evolution of genome orientation and dsRNA viruses | p. 113 |
| The evolution of overlapping reading frames | p. 114 |
| The processes of genome evolution | p. 116 |
| Gene duplication in RNA virus evolution | p. 117 |
| LGT among viruses and hosts | p. 118 |
| Modular evolution | p. 119 |
| Patterns and processes of macroevolution in RNA viruses | p. 120 |
| Speciation in RNA viruses | p. 121 |
| A birth-death model of viral evolution | p. 124 |
| The birth and death of endogenous retroviruses | p. 128 |
| The molecular epidemiology, phylogeography, and emergence of RNA viruses | p. 131 |
| Phylodynamics; linking viral evolution at the phylogenetic and epidemiological scales | p. 131 |
| Coalescent approaches to viral epidemiology | p. 133 |
| Cross-species transmission, co-divergence, and emergence | p. 135 |
| The RNA/DNA divide again | p. 135 |
| Inferring co-divergence | p. 137 |
| The evolution of persistence in RNA viruses | p. 138 |
| Host phylogeny and viral emergence | p. 139 |
| The evolutionary genetics of viral emergence | p. 142 |
| Adaptation and emergence | p. 142 |
| ÆOff-the-shelf emergence | p. 144 |
| The fitness landscapes of emergence | p. 146 |
| Recombination, reassortment, and viral emergence | p. 147 |
| The phylogeography of human viruses | p. 148 |
| Viruses differ in phylogeographic pattern | p. 149 |
| Major transitions in human ecology and viral evolution | p. 153 |
| The transitions | p. 154 |
| Immunodeficiency and disease emergence | p. 155 |
| Case studies in RNA virus evolution and emergence | p. 156 |
| The evolutionary biology of influenza virus | p. 156 |
| The diversity of influenza virus | p. 156 |
| The evolution of avian influenza virus | p. 158 |
| Antigenic drift and shift | p. 161 |
| Antigenic cartography and the punctuated evolution of HA | p. 162 |
| Genome-wide evolutionary processes | p. 165 |
| The emergence and evolution of HIV | p. 167 |
| A brief history of HIV/AIDS | p. 167 |
| The genetic diversity of HIV | p. 169 |
| What and why are subtypes? | p. 172 |
| The origins and spread of HIV | p. 173 |
| The intra- and inter-host evolutionary dynamics of HIV | p. 176 |
| The great obsession moves to HIV | p. 177 |
| Epidemiological scale dynamics | p. 178 |
| The evolution of dengue virus | p. 180 |
| The origins of DENV | p. 182 |
| DENV biodiversity | p. 184 |
| Lineage birth-death in DENV | p. 186 |
| DENV fitness | p. 187 |
| Comparing dengue and yellow fever | p. 188 |
| Why no yellow fever in Asia? | p. 190 |
| The phylogeography and evolution of rabies virus | p. 191 |
| The world of lyssaviruses | p. 192 |
| The spatiotemporal dynamics of RABV | p. 195 |
| Epilogue | p. 198 |
| References | p. 201 |
| Index | p. 209 |
| Table of Contents provided by Ingram. All Rights Reserved. |
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