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This study entailed an evaluation of HIV-1 drug resistance-associated mutations (RAMs) among minor viral populations through high-throughput sequencing genotypic resistance testing (HTS-GRT) in patients on the South African national second-line cART regimen receiving bPIs.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      During 2017 and 2018, 67 patient samples were sequenced using high-throughput sequencing (HTS), of which 56 samples were included in the final analysis because the patient\u2019s treatment regimen was available at the time of sampling. All patients were receiving bPIs as part of their cART. Viral RNA was extracted, and complete\n                      <jats:italic>pol<\/jats:italic>\n                      genes were amplified and sequenced using Illumina HiSeq2500, followed by bioinformatics analysis to quantify the RAMs according to the Stanford HIV Drug Resistance Database.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Statistically significantly higher PI RAMs were observed in minor viral quasispecies (25%; 14\/56) compared to non-nucleoside reverse transcriptase inhibitors (9%; 5\/56;\n                      <jats:italic>p<\/jats:italic>\n                      \u2009=\u20090.042) and integrase inhibitor RAM (4%; 2\/56;\n                      <jats:italic>p<\/jats:italic>\n                      \u2009=\u20090.002). The majority of the drug resistance mutations in the minor viral quasispecies were observed in the V82A mutation (\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u200913) in protease and K65R (\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u20095), K103N (\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u20097) and M184V (n\u2009=\u20095) in reverse transcriptase.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>HTS-GRT improved the identification of PI and reverse transcriptase inhibitor (RTI) RAMs in second-line cART patients from South Africa compared to the conventional GRT with \u226520% used in Sanger-based sequencing. Several RTI RAMs, such as K65R, M184V or K103N and PI RAM V82A, were identified in &lt;\u200920% of the population. Deep sequencing could be of greater value in detecting acquired resistance mutations early.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12879-021-05905-2","type":"journal-article","created":{"date-parts":[[2021,2,25]],"date-time":"2021-02-25T09:09:41Z","timestamp":1614244181000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Increased acquired protease inhibitor drug resistance mutations in minor HIV-1 quasispecies from infected patients suspected of failing on national second-line therapy in South Africa"],"prefix":"10.1186","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0934-9586","authenticated-orcid":false,"given":"Adetayo Emmanuel","family":"Obasa","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anoop T.","family":"Ambikan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Soham","family":"Gupta","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ujjwal","family":"Neogi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Graeme Brendon","family":"Jacobs","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2021,2,25]]},"reference":[{"key":"5905_CR1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/jia2.25193","volume":"21","author":"H Ji","year":"2018","unstructured":"Ji H, Enns E, Brumme CJ, Parkin N, Howison M, Lee ER, et al. 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The study was conducted according to the ethical guidelines and principles of the Declaration of Helsinki 2013, the South African Guidelines for Good Clinical Practice and the Medical Research Council Ethical Guidelines for Research. A waiver of written informed consent was awarded to conduct sequence analyses on these samples by the Health Research Ethics Committee of Stellenbosch University, South Africa.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"214"}}