{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T20:34:30Z","timestamp":1790541270191,"version":"4.1.0"},"reference-count":36,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2021,4,29]],"date-time":"2021-04-29T00:00:00Z","timestamp":1619654400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>The latent HIV-1 reservoir is comprised of stably integrated and intact proviruses with limited to no viral transcription. It has been proposed that latent infection may be maintained by methylation of pro-viral DNA. Here, for the first time, we investigate the cytosine methylation of a replication competent provirus (AMBI-1) found in a T cell clone in a donor on antiretroviral therapy (ART). Methylation profiles of the AMBI-1 provirus were compared to other proviruses in the same donor and in samples from three other individuals on ART, including proviruses isolated from lymph node mononuclear cells (LNMCs) and peripheral blood mononuclear cells (PBMCs). We also evaluated the apparent methylation of cytosines outside of CpG (i.e., CpH) motifs. We found no evidence for methylation in AMBI-1 or any other provirus tested within the 5\u2032 LTR promoter. In contrast, CpG methylation was observed in the env-tat-rev overlapping reading frame. In addition, we found evidence for differential provirus methylation in cells isolated from LNMCs vs. PBMCs in some individuals, possibly from the expansion of infected cell clones. Finally, we determined that apparent low-level methylation of CpH cytosines is consistent with occasional bisulfite reaction failures. In conclusion, our data do not support the proposition that latent HIV infection is associated with methylation of the HIV 5\u2032 LTR promoter.<\/jats:p>","DOI":"10.3390\/v13050799","type":"journal-article","created":{"date-parts":[[2021,4,30]],"date-time":"2021-04-30T05:10:55Z","timestamp":1619759455000},"page":"799","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["CpG Methylation Profiles of HIV-1 Proviral DNA in Individuals on ART"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8872-5599","authenticated-orcid":false,"given":"Valerie F.","family":"Boltz","sequence":"first","affiliation":[{"name":"HIV Dynamics and Replication Program, Center for Cancer Research, NCI-Frederick, Frederick, MD 21702, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cristina","family":"Ceriani","sequence":"additional","affiliation":[{"name":"HIV Dynamics and Replication Program, Center for Cancer Research, NCI-Frederick, Frederick, MD 21702, USA"},{"name":"University of North Carolina HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason W.","family":"Rausch","sequence":"additional","affiliation":[{"name":"HIV Dynamics and Replication Program, Center for Cancer Research, NCI-Frederick, Frederick, MD 21702, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Shao","sequence":"additional","affiliation":[{"name":"Advanced Biomedical Computing Center, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6899-1459","authenticated-orcid":false,"given":"Michael J.","family":"Bale","sequence":"additional","affiliation":[{"name":"HIV Dynamics and Replication Program, Center for Cancer Research, NCI-Frederick, Frederick, MD 21702, USA"},{"name":"Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2381-1151","authenticated-orcid":false,"given":"Brandon F.","family":"Keele","sequence":"additional","affiliation":[{"name":"AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca","family":"Hoh","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of California, San Francisco, CA 94143, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeffrey M.","family":"Milush","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of California, San Francisco, CA 94143, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6371-747X","authenticated-orcid":false,"given":"Steve G.","family":"Deeks","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of California, San Francisco, CA 94143, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frank","family":"Maldarelli","sequence":"additional","affiliation":[{"name":"HIV Dynamics and Replication Program, Center for Cancer Research, NCI-Frederick, Frederick, MD 21702, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mary F.","family":"Kearney","sequence":"additional","affiliation":[{"name":"HIV Dynamics and Replication Program, Center for Cancer Research, NCI-Frederick, Frederick, MD 21702, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John M.","family":"Coffin","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02129, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,4,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"e128432","DOI":"10.1172\/jci.insight.128432","article-title":"Clones of infected cells arise early in HIV-infected individuals","volume":"4","author":"Coffin","year":"2019","journal-title":"JCI Insight"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"8869","DOI":"10.1073\/pnas.95.15.8869","article-title":"Early establishment of a pool of latently infected, resting CD4(+) T cells during primary HIV-1 infection","volume":"95","author":"Chun","year":"1998","journal-title":"Proc. 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