{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T20:34:31Z","timestamp":1790541271093,"version":"4.1.0"},"reference-count":41,"publisher":"Elsevier BV","issue":"4","license":[{"start":{"date-parts":[[2023,4,1]],"date-time":"2023-04-01T00:00:00Z","timestamp":1680307200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2023,4,1]],"date-time":"2023-04-01T00:00:00Z","timestamp":1680307200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2023,3,13]],"date-time":"2023-03-13T00:00:00Z","timestamp":1678665600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100010431","name":"Institut de M\u00e9decine et d'Epid\u00e9miologie Appliqu\u00e9e","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100010431","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["114"],"award-info":[{"award-number":["114"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["ARP-11346"],"award-info":[{"award-number":["ARP-11346"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["HIV-1 NL4-3"],"award-info":[{"award-number":["HIV-1 NL4-3"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["pNL4-3"],"award-info":[{"award-number":["pNL4-3"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["SFB 992\/1 2012"],"award-info":[{"award-number":["SFB 992\/1 2012"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001677","name":"Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale","doi-asserted-by":"publisher","award":["U1016"],"award-info":[{"award-number":["U1016"]}],"id":[{"id":"10.13039\/501100001677","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["031 A538A\/A538C RBC"],"award-info":[{"award-number":["031 A538A\/A538C RBC"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["031L0106 de.STAIR"],"award-info":[{"award-number":["031L0106 de.STAIR"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003323","name":"Agence Nationale de Recherches sur le Sida et les H\u00e9patites Virales","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003323","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Reports Methods"],"published-print":{"date-parts":[[2023,4]]},"DOI":"10.1016\/j.crmeth.2023.100443","type":"journal-article","created":{"date-parts":[[2023,4,5]],"date-time":"2023-04-05T21:10:37Z","timestamp":1680729037000},"page":"100443","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":4,"title":["DNA ultra-sensitive quantification, a technology for studying HIV unintegrated linear DNA"],"prefix":"10.1016","volume":"3","author":[{"given":"H\u00e9l\u00e8ne Marie","family":"Roux","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suzanne","family":"Figueiredo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucas","family":"Sareoua","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maud","family":"Salmona","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juliette","family":"Hamroune","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucie","family":"Adoux","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julie","family":"Migraine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Allan","family":"Hance","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fran\u00e7ois","family":"Clavel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"R\u00e9mi","family":"Cheynier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4416-6136","authenticated-orcid":false,"given":"Jacques","family":"Dutrieux","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.crmeth.2023.100443_bib1","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1186\/1742-4690-8-52","article-title":"The role of unintegrated DNA in HIV infection","volume":"8","author":"Sloan","year":"2011","journal-title":"Retrovirology"},{"key":"10.1016\/j.crmeth.2023.100443_bib2","doi-asserted-by":"crossref","first-page":"1503","DOI":"10.1126\/science.1061548","article-title":"Selective transcription and modulation of resting T\u00a0cell activity by preintegrated HIV DNA","volume":"293","author":"Wu","year":"2001","journal-title":"Science"},{"key":"10.1016\/j.crmeth.2023.100443_bib3","doi-asserted-by":"crossref","first-page":"10376","DOI":"10.1128\/JVI.77.19.10376-10382.2003","article-title":"Early transcription from nonintegrated DNA in human immunodeficiency virus infection","volume":"77","author":"Wu","year":"2003","journal-title":"J.\u00a0Virol."},{"key":"10.1016\/j.crmeth.2023.100443_bib4","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1186\/1742-4690-5-60","article-title":"Viral complementation allows HIV-1 replication without integration","volume":"5","author":"Gelderblom","year":"2008","journal-title":"Retrovirology"},{"key":"10.1016\/j.crmeth.2023.100443_bib5","doi-asserted-by":"crossref","first-page":"5832","DOI":"10.1093\/emboj\/17.19.5832","article-title":"Sequence specificity of viral end DNA binding by HIV-1 integrase reveals critical regions for protein-DNA interaction","volume":"17","author":"Esposito","year":"1998","journal-title":"EMBO J."},{"key":"10.1016\/j.crmeth.2023.100443_bib6","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1038\/nature09517","article-title":"The mechanism of retroviral integration from X-ray structures of its key intermediates","volume":"468","author":"Maertens","year":"2010","journal-title":"Nature"},{"key":"10.1016\/j.crmeth.2023.100443_bib7","doi-asserted-by":"crossref","first-page":"4622","DOI":"10.1073\/pnas.0509828103","article-title":"The DNA repair genes XPB and XPD defend cells from retroviral infection","volume":"103","author":"Yoder","year":"2006","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.crmeth.2023.100443_bib8","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1038\/387188a0","article-title":"Decay characteristics of HIV-1-infected compartments during combination therapy","volume":"387","author":"Perelson","year":"1997","journal-title":"Nature"},{"key":"10.1016\/j.crmeth.2023.100443_bib9","doi-asserted-by":"crossref","first-page":"2315","DOI":"10.1097\/QAD.0b013e3282f12377","article-title":"Antiretroviral therapy with the integrase inhibitor raltegravir alters decay kinetics of HIV, significantly reducing the second phase","volume":"21","author":"Murray","year":"2007","journal-title":"AIDS"},{"key":"10.1016\/j.crmeth.2023.100443_bib10","doi-asserted-by":"crossref","first-page":"e1006478","DOI":"10.1371\/journal.ppat.1006478","article-title":"Treatment with integrase inhibitor suggests a new interpretation of HIV RNA decay curves that reveals a subset of cells with slow integration","volume":"13","author":"Cardozo","year":"2017","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.crmeth.2023.100443_bib11","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/0092-8674(90)90802-L","article-title":"HIV-1 entry into quiescent primary lymphocytes: molecular analysis reveals a labile, latent viral structure","volume":"61","author":"Zack","year":"1990","journal-title":"Cell"},{"key":"10.1016\/j.crmeth.2023.100443_bib12","doi-asserted-by":"crossref","first-page":"1717","DOI":"10.1128\/jvi.66.3.1717-1725.1992","article-title":"Incompletely reverse-transcribed human immunodeficiency virus type 1 genomes in quiescent cells can function as intermediates in the retroviral life cycle","volume":"66","author":"Zack","year":"1992","journal-title":"J.\u00a0Virol."},{"key":"10.1016\/j.crmeth.2023.100443_bib13","doi-asserted-by":"crossref","first-page":"8518","DOI":"10.1128\/JVI.76.17.8518-8513.2002","article-title":"Molecular characterization of preintegration latency in human immunodeficiency virus type 1 infection","volume":"76","author":"Pierson","year":"2002","journal-title":"J.\u00a0Virol."},{"key":"10.1016\/j.crmeth.2023.100443_bib14","doi-asserted-by":"crossref","first-page":"1551","DOI":"10.1002\/j.1460-2075.1990.tb08274.x","article-title":"HIV-1 replication is controlled at the level of T\u00a0cell activation and proviral integration","volume":"9","author":"Stevenson","year":"1990","journal-title":"The EMBO Journal"},{"key":"10.1016\/j.crmeth.2023.100443_bib15","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/1742-4690-10-11","article-title":"Cellular and molecular mechanisms involved in the establishment of HIV-1 latency","volume":"10","author":"Donahue","year":"2013","journal-title":"Retrovirology"},{"key":"10.1016\/j.crmeth.2023.100443_bib16","doi-asserted-by":"crossref","first-page":"2199","DOI":"10.1128\/JVI.79.4.2199-2210.2005","article-title":"Kinetics of human immunodeficiency virus type 1 decay following entry into resting CD4+ T\u00a0cells","volume":"79","author":"Zhou","year":"2005","journal-title":"J.\u00a0Virol."},{"key":"10.1016\/j.crmeth.2023.100443_bib17","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1186\/1742-4690-4-60","article-title":"Unintegrated HIV-1 provides an inducible and functional reservoir in untreated and highly active antiretroviral therapy-treated patients","volume":"4","author":"Petitjean","year":"2007","journal-title":"Retrovirology"},{"key":"10.1016\/j.crmeth.2023.100443_bib18","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1186\/1742-4690-4-63","article-title":"Centrosomal pre-integration latency of HIV-1 in quiescent cells","volume":"4","author":"Zamborlini","year":"2007","journal-title":"Retrovirology"},{"key":"10.1016\/j.crmeth.2023.100443_bib19","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1038\/387183a0","article-title":"Quantification of latent tissue reservoirs and total body viral load in HIV-1 infection","volume":"387","author":"Chun","year":"1997","journal-title":"Nature"},{"key":"10.1016\/j.crmeth.2023.100443_bib20","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1186\/1742-4690-10-87","article-title":"Quantitative analysis of the time-course of viral DNA forms during the HIV-1 life cycle","volume":"10","author":"Munir","year":"2013","journal-title":"Retrovirology"},{"key":"10.1016\/j.crmeth.2023.100443_bib21","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s12977-017-0339-4","article-title":"Spatiotemporal dynamics of HIV-1 transmission in France (1999-2014) and impact of targeted prevention strategies","volume":"14","author":"Chaillon","year":"2017","journal-title":"Retrovirology"},{"key":"10.1016\/j.crmeth.2023.100443_bib22","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"10.1016\/j.crmeth.2023.100443_bib23","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"key":"10.1016\/j.crmeth.2023.100443_bib24","doi-asserted-by":"crossref","first-page":"1691","DOI":"10.1093\/bioinformatics\/btr174","article-title":"BamTools: a C++ API and toolkit for analyzing and managing BAM files","volume":"27","author":"Barnett","year":"2011","journal-title":"Bioinformatics"},{"key":"10.1016\/j.crmeth.2023.100443_bib25","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1101\/gr.209601.116","article-title":"UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy","volume":"27","author":"Smith","year":"2017","journal-title":"Genome Res."},{"key":"10.1016\/j.crmeth.2023.100443_bib26","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.crmeth.2023.100443_bib27","doi-asserted-by":"crossref","first-page":"i202","DOI":"10.1093\/bioinformatics\/bty264","article-title":"AmpUMI: design and analysis of unique molecular identifiers for deep amplicon sequencing","volume":"34","author":"Clement","year":"2018","journal-title":"Bioinformatics"},{"key":"10.1016\/j.crmeth.2023.100443_bib28","doi-asserted-by":"crossref","first-page":"e0146638","DOI":"10.1371\/journal.pone.0146638","article-title":"Benefits and challenges with applying unique molecular identifiers in next generation sequencing to detect low frequency mutations","volume":"11","author":"Kou","year":"2016","journal-title":"PLoS One"},{"key":"10.1016\/j.crmeth.2023.100443_bib38","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1101\/gr.849004","article-title":"WebLogo: a sequence logo generator","volume":"14","author":"Crooks","year":"2004","journal-title":"Genome Res."},{"key":"10.1016\/j.crmeth.2023.100443_bib29","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1038\/nprot.2011.327","article-title":"A simple, versatile and efficient method to genetically modify human monocyte-derived dendritic cells with HIV-1-derived lentiviral vectors","volume":"6","author":"Berger","year":"2011","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.crmeth.2023.100443_bib30","doi-asserted-by":"crossref","first-page":"2100","DOI":"10.1016\/j.celrep.2016.02.022","article-title":"IL-7 induces SAMHD1 phosphorylation in CD4+ T lymphocytes, improving early steps of HIV-1 life cycle","volume":"14","author":"Coiras","year":"2016","journal-title":"Cell Rep."},{"key":"10.1016\/j.crmeth.2023.100443_bib31","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1186\/s12967-020-02368-y","article-title":"A comparative analysis of unintegrated HIV-1 DNA measurement as a potential biomarker of the cellular reservoir in the blood of patients controlling and non-controlling viral replication","volume":"18","author":"Orlandi","year":"2020","journal-title":"J.\u00a0Transl. Med."},{"key":"10.1016\/j.crmeth.2023.100443_bib32","doi-asserted-by":"crossref","first-page":"658","DOI":"10.1073\/pnas.98.2.658","article-title":"Macrophage are the principal reservoir and sustain high virus loads in rhesus macaques after the depletion of CD4+ T\u00a0cells by a highly pathogenic simian immunodeficiency virus\/HIV type 1 chimera (SHIV): implications for HIV-1 infections of humans","volume":"98","author":"Igarashi","year":"2001","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.crmeth.2023.100443_bib33","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/j.antiviral.2010.05.005","article-title":"Macrophage HIV-1 infection in duodenal tissue of patients on long term HAART","volume":"87","author":"Zalar","year":"2010","journal-title":"Antiviral Res."},{"key":"10.1016\/j.crmeth.2023.100443_bib34","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1089\/aid.2014.0133","article-title":"Healthy HIV-1-infected individuals on highly active antiretroviral therapy harbor HIV-1 in their alveolar macrophages","volume":"31","author":"Cribbs","year":"2015","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"10.1016\/j.crmeth.2023.100443_bib35","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1007\/s11481-018-9809-2","article-title":"Macrophages but not astrocytes harbor HIV DNA in the brains of HIV-1-Infected aviremic individuals on suppressive antiretroviral therapy","volume":"14","author":"Ko","year":"2019","journal-title":"J.\u00a0Neuroimmune Pharmacol."},{"key":"10.1016\/j.crmeth.2023.100443_bib36","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1038\/s41564-018-0335-z","article-title":"HIV-1 reservoirs in urethral macrophages of patients under suppressive antiretroviral therapy","volume":"4","author":"Ganor","year":"2019","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.crmeth.2023.100443_bib37","doi-asserted-by":"crossref","first-page":"W537","DOI":"10.1093\/nar\/gky379","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update","volume":"46","author":"Afgan","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.crmeth.2023.100443_bib39","doi-asserted-by":"crossref","first-page":"2550","DOI":"10.1128\/JVI.77.4.2550-2558.2003","article-title":"G protein-dependent CCR5 signaling is not required for efficient infection of primary T lymphocytes and macrophages by R5 human immunodeficiency virus type 1 isolates","volume":"77","author":"Amara","year":"2003","journal-title":"J.\u00a0Virol."},{"key":"10.1016\/j.crmeth.2023.100443_bib41","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/nmeth.2019","article-title":"Fiji: an open-source platform for biological-image analysis","volume":"9","author":"Schindelin","year":"2012","journal-title":"Nature methods"},{"key":"10.1016\/j.crmeth.2023.100443_bib40","doi-asserted-by":"crossref","first-page":"2212","DOI":"10.1093\/bioinformatics\/btx154","article-title":"Aozan: an automated post-sequencing data-processing pipeline","volume":"33","author":"Perrin","year":"2017","journal-title":"Bioinformatics"}],"container-title":["Cell Reports Methods"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2667237523000589?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2667237523000589?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,11,8]],"date-time":"2025-11-08T22:58:24Z","timestamp":1762642704000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2667237523000589"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,4]]},"references-count":41,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2023,4]]}},"alternative-id":["S2667237523000589"],"URL":"https:\/\/doi.org\/10.1016\/j.crmeth.2023.100443","relation":{},"ISSN":["2667-2375"],"issn-type":[{"value":"2667-2375","type":"print"}],"subject":[],"published":{"date-parts":[[2023,4]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"DNA ultra-sensitive quantification, a technology for studying HIV unintegrated linear DNA","name":"articletitle","label":"Article Title"},{"value":"Cell Reports Methods","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.crmeth.2023.100443","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2023 The Authors.","name":"copyright","label":"Copyright"}],"article-number":"100443"}}