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The evolution and emergence of RNA viruses 1st Edition by Edward C Holmes ISBN 0199211132 9780199211135

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Author(s): Edward C. Holmes
ISBN(s): 9780199211135, 0199211132
Edition: 1
File Details: PDF, 7.46 MB
Year: 2009
Language: english
SKU: EB-1295292 Category: Tag:

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ISBN 10: 0199211132 
ISBN 13: 9780199211135
Author: Edward C Holmes

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 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 and evolution 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.

The evolution and emergence of RNA viruses 1st Table of contents:

1. Introduction

1.1 Why study RNA virus evolution?
1.1.1 Ways to study viral evolution
1.1.2 The scope of this book
1.2 RNA viruses and evolutionary biology
1.2.1 The RNA virus world
1.3 The basics of viral biology
1.3.1 A cursory history of virology
1.3.2 Virology 101
1.3.3 Exploring the virosphere

2. The Origins of RNA Viruses

2.1 Introduction
2.1.1 The perils of deep viral phylogeny
2.2 Theories for the origin of RNA viruses
2.2.1 The regressive origin theory
2.2.2 RNA viruses as escaped genes
2.2.3 RNA viruses and the RNA world
2.2.4 Eigen’s paradox
2.2.5 The taxonomic distribution of RNA viruses
2.2.6 Conserved protein structures
2.3 Deep phylogenetic relationships among RNA viruses
2.3.1 The ‘higher-order’ relationships of RNA viruses
2.3.2 Phylogenies based on genome organization
2.3.3 Phylogenies based on protein structure
2.4 RNA viruses and the evolution of the genetic code

3. The Mechanisms of RNA Virus Evolution

3.1 The evolutionary dynamics of RNA viruses
3.1.1 Mutation rates in RNA viruses and their determinants
3.1.2 A comparison of substitution rates in viruses
3.1.3 Differences in viral generation time
3.1.4 Slowly evolving RNA viruses?
3.1.5 Rapidly evolving ssDNA viruses
3.1.6 What sets the rate of RNA virus evolution?
3.1.7 Trade-offs and the evolution of mutation rates
3.1.8 Mutation rates and mutational loads
3.1.9 Are RNA viruses trapped by high mutation rates?
3.2 Recombination and reassortment in RNA virus evolution
3.2.1 Recombination frequency in RNA viruses
3.2.2 Detecting recombination in RNA viruses
3.2.3 What determines the rate of recombination in RNA viruses?
3.2.4 Recombination and deleterious mutation
3.3 Natural selection, genetic drift, and the genetics of adaptation
3.3.1 Effective population sizes in viral evolution
3.3.2 Transmission bottlenecks
3.3.3 The dynamics of allele fixation: estimating selection coefficients
3.3.4 The importance of hitch-hiking
3.3.5 Patterns of synonymous and nonsynonymous evolution
3.3.6 Natural selection and transmission mode
3.3.7 Escape from intrinsic immunity
3.3.8 Strictly neutral evolution in RNA viruses?
3.3.9 Determinants of codon bias (and nucleotide composition) in RNA viruses
3.4 Deleterious mutation and RNA virus evolution
3.4.1 Deleterious mutation and intra-host genetic diversity
3.4.2 The importance of defective interfering particles and complementation
3.4.3 Complementation may be commonplace in RNA viruses
3.5 Epistasis in RNA virus evolution
3.5.1 Epistasis and robustness
3.5.2 The importance of RNA secondary structure
3.5.3 Convergence and pleiotropy
3.6 The importance of intra-host viral diversity

4. The RNA Virus Quasispecies

4.1 What is a quasispecies?
4.2 The great quasispecies debate
4.2.1 What’s in a name: quasispecies or polymorphism?
4.2.2 Is quasispecies theory different from ‘classical’ population genetics?
4.2.3 Does genetic drift destroy the quasispecies?
4.2.4 The evidence from ‘digital organisms’
4.2.5 Experimental tests of quasispecies theory
4.2.6 Comparative analyses of RNA virus quasispecies
4.2.7 Recombination and the quasispecies
4.2.8 ‘Memory’ in viral quasispecies
4.3 Error thresholds, extinction thresholds, and error catastrophes
4.4 Concluding remarks

5. Comparative Genomics and the Macroevolution of RNA Viruses

5.1 The evolution of genome architecture in RNA viruses
5.1.1 The evolution of genome size
5.1.2 The exceptions: coronaviruses and roniviruses
5.1.3 The evolution of genome organization: an overview
5.1.4 The evolution of genome segmentation
5.1.5 The evolution of genome orientation and dsRNA viruses
5.1.6 The evolution of overlapping reading frames
5.2 The processes of genome evolution
5.2.1 Gene duplication in RNA virus evolution
5.2.2 LGT among viruses and hosts
5.2.3 Modular evolution
5.3 Patterns and processes of macroevolution in RNA viruses
5.3.1 Speciation in RNA viruses
5.3.2 A birth-death model of viral evolution
5.3.3 The birth and death of endogenous retroviruses

6. The Molecular Epidemiology, Phylogeography, and Emergence of RNA Viruses

6.1 Phylodynamics: linking viral evolution at the phylogenetic and epidemiological scales
6.1.1 Coalescent approaches to viral epidemiology
6.2 Cross-species transmission, co-divergence, and emergence
6.2.1 The RNA/DNA divide again
6.2.2 Inferring co-divergence
6.2.3 The evolution of persistence in RNA viruses
6.2.4 Host phylogeny and viral emergence
6.3 The evolutionary genetics of viral emergence
6.3.1 Adaptation and emergence
6.3.2 ‘Off-the-shelf’ emergence
6.3.3 The fitness landscapes of emergence
6.3.4 Recombination, reassortment, and viral emergence
6.4 The phylogeography of human viruses
6.4.1 Viruses differ in phylogeographic pattern
6.5 Major transitions in human ecology and viral evolution
6.5.1 The transitions
6.5.2 Immunodeficiency and disease emergence

7. Case Studies in RNA Virus Evolution and Emergence

7.1 The evolutionary biology of influenza virus
7.1.1 The diversity of influenza virus
7.1.2 The evolution of avian influenza virus
7.1.3 Antigenic drift and shift
7.1.4 Antigenic cartography and the punctuated evolution of HA
7.1.5 Genome-wide evolutionary processes
7.2 The emergence and evolution of HIV
7.2.1 A brief history of HIV/AIDS
7.2.2 The genetic diversity of HIV
7.2.3 What and why are subtypes?
7.2.4 The origins and spread of HIV
7.2.5 The intra- and inter-host evolutionary dynamics of HIV
7.2.6 The great obsession moves to HIV
7.2.7 Epidemiological scale dynamics
7.3 The evolution of dengue virus
7.3.1 The origins of DENV
7.3.2 DENV biodiversity
7.3.3 Lineage birth-death in DENV
7.3.4 DENV fitness
7.3.5 Comparing dengue and yellow fever
7.3.6 Why no yellow fever in Asia?
7.4 The phylogeography and evolution of rabies virus
7.4.1 The world of lyssaviruses
7.4.2 The spatiotemporal dynamics of RABV

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