Title The Evolution and Emergence of RNA Viruses

Published OUP Oxford 2009

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Description 1 online resource (272 pages) 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 viruses2.2.6 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 adaptation3.3.1 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 diversity3.4.2 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? 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 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 Subject RNA viruses. Viral genetics. Virus diseases. Viruses -- Evolution. Molecular evolution. Viral genomes. Phylogeny. RNA Viruses -- genetics Communicable Diseases, Emerging -- genetics Evolution, Molecular Genome, Viral Phylogeny RNA Virus Infections -- genetics RNA Viruses Virus Diseases SCIENCE -- Life Sciences -- Biology. SCIENCE -- Life Sciences -- Microbiology. Viral genomes Phylogeny Molecular evolution RNA viruses Viral genetics Virus diseases Viruses -- Evolution Form Electronic book ISBN 1282346717 9781282346710

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