{"doi":"10.3390/life11121410","title":"Measuring Proviral HIV-1 DNA: Hurdles and Improvements to an Assay Monitoring Integration Events Utilising Human Alu Repeat Sequences","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 Alu-5LTR PCR, which utilises novel primer combinations. We tested the Alu-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 Alu-gag assay. The numbers of median integrated HIV-1 DNA copies were 5 (range: 1–12) and 14 (5–26) with the Alu-gag and Alu-5LTR, respectively. The ratios between Alu-gag vs Alu-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. Alu-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.","journal":"Life","year":2021,"id":201901,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":7,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9476,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":781362,"name":"Jordan Thomas","orcid":"0000-0003-2725-5233","position":1,"is_corresponding":false},{"id":411949,"name":"Ward De Spiegelaere","orcid":"0000-0003-2097-8439","position":2,"is_corresponding":false},{"id":408656,"name":"Sofie Rutsaert","orcid":"0000-0003-4623-0939","position":3,"is_corresponding":false},{"id":781363,"name":"Anna María Geretti","orcid":"0000-0002-3670-6588","position":4,"is_corresponding":false},{"id":83861,"name":"Georgios Pollakis","orcid":"0000-0002-9659-5461","position":5,"is_corresponding":false},{"id":83860,"name":"William A. Paxton","orcid":"0000-0001-5200-0801","position":6,"is_corresponding":false},{"id":408658,"name":"Linos Vandekerckhove","orcid":"0000-0002-8600-1631","position":7,"is_corresponding":false},{"id":380961,"name":"Alessandra Ruggiero","orcid":"0000-0002-1041-7489","position":8,"is_corresponding":false},{"id":412867,"name":"Eva Malatinková","orcid":null,"position":0,"is_corresponding":true}],"reference_count":97,"raw_metadata":null,"created_at":"2026-07-18T23:51:05.955461Z","pmid":"34947941","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}