Genealogical evidence for positive selection in the nef gene of HIV-1
Autor(a) principal: | |
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Data de Publicação: | 1999 |
Outros Autores: | , , |
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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Repositório Institucional da UNIFESP |
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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 |
_version_ |
1818602581291696128 |