ArticleBMC evolutionary biology2008
Selection dramatically reduces effective population size in HIV-1 infection.
Article in BMC evolutionary biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- A theoretical analysis of taxonomic binning accuracy.Molecular ecology resources · 2022Article
- Two-year longitudinal survey reveals high genetic diversity of Schistosoma mansoni with adult worms surviving praziquantel treatment at the start of mass drug administration in Uganda.Parasites & vectors · 2019Article
- Understanding Past Population Dynamics: Bayesian Coalescent-Based Modeling with Covariates.Systematic biology · 2016Article
- Estimating the Effective Population Size from Temporal Allele Frequency Changes in Experimental Evolution.Genetics · 2016Article
- Investigating the Consequences of Interference between Multiple CD8+ T Cell Escape Mutations in Early HIV Infection.PLoS computational biology · 2016Article
- Population genetics inference for longitudinally-sampled mutants under strong selection.Genetics · 2014Article
- HIV populations are large and accumulate high genetic diversity in a nonlinear fashion.Journal of virology · 2013Article
- The dynamics of HIV-1 adaptation in early infection.Genetics · 2012Article
- Stochastic simulations suggest that HIV-1 survives close to its error threshold.PLoS computational biology · 2012Article
- Fitness costs and diversity of the cytotoxic T lymphocyte (CTL) response determine the rate of CTL escape during acute and chronic phases of HIV infection.Journal of virology · 2011Article
- Genetic drift of HIV populations in culture.PLoS genetics · 2009Article
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Authors and funding
2 authors.
Funding
Abstract
backgroundIn HIV-1 evolution, a 100-100,000 fold discrepancy between census size and effective population size (Ne) has been noted. Although it is well known that selection can reduce Ne, high in vivo mutation and recombination rates complicate attempts to quantify the effects of selection on HIV-1 effective size.
resultsWe use the inbreeding coefficient and the variance in allele frequency at a linked neutral locus to estimate the reduction in Ne due to selection in the presence of mutation and recombination. With biologically realistic mutation rates, the reduction in Ne due to selection is determined by the strength of selection, i.e., the stronger the selection, the greater the reduction. However, the dependence of Ne on selection can break down if recombination rates are very high (e.g., r > or = 0.1). With biologically likely recombination rates, our model suggests that recurrent selective sweeps similar to those observed in vivo can reduce within-host HIV-1 effective population sizes by a factor of 300 or more.
conclusionAlthough other factors, such as unequal viral reproduction rates and limited migration between tissue compartments contribute to reductions in Ne, our model suggests that recurrent selection plays a significant role in reducing HIV-1 effective population sizes in vivo.
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