Frequent toggling between alternative amino acids is driven by selection in HIV-1

 

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dc.contributor.author Delport, Wayne en_ZA
dc.contributor.author Scheffler, Konrad en_ZA
dc.contributor.author Seoighe, Cathal en_ZA
dc.date.accessioned 2016-01-02T05:05:50Z
dc.date.available 2016-01-02T05:05:50Z
dc.date.issued 2008 en_ZA
dc.identifier.citation Delport, W., Scheffler, K., & Seoighe, C. (2008). Frequent toggling between alternative amino acids is driven by selection in HIV-1. PLoS pathogens, 4(12), e1000242. doi:10.1371/journal.ppat.1000242 en_ZA
dc.identifier.uri http://hdl.handle.net/11427/16167
dc.identifier.uri http://dx.doi.org/10.1371/journal.ppat.1000242
dc.description.abstract Author Summary Viruses, such as HIV, are able to evade host immune responses through escape mutations, yet sometimes they do so at a cost. This cost is the reduction in the ability of the virus to replicate, and thus selective pressure exists for a virus to revert to its original state in the absence of the host immune response that caused the initial escape mutation. This pattern of escape and reversion typically occurs when viruses are transmitted between individuals with different immune responses. We develop a phylogenetic model of immune escape and reversion and provide evidence that it outperforms existing models for the detection of selective pressure associated with host immune responses. Finally, we demonstrate that amino acid toggling is a pervasive process in HIV-1 evolution, such that many of the positions in the virus that evolve rapidly, under the influence of positive Darwinian selection, nonetheless display quite low sequence diversity. This highlights the limitations of HIV-1 evolution, and sites such as these are potentially good targets for HIV-1 vaccines. en_ZA
dc.language.iso eng en_ZA
dc.publisher Public Library of Science en_ZA
dc.rights This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. en_ZA
dc.rights.uri http://creativecommons.org/licenses/by/4.0 en_ZA
dc.source PLoS One en_ZA
dc.source.uri http://journals.plos.org/plospathogens en_ZA
dc.subject.other Natural selection en_ZA
dc.subject.other Immune response en_ZA
dc.subject.other HIV-1 en_ZA
dc.subject.other Phylogenetic analysis en_ZA
dc.subject.other Amino acid substitution en_ZA
dc.subject.other Phylogenetics en_ZA
dc.subject.other Sequence alignment en_ZA
dc.subject.other Simulation and modeling en_ZA
dc.title Frequent toggling between alternative amino acids is driven by selection in HIV-1 en_ZA
dc.type Journal Article en_ZA
dc.rights.holder © 2008 Delport et al en_ZA
uct.type.publication Research en_ZA
uct.type.resource Article en_ZA
dc.publisher.institution University of Cape Town
dc.publisher.faculty Faculty of Health Sciences en_ZA
dc.publisher.department Institute of Infectious Disease and Molecular Medicine en_ZA
uct.type.filetype Text
uct.type.filetype Image


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This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Except where otherwise noted, this item's license is described as This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.