{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T18:58:56Z","timestamp":1787165936270,"version":"build-2736575974"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2021,11,6]],"date-time":"2021-11-06T00:00:00Z","timestamp":1636156800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"President\u2019s Emergency Plan for AIDS Relief (PEPFAR) through the Centers for Disease Control and Prevention","award":["U2G GH002099-01"],"award-info":[{"award-number":["U2G GH002099-01"]}]},{"name":"President\u2019s Emergency Plan for AIDS Relief (PEPFAR) through the Centers for Disease Control and Prevention","award":["PA GH17-1753"],"award-info":[{"award-number":["PA GH17-1753"]}]},{"name":"Wellcome Trust Clinical Ph.D. fellowship","award":["WT170461"],"award-info":[{"award-number":["WT170461"]}]},{"name":"ICONIC project"},{"name":"Health Innovation Challenge Fund","award":["T5-344"],"award-info":[{"award-number":["T5-344"]}]},{"name":"National Institute of Health Research University College London\/University College London Hospital Biomedical Research Centre"},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 AI147331-01"],"award-info":[{"award-number":["R01 AI147331-01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Wellcome Trust Senior Fellowship in Clinical Science","award":["WT108082AIA"],"award-info":[{"award-number":["WT108082AIA"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,2,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Deep sequencing could improve understanding of HIV treatment failure and viral population dynamics. However, this tool is often inaccessible in low- and middle-income countries.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Objectives<\/jats:title>\n                    <jats:p>To determine the genetic patterns of resistance emerging in West African HIV-1 subtypes during first-line virological failure, and the implications for future antiretroviral options.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Patients and methods<\/jats:title>\n                    <jats:p>Participants were selected from a Nigerian cohort of people living with HIV who had failed first-line ART and subsequently switched to second-line therapy. Whole HIV-1 genome sequences were generated from first-line virological failure samples with Illumina MiSeq. Mutations detected at \u22652% frequency were analysed and compared by subtype.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>HIV-1 sequences were obtained from 101 participants (65% female, median age 30 years, median 32.9 months of nevirapine- or efavirenz-based ART). Thymidine analogue mutations (TAMs) were detected in 61%, other core NRTI mutations in 92% and NNRTI mutations in 99%. Minority variants (&amp;lt;20% frequency) comprised 18% of all mutations. K65R was more prevalent in CRF02_AG than G subtypes (33% versus 7%; P\u200a=\u200a0.002), and \u22653 TAMs were more common in G than CRF02_AG (52% versus 24%; P\u200a=\u200a0.004). Subtype G viruses also contained more RT cleavage site mutations. Cross-resistance to at least one of the newer NNRTIs, doravirine, etravirine or rilpivirine, was predicted in 81% of participants.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Extensive drug resistance had accumulated in people with West African HIV-1 subtypes, prior to second-line ART. Deep sequencing significantly increased the detection of resistance-associated mutations. Caution should be used if considering newer-generation NNRTI agents in this setting.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/jac\/dkab385","type":"journal-article","created":{"date-parts":[[2021,10,12]],"date-time":"2021-10-12T18:01:36Z","timestamp":1634061696000},"page":"474-482","source":"Crossref","is-referenced-by-count":15,"title":["Deep sequencing of HIV-1 reveals extensive subtype variation and drug resistance after failure of first-line antiretroviral regimens in Nigeria"],"prefix":"10.1093","volume":"77","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3614-4570","authenticated-orcid":false,"given":"Kate","family":"El Bouzidi","sequence":"first","affiliation":[{"name":"Division of Infection & Immunity, University College London, London, UK"},{"name":"Institute for Global Health, University College London, London, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rawlings 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