{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:14:49Z","timestamp":1790813689037,"version":"4.1.0"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2020,8,9]],"date-time":"2020-08-09T00:00:00Z","timestamp":1596931200000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001322","name":"South African Medical Research Council","doi-asserted-by":"publisher","award":["MRC-RFA-UFSP-01-2013\/UKZN HIVEPI"],"award-info":[{"award-number":["MRC-RFA-UFSP-01-2013\/UKZN HIVEPI"]}],"id":[{"id":"10.13039\/501100001322","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Centre for AIDS Programme Research in South Africa"},{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"publisher","award":["55007065"],"award-info":[{"award-number":["55007065"]}],"id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000030","name":"Centers for Disease Control and Prevention","doi-asserted-by":"crossref","award":["UY2G\/PS001350-02"],"award-info":[{"award-number":["UY2G\/PS001350-02"]}],"id":[{"id":"10.13039\/100000030","id-type":"DOI","asserted-by":"crossref"}]},{"name":"KwaZulu-Natal Department of Health"},{"name":"US President\u2019s Emergency Plan for AIDS Relief"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Objectives<\/jats:title>\n                  <jats:p>To determine the impact of pretreatment low-abundance HIV-1 drug-resistant variants (LA-DRVs) on virological failure (VF) among HIV-1\/TB-co-infected individuals treated with NNRTI first-line ART.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>We conducted a case\u2013control study of 170 adults with HIV-1\/TB co-infection. Cases had at least one viral load (VL) \u22651000 RNA copies\/mL after \u22656\u2009months on NNRTI-based ART, and controls had sustained VLs &amp;lt;1000 copies\/mL. We sequenced plasma viruses by Sanger and MiSeq next-generation sequencing (NGS). We assessed drug resistance mutations (DRMs) using the Stanford drug resistance database, and analysed NGS data for DRMs at \u226520%, 10%, 5% and 2% thresholds. We assessed the effect of pretreatment drug resistance (PDR) on VF.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We analysed sequences from 45 cases and 125 controls. Overall prevalence of PDR detected at a \u226520% threshold was 4.7% (8\/170) and was higher in cases than in controls (8.9% versus 3.2%), P\u2009=\u20090.210. Participants with PDR at \u226520% had almost 4-fold higher odds of VF (adjusted OR 3.7, 95% CI 0.8\u201318.3) compared with those without, P\u2009=\u20090.104. PDR prevalence increased to 18.2% (31\/170) when LA-DRVs at \u22652% were included. Participants with pretreatment LA-DRVs only had 1.6-fold higher odds of VF (adjusted OR 1.6, 95% CI 0.6\u20134.3) compared with those without, P\u2009=\u20090.398.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>Pretreatment DRMs and LA-DRVs increased the odds of developing VF on NNRTI-based ART, although without statistical significance. NGS increased detection of DRMs but provided no additional benefit in identifying participants at risk of VF at lower thresholds. More studies assessing mutation thresholds predictive of VF are required to inform use of NGS in treatment decisions.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/jac\/dkaa343","type":"journal-article","created":{"date-parts":[[2020,7,22]],"date-time":"2020-07-22T19:16:19Z","timestamp":1595445379000},"page":"3319-3326","source":"Crossref","is-referenced-by-count":14,"title":["Impact of pretreatment low-abundance HIV-1 drug-resistant variants on virological failure among HIV-1\/TB-co-infected individuals"],"prefix":"10.1093","volume":"75","author":[{"given":"Benjamin","family":"Chimukangara","sequence":"first","affiliation":[{"name":"KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa"},{"name":"Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa"},{"name":"Department of Virology, 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Medical Research Institute, Durban, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Babill","family":"Stray-Pedersen","sequence":"additional","affiliation":[{"name":"Institute of Clinical Medicine, University of Oslo, Oslo University Hospital, Oslo, Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pravi","family":"Moodley","sequence":"additional","affiliation":[{"name":"Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karin J","family":"Metzner","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland"},{"name":"Institute of Medical Virology, University of Zurich, Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nesri","family":"Padayatchi","sequence":"additional","affiliation":[{"name":"Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa"},{"name":"South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kogieleum","family":"Naidoo","sequence":"additional","affiliation":[{"name":"Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa"},{"name":"South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tulio","family":"De Oliveira","sequence":"additional","affiliation":[{"name":"KwaZulu-Natal Research Innovation and Sequencing 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