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

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dc.contributor.authorDelport, Wayneen_ZA
dc.contributor.authorScheffler, Konraden_ZA
dc.contributor.authorSeoighe, Cathalen_ZA
dc.date.accessioned2016-01-02T05:05:50Z
dc.date.available2016-01-02T05:05:50Z
dc.date.issued2008en_ZA
dc.description.abstractAuthor 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.identifier.apacitationDelport, W., Scheffler, K., & Seoighe, C. (2008). Frequent toggling between alternative amino acids is driven by selection in HIV-1. <i>PLoS One</i>, http://hdl.handle.net/11427/16167en_ZA
dc.identifier.chicagocitationDelport, Wayne, Konrad Scheffler, and Cathal Seoighe "Frequent toggling between alternative amino acids is driven by selection in HIV-1." <i>PLoS One</i> (2008) http://hdl.handle.net/11427/16167en_ZA
dc.identifier.citationDelport, 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.1000242en_ZA
dc.identifier.ris TY - Journal Article AU - Delport, Wayne AU - Scheffler, Konrad AU - Seoighe, Cathal AB - 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. DA - 2008 DB - OpenUCT DO - 10.1371/journal.ppat.1000242 DP - University of Cape Town J1 - PLoS One LK - https://open.uct.ac.za PB - University of Cape Town PY - 2008 T1 - Frequent toggling between alternative amino acids is driven by selection in HIV-1 TI - Frequent toggling between alternative amino acids is driven by selection in HIV-1 UR - http://hdl.handle.net/11427/16167 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/16167
dc.identifier.urihttp://dx.doi.org/10.1371/journal.ppat.1000242
dc.identifier.vancouvercitationDelport W, Scheffler K, Seoighe C. Frequent toggling between alternative amino acids is driven by selection in HIV-1. PLoS One. 2008; http://hdl.handle.net/11427/16167.en_ZA
dc.language.isoengen_ZA
dc.publisherPublic Library of Scienceen_ZA
dc.publisher.departmentInstitute of Infectious Disease and Molecular Medicineen_ZA
dc.publisher.facultyFaculty of Health Sciencesen_ZA
dc.publisher.institutionUniversity of Cape Town
dc.rightsThis 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.holder© 2008 Delport et alen_ZA
dc.rights.urihttp://creativecommons.org/licenses/by/4.0en_ZA
dc.sourcePLoS Oneen_ZA
dc.source.urihttp://journals.plos.org/plospathogensen_ZA
dc.subject.otherNatural selectionen_ZA
dc.subject.otherImmune responseen_ZA
dc.subject.otherHIV-1en_ZA
dc.subject.otherPhylogenetic analysisen_ZA
dc.subject.otherAmino acid substitutionen_ZA
dc.subject.otherPhylogeneticsen_ZA
dc.subject.otherSequence alignmenten_ZA
dc.subject.otherSimulation and modelingen_ZA
dc.titleFrequent toggling between alternative amino acids is driven by selection in HIV-1en_ZA
dc.typeJournal Articleen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceArticleen_ZA
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