An integrated map of HIV genome-wide variation from a population perspective
| Autor(a) principal: | |
|---|---|
| Data de Publicação: | 2015 |
| Outros Autores: | , , , , , , , |
| Tipo de documento: | Artigo |
| Idioma: | eng |
| Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
| Texto Completo: | https://doi.org/10.1186/s12977-015-0148-6 |
Resumo: | PMID: 25808207 WOS:000350853000001 |
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oai:run.unl.pt:10362/36934 |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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7160 |
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An integrated map of HIV genome-wide variation from a population perspectiveConservationGenomic diversityHIV genomeHIV inter- and inter-clade genetic diversityHIV phylogenetic treeHIV-human protein interactionPeptide inhibitorProtein intrinsic disorderProtein multimerizationSelective pressureVirologyInfectious DiseasesSDG 3 - Good Health and Well-beingPMID: 25808207 WOS:000350853000001Background: 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.Instituto de Higiene e Medicina Tropical (IHMT)TB, HIV and opportunistic diseases and pathogens (THOP)Global Health and Tropical Medicine (GHTM)RUNLi, GuangdiPiampongsant, SupinyaFaria, Rodrigues N.Voet, ArnoutPineda-Peña, Andrea ClemenciaKhouri, RicardoLemey, PhilippeVandamme, Anne MiekeTheys, Kristof2018-05-14T22:01:54Z2015-02-152015-02-15T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttps://doi.org/10.1186/s12977-015-0148-6eng1742-4690PURE: 1726983http://www.scopus.com/inward/record.url?scp=84928747332&partnerID=8YFLogxKhttps://doi.org/10.1186/s12977-015-0148-6info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-03-11T04:20:29Zoai:run.unl.pt:10362/36934Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:30:42.588043Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
| dc.title.none.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 Conservation Genomic diversity HIV genome HIV inter- and inter-clade genetic diversity HIV phylogenetic tree HIV-human protein interaction Peptide inhibitor Protein intrinsic disorder Protein multimerization Selective pressure Virology Infectious Diseases SDG 3 - Good Health and Well-being |
| 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, Rodrigues N. Voet, Arnout Pineda-Peña, Andrea Clemencia Khouri, Ricardo Lemey, Philippe Vandamme, Anne Mieke Theys, Kristof |
| author_role |
author |
| author2 |
Piampongsant, Supinya Faria, Rodrigues N. Voet, Arnout Pineda-Peña, Andrea Clemencia Khouri, Ricardo Lemey, Philippe Vandamme, Anne Mieke Theys, Kristof |
| author2_role |
author author author author author author author author |
| dc.contributor.none.fl_str_mv |
Instituto de Higiene e Medicina Tropical (IHMT) TB, HIV and opportunistic diseases and pathogens (THOP) Global Health and Tropical Medicine (GHTM) RUN |
| dc.contributor.author.fl_str_mv |
Li, Guangdi Piampongsant, Supinya Faria, Rodrigues N. Voet, Arnout Pineda-Peña, Andrea Clemencia Khouri, Ricardo Lemey, Philippe Vandamme, Anne Mieke Theys, Kristof |
| dc.subject.por.fl_str_mv |
Conservation Genomic diversity HIV genome HIV inter- and inter-clade genetic diversity HIV phylogenetic tree HIV-human protein interaction Peptide inhibitor Protein intrinsic disorder Protein multimerization Selective pressure Virology Infectious Diseases SDG 3 - Good Health and Well-being |
| topic |
Conservation Genomic diversity HIV genome HIV inter- and inter-clade genetic diversity HIV phylogenetic tree HIV-human protein interaction Peptide inhibitor Protein intrinsic disorder Protein multimerization Selective pressure Virology Infectious Diseases SDG 3 - Good Health and Well-being |
| description |
PMID: 25808207 WOS:000350853000001 |
| publishDate |
2015 |
| dc.date.none.fl_str_mv |
2015-02-15 2015-02-15T00:00:00Z 2018-05-14T22:01:54Z |
| 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.uri.fl_str_mv |
https://doi.org/10.1186/s12977-015-0148-6 |
| url |
https://doi.org/10.1186/s12977-015-0148-6 |
| dc.language.iso.fl_str_mv |
eng |
| language |
eng |
| dc.relation.none.fl_str_mv |
1742-4690 PURE: 1726983 http://www.scopus.com/inward/record.url?scp=84928747332&partnerID=8YFLogxK https://doi.org/10.1186/s12977-015-0148-6 |
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info:eu-repo/semantics/openAccess |
| eu_rights_str_mv |
openAccess |
| dc.format.none.fl_str_mv |
application/pdf |
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reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
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RCAAP |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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