Genealogical evidence for positive selection in the nef gene of HIV-1

Detalhes bibliográficos
Autor(a) principal: Zanotto, Paolo Marinho de Andrade [UNIFESP]
Data de Publicação: 1999
Outros Autores: Kallas, Esper Georges [UNIFESP], Souza, Robson F. de, Holmes, Edward C.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UNIFESP
dARK ID: ark:/48912/0013000016bcz
Texto Completo: http://www.genetics.org/content/153/3/1077.long
http://repositorio.unifesp.br/handle/11600/43725
Resumo: The pattern and process of evolution in the nef gene of HIV-1 was analyzed within and among patients. Using a maximum likelihood method that allows for variable intensity of selection pressure among codons, strong positive selection was detected in a hemophiliac patient over 30 mo of infection. By reconstructing the process of allele substitution in this patient using parsimony, the synapomorphic amino acid changes separating each time point were found to have high probabilities of being under positive selection, with selective coefficients of at least 3.6%. Positive selection was also detected among 39 nef sequences from HIV-1 subtype B. Tn contrast, multiple pairwise comparisons of nonsynonymous and synonymous substitution rates provided no good evidence for positive selection and sliding window analyses failed to detect most positively selected sites. These findings demonstrate that positive selection is an important determinant of nef gene evolution and that genealogy-based methods outperform pairwise methods in the detection of adaptive evolution. Mapping the locations of positively selected sites may also be of use in identifying targets of the immune response and hence aid vaccine design.
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spelling Genealogical evidence for positive selection in the nef gene of HIV-1The pattern and process of evolution in the nef gene of HIV-1 was analyzed within and among patients. Using a maximum likelihood method that allows for variable intensity of selection pressure among codons, strong positive selection was detected in a hemophiliac patient over 30 mo of infection. By reconstructing the process of allele substitution in this patient using parsimony, the synapomorphic amino acid changes separating each time point were found to have high probabilities of being under positive selection, with selective coefficients of at least 3.6%. Positive selection was also detected among 39 nef sequences from HIV-1 subtype B. Tn contrast, multiple pairwise comparisons of nonsynonymous and synonymous substitution rates provided no good evidence for positive selection and sliding window analyses failed to detect most positively selected sites. These findings demonstrate that positive selection is an important determinant of nef gene evolution and that genealogy-based methods outperform pairwise methods in the detection of adaptive evolution. Mapping the locations of positively selected sites may also be of use in identifying targets of the immune response and hence aid vaccine design.Univ Sao Paulo, Escola Paulista Med, Bioinformat & Retrovirol Lab, BR-05508900 Sao Paulo, BrazilUniv Sao Paulo, Escola Paulista Med, Immunol Lab, DIPA, BR-05508900 Sao Paulo, BrazilUniv Oxford, Dept Zool, Wellcome Trust Ctr Epidemiol Infect Dis, Oxford OX1 3PS, EnglandUniv Sao Paulo, Escola Paulista Med, Bioinformat & Retrovirol Lab, BR-05508900 Sao Paulo, BrazilUniv Sao Paulo, Escola Paulista Med, Immunol Lab, DIPA, BR-05508900 Sao Paulo, BrazilWeb of ScienceGeneticsUniversidade Federal de São Paulo (UNIFESP)Univ OxfordZanotto, Paolo Marinho de Andrade [UNIFESP]Kallas, Esper Georges [UNIFESP]Souza, Robson F. deHolmes, Edward C.2018-06-15T17:30:21Z2018-06-15T17:30:21Z1999-11-01info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersion1077-1089http://www.genetics.org/content/153/3/1077.longGenetics. Baltimore: Genetics, v. 153, n. 3, p. 1077-1089, 1999.0016-6731http://repositorio.unifesp.br/handle/11600/43725WOS:000083539500002ark:/48912/0013000016bczengGeneticsinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da UNIFESPinstname:Universidade Federal de São Paulo (UNIFESP)instacron:UNIFESP2024-05-02T11:58:36Zoai:repositorio.unifesp.br/:11600/43725Repositório InstitucionalPUBhttp://www.repositorio.unifesp.br/oai/requestbiblioteca.csp@unifesp.bropendoar:34652024-12-11T20:59:16.652304Repositório Institucional da UNIFESP - Universidade Federal de São Paulo (UNIFESP)false
dc.title.none.fl_str_mv Genealogical evidence for positive selection in the nef gene of HIV-1
title Genealogical evidence for positive selection in the nef gene of HIV-1
spellingShingle Genealogical evidence for positive selection in the nef gene of HIV-1
Zanotto, Paolo Marinho de Andrade [UNIFESP]
title_short Genealogical evidence for positive selection in the nef gene of HIV-1
title_full Genealogical evidence for positive selection in the nef gene of HIV-1
title_fullStr Genealogical evidence for positive selection in the nef gene of HIV-1
title_full_unstemmed Genealogical evidence for positive selection in the nef gene of HIV-1
title_sort Genealogical evidence for positive selection in the nef gene of HIV-1
author Zanotto, Paolo Marinho de Andrade [UNIFESP]
author_facet Zanotto, Paolo Marinho de Andrade [UNIFESP]
Kallas, Esper Georges [UNIFESP]
Souza, Robson F. de
Holmes, Edward C.
author_role author
author2 Kallas, Esper Georges [UNIFESP]
Souza, Robson F. de
Holmes, Edward C.
author2_role author
author
author
dc.contributor.none.fl_str_mv Universidade Federal de São Paulo (UNIFESP)
Univ Oxford
dc.contributor.author.fl_str_mv Zanotto, Paolo Marinho de Andrade [UNIFESP]
Kallas, Esper Georges [UNIFESP]
Souza, Robson F. de
Holmes, Edward C.
description The pattern and process of evolution in the nef gene of HIV-1 was analyzed within and among patients. Using a maximum likelihood method that allows for variable intensity of selection pressure among codons, strong positive selection was detected in a hemophiliac patient over 30 mo of infection. By reconstructing the process of allele substitution in this patient using parsimony, the synapomorphic amino acid changes separating each time point were found to have high probabilities of being under positive selection, with selective coefficients of at least 3.6%. Positive selection was also detected among 39 nef sequences from HIV-1 subtype B. Tn contrast, multiple pairwise comparisons of nonsynonymous and synonymous substitution rates provided no good evidence for positive selection and sliding window analyses failed to detect most positively selected sites. These findings demonstrate that positive selection is an important determinant of nef gene evolution and that genealogy-based methods outperform pairwise methods in the detection of adaptive evolution. Mapping the locations of positively selected sites may also be of use in identifying targets of the immune response and hence aid vaccine design.
publishDate 1999
dc.date.none.fl_str_mv 1999-11-01
2018-06-15T17:30:21Z
2018-06-15T17:30:21Z
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://www.genetics.org/content/153/3/1077.long
Genetics. Baltimore: Genetics, v. 153, n. 3, p. 1077-1089, 1999.
0016-6731
http://repositorio.unifesp.br/handle/11600/43725
WOS:000083539500002
dc.identifier.dark.fl_str_mv ark:/48912/0013000016bcz
url http://www.genetics.org/content/153/3/1077.long
http://repositorio.unifesp.br/handle/11600/43725
identifier_str_mv Genetics. Baltimore: Genetics, v. 153, n. 3, p. 1077-1089, 1999.
0016-6731
WOS:000083539500002
ark:/48912/0013000016bcz
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Genetics
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 1077-1089
dc.publisher.none.fl_str_mv Genetics
publisher.none.fl_str_mv Genetics
dc.source.none.fl_str_mv reponame:Repositório Institucional da UNIFESP
instname:Universidade Federal de São Paulo (UNIFESP)
instacron:UNIFESP
instname_str Universidade Federal de São Paulo (UNIFESP)
instacron_str UNIFESP
institution UNIFESP
reponame_str Repositório Institucional da UNIFESP
collection Repositório Institucional da UNIFESP
repository.name.fl_str_mv Repositório Institucional da UNIFESP - Universidade Federal de São Paulo (UNIFESP)
repository.mail.fl_str_mv biblioteca.csp@unifesp.br
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