{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T17:15:40Z","timestamp":1774372540972,"version":"3.50.1"},"reference-count":30,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T00:00:00Z","timestamp":1761868800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NIH","award":["R21AI150398 (GQL)"],"award-info":[{"award-number":["R21AI150398 (GQL)"]}]},{"name":"NIH","award":["R01AI162221 (GQL)"],"award-info":[{"award-number":["R01AI162221 (GQL)"]}]},{"name":"NIH","award":["UM1AI164565 (GQL)"],"award-info":[{"award-number":["UM1AI164565 (GQL)"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>The Intact Proviral DNA Assay (IPDA) is widely used to quantify genome-intact HIV proviruses in people living with HIV, but viral sequence diversity has been observed to cause assay failures due to primer\/probe mismatches. Adapted for subtype C, IPDA-BC is a modified version of the IPDA validated on South African HIV-1 subtype C. India is also impacted by subtype C, but IPDA performance within-subtype across geographical regions is not well studied. We analyzed Indian (IN) and South African (ZA) subtype C sequences in silico, hypothesizing that IPDA-BC may underperform with IN viruses. Primer\/probe binding was predicted using three increasingly stringent nucleotide mismatch criteria, whose sensitivity and specificity were evaluated against experimental IPDA outcomes. Phylogenetic analyses confirmed that IN and ZA subtype C sequences form distinct clusters with significant compartmentalization (p &lt; 0.003). Across criteria, up to 6\u201310% decreases in primer\/probe binding were observed in IN versus ZA, with the env forward primer being the most affected. These criteria showed low sensitivity (18\u201353%) and variable specificity (67\u2013100%) in predicting experimental outcomes. In conclusion, even within subtype, HIV-1 variation across geographical regions may impact IPDA performance, underscoring the need for improved predictive models to guide assay design for global HIV cure research.<\/jats:p>","DOI":"10.3390\/v17111453","type":"journal-article","created":{"date-parts":[[2025,11,3]],"date-time":"2025-11-03T13:47:58Z","timestamp":1762177678000},"page":"1453","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Within-Subtype HIV-1 Polymorphisms and Their Impacts on Intact Proviral DNA Assay (IPDA) for Viral Reservoir Quantification"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7199-4570","authenticated-orcid":false,"given":"Mohith Reddy","family":"Arikatla","sequence":"first","affiliation":[{"name":"Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9487-7775","authenticated-orcid":false,"given":"Jyoti S.","family":"Mathad","sequence":"additional","affiliation":[{"name":"Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA"},{"name":"Center for Global Health, Weill Cornell Medicine, New York, NY 10065, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7024-0574","authenticated-orcid":false,"given":"Kavidha","family":"Reddy","sequence":"additional","affiliation":[{"name":"Africa Health Research Institute, Durban 4001, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicole","family":"Reddy","sequence":"additional","affiliation":[{"name":"Africa Health Research Institute, Durban 4001, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2962-3992","authenticated-orcid":false,"given":"Thumbi","family":"Ndung\u2019u","sequence":"additional","affiliation":[{"name":"Africa Health Research Institute, Durban 4001, South Africa"},{"name":"Division of Infection and Immunity, University College London (UCL), London WC1E 6JF, UK"},{"name":"HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4001, South Africa"},{"name":"Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7100-2917","authenticated-orcid":false,"given":"Kathryn M.","family":"Dupnik","sequence":"additional","affiliation":[{"name":"Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA"},{"name":"Center for Global Health, Weill Cornell Medicine, New York, NY 10065, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9412-886X","authenticated-orcid":false,"given":"Guinevere Q.","family":"Lee","sequence":"additional","affiliation":[{"name":"Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA"},{"name":"Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,10,31]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1038\/s41586-019-0898-8","article-title":"A Quantitative Approach for Measuring the Reservoir of Latent HIV-1 Proviruses","volume":"566","author":"Bruner","year":"2019","journal-title":"Nature"},{"key":"ref_2","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":"ref_3","doi-asserted-by":"crossref","unstructured":"Lee, G.Q. 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