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Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy
Most HIV-1-infected individuals with virological failure on a pharmacologically-boosted protease inhibitor (PI) regimen do not develop PI-resistance protease mutations. One proposed explanation is that HIV-1 gag or gp41 cytoplasmic domain mutations might also reduce PI susceptibility. In a recent st...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6057438/ https://www.ncbi.nlm.nih.gov/pubmed/30040081 http://dx.doi.org/10.1038/sdata.2018.147 |
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author | Tzou, Philip L. Rhee, Soo-Yon Pond, Sergei L. Kosakovsky Manasa, Justen Shafer, Robert W. |
author_facet | Tzou, Philip L. Rhee, Soo-Yon Pond, Sergei L. Kosakovsky Manasa, Justen Shafer, Robert W. |
author_sort | Tzou, Philip L. |
collection | PubMed |
description | Most HIV-1-infected individuals with virological failure on a pharmacologically-boosted protease inhibitor (PI) regimen do not develop PI-resistance protease mutations. One proposed explanation is that HIV-1 gag or gp41 cytoplasmic domain mutations might also reduce PI susceptibility. In a recent study of paired gag and gp41 sequences from individuals with virological failure on a PI regimen, we did not identify PI-selected mutations and concluded that if such mutations existed, larger numbers of paired sequences from multiple studies would be needed for their identification. In this study, we generated site-specific amino acid profiles using gag and gp41 published sequences from 5,338 and 4,242 ART-naïve individuals, respectively, to assist researchers identify unusual mutations arising during therapy and to provide scripts for performing established and novel maximal likelihood estimates of dN/dS substitution rates in paired sequences. The pipelines used to generate the curated sequences, amino acid profiles, and dN/dS analyses will facilitate the application of consistent methods to paired gag and gp41 sequence datasets and expedite the identification of potential sites under PI-selection pressure. |
format | Online Article Text |
id | pubmed-6057438 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-60574382018-07-27 Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy Tzou, Philip L. Rhee, Soo-Yon Pond, Sergei L. Kosakovsky Manasa, Justen Shafer, Robert W. Sci Data Data Descriptor Most HIV-1-infected individuals with virological failure on a pharmacologically-boosted protease inhibitor (PI) regimen do not develop PI-resistance protease mutations. One proposed explanation is that HIV-1 gag or gp41 cytoplasmic domain mutations might also reduce PI susceptibility. In a recent study of paired gag and gp41 sequences from individuals with virological failure on a PI regimen, we did not identify PI-selected mutations and concluded that if such mutations existed, larger numbers of paired sequences from multiple studies would be needed for their identification. In this study, we generated site-specific amino acid profiles using gag and gp41 published sequences from 5,338 and 4,242 ART-naïve individuals, respectively, to assist researchers identify unusual mutations arising during therapy and to provide scripts for performing established and novel maximal likelihood estimates of dN/dS substitution rates in paired sequences. The pipelines used to generate the curated sequences, amino acid profiles, and dN/dS analyses will facilitate the application of consistent methods to paired gag and gp41 sequence datasets and expedite the identification of potential sites under PI-selection pressure. Nature Publishing Group 2018-07-24 /pmc/articles/PMC6057438/ /pubmed/30040081 http://dx.doi.org/10.1038/sdata.2018.147 Text en Copyright © 2018, The Author(s) http://creativecommons.org/licenses/by/4.0/ Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ The Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the metadata files made available in this article. |
spellingShingle | Data Descriptor Tzou, Philip L. Rhee, Soo-Yon Pond, Sergei L. Kosakovsky Manasa, Justen Shafer, Robert W. Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy |
title | Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy |
title_full | Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy |
title_fullStr | Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy |
title_full_unstemmed | Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy |
title_short | Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy |
title_sort | selection analyses of paired hiv-1 gag and gp41 sequences obtained before and after antiretroviral therapy |
topic | Data Descriptor |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6057438/ https://www.ncbi.nlm.nih.gov/pubmed/30040081 http://dx.doi.org/10.1038/sdata.2018.147 |
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