The evolution and emergence of RNA viruses:
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| Main Author: | |
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| Format: | Book |
| Language: | English |
| Published: |
Oxford
Oxford Univ. Press
2009
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| Series: | Oxford series in ecology and evolution
|
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XII, 254 S. graph. Darst. |
| ISBN: | 9780199211128 9780199211135 |
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Record in the Search Index
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| adam_text | THE EVOLUTION AND EMERGENCE OF RNA VIRUSES EDWARD C. HOLMES CENTER FOR
INFECTIOUS DISEASE DYNAMICS, DEPARTMENT OF BIOLOGY, THE PENNSYLVANIA
STATE UNIVERSITY, PENNSYLVANIA, USA AND FOGARTY INTERNATIONAL CENTER,
NATIONAL INSTITUTES OF HEALTH, BETHESDA, USA OXFORD UNIVERSITY PRESS
CONTENTS 1 INTRODUCTION 1 1.1 WHY STUDY RNA VIRUS EVOLUTION? 1 1.1.1
WAYS TO STUDY VIRAL EVOLUTION 2 1.1.2 THE SCOPE OF THIS BOOK 4 1.2 RNA
VIRUSES AND EVOLUTIONARY BIOLOGY 5 1.2.1 THE RNA VIRUS WORLD 6 1.3 THE
BASICS OF VIRAL BIOLOGY 8 1.3.1 A CURSORY HISTORY OF VIROLOGY 8 1.3.2
VIROLOGY 101 9 1.3.3 EXPLORING THE VIROSPHERE 13 2 THE ORIGINS OF RNA
VIRUSES 15 2.1 INTRODUCTION 15 2.1.1 THE PERILS OF DEEP VIRAL PHYLOGENY
15 2.2 THEORIES FOR THE ORIGIN OF RNA VIRUSES 16 2.2.1 THE REGRESSIVE
ORIGIN THEORY 17 2.2.2 RNA VIRUSES AS ESCAPED GENES 18 2.2.3 RNA VIRUSES
AND THE RNA WORLD 20 2.2.4 EIGEN S PARADOX 22 2.2.5 THE TAXONOMIC
DISTRIBUTION OF RNA VIRUSES 24 2.2.6 CONSERVED PROTEIN STRUCTURES 25 2.3
DEEP PHYLOGENETIC RELATIONSHIPS AMONG RNA VIRUSES 28 2.3.1
THE HIGHER-ORDER RELATIONSHIPS OF RNA VIRUSES 29 2.3.2 PHYLOGENIES BASED
ON GENOME ORGANIZATION 34 2.3.3 PHYLOGENIES BASED ON PROTEIN STRUCTURE
34 2.4 RNA VIRUSES AND THE EVOLUTION OF THE GENETIC CODE 35 3 THE
MECHANISMS OF RNA VIRUS EVOLUTION 37 3.1 THE EVOLUTIONARY DYNAMICS OF
RNA VIRUSES 37 3.1.1 MUTATION RATES IN RNA VIRUSES AND THEIR
DETERMINANTS 37 3.1.2 A COMPARISON OF SUBSTITUTION RATES IN VIRUSES 39
3.1.3 DIFFERENCES IN VIRAL GENERATION TIME 42 X * CONTENTS .4 SLOWLY
EVOLVING RNA VIRUSES? 43 .5 RAPIDLY EVOLVING SSDNA VIRUSES 44 .6 WHAT
SETS THE RATE OF RNA VIRUS EVOLUTION? 45 .7 TRADE-OFFS AND THE EVOLUTION
OF MUTATION RATES 46 .8 MUTATION RATES AND MUTATIONAL LOADS 47 .9 ARE
RNA VIRUSES TRAPPED BY HIGH MUTATION RATES? 48 3.2 RECOMBINATION AND
REASSORTMENT IN RNA VIRUS EVOLUTION 48 3.2.1 RECOMBINATION FREQUENCY IN
RNA VIRUSES 50 3.2.2 DETECTING RECOMBINATION IN RNA VIRUSES 51 3.2.3
WHAT DETERMINES THE RATE OF RECOMBINATION IN RNA VIRUSES? 52 3.2.4
RECOMBINATION AND DELETERIOUS MUTATION 53 3.3 NATURAL SELECTION, GENETIC
DRIFT, AND THE GENETICS OF ADAPTATION 55 3.3.1 EFFECTIVE POPULATION
SIZES IN VIRAL EVOLUTION 56 3.3.2 TRANSMISSION BOTTLENECKS 58 3.3.3 THE
DYNAMICS OF ALLELE FIXATION: ESTIMATING SELECTION COEFFICIENTS 59 3.3.4
THE IMPORTANCE OF HITCH-HIKING 62 3.3.5 PATTERNS OF SYNONYMOUS AND
NONSYNONYMOUS EVOLUTION 63 3.3.6 NATURAL SELECTION AND TRANSMISSION MODE
63 3.3.7 ESCAPE FROM INTRINSIC IMMUNITY 65 3.3.8 STRICTLY NEUTRAL
EVOLUTION IN RNA VIRUSES? 66 3.3.9 DETERMINANTS OF CODON BIAS (AND
NUCLEOTIDE COMPOSITION) IN RNA VIRUSES 68 3.4 DELETERIOUS MUTATION AND
RNA VIRUS EVOLUTION 70 3.4.1 DELETERIOUS MUTATION AND INTRA-HOST GENETIC
DIVERSITY * 73 3.4.2 THE IMPORTANCE OF DEFECTIVE INTERFERING PARTICLES
AND COMPLEMENTATION 74 3.4.3 COMPLEMENTATION MAY BE COMMONPLACE IN RNA
VIRUSES 75 3.5 EPISTASIS IN RNA VIRUS EVOLUTION 77 3.5.1 EPISTASIS AND
ROBUSTNESS 78 3.5.2 THE IMPORTANCE OF RNA SECONDARY STRUCTURE 80 3.5.3
CONVERGENCE AND PLEIOTROPY 82 3.6 THE IMPORTANCE OF INTRA-HOST VIRAL
DIVERSITY 83 4 THE RNA VIRUS QUASISPECIES 87 4.1 WHAT IS A QUASISPECIES?
87 4.2 THE GREAT QUASISPECIES DEBATE 90 4.2.1 WHAT S IN A NAME:
QUASISPECIES OR POLYMORPHISM? 91 4.2.2 IS QUASISPECIES THEORY DIFFERENT
FROM CLASSICAL POPULATION GENETICS? 92 4.2.3 DOES GENETIC DRIFT
DESTROY THE QUASISPECIES? 92 4.2.4 THE EVIDENCE FROM DIGITAL ORGANISMS
93 4.2.5 EXPERIMENTAL TESTS OF QUASISPECIES THEORY 93 4.2.6 COMPARATIVE
ANALYSES OF RNA VIRUS QUASISPECIES 96 CONTENTS * XI 4.2.7 RECOMBINATION
AND THE QUASISPECIES 99 4.2.8 MEMORY IN VIRAL QUASISPECIES 99 4.3
ERROR THRESHOLDS, EXTINCTION THRESHOLDS, AND ERROR CATASTROPHES 100 4.4
CONCLUDING REMARKS 103 5 COMPARATIVE GENOMICS AND THE MACROEVOLUTION OF
RNA VIRUSES 104 5.1 THE EVOLUTION OF GENOME ARCHITECTURE IN RNA VIRUSES
104 .1 THE EVOLUTION OF GENOME SIZE 104 .2 THE EXCEPTIONS: CORONAVIRUSES
AND RONIVIRUSES 107 .3 THE EVOLUTION OF GENOME ORGANIZATION: AN OVERVIEW
109 .4 THE EVOLUTION OF GENOME SEGMENTATION 111 .5 THE EVOLUTION OF
GENOME ORIENTATION AND DSRNA VIRUSES 113 .6 THE EVOLUTION OF OVERLAPPING
READING FRAMES 114 5.2 THE PROCESSES OF GENOME EVOLUTION 116 5.2.1 GENE
DUPLICATION IN RNA VIRUS EVOLUTION 117 5.2.2 LGT AMONG VIRUSES AND HOSTS
118 5.2.3 MODULAR EVOLUTION 119 5.3 PATTERNS AND PROCESSES OF
MACROEVOLUTION IN RNA VIRUSES 120 5.3.1 SPECIATION IN RNA VIRUSES 121
5.3.2 A BIRTH-DEATH MODEL OF VIRAL EVOLUTION 124 5.3.3 THE BIRTH AND
DEATH OF ENDOGENOUS RETROVIRUSES 128 6 THE MOLECULAR EPIDEMIOLOGY,
PHYLOGEOGRAPHY, AND EMERGENCE OF RNA VIRUSES 131 6.1 PHYLODYNAMICS:
LINKING VIRAL EVOLUTION AT THE PHYLOGENETIC AND EPIDEMIOLOGICAL SCALES
131 6.1.1 COALESCENT APPROACHES TO VIRAL EPIDEMIOLOGY 133 6.2
CROSS-SPECIES TRANSMISSION, CO-DIVERGENCE, AND EMERGENCE 135 6.2.1 THE
RNA/DNA DIVIDE AGAIN 135 6.2.2 INFERRING CO-DIVERGENCE 137 6.2.3 THE
EVOLUTION OF PERSISTENCE IN RNA VIRUSES 138 6.2.4 HOST PHYLOGENY AND
VIRAL EMERGENCE 139 6.3 THE EVOLUTIONARY GENETICS OF VIRAL EMERGENCE 142
6.3.1 ADAPTATION AND EMERGENCE 142 6.3.2 OFF-THE-SHELF EMERGENCE 144
6.3.3 THE FITNESS LANDSCAPES OF EMERGENCE 146 6.3.4 RECOMBINATION,
REASSORTMENT, AND VIRAL EMERGENCE 147 6.4 THE PHYLOGEOGRAPHY OF HUMAN
VIRUSES 148 6.4.1 VIRUSES DIFFER IN PHYLOGEOGRAPHIC PATTERN 149 6.5
MAJOR TRANSITIONS IN HUMAN ECOLOGY AND VIRAL EVOLUTION 153 6.5.1 THE
TRANSITIONS 154 6.5.2 IMMUNODEFICIENCY AND DISEASE EMERGENCE 155 XII *
CONTENTS 7 CASE STUDIES IN RNA VIRUS EVOLUTION AND EMERGENCE 156 7.1 THE
EVOLUTIONARY BIOLOGY OF INFLUENZA VIRUS 156 7.1.1 THE DIVERSITY OF
INFLUENZA VIRUS 156 7.1.2 THE EVOLUTION OF AVIAN INFLUENZA VIRUS 158
7.1.3 ANTIGENIC DRIFT AND SHIFT 161 7.1.4 ANTIGENIC CARTOGRAPHY AND THE
PUNCTUATED EVOLUTION OF HA 162 7.1.5 GENOME-WIDE EVOLUTIONARY PROCESSES
165 7.2 THE EMERGENCE AND EVOLUTION OF HIV 167 7.2.1 A BRIEF HISTORY OF
HIV/AIDS 167 7.2.2 THE GENETIC DIVERSITY OF HIV 169 7.2.3 WHAT AND WHY
ARE SUBTYPES? 172 7.2.4 THE ORIGINS AND SPREAD OF HIV 173 7.2.5 THE
INTRA-AND INTER-HOST EVOLUTIONARY DYNAMICS OF HIV 176 7.2.6 THE GREAT
OBSESSION MOVES TO HIV 177 7.2.7 EPIDEMIOLOGICAL SCALE DYNAMICS 178 7.3
THE EVOLUTION OF DENGUE VIRUS 180 7.3.1 THE ORIGINS OF DEN V 182 7.3.2
DENV BIODIVERSITY 184 7.3.3 LINEAGE BIRTH-DEATH IN DENV 186 7.3.4 DENV
FITNESS 187 7.3.5 COMPARING DENGUE AND YELLOW FEVER 188 7.3.6 WHY NO
YELLOW FEVER IN ASIA? 190 7.4 THE PHYLOGEOGRAPHY AND EVOLUTION OF RABIES
VIRUS 191 7.4.1 THE WORLD OF LYSSAVIRUSES 192 7.4.2 THE SPATIOTEMPORAL
DYNAMICS OF RABV . 195 8 EPILOGUE 198 REFERENCES 201 INDEX 249
|
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| spelling | Holmes, Edward C. Verfasser aut The evolution and emergence of RNA viruses Edward C. Holmes Oxford Oxford Univ. Press 2009 XII, 254 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Oxford series in ecology and evolution HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020146559&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Holmes, Edward C. The evolution and emergence of RNA viruses |
| title | The evolution and emergence of RNA viruses |
| title_auth | The evolution and emergence of RNA viruses |
| title_exact_search | The evolution and emergence of RNA viruses |
| title_full | The evolution and emergence of RNA viruses Edward C. Holmes |
| title_fullStr | The evolution and emergence of RNA viruses Edward C. Holmes |
| title_full_unstemmed | The evolution and emergence of RNA viruses Edward C. Holmes |
| title_short | The evolution and emergence of RNA viruses |
| title_sort | the evolution and emergence of rna viruses |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020146559&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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