{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T21:36:23Z","timestamp":1793223383346,"version":"4.5.0"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2024,7,15]],"date-time":"2024-07-15T00:00:00Z","timestamp":1721001600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/100005564","name":"Gilead Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100005564","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010877","name":"ViiV Healthcare","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010877","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Theratechnologies"},{"DOI":"10.13039\/100009947","name":"Merck Sharp & Dohme","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009947","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,9,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>To clarify whether next-generation sequencing (NGS) can be useful for resistance assessment in virologically suppressed highly treatment-experienced (HTE) individuals with MDR HIV.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>Ninety-one participants from the PRESTIGIO Registry were included. NGS was performed on HIV-DNA at 1%, 5% and 20% cut-offs; major drug resistance mutations (DRMs) were evaluated and compared with those detected in historical plasma genotypic resistance testing (h-GRT). APOBEC editing was also characterized.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Participants had a complex and long treatment history [median 23 (IQR 21\u201325) years of ART exposure) and had been virologically suppressed since a median of 3 (IQR 2\u20135) years. Among all major DRMs detected by HIV-DNA NGS and\/or h-GRT, 30% were exclusively found through NGS. The highest detection rate of historical major DRMs was reached with NGS set at 1%, but unusual substitutions and extensive APOBEC hypermutations suggest technical issues and poor clinical relevance in the 1%\u20135% interval. At NGS set at 5%, 67.2% of historical major DRMs were detected. The number of major DRMs detected exclusively by DNA-NGS as minority variants (frequency 5%\u201320%) was significantly higher in individuals who later experienced virological rebound compared with those who maintained virological control [median 2 (IQR 1\u20133) versus 1 (0\u20132), P\u200a=\u200a0.030] and positively correlated with viraemia levels at rebound (rho\u200a=\u200a0.474, P\u200a=\u200a0.030).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>In non-viraemic people with an MDR virus, HIV-1 DNA NGS set at 5% is an acceptable technical cut-off that might help to reveal mutations with a potential clinical relevance. Moreover, the number of minority resistance mutations additionally detected by NGS might be associated with loss of virological control.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/jac\/dkae236","type":"journal-article","created":{"date-parts":[[2024,7,15]],"date-time":"2024-07-15T06:32:35Z","timestamp":1721025155000},"page":"2354-2363","source":"Crossref","is-referenced-by-count":7,"title":["Use of next-generation sequencing on HIV-1 DNA to assess archived resistance in highly treatment-experienced people with multidrug-resistant HIV under virological control: data from the PRESTIGIO Registry"],"prefix":"10.1093","volume":"79","author":[{"given":"Daniele","family":"Armenia","sequence":"first","affiliation":[{"name":"Departmental Faculty, Saint Camillus International University of Health Sciences , Rome , Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9656-7217","authenticated-orcid":false,"given":"Vincenzo","family":"Spagnuolo","sequence":"additional","affiliation":[{"name":"Clinic of Infectious Diseases, Istituto Scientifico San Raffaele , Milan , Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria C","family":"Bellocchi","sequence":"additional","affiliation":[{"name":"Department of Experimental Medicine, University of Rome \u2018Tor Vergata\u2019 , Rome , Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Galli","sequence":"additional","affiliation":[{"name":"Clinic of Infectious Diseases, Istituto Scientifico San Raffaele , Milan , Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leonardo","family":"Duca","sequence":"additional","affiliation":[{"name":"Department of Experimental Medicine, University of Rome \u2018Tor Vergata\u2019 , Rome , Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Greta","family":"Marchegiani","sequence":"additional","affiliation":[{"name":"Department of Experimental Medicine, University of Rome \u2018Tor Vergata\u2019 , Rome , Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6548-3427","authenticated-orcid":false,"given":"Tommaso","family":"Clemente","sequence":"additional","affiliation":[{"name":"Clinic of Infectious Diseases, Istituto Scientifico San Raffaele , Milan , Italy"},{"name":"Faculty of Medicine and Surgery, Vita-Salute San Raffaele University , Milan , Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luca","family":"Carioti","sequence":"additional","affiliation":[{"name":"Department of Experimental Medicine, University of Rome \u2018Tor Vergata\u2019 , Rome , Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Riccardo","family":"Lolatto","sequence":"additional","affiliation":[{"name":"Clinic of Infectious Diseases, Istituto Scientifico San Raffaele , Milan , Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leonardo","family":"Calza","sequence":"additional","affiliation":[{"name":"Department of Medical and Surgical Sciences, Unit of Infectious Diseases, Policlinico Sant\u2019Orsola-Malpighi , Bologna , Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benedetto M","family":"Celesia","sequence":"additional","affiliation":[{"name":"Unit of Infectious Diseases, Garibaldi Hospital , Catania , Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonio","family":"Cascio","sequence":"additional","affiliation":[{"name":"Infectious and Tropical Diseases Unit\u2014Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo , Palermo , Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniela","family":"Francisci","sequence":"additional","affiliation":[{"name":"Clinic of Infectious Diseases, Department of Medicine and Surgery, University of Perugia , Perugia , Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Annalisa","family":"Saracino","sequence":"additional","affiliation":[{"name":"Clinic of Infectious Diseases, University of Bari , Bari , Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlo","family":"Torti","sequence":"additional","affiliation":[{"name":"Dipartimento di Scienze di Mediche e Chirurgiche, Fondazione Policlinico Universitario \"A. 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