{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,9]],"date-time":"2026-03-09T21:36:46Z","timestamp":1773092206067,"version":"3.50.1"},"reference-count":29,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2016,2,11]],"date-time":"2016-02-11T00:00:00Z","timestamp":1455148800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["T32 AI052073"],"award-info":[{"award-number":["T32 AI052073"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["KL2 TR001083"],"award-info":[{"award-number":["KL2 TR001083"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["UL1 TR001085"],"award-info":[{"award-number":["UL1 TR001085"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 AI068581"],"award-info":[{"award-number":["R01 AI068581"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC) 2015 Mobility Program"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>A hybridization-based point-of-care (POC) assay for HIV-1 drug resistance would be useful in low- and middle-income countries (LMICs) where resistance testing is not routinely available. The major obstacle in developing such an assay is the extreme genetic variability of  HIV-1. We analyzed 27,203 reverse transcriptase (RT) sequences from the Stanford HIV Drug Resistance Database originating from six LMIC regions. We characterized the variability in a  27-nucleotide window surrounding six clinically important drug resistance mutations (DRMs) at positions 65, 103, 106, 181, 184, and 190. The number of distinct codons at each DRM position ranged from four at position 184 to 11 at position 190. Depending on the mutation, between 11 and 15 of the 24 flanking nucleotide positions were variable. Nonetheless, most flanking sequences differed from a core set of 10 flanking sequences by just one or two nucleotides. Flanking sequence variability was also lower in each LMIC region compared with overall variability in all regions. We also describe an online program that we developed to perform similar analyses for mutations at any position in RT, protease, or integrase.<\/jats:p>","DOI":"10.3390\/v8020048","type":"journal-article","created":{"date-parts":[[2016,2,11]],"date-time":"2016-02-11T21:03:56Z","timestamp":1455224636000},"page":"48","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["Genetic Variability of HIV-1 for Drug Resistance Assay Development"],"prefix":"10.3390","volume":"8","author":[{"given":"Dana","family":"Clutter","sequence":"first","affiliation":[{"name":"Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine,  300 Pasteur Drive, L-134, Stanford, CA 94035, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patricia","family":"S\u00e1nchez","sequence":"additional","affiliation":[{"name":"HIV-1 Molecular Epidemiology Laboratory, Microbiology and Parasitology Department,  Hospital Ramo\u0301n y Cajal-IRYCIS and CIBER-ESP, Madrid 28034, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Soo-Yon","family":"Rhee","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine,  300 Pasteur Drive, L-134, Stanford, CA 94035, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2513-2643","authenticated-orcid":false,"given":"Robert","family":"Shafer","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine,  300 Pasteur Drive, L-134, Stanford, CA 94035, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2016,2,11]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Rhee, S.Y., Blanco, J.L., Jordan, M.R., Taylor, J., Lemey, P., Varghese, V., Hamers, R.L., Bertagnolio, S., de Wit, T.F., and Aghokeng, A.F. 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DNA PNA XNA"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/8\/2\/48\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T19:19:05Z","timestamp":1760210345000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/8\/2\/48"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,2,11]]},"references-count":29,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2016,2]]}},"alternative-id":["v8020048"],"URL":"https:\/\/doi.org\/10.3390\/v8020048","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,2,11]]}}}