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In Vivo Emergence of a Novel Protease Inhibitor Resistance Signature in HIV-1 Matrix

Protease inhibitors (PIs) are the second- and last-line therapy for the majority of HIV-infected patients worldwide. Only around 20% of individuals who fail PI regimens develop major resistance mutations in protease. We sought to explore the role of mutations in gag-pro genotypic and phenotypic chan...

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Autores principales: Datir, Rawlings, Kemp, Steven, El Bouzidi, Kate, Mlchocova, Petra, Goldstein, Richard, Breuer, Judy, Towers, Greg J., Jolly, Clare, Quiñones-Mateu, Miguel E., Dakum, Patrick S., Ndembi, Nicaise, Gupta, Ravindra K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Society for Microbiology 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7642677/
https://www.ncbi.nlm.nih.gov/pubmed/33144375
http://dx.doi.org/10.1128/mBio.02036-20
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author Datir, Rawlings
Kemp, Steven
El Bouzidi, Kate
Mlchocova, Petra
Goldstein, Richard
Breuer, Judy
Towers, Greg J.
Jolly, Clare
Quiñones-Mateu, Miguel E.
Dakum, Patrick S.
Ndembi, Nicaise
Gupta, Ravindra K.
author_facet Datir, Rawlings
Kemp, Steven
El Bouzidi, Kate
Mlchocova, Petra
Goldstein, Richard
Breuer, Judy
Towers, Greg J.
Jolly, Clare
Quiñones-Mateu, Miguel E.
Dakum, Patrick S.
Ndembi, Nicaise
Gupta, Ravindra K.
author_sort Datir, Rawlings
collection PubMed
description Protease inhibitors (PIs) are the second- and last-line therapy for the majority of HIV-infected patients worldwide. Only around 20% of individuals who fail PI regimens develop major resistance mutations in protease. We sought to explore the role of mutations in gag-pro genotypic and phenotypic changes in viruses from six Nigerian patients who failed PI-based regimens without known drug resistance-associated protease mutations in order to identify novel determinants of PI resistance. Target enrichment and next-generation sequencing (NGS) with the Illumina MiSeq system were followed by haplotype reconstruction. Full-length Gag-protease gene regions were amplified from baseline (pre-PI) and virologic failure (VF) samples, sequenced, and used to construct gag-pro-pseudotyped viruses. Phylogenetic analysis was performed using maximum-likelihood methods. Susceptibility to lopinavir (LPV) and darunavir (DRV) was measured using a single-cycle replication assay. Western blotting was used to analyze Gag cleavage. In one of six participants (subtype CRF02_AG), we found 4-fold-lower LPV susceptibility in viral clones during failure of second-line treatment. A combination of four mutations (S126del, H127del, T122A, and G123E) in the p17 matrix of baseline virus generated a similar 4-fold decrease in susceptibility to LPV but not darunavir. These four amino acid changes were also able to confer LPV resistance to a subtype B Gag-protease backbone. Western blotting demonstrated significant Gag cleavage differences between sensitive and resistant isolates in the presence of drug. Resistant viruses had around 2-fold-lower infectivity than sensitive clones in the absence of drug. NGS combined with haplotype reconstruction revealed that resistant, less fit clones emerged from a minority population at baseline and thereafter persisted alongside sensitive fitter viruses. We used a multipronged genotypic and phenotypic approach to document emergence and temporal dynamics of a novel protease inhibitor resistance signature in HIV-1 matrix, revealing the interplay between Gag-associated resistance and fitness.
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spelling pubmed-76426772020-11-17 In Vivo Emergence of a Novel Protease Inhibitor Resistance Signature in HIV-1 Matrix Datir, Rawlings Kemp, Steven El Bouzidi, Kate Mlchocova, Petra Goldstein, Richard Breuer, Judy Towers, Greg J. Jolly, Clare Quiñones-Mateu, Miguel E. Dakum, Patrick S. Ndembi, Nicaise Gupta, Ravindra K. mBio Research Article Protease inhibitors (PIs) are the second- and last-line therapy for the majority of HIV-infected patients worldwide. Only around 20% of individuals who fail PI regimens develop major resistance mutations in protease. We sought to explore the role of mutations in gag-pro genotypic and phenotypic changes in viruses from six Nigerian patients who failed PI-based regimens without known drug resistance-associated protease mutations in order to identify novel determinants of PI resistance. Target enrichment and next-generation sequencing (NGS) with the Illumina MiSeq system were followed by haplotype reconstruction. Full-length Gag-protease gene regions were amplified from baseline (pre-PI) and virologic failure (VF) samples, sequenced, and used to construct gag-pro-pseudotyped viruses. Phylogenetic analysis was performed using maximum-likelihood methods. Susceptibility to lopinavir (LPV) and darunavir (DRV) was measured using a single-cycle replication assay. Western blotting was used to analyze Gag cleavage. In one of six participants (subtype CRF02_AG), we found 4-fold-lower LPV susceptibility in viral clones during failure of second-line treatment. A combination of four mutations (S126del, H127del, T122A, and G123E) in the p17 matrix of baseline virus generated a similar 4-fold decrease in susceptibility to LPV but not darunavir. These four amino acid changes were also able to confer LPV resistance to a subtype B Gag-protease backbone. Western blotting demonstrated significant Gag cleavage differences between sensitive and resistant isolates in the presence of drug. Resistant viruses had around 2-fold-lower infectivity than sensitive clones in the absence of drug. NGS combined with haplotype reconstruction revealed that resistant, less fit clones emerged from a minority population at baseline and thereafter persisted alongside sensitive fitter viruses. We used a multipronged genotypic and phenotypic approach to document emergence and temporal dynamics of a novel protease inhibitor resistance signature in HIV-1 matrix, revealing the interplay between Gag-associated resistance and fitness. American Society for Microbiology 2020-11-03 /pmc/articles/PMC7642677/ /pubmed/33144375 http://dx.doi.org/10.1128/mBio.02036-20 Text en Copyright © 2020 Datir et al. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Research Article
Datir, Rawlings
Kemp, Steven
El Bouzidi, Kate
Mlchocova, Petra
Goldstein, Richard
Breuer, Judy
Towers, Greg J.
Jolly, Clare
Quiñones-Mateu, Miguel E.
Dakum, Patrick S.
Ndembi, Nicaise
Gupta, Ravindra K.
In Vivo Emergence of a Novel Protease Inhibitor Resistance Signature in HIV-1 Matrix
title In Vivo Emergence of a Novel Protease Inhibitor Resistance Signature in HIV-1 Matrix
title_full In Vivo Emergence of a Novel Protease Inhibitor Resistance Signature in HIV-1 Matrix
title_fullStr In Vivo Emergence of a Novel Protease Inhibitor Resistance Signature in HIV-1 Matrix
title_full_unstemmed In Vivo Emergence of a Novel Protease Inhibitor Resistance Signature in HIV-1 Matrix
title_short In Vivo Emergence of a Novel Protease Inhibitor Resistance Signature in HIV-1 Matrix
title_sort in vivo emergence of a novel protease inhibitor resistance signature in hiv-1 matrix
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7642677/
https://www.ncbi.nlm.nih.gov/pubmed/33144375
http://dx.doi.org/10.1128/mBio.02036-20
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