{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T04:51:50Z","timestamp":1783054310242,"version":"3.54.6"},"reference-count":71,"publisher":"Elsevier BV","issue":"8","license":[{"start":{"date-parts":[[2021,12,1]],"date-time":"2021-12-01T00:00:00Z","timestamp":1638316800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2021,12,1]],"date-time":"2021-12-01T00:00:00Z","timestamp":1638316800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2021,11,6]],"date-time":"2021-11-06T00:00:00Z","timestamp":1636156800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["JP20fk0410015"],"award-info":[{"award-number":["JP20fk0410015"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["JP21fk0410023"],"award-info":[{"award-number":["JP21fk0410023"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["JP19fk0410009"],"award-info":[{"award-number":["JP19fk0410009"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"publisher","award":["JP19fk0410014"],"award-info":[{"award-number":["JP19fk0410014"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["JP17890606"],"award-info":[{"award-number":["JP17890606"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012319","name":"National Center for Global Health and Medicine","doi-asserted-by":"publisher","award":["20A1018"],"award-info":[{"award-number":["20A1018"]}],"id":[{"id":"10.13039\/100012319","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012319","name":"National Center for Global Health and Medicine","doi-asserted-by":"publisher","award":["20K17480"],"award-info":[{"award-number":["20K17480"]}],"id":[{"id":"10.13039\/100012319","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001700","name":"Ministry of Education, Culture, Sports, Science and Technology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001700","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":[[2021,12]]},"DOI":"10.1016\/j.crmeth.2021.100122","type":"journal-article","created":{"date-parts":[[2021,11,29]],"date-time":"2021-11-29T10:47:44Z","timestamp":1638182864000},"page":"100122","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":13,"title":["A widely distributed HIV-1 provirus elimination assay to evaluate latency-reversing agents in\u00a0vitro"],"prefix":"10.1016","volume":"1","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4757-7128","authenticated-orcid":false,"given":"Kouki","family":"Matsuda","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5777-9164","authenticated-orcid":false,"given":"Saiful","family":"Islam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Toru","family":"Takada","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8233-6653","authenticated-orcid":false,"given":"Kiyoto","family":"Tsuchiya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjy Jek","family":"Yang Tan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shin-ichiro","family":"Hattori","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hiroo","family":"Katsuya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3108-2152","authenticated-orcid":false,"given":"Kosaku","family":"Kitagawa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kwang Su","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Misaki","family":"Matsuo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kenji","family":"Sugata","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicole S.","family":"Delino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hiroyuki","family":"Gatanaga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kazuhisa","family":"Yoshimura","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9649-8821","authenticated-orcid":false,"given":"Shuzo","family":"Matsushita","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9274-3853","authenticated-orcid":false,"given":"Hiroaki","family":"Mitsuya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shingo","family":"Iwami","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yorifumi","family":"Satou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9424-1491","authenticated-orcid":false,"given":"Kenji","family":"Maeda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.crmeth.2021.100122_bib1","doi-asserted-by":"crossref","first-page":"136","DOI":"10.3390\/v12020136","article-title":"Dynamic shifts in the HIV proviral landscape during long term combination antiretroviral therapy: implications for persistence and control of HIV infections","volume":"12","author":"Anderson","year":"2020","journal-title":"Viruses"},{"key":"10.1016\/j.crmeth.2021.100122_bib2","doi-asserted-by":"crossref","first-page":"482","DOI":"10.1038\/nature11286","article-title":"Administration of vorinostat disrupts HIV-1 latency in patients on antiretroviral therapy","volume":"487","author":"Archin","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.crmeth.2021.100122_bib3","doi-asserted-by":"crossref","first-page":"e718","DOI":"10.1038\/cddis.2013.248","article-title":"Altering cell death pathways as an approach to cure HIV infection","volume":"4","author":"Badley","year":"2013","journal-title":"Cell Death Dis."},{"key":"10.1016\/j.crmeth.2021.100122_bib4","doi-asserted-by":"crossref","first-page":"e34655","DOI":"10.7554\/eLife.34655","article-title":"Distinct chromatin functional states correlate with HIV latency reactivation in infected primary CD4(+) T\u00a0cells","volume":"7","author":"Battivelli","year":"2018","journal-title":"eLife"},{"key":"10.1016\/j.crmeth.2021.100122_bib5","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1038\/s41586-018-0600-6","article-title":"Antibody and TLR7 agonist delay viral rebound in SHIV-infected monkeys","volume":"563","author":"Borducchi","year":"2018","journal-title":"Nature"},{"key":"10.1016\/j.crmeth.2021.100122_bib6","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1182\/blood-2008-07-168393","article-title":"Induction of HIV-1 latency and reactivation in primary memory CD4+ T\u00a0cells","volume":"113","author":"Bosque","year":"2009","journal-title":"Blood"},{"key":"10.1016\/j.crmeth.2021.100122_bib7","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1016\/S1074-7613(03)00236-X","article-title":"Molecular characterization, reactivation, and depletion of latent HIV","volume":"19","author":"Brooks","year":"2003","journal-title":"Immunity"},{"key":"10.1016\/j.crmeth.2021.100122_bib8","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1038\/nm.4156","article-title":"Defective proviruses rapidly accumulate during acute HIV-1 infection","volume":"22","author":"Bruner","year":"2016","journal-title":"Nat. Med."},{"key":"10.1016\/j.crmeth.2021.100122_bib9","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1038\/nm.3489","article-title":"New ex\u00a0vivo approaches distinguish effective and ineffective single agents for reversing HIV-1 latency in\u00a0vivo","volume":"20","author":"Bullen","year":"2014","journal-title":"Nat. Med."},{"key":"10.1016\/j.crmeth.2021.100122_bib10","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1038\/87979","article-title":"A quantitative assay for HIV DNA integration in\u00a0vivo","volume":"7","author":"Butler","year":"2001","journal-title":"Nat. Med."},{"key":"10.1016\/j.crmeth.2021.100122_bib11","doi-asserted-by":"crossref","first-page":"13193","DOI":"10.1073\/pnas.94.24.13193","article-title":"Presence of an inducible HIV-1 latent reservoir during highly active antiretroviral therapy","volume":"94","author":"Chun","year":"1997","journal-title":"Proc. Natl. Acad. Sci. U S A"},{"key":"10.1016\/j.crmeth.2021.100122_bib12","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1016\/j.cell.2015.01.020","article-title":"HIV-1 integration landscape during latent and active infection","volume":"160","author":"Cohn","year":"2015","journal-title":"Cell"},{"key":"10.1016\/j.crmeth.2021.100122_bib13","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1016\/j.it.2016.12.003","article-title":"HIV latency: should we shock or lock?","volume":"38","author":"Darcis","year":"2017","journal-title":"Trends Immunol."},{"key":"10.1016\/j.crmeth.2021.100122_bib14","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1038\/487439a","article-title":"HIV: shock and kill","volume":"487","author":"Deeks","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.crmeth.2021.100122_bib15","doi-asserted-by":"crossref","first-page":"e00337-19","DOI":"10.1128\/mBio.00337-19","article-title":"Entry of polarized effector cells into quiescence forces HIV latency","volume":"10","author":"Dobrowolski","year":"2019","journal-title":"mBio"},{"key":"10.1016\/j.crmeth.2021.100122_bib16","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1038\/417095a","article-title":"HIV preferentially infects HIV-specific CD4+ T\u00a0cells","volume":"417","author":"Douek","year":"2002","journal-title":"Nature"},{"key":"10.1016\/j.crmeth.2021.100122_bib17","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.crmeth.2021.100122_bib18","series-title":"An Introduction to the Bootstrap","author":"Efron","year":"1994"},{"key":"10.1016\/j.crmeth.2021.100122_bib19","doi-asserted-by":"crossref","first-page":"988","DOI":"10.1172\/JCI124291","article-title":"Intact HIV-1 proviruses accumulate at distinct chromosomal positions during prolonged antiretroviral therapy","volume":"129","author":"Einkauf","year":"2019","journal-title":"J.\u00a0Clin. Invest."},{"key":"10.1016\/j.crmeth.2021.100122_bib20","doi-asserted-by":"crossref","first-page":"1295","DOI":"10.1126\/science.278.5341.1295","article-title":"Identification of a reservoir for HIV-1 in patients on highly active antiretroviral therapy","volume":"278","author":"Finzi","year":"1997","journal-title":"Science"},{"key":"10.1016\/j.crmeth.2021.100122_bib21","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.2021.100122_bib22","doi-asserted-by":"crossref","first-page":"3113","DOI":"10.1182\/blood-2010-10-312926","article-title":"The host genomic environment of the provirus determines the abundance of HTLV-1-infected T-cell clones","volume":"117","author":"Gillet","year":"2011","journal-title":"Blood"},{"key":"10.1016\/j.crmeth.2021.100122_bib23","first-page":"618","article-title":"The use of real-time quantitative polymerase chain reaction and comparative genomic hybridization to identify amplification of the REL gene in follicular lymphoma","volume":"111","author":"Goff","year":"2000","journal-title":"Br. J. Haematol."},{"key":"10.1016\/j.crmeth.2021.100122_bib24","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1007\/s11222-006-9438-0","article-title":"DRAM: efficient adaptive MCMC","volume":"16","author":"Haario","year":"2006","journal-title":"Stat. Comput."},{"key":"10.1016\/j.crmeth.2021.100122_bib25","doi-asserted-by":"crossref","first-page":"6122","DOI":"10.1128\/JVI.78.12.6122-6133.2004","article-title":"Resting CD4+ T\u00a0cells from human immunodeficiency virus type 1 (HIV-1)-infected individuals carry integrated HIV-1 genomes within actively transcribed host genes","volume":"78","author":"Han","year":"2004","journal-title":"J.\u00a0Virol."},{"key":"10.1016\/j.crmeth.2021.100122_bib26","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1016\/j.chom.2008.06.008","article-title":"Orientation-dependent regulation of integrated HIV-1 expression by host gene transcriptional readthrough","volume":"4","author":"Han","year":"2008","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.crmeth.2021.100122_bib27","doi-asserted-by":"crossref","first-page":"2022","DOI":"10.3389\/fmicb.2018.02022","article-title":"Combination of a latency-reversing agent with a Smac mimetic minimizes secondary HIV-1 infection in\u00a0vitro","volume":"9","author":"Hattori","year":"2018","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.crmeth.2021.100122_bib28","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1016\/j.cell.2013.09.020","article-title":"Replication-competent noninduced proviruses in the latent reservoir increase barrier to HIV-1 cure","volume":"155","author":"Ho","year":"2013","journal-title":"Cell"},{"key":"10.1016\/j.crmeth.2021.100122_bib29","doi-asserted-by":"crossref","first-page":"13","DOI":"10.4137\/CIN.S13495","article-title":"OmicCircos: a simple-to-use R package for the circular visualization of multidimensional omics data","volume":"13","author":"Hu","year":"2014","journal-title":"Cancer Inform."},{"key":"10.1016\/j.crmeth.2021.100122_bib30","doi-asserted-by":"crossref","first-page":"876","DOI":"10.1172\/JCI97555","article-title":"Latent HIV reservoirs exhibit inherent resistance to elimination by CD8+ T\u00a0cells","volume":"128","author":"Huang","year":"2018","journal-title":"J.\u00a0Clin. Invest."},{"key":"10.1016\/j.crmeth.2021.100122_bib31","doi-asserted-by":"crossref","first-page":"8783","DOI":"10.1073\/pnas.1609057113","article-title":"Defective HIV-1 proviruses produce novel protein-coding RNA species in HIV-infected patients on combination antiretroviral therapy","volume":"113","author":"Imamichi","year":"2016","journal-title":"Proc. Natl. Acad. Sci. U S A"},{"key":"10.1016\/j.crmeth.2021.100122_bib32","doi-asserted-by":"crossref","first-page":"3704","DOI":"10.1073\/pnas.1917876117","article-title":"Defective HIV-1 proviruses produce viral proteins","volume":"117","author":"Imamichi","year":"2020","journal-title":"Proc. Natl. Acad. Sci. U S A"},{"key":"10.1016\/j.crmeth.2021.100122_bib33","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1186\/1742-4690-9-18","article-title":"Quantification system for the viral dynamics of a highly pathogenic simian\/human immunodeficiency virus based on an in\u00a0vitro experiment and a mathematical model","volume":"9","author":"Iwami","year":"2012","journal-title":"Retrovirology"},{"key":"10.1016\/j.crmeth.2021.100122_bib34","doi-asserted-by":"crossref","first-page":"e08150","DOI":"10.7554\/eLife.08150","article-title":"Cell-to-cell infection by HIV contributes over half of virus infection","volume":"4","author":"Iwami","year":"2015","journal-title":"eLife"},{"key":"10.1016\/j.crmeth.2021.100122_bib71","article-title":"Clonality of HIV-1 and HTLV-1 infected cells in naturally coinfected individuals","author":"Katsuya","year":"2021","journal-title":"J. Infect Dis."},{"key":"10.1016\/j.crmeth.2021.100122_bib35","doi-asserted-by":"crossref","first-page":"600","DOI":"10.1016\/j.celrep.2017.09.080","article-title":"In\u00a0vivo suppression of HIV rebound by didehydro-cortistatin A, a \u201cblock-and-lock\u201d strategy for HIV-1 treatment","volume":"21","author":"Kessing","year":"2017","journal-title":"Cell Rep."},{"key":"10.1016\/j.crmeth.2021.100122_bib36","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/j.chom.2017.12.004","article-title":"Getting the \u201ckill\u201d into \u201cshock and kill\u201d: strategies to eliminate latent HIV","volume":"23","author":"Kim","year":"2018","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.crmeth.2021.100122_bib37","doi-asserted-by":"crossref","first-page":"1901","DOI":"10.1172\/JCI80142","article-title":"Ex\u00a0vivo analysis identifies effective HIV-1 latency-reversing drug combinations","volume":"125","author":"Laird","year":"2015","journal-title":"J.\u00a0Clin. Invest."},{"key":"10.1016\/j.crmeth.2021.100122_bib38","doi-asserted-by":"crossref","first-page":"e30176","DOI":"10.1371\/journal.pone.0030176","article-title":"A flexible model of HIV-1 latency permitting evaluation of many primary CD4 T-cell reservoirs","volume":"7","author":"Lassen","year":"2012","journal-title":"PLoS One"},{"key":"10.1016\/j.crmeth.2021.100122_bib39","doi-asserted-by":"crossref","first-page":"2689","DOI":"10.1172\/JCI93289","article-title":"Clonal expansion of genome-intact HIV-1 in functionally polarized Th1 CD4+ T\u00a0cells","volume":"127","author":"Lee","year":"2017","journal-title":"J.\u00a0Clin. Invest."},{"key":"10.1016\/j.crmeth.2021.100122_bib40","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1016\/j.chom.2008.05.016","article-title":"Transcriptional interference antagonizes proviral gene expression to promote HIV latency","volume":"4","author":"Lenasi","year":"2008","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.crmeth.2021.100122_bib41","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.crmeth.2021.100122_bib42","doi-asserted-by":"crossref","first-page":"eaaz0802","DOI":"10.1126\/scitranslmed.aaz0802","article-title":"Single-cell transcriptional landscapes reveal HIV-1-driven aberrant host gene transcription as a potential therapeutic target","volume":"12","author":"Liu","year":"2020","journal-title":"Sci. Transl. Med."},{"key":"10.1016\/j.crmeth.2021.100122_bib43","doi-asserted-by":"crossref","first-page":"179","DOI":"10.3851\/IMP2697","article-title":"Delayed emergence of HIV-1 variants resistant to 4'-ethynyl-2-fluoro-2'-deoxyadenosine: comparative sequential passage study with lamivudine, tenofovir, emtricitabine and BMS-986001","volume":"19","author":"Maeda","year":"2014","journal-title":"Antivir. Ther."},{"key":"10.1016\/j.crmeth.2021.100122_bib44","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1126\/science.1254194","article-title":"HIV latency. Specific HIV integration sites are linked to clonal expansion and persistence of infected cells","volume":"345","author":"Maldarelli","year":"2014","journal-title":"Science"},{"key":"10.1016\/j.crmeth.2021.100122_bib45","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1074\/jbc.RA118.005798","article-title":"Benzolactam-related compounds promote apoptosis of HIV-infected human cells via protein kinase C-induced HIV latency reversal","volume":"294","author":"Matsuda","year":"2019","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.crmeth.2021.100122_bib46","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1038\/s41586-020-1946-0","article-title":"Robust and persistent reactivation of SIV and HIV by N-803 and depletion of CD8(+) cells","volume":"578","author":"McBrien","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.crmeth.2021.100122_bib47","doi-asserted-by":"crossref","first-page":"2701","DOI":"10.1128\/AAC.00277-07","article-title":"Activity against human immunodeficiency virus type 1, intracellular metabolism, and effects on human DNA polymerases of 4'-ethynyl-2-fluoro-2'-deoxyadenosine","volume":"51","author":"Nakata","year":"2007","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.crmeth.2021.100122_bib48","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1038\/s41586-020-1951-3","article-title":"Systemic HIV and SIV latency reversal via non-canonical NF-kappaB signalling in\u00a0vivo","volume":"578","author":"Nixon","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.crmeth.2021.100122_bib49","doi-asserted-by":"crossref","first-page":"e1007619","DOI":"10.1371\/journal.ppat.1007619","article-title":"Single-cell characterization and quantification of translation-competent viral reservoirs in treated and untreated HIV infection","volume":"15","author":"Pardons","year":"2019","journal-title":"Plos Pathog."},{"key":"10.1016\/j.crmeth.2021.100122_bib50","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1038\/nri700","article-title":"Modelling viral and immune system dynamics","volume":"2","author":"Perelson","year":"2002","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.crmeth.2021.100122_bib51","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.2021.100122_bib52","first-page":"7","article-title":"CODA: convergence diagnosis and output analysis for MCMC","volume":"6","author":"Plummer","year":"2006","journal-title":"R.\u00a0News"},{"key":"10.1016\/j.crmeth.2021.100122_bib53","series-title":"R: A Language and Environment for Statistical Computing","year":"2019"},{"key":"10.1016\/j.crmeth.2021.100122_bib54","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative genomics viewer","volume":"29","author":"Robinson","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.crmeth.2021.100122_bib55","doi-asserted-by":"crossref","first-page":"e1000533","DOI":"10.1371\/journal.pcbi.1000533","article-title":"Modeling latently infected cell activation: viral and latent reservoir persistence, and viral blips in HIV-infected patients on potent therapy","volume":"5","author":"Rong","year":"2009","journal-title":"Plos Comput. Biol."},{"key":"10.1016\/j.crmeth.2021.100122_bib56","doi-asserted-by":"crossref","first-page":"4161","DOI":"10.1182\/blood-2007-06-097907","article-title":"CCR7 ligands CCL19 and CCL21 increase permissiveness of resting memory CD4+ T\u00a0cells to HIV-1 infection: a novel model of HIV-1 latency","volume":"110","author":"Saleh","year":"2007","journal-title":"Blood"},{"key":"10.1016\/j.crmeth.2021.100122_bib57","doi-asserted-by":"crossref","first-page":"2233","DOI":"10.1128\/jvi.71.3.2233-2240.1997","article-title":"Accumulation of defective viral genomes in peripheral blood mononuclear cells of human immunodeficiency virus type 1-infected individuals","volume":"71","author":"Sanchez","year":"1997","journal-title":"J.\u00a0Virol."},{"key":"10.1016\/j.crmeth.2021.100122_bib58","doi-asserted-by":"crossref","first-page":"6913","DOI":"10.1038\/s41598-017-07307-4","article-title":"Dynamics and mechanisms of clonal expansion of HIV-1-infected cells in a humanized mouse model","volume":"7","author":"Satou","year":"2017","journal-title":"Sci. Rep."},{"key":"10.1016\/j.crmeth.2021.100122_bib59","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1016\/S0092-8674(02)00864-4","article-title":"HIV-1 integration in the human genome favors active genes and local hotspots","volume":"110","author":"Schroder","year":"2002","journal-title":"Cell"},{"key":"10.1016\/j.crmeth.2021.100122_bib60","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1016\/j.immuni.2012.01.014","article-title":"Stimulation of HIV-1-specific cytolytic T lymphocytes facilitates elimination of latent viral reservoir after virus reactivation","volume":"36","author":"Shan","year":"2012","journal-title":"Immunity"},{"key":"10.1016\/j.crmeth.2021.100122_bib61","first-page":"1","article-title":"Inverse modelling, sensitivity and Monte Carlo analysis in R using package FME","volume":"33","author":"Soetaert","year":"2010","journal-title":"J.\u00a0Stat. Softw."},{"key":"10.1016\/j.crmeth.2021.100122_bib62","doi-asserted-by":"crossref","first-page":"e1003834","DOI":"10.1371\/journal.ppat.1003834","article-title":"An in-depth comparison of latent HIV-1 reactivation in multiple cell model systems and resting CD4+ T\u00a0cells from aviremic patients","volume":"9","author":"Spina","year":"2013","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.crmeth.2021.100122_bib63","doi-asserted-by":"crossref","first-page":"883","DOI":"10.1093\/cid\/cit813","article-title":"A pilot study assessing the safety and latency-reversing activity of disulfiram in HIV-1-infected adults on antiretroviral therapy","volume":"58","author":"Spivak","year":"2014","journal-title":"Clin. Infect. Dis."},{"key":"10.1016\/j.crmeth.2021.100122_bib64","doi-asserted-by":"crossref","first-page":"6425","DOI":"10.1128\/JVI.01519-09","article-title":"Establishment of HIV latency in primary CD4+ cells is due to epigenetic transcriptional silencing and P-TEFb restriction","volume":"84","author":"Tyagi","year":"2010","journal-title":"J.\u00a0Virol."},{"key":"10.1016\/j.crmeth.2021.100122_bib65","doi-asserted-by":"crossref","first-page":"1315","DOI":"10.1097\/QAD.0000000000002213","article-title":"Effects of 24-week Toll-like receptor 9 agonist treatment in HIV type 1+ individuals","volume":"33","author":"Vibholm","year":"2019","journal-title":"AIDS"},{"key":"10.1016\/j.crmeth.2021.100122_bib66","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1126\/science.1256304","article-title":"HIV latency. Proliferation of cells with HIV integrated into cancer genes contributes to persistent infection","volume":"345","author":"Wagner","year":"2014","journal-title":"Science"},{"key":"10.1016\/j.crmeth.2021.100122_bib67","doi-asserted-by":"crossref","first-page":"E3659","DOI":"10.1073\/pnas.1617961114","article-title":"Single-cell analysis of HIV-1 transcriptional activity reveals expression of proviruses in expanded clones during ART","volume":"114","author":"Wiegand","year":"2017","journal-title":"Proc. Natl. Acad. Sci. U S A"},{"key":"10.1016\/j.crmeth.2021.100122_bib68","doi-asserted-by":"crossref","first-page":"1291","DOI":"10.1126\/science.278.5341.1291","article-title":"Recovery of replication-competent HIV despite prolonged suppression of plasma viremia","volume":"278","author":"Wong","year":"1997","journal-title":"Science"},{"key":"10.1016\/j.crmeth.2021.100122_bib69","first-page":"3473","article-title":"Small-molecule screening using a human primary cell model of HIV latency identifies compounds that reverse latency without cellular activation","volume":"119","author":"Yang","year":"2009","journal-title":"J.\u00a0Clin. Invest."},{"key":"10.1016\/j.crmeth.2021.100122_bib70","doi-asserted-by":"crossref","first-page":"1624","DOI":"10.1038\/s41598-018-19602-9","article-title":"HIV-1 with HBV-associated Q151M substitution in RT becomes highly susceptible to entecavir: structural insights into HBV-RT inhibition by entecavir","volume":"8","author":"Yasutake","year":"2018","journal-title":"Sci. Rep."}],"container-title":["Cell Reports Methods"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2667237521001867?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2667237521001867?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,5,16]],"date-time":"2026-05-16T11:17:48Z","timestamp":1778930268000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2667237521001867"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,12]]},"references-count":71,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2021,12]]}},"alternative-id":["S2667237521001867"],"URL":"https:\/\/doi.org\/10.1016\/j.crmeth.2021.100122","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/842419","asserted-by":"object"}]},"ISSN":["2667-2375"],"issn-type":[{"value":"2667-2375","type":"print"}],"subject":[],"published":{"date-parts":[[2021,12]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"A widely distributed HIV-1 provirus elimination assay to evaluate latency-reversing agents in\u00a0vitro","name":"articletitle","label":"Article Title"},{"value":"Cell Reports Methods","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.crmeth.2021.100122","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2021 The Author(s).","name":"copyright","label":"Copyright"}],"article-number":"100122"}}