Malatinkova, Eva, Thomas, Jordan 
ORCID: 0000-0003-2725-5233, De Spiegelaere, Ward, Rutsaert, Sofie, Geretti, Anna Maria, Pollakis, Georgios ORCID: 0000-0002-9659-5461, Paxton, William A ORCID: 0000-0001-5200-0801, Vandekerckhove, Linos and Ruggiero, Alessandra ORCID: 0000-0001-6436-8814
(2021)
Measuring Proviral HIV-1 DNA: Hurdles and Improvements to an Assay Monitoring Integration Events Utilising Human <i>Alu</i> Repeat Sequences.
LIFE-BASEL, 11 (12).
1410-.
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Abstract
Integrated HIV-1 DNA persists despite antiretroviral therapy and can fuel viral rebound following treatment interruption. Hence, methods to specifically measure the integrated HIV-1 DNA portion only are important to monitor the reservoir in eradication trials. Here, we provide an up-to-date overview of the literature on the different approaches used to measure integrated HIV-1 DNA. Further, we propose an implemented standard-curve free assay to quantify integrated HIV-1 DNA, so-called <i>Alu</i>-5LTR PCR, which utilises novel primer combinations. We tested the <i>Alu</i>-5LTR PCR in 20 individuals on suppressive ART for a median of nine years; the results were compared to those produced with the standard-free <i>Alu</i>-gag assay. The numbers of median integrated HIV-1 DNA copies were 5 (range: 1-12) and 14 (5-26) with the <i>Alu</i>-gag and <i>Alu</i>-5LTR, respectively. The ratios between <i>Alu</i>-gag vs <i>Alu</i>-5LTR results were distributed within the cohort as follows: most patients (12/20, 60%) provided ratios between 2-5, with 3/20 (15%) and 5/20 (25%) being below or above this range, respectively. <i>Alu</i>-5LTR assay sensitivity was also determined using an "integrated standard"; the data confirmed the increased sensitivity of the assay, i.e., equal to 0.25 proviruses in 10,000 genomes. This work represents an improvement in the field of measuring proviral HIV-1 DNA that could be employed in future HIV-1 persistence and eradication studies.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | integrated HIV-1, Alu-gag, Alu-5LTR, quantification, reservoir |
| Divisions: | Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Infection, Veterinary and Ecological Sciences |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 12 Jan 2022 15:28 |
| Last Modified: | 07 Feb 2024 15:43 |
| DOI: | 10.3390/life11121410 |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3146680 |
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