Why do RNA viruses recombine
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TLDR
There is little evidence that recombination is favoured by natural selection to create advantageous genotypes or purge deleterious mutations, as predicted if recombination functions as a form of sexual reproduction, and recombination may be a mechanistic by-product of the evolutionary pressures acting on other aspects of virus biology.Abstract:
Recombination occurs in many RNA viruses and can be of major evolutionary significance However, rates of recombination vary dramatically among RNA viruses, which can range from clonal to highly recombinogenic Here, we review the factors that might explain this variation in recombination frequency and show that there is little evidence that recombination is favoured by natural selection to create advantageous genotypes or purge deleterious mutations, as predicted if recombination functions as a form of sexual reproduction Rather, recombination rates seemingly reflect larger-scale patterns of viral genome organization, such that recombination may be a mechanistic by-product of the evolutionary pressures acting on other aspects of virus biologyread more
Citations
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Replication-Competent Noninduced Proviruses in the Latent Reservoir Increase Barrier to HIV-1 Cure
Ya Chi Ho,Liang Shan,Nina N. Hosmane,Jeffrey C. Wang,Sarah B. Laskey,Daniel I. S. Rosenbloom,Jun Lai,Joel N. Blankson,Janet D. Siliciano,Robert F. Siliciano,Robert F. Siliciano +10 more
TL;DR: The identification of replication-competent noninduced proviruses indicates that the size of the latent reservoir-and, hence, the barrier to cure-may be up to 60-fold greater than previously estimated.
Journal ArticleDOI
Molecular Evolution of Zika Virus during Its Emergence in the 20th Century
Oumar Faye,Caio César de Melo Freire,Atila Iamarino,Ousmane Faye,Juliana Velasco Castro de Oliveira,Mawlouth Diallo,Paolo Marinho de Andrade Zanotto,Amadou A. Sall +7 more
TL;DR: Evidence is presented that ZIKV has possibly undergone recombination in nature and that a loss of the N154 glycosylation site in the envelope protein was a possible adaptive response to the Aedes dalzieli vector.
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The role of mutational robustness in RNA virus evolution.
TL;DR: This Review discusses the strategies used by RNA viruses to deal with the increased mutational load and considers how this mutational robustness might influence viral evolution and pathogenesis.
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Recombination in viruses: mechanisms, methods of study, and evolutionary consequences.
Marcos Pérez-Losada,Miguel Arenas,Juan Carlos Galán,Ferran Palero,Fernando González-Candelas +4 more
TL;DR: This review presents an overview of three major areas related to viral recombination, including the molecular mechanisms that underlie recombination in model viruses, the application of evolutionary reconstructions in the characterization of centralized genes for vaccine design, and the evaluation of linkage disequilibrium and population structure.
Journal ArticleDOI
Reassortment in segmented RNA viruses: mechanisms and outcomes.
TL;DR: Recent studies that examined the mechanisms and outcomes of reassortment for three well-studied viral families are discussed and how these findings provide new perspectives on the replication and evolution of segmented RNA viruses are discussed.
References
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The relation of recombination to mutational advance.
TL;DR: It is shown that this calculation does not apply for mutant genes that act advantageously only when in some special combinations with one or more other mutant genes, and that as far as these cases of special synergism are concerned recombining lines have no evolutionary advantage over non-recombining ones.
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Rates of evolutionary change in viruses: patterns and determinants.
TL;DR: It is shown that the high rate of nucleotide substitution in RNA viruses is matched by some DNA viruses, suggesting that evolutionary rates in viruses are explained by diverse aspects of viral biology, such as genomic architecture and replication speed, and not simply by polymerase fidelity.
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Viral mutation rates.
TL;DR: There appears to be a negative correlation between mutation rate and genome size among RNA viruses, and nucleotide substitutions are on average four times more common than insertions/deletions (indels) in retroviruses.
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Deleterious mutations and the evolution of sexual reproduction
TL;DR: If the deleterious mutation rate per genome per generation is greater than 1, then the greater efficiency of selection against these mutations in sexual populations may be responsible for the evolution of sex and related phenomena.
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A coalescent-based method for detecting and estimating recombination from gene sequences.
TL;DR: The extremely high level of recombination detected in both HIV1 and HIV2 sequences demonstrates that recombination cannot be ignored in the analysis of viral population genetic data and develops a powerful permutation-based method for detecting recombination that is both more powerful and robust to misspecification of the model of sequence evolution.