An integrated map of HIV genome-wide variation from a population perspective.

Detalhes bibliográficos
Autor(a) principal: Li, Guangdi
Data de Publicação: 2015
Outros Autores: Piampongsant, Supinya, Faria, Nuno Rodrigues, Voet, Arnout, Peña, Andrea-Clemencia Pineda, Cunha, Antonio Ricardo Khouri, Lemey, Philippe, Vandamme, Anne-Mieke, Theys, Kristof
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
DOI: 10.1186/s12977-015-0148-6
Texto Completo: https://www.arca.fiocruz.br/handle/icict/10577
Resumo: Central South University. Metabolic Syndrome Research Center. Second Xiangya Hospital. Changsha, Hunan, China / Rega Institute for Medical Research. Department of Microbiology and Immunology. KU Leuven, Leuven, Belgium
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spelling Li, GuangdiPiampongsant, SupinyaFaria, Nuno RodriguesVoet, ArnoutPeña, Andrea-Clemencia PinedaCunha, Antonio Ricardo KhouriLemey, PhilippeVandamme, Anne-MiekeTheys, Kristof2015-05-28T16:52:46Z2015-05-28T16:52:46Z2015LI, G. et al. An integrated map of HIV genome-wide variation from a population perspective. Retrovirology, v. 12, n. 1, p. 18, 2015.1742-4690https://www.arca.fiocruz.br/handle/icict/1057710.1186/s12977-015-0148-6engBioMed CentralAn integrated map of HIV genome-wide variation from a population perspective.info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleCentral South University. Metabolic Syndrome Research Center. Second Xiangya Hospital. Changsha, Hunan, China / Rega Institute for Medical Research. Department of Microbiology and Immunology. KU Leuven, Leuven, BelgiumCentral South University. Metabolic Syndrome Research Center. Second Xiangya Hospital. Changsha, Hunan, China / Rega Institute for Medical Research. Department of Microbiology and Immunology. KU Leuven, Leuven, BelgiumUniversity of Oxford. Department of Zoology. Oxford, UKRIKEN Institute Laboratories. Zhang IRU. Hirosawa, Wako-shi, Saitama, JapanRega Institute for Medical Research. Department of Microbiology and Immunology. KU Leuven, Leuven, Belgium / Universidad del Rosario. Faculty of Sciences and Mathematics. Clinical and Molecular Infectious Disease Group. Bogotá, ColombiaRega Institute for Medical Research. Department of Microbiology and Immunology. KU Leuven, Leuven, Belgium / Fundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz. Salvador, BA, BrasilRega Institute for Medical Research. Department of Microbiology and Immunology. KU Leuven, Leuven, BelgiumRega Institute for Medical Research. Department of Microbiology and Immunology. KU Leuven, Leuven, Belgium / Universidade Nova de Lisboa. Instituto de Higiene e Medicina Tropical. Centro de Malária e Outras Doenças Tropicais and Unidade de Microbiologia. Lisbon, PortugalRega Institute for Medical Research. Department of Microbiology and Immunology. KU Leuven, Leuven, BelgiumBACKGROUND: The HIV pandemic is characterized by extensive genetic variability, which has challenged the development of HIV drugs and vaccines. Although HIV genomes have been classified into different types, groups, subtypes and recombinants, a comprehensive study that maps HIV genome-wide diversity at the population level is still lacking to date. This study aims to characterize HIV genomic diversity in large-scale sequence populations, and to identify driving factors that shape HIV genome diversity. RESULTS: A total of 2996 full-length genomic sequences from 1705 patients infected with 16 major HIV groups, subtypes and circulating recombinant forms (CRFs) were analyzed along with structural, immunological and peptide inhibitor information. Average nucleotide diversity of HIV genomes was almost 50% between HIV-1 and HIV-2 types, 37.5% between HIV-1 groups, 14.7% between HIV-1 subtypes, 8.2% within individual HIV-1 subtypes and less than 1% within single patients. Along the HIV genome, diversity patterns and compositions of nucleotides and amino acids were highly similar across different groups, subtypes and CRFs. Current HIV-derived peptide inhibitors were predominantly derived from conserved, solvent accessible and intrinsically ordered structures in the HIV-1 subtype B genome. We identified these conserved regions in Capsid, Nucleocapsid, Protease, Integrase, Reverse transcriptase, Vpr and the GP41 N terminus as potential drug targets. In the analysis of factors that impact HIV-1 genomic diversity, we focused on protein multimerization, immunological constraints and HIV-human protein interactions. We found that amino acid diversity in monomeric proteins was higher than in multimeric proteins, and diversified positions were preferably located within human CD4 T cell and antibody epitopes. Moreover, intrinsic disorder regions in HIV-1 proteins coincided with high levels of amino acid diversity, facilitating a large number of interactions between HIV-1 and human proteins. CONCLUSIONS: This first large-scale analysis provided a detailed mapping of HIV genomic diversity and highlighted drug-target regions conserved across different groups, subtypes and CRFs. Our findings suggest that, in addition to the impact of protein multimerization and immune selective pressure on HIV-1 diversity, HIV-human protein interactions are facilitated by high variability within intrinsically disordered structures.HIV genomeGenomic diversityConservationPeptide inhibitorHIV-human protein interactionHIVPhylogenetic treeHIV inter- and inter-clade genetic diversitySelective pressureProtein multimerizationProtein intrinsic disorderinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82352https://www.arca.fiocruz.br/bitstream/icict/10577/1/license.txtafbdf7d7a9bcf771a1cc7edf5f618413MD51ORIGINALLi G An integrated....pdfLi G An integrated....pdfapplication/pdf2975526https://www.arca.fiocruz.br/bitstream/icict/10577/2/Li%20G%20An%20integrated....pdf76e738ffcb4e9d5712da80b51e3b1116MD52TEXTLi G An integrated....pdf.txtLi G An integrated....pdf.txtExtracted texttext/plain69653https://www.arca.fiocruz.br/bitstream/icict/10577/3/Li%20G%20An%20integrated....pdf.txt4ae45255f303a707beac71ced6a9ead2MD53icict/105772023-03-15 14:33:22.352oai:www.arca.fiocruz.br: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ório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352023-03-15T17:33:22Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false
dc.title.pt_BR.fl_str_mv An integrated map of HIV genome-wide variation from a population perspective.
title An integrated map of HIV genome-wide variation from a population perspective.
spellingShingle An integrated map of HIV genome-wide variation from a population perspective.
Li, Guangdi
HIV genome
Genomic diversity
Conservation
Peptide inhibitor
HIV-human protein interaction
HIV
Phylogenetic tree
HIV inter- and inter-clade genetic diversity
Selective pressure
Protein multimerization
Protein intrinsic disorder
title_short An integrated map of HIV genome-wide variation from a population perspective.
title_full An integrated map of HIV genome-wide variation from a population perspective.
title_fullStr An integrated map of HIV genome-wide variation from a population perspective.
title_full_unstemmed An integrated map of HIV genome-wide variation from a population perspective.
title_sort An integrated map of HIV genome-wide variation from a population perspective.
author Li, Guangdi
author_facet Li, Guangdi
Piampongsant, Supinya
Faria, Nuno Rodrigues
Voet, Arnout
Peña, Andrea-Clemencia Pineda
Cunha, Antonio Ricardo Khouri
Lemey, Philippe
Vandamme, Anne-Mieke
Theys, Kristof
author_role author
author2 Piampongsant, Supinya
Faria, Nuno Rodrigues
Voet, Arnout
Peña, Andrea-Clemencia Pineda
Cunha, Antonio Ricardo Khouri
Lemey, Philippe
Vandamme, Anne-Mieke
Theys, Kristof
author2_role author
author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv Li, Guangdi
Piampongsant, Supinya
Faria, Nuno Rodrigues
Voet, Arnout
Peña, Andrea-Clemencia Pineda
Cunha, Antonio Ricardo Khouri
Lemey, Philippe
Vandamme, Anne-Mieke
Theys, Kristof
dc.subject.en.pt_BR.fl_str_mv HIV genome
Genomic diversity
Conservation
Peptide inhibitor
HIV-human protein interaction
HIV
Phylogenetic tree
HIV inter- and inter-clade genetic diversity
Selective pressure
Protein multimerization
Protein intrinsic disorder
topic HIV genome
Genomic diversity
Conservation
Peptide inhibitor
HIV-human protein interaction
HIV
Phylogenetic tree
HIV inter- and inter-clade genetic diversity
Selective pressure
Protein multimerization
Protein intrinsic disorder
description Central South University. Metabolic Syndrome Research Center. Second Xiangya Hospital. Changsha, Hunan, China / Rega Institute for Medical Research. Department of Microbiology and Immunology. KU Leuven, Leuven, Belgium
publishDate 2015
dc.date.accessioned.fl_str_mv 2015-05-28T16:52:46Z
dc.date.available.fl_str_mv 2015-05-28T16:52:46Z
dc.date.issued.fl_str_mv 2015
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.citation.fl_str_mv LI, G. et al. An integrated map of HIV genome-wide variation from a population perspective. Retrovirology, v. 12, n. 1, p. 18, 2015.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/10577
dc.identifier.issn.none.fl_str_mv 1742-4690
dc.identifier.doi.none.fl_str_mv 10.1186/s12977-015-0148-6
identifier_str_mv LI, G. et al. An integrated map of HIV genome-wide variation from a population perspective. Retrovirology, v. 12, n. 1, p. 18, 2015.
1742-4690
10.1186/s12977-015-0148-6
url https://www.arca.fiocruz.br/handle/icict/10577
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
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