{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T23:36:39Z","timestamp":1783121799799,"version":"3.54.6"},"reference-count":28,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2024,11,30]],"date-time":"2024-11-30T00:00:00Z","timestamp":1732924800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"CDC"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>The HIV integrase inhibitor, dolutegravir (DTG), in the absence of eliciting integrase (int) resistance, has been reported to select mutations in the virus 3\u2032-polypurine tract (3\u2032-PPT) adjacent to the 3\u2032-LTR U3. An analog of DTG, cabotegravir (CAB), has a high genetic barrier to drug resistance and is used in formulations for treatment and long-acting pre-exposure prophylaxis. We examined whether mutations observed for DTG would emerge in vitro with CAB. HIV-1IIIB was cultured in paired experiments of continuous high (300 nM) CAB initiated 2 h or 24 h after infection. After eight months of CAB treatment, no int resistance was detected. Conversely, HIV RNA 3\u2032-PPT mutants were detected within one month and were the majority virus by day 98. The appearance of 3\u2032-PPT variants coincided with a rapid accumulation of HIV 1-LTR and 2-LTR circles. RNA amplification from the 3\u2032-LTR TAR identified transcripts crossing 2-LTR circle junctions, which incorporated the adjacent U5 sequence identical to the 3\u2032-PPT mutants. 3\u2032-PPT variants were only identified in LTR circles and transcripts. Additionally, we found evidence of linear HIV and LTR circle recombination with human DNA at motifs homologous to 3\u2032-PPT sequences. HIV persistence under CAB was associated with transcription and recombination of LTR circle sequences.<\/jats:p>","DOI":"10.3390\/v16121874","type":"journal-article","created":{"date-parts":[[2024,12,2]],"date-time":"2024-12-02T06:58:58Z","timestamp":1733122738000},"page":"1874","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["HIV Replication Under High-Level Cabotegravir Is Associated with the Appearance of 3\u2032-PPT Mutations, Circular DNA Transcription and Recombination"],"prefix":"10.3390","volume":"16","author":[{"given":"Xierong","family":"Wei","sequence":"first","affiliation":[{"name":"Laboratory Branch, Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6673-0207","authenticated-orcid":false,"given":"Jonathan T.","family":"Lipscomb","sequence":"additional","affiliation":[{"name":"Laboratory Branch, Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ariana Santos","family":"Tino","sequence":"additional","affiliation":[{"name":"Laboratory Branch, Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"},{"name":"Anyar Inc., 2113 Lewis Turner Blvd, Fort Walton Beach, FL 32547, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mian-er","family":"Cong","sequence":"additional","affiliation":[{"name":"Laboratory Branch, Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0648-7038","authenticated-orcid":false,"given":"Susan","family":"Ruone","sequence":"additional","affiliation":[{"name":"Laboratory Branch, Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meghan L.","family":"Bentz","sequence":"additional","affiliation":[{"name":"Advanced Diagnostics and Biotechnologies Branch, Division of Core Laboratory Services and Response, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mili","family":"Sheth","sequence":"additional","affiliation":[{"name":"Advanced Diagnostics and Biotechnologies Branch, Division of Core Laboratory Services and Response, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6437-7745","authenticated-orcid":false,"given":"Gerardo","family":"Garcia-Lerma","sequence":"additional","affiliation":[{"name":"Laboratory Branch, Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeffrey A.","family":"Johnson","sequence":"additional","affiliation":[{"name":"Laboratory Branch, Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,11,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"a006890","DOI":"10.1101\/cshperspect.a006890","article-title":"HIV DNA integration","volume":"2","author":"Craigie","year":"2012","journal-title":"Cold Spring Harb. Perspect. Med."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1126\/science.aah5163","article-title":"Cryo-EM structures and atomic model of the HIV-1 strand transfer complex intasome","volume":"355","author":"Passos","year":"2017","journal-title":"Science"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"810","DOI":"10.1126\/science.aay8015","article-title":"Structural basis for strand-transfer inhibitor binding to HIV intasomes","volume":"367","author":"Passos","year":"2020","journal-title":"Science"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.sbi.2017.04.005","article-title":"Retroviral intasomes arising","volume":"47","author":"Engelman","year":"2017","journal-title":"Curr. Opin. Struct. Biol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1016\/0092-8674(91)90297-C","article-title":"HIV-1 DNA integration: Mecshanism of viral DNA cleavage and DNA strand transfer","volume":"67","author":"Engelman","year":"1991","journal-title":"Cell"},{"key":"ref_6","unstructured":"(2024, August 01). US Food and Drug Administration, Available online: https:\/\/www.fda.gov\/drugs\/human-immunodeficiency-virus-hiv\/fda-approves-cabenuva-and-vocabria-treatment-hiv-1-infection."},{"key":"ref_7","unstructured":"(2024, August 01). US Food and Drug Administration, Available online: https:\/\/www.fda.gov\/news-events\/press-announcements\/fda-approves-first-injectable-treatment-hiv-pre-exposure-prevention."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"e00922-17","DOI":"10.1128\/mBio.00922-17","article-title":"Mutations Located outside the Integrase Gene Can Confer Resistance to HIV-1 Integrase Strand Transfer Inhibitors","volume":"8","author":"Malet","year":"2017","journal-title":"mBio"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1093\/infdis\/jiy176","article-title":"HIV-1 Resistance Dynamics in Patients with Virologic Failure to Dolutegravir Maintenance Monotherapy","volume":"218","author":"Wijting","year":"2018","journal-title":"J. Infect. Dis."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"e01695-17","DOI":"10.1128\/AAC.01695-17","article-title":"Antiviral Activity of Bictegravir and Cabotegravir against Integrase Inhibitor-Resistant SIVmac239 and HIV-1","volume":"61","author":"Hassounah","year":"2017","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_11","unstructured":"US Food and Drug Administration (2024, August 01). Integrated Review, Available online: https:\/\/www.accessdata.fda.gov\/drugsatfda_docs\/nda\/2021\/212887Orig1s000,212888Orig1s000IntegratedR.pdf."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"4903","DOI":"10.1128\/jvi.64.10.4903-4906.1990","article-title":"Sequence of the circle junction of human immunodeficiency virus type 1: Implications for reverse transcription and integration","volume":"64","author":"Whitcomb","year":"1990","journal-title":"J. Virol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"2960","DOI":"10.1128\/jvi.65.6.2960-2967.1991","article-title":"Quantitation of relative fitness and great adaptability of clonal populations of RNA viruses","volume":"65","author":"Holland","year":"1991","journal-title":"J. Virol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"3037","DOI":"10.1128\/JVI.02712-06","article-title":"The fitness cost of mutations associated with human immunodeficiency virus type 1 drug resistance is modulated by mutational interactions","volume":"81","author":"Cong","year":"2007","journal-title":"J. Virol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1537","DOI":"10.1099\/0022-1317-73-6-1537","article-title":"Analysis of human immunodeficiency virus type 1 LTR-LTR junctions in peripheral blood mononuclear cells of infected individuals","volume":"73","author":"Jurriaans","year":"1992","journal-title":"J. Gen. Virol."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Delelis, O., Parissi, V., Leh, H., Mbemba, G., Petit, C., Sonigo, P., Deprez, E., and Mouscadet, J.F. (2007). Efficient and specific internal cleavage of a retroviral palindromic DNA sequence by tetrameric HIV-1 integrase. PLoS ONE, 2.","DOI":"10.1371\/journal.pone.0000608"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1186\/1742-4690-5-114","article-title":"Integrase and integration: Biochemical activities of HIV-1 integrase","volume":"5","author":"Delelis","year":"2008","journal-title":"Retrovirology"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"e0033524","DOI":"10.1128\/jvi.00335-24","article-title":"Reverse Transcription of HIV-1 2-LTR circle transcripts does frequently cause 3\u2032-polypurine tract mutations implicated in dolutegravir resistance","volume":"98","author":"Dekker","year":"2024","journal-title":"J. Virol."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Kirk, P.D., Huvet, M., Melamed, A., Maertens, G.N., and Bangham, C.R. (2016). Retroviruses integrate into a shared, non-palindromic DNA motif. Nat. Microbiol., 2.","DOI":"10.1038\/nmicrobiol.2016.212"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"13315","DOI":"10.1128\/JVI.78.23.13315-13324.2004","article-title":"Effects of mutations in the G tract of the human immunodeficiency virus type 1 polypurine tract on virus replication and RNase H cleavage","volume":"78","author":"Julias","year":"2004","journal-title":"J. Virol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"5104","DOI":"10.1128\/JVI.01897-07","article-title":"Mutations in the human immunodeficiency virus type 1 polypurine tract (PPT) reduce the rate of PPT cleavage and plus-strand DNA synthesis","volume":"82","author":"McWilliams","year":"2008","journal-title":"J. Virol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"e0067622","DOI":"10.1128\/jvi.00676-22","article-title":"Mutations in the 3\u2032-PPT Lead to HIV-1 Replication without Integration","volume":"96","author":"Richetta","year":"2022","journal-title":"J. Virol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"e0036123","DOI":"10.1128\/jvi.00361-23","article-title":"HIV-1 3\u2032-Polypurine Tract Mutations Confer Dolutegravir Resistance by Switching to an Integration-Independent Replication Mechanism via 1-LTR Circles","volume":"97","author":"Dekker","year":"2023","journal-title":"J. Virol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1186\/1742-4690-10-80","article-title":"HIV-1 Nef promotes the localization of Gag to the cell membrane and facilitates viral cell-to-cell transfer","volume":"10","author":"Malbec","year":"2013","journal-title":"Retrovirology"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"8286","DOI":"10.1074\/jbc.RA118.006755","article-title":"Two-long terminal repeat (LTR) DNA circles are a substrate for HIV-1 integrase","volume":"294","author":"Richetta","year":"2019","journal-title":"J. Biol. Chem."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1755","DOI":"10.1093\/nar\/gkn1045","article-title":"Fidelity of plus-strand priming requires the nucleic acid chaperone activity of HIV-1 nucleocapsid protein","volume":"37","author":"Post","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1149","DOI":"10.3851\/IMP1919","article-title":"Pharmacokinetics of antiretroviral drugs in anatomical sanctuary sites: The male and female genital tract","volume":"16","author":"Else","year":"2011","journal-title":"Antivir. Ther."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1097\/QAI.0b013e31829ed7a4","article-title":"Dolutegravir pharmacokinetics in the genital tract and colorectum of HIV-negative men after single and multiple dosing","volume":"64","author":"Greener","year":"2013","journal-title":"J. Acquir. Immune Defic. Syndr."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/16\/12\/1874\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T16:44:02Z","timestamp":1760114642000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/16\/12\/1874"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11,30]]},"references-count":28,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["v16121874"],"URL":"https:\/\/doi.org\/10.3390\/v16121874","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,11,30]]}}}