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Measuring integrated HIV DNA ex vivo and in vitro provides insights about how reservoirs are formed and maintained
The identification of the most appropriate marker to measure reservoir size has been a great challenge for the HIV field. Quantitative viral outgrowth assay (QVOA), the reference standard to quantify the amount of replication-competent virus, has several limitations, as it is laborious, expensive, a...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5816390/ https://www.ncbi.nlm.nih.gov/pubmed/29452580 http://dx.doi.org/10.1186/s12977-018-0396-3 |
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author | Pinzone, Marilia Rita O’Doherty, Una |
author_facet | Pinzone, Marilia Rita O’Doherty, Una |
author_sort | Pinzone, Marilia Rita |
collection | PubMed |
description | The identification of the most appropriate marker to measure reservoir size has been a great challenge for the HIV field. Quantitative viral outgrowth assay (QVOA), the reference standard to quantify the amount of replication-competent virus, has several limitations, as it is laborious, expensive, and unable to robustly reactivate every single integrated provirus. PCR-based assays have been developed as an easier, cheaper and less error-prone alternative to QVOA, but also have limitations. Historically, measuring integrated HIV DNA has provided insights about how reservoirs are formed and maintained. In the 1990s, measuring integrated HIV DNA was instrumental in understanding that a subset of resting CD4 T cells containing integrated HIV DNA were the major source of replication-competent virus. Follow-up studies have further characterized the phenotype of these cells containing integrated HIV DNA, as well as shown the correlation between the integration levels and clinical parameters, such as duration of infection, CD4 count and viral load. Integrated HIV DNA correlates with total HIV measures and with QVOA. The integration assay has several limitations. First, it largely overestimates the reservoir size, as both defective and replication-competent proviruses are detected. Since defective proviruses are the majority in patients on ART, it follows that the number of proviruses capable of reactivating and releasing new virions is significantly smaller than the number of integrated proviruses. Second, in patients on ART clonal expansion could theoretically lead to the preferential amplification of proviruses close to an Alu sequence though longitudinal studies have not captured this effect. Proviral sequencing combined with integration measures is probably the best estimate of reservoir size, but it is expensive, time-consuming and requires considerable bioinformatics expertise. All these reasons limit its use on a large scale. Herein, we review the utility of measuring HIV integration and suggest combining it with sequencing and total HIV measurements can provide insights that underlie reservoir maintenance. |
format | Online Article Text |
id | pubmed-5816390 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-58163902018-02-21 Measuring integrated HIV DNA ex vivo and in vitro provides insights about how reservoirs are formed and maintained Pinzone, Marilia Rita O’Doherty, Una Retrovirology Review The identification of the most appropriate marker to measure reservoir size has been a great challenge for the HIV field. Quantitative viral outgrowth assay (QVOA), the reference standard to quantify the amount of replication-competent virus, has several limitations, as it is laborious, expensive, and unable to robustly reactivate every single integrated provirus. PCR-based assays have been developed as an easier, cheaper and less error-prone alternative to QVOA, but also have limitations. Historically, measuring integrated HIV DNA has provided insights about how reservoirs are formed and maintained. In the 1990s, measuring integrated HIV DNA was instrumental in understanding that a subset of resting CD4 T cells containing integrated HIV DNA were the major source of replication-competent virus. Follow-up studies have further characterized the phenotype of these cells containing integrated HIV DNA, as well as shown the correlation between the integration levels and clinical parameters, such as duration of infection, CD4 count and viral load. Integrated HIV DNA correlates with total HIV measures and with QVOA. The integration assay has several limitations. First, it largely overestimates the reservoir size, as both defective and replication-competent proviruses are detected. Since defective proviruses are the majority in patients on ART, it follows that the number of proviruses capable of reactivating and releasing new virions is significantly smaller than the number of integrated proviruses. Second, in patients on ART clonal expansion could theoretically lead to the preferential amplification of proviruses close to an Alu sequence though longitudinal studies have not captured this effect. Proviral sequencing combined with integration measures is probably the best estimate of reservoir size, but it is expensive, time-consuming and requires considerable bioinformatics expertise. All these reasons limit its use on a large scale. Herein, we review the utility of measuring HIV integration and suggest combining it with sequencing and total HIV measurements can provide insights that underlie reservoir maintenance. BioMed Central 2018-02-17 /pmc/articles/PMC5816390/ /pubmed/29452580 http://dx.doi.org/10.1186/s12977-018-0396-3 Text en © The Author(s) 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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 Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Review Pinzone, Marilia Rita O’Doherty, Una Measuring integrated HIV DNA ex vivo and in vitro provides insights about how reservoirs are formed and maintained |
title | Measuring integrated HIV DNA ex vivo and in vitro provides insights about how reservoirs are formed and maintained |
title_full | Measuring integrated HIV DNA ex vivo and in vitro provides insights about how reservoirs are formed and maintained |
title_fullStr | Measuring integrated HIV DNA ex vivo and in vitro provides insights about how reservoirs are formed and maintained |
title_full_unstemmed | Measuring integrated HIV DNA ex vivo and in vitro provides insights about how reservoirs are formed and maintained |
title_short | Measuring integrated HIV DNA ex vivo and in vitro provides insights about how reservoirs are formed and maintained |
title_sort | measuring integrated hiv dna ex vivo and in vitro provides insights about how reservoirs are formed and maintained |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5816390/ https://www.ncbi.nlm.nih.gov/pubmed/29452580 http://dx.doi.org/10.1186/s12977-018-0396-3 |
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