{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,23]],"date-time":"2026-06-23T16:02:38Z","timestamp":1782230558821,"version":"3.54.5"},"reference-count":25,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2015,12,7]],"date-time":"2015-12-07T00:00:00Z","timestamp":1449446400000},"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>At Week 96 of the Single-Tablet Regimen (STaR) study, more treatment-na\u00efve subjects that received rilpivirine\/emtricitabine\/tenofovir DF (RPV\/FTC\/TDF) developed resistance mutations compared to those treated with efavirenz (EFV)\/FTC\/TDF by population sequencing. Furthermore, more RPV\/FTC\/TDF-treated subjects with baseline HIV-1 RNA &gt;100,000 copies\/mL developed resistance compared to subjects with baseline HIV-1 RNA \u2264100,000 copies\/mL. Here, deep sequencing was utilized to assess the presence of pre-existing low-frequency variants in subjects with and without resistance development in the STaR study. Deep sequencing (Illumina MiSeq) was performed on baseline and virologic failure samples for all subjects analyzed for resistance by population sequencing during the clinical study (n = 33), as well as baseline samples from control subjects with virologic response (n = 118). Primary NRTI or NNRTI drug resistance mutations present at low frequency (\u22652% to 20%) were detected in 6.6% of baseline samples by deep sequencing, all of which occurred in control subjects. Deep sequencing results were generally consistent with population sequencing but detected additional primary NNRTI and NRTI resistance mutations at virologic failure in seven samples. HIV-1 drug resistance mutations emerging while on RPV\/FTC\/TDF or EFV\/FTC\/TDF treatment were not present at low frequency at baseline in the STaR study.<\/jats:p>","DOI":"10.3390\/v7122943","type":"journal-article","created":{"date-parts":[[2015,12,9]],"date-time":"2015-12-09T07:06:30Z","timestamp":1449644790000},"page":"6360-6370","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["Emergent HIV-1 Drug Resistance Mutations Were Not Present at Low-Frequency at Baseline in Non-Nucleoside Reverse Transcriptase Inhibitor-Treated Subjects in the STaR Study"],"prefix":"10.3390","volume":"7","author":[{"given":"Danielle","family":"Porter","sequence":"first","affiliation":[{"name":"Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Daeumer","sequence":"additional","affiliation":[{"name":"Seq-IT GmbH &amp; Co. KG, Pfaffplatz 10, 67655 Kaiserslautern, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Thielen","sequence":"additional","affiliation":[{"name":"Seq-IT GmbH &amp; Co. KG, Pfaffplatz 10, 67655 Kaiserslautern, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silvia","family":"Chang","sequence":"additional","affiliation":[{"name":"Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ross","family":"Martin","sequence":"additional","affiliation":[{"name":"Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cal","family":"Cohen","sequence":"additional","affiliation":[{"name":"Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Miller","sequence":"additional","affiliation":[{"name":"Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kirsten","family":"White","sequence":"additional","affiliation":[{"name":"Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2015,12,7]]},"reference":[{"key":"ref_1","unstructured":"Department for Health and Human Services (DHHS) Guidelines for the Use of Antiretroviral Agents in HIV-1-Infected Adults and Adolescents. 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