{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,29]],"date-time":"2026-08-29T07:30:21Z","timestamp":1787988621946,"version":"build-2784847793"},"reference-count":28,"publisher":"SAGE Publications","issue":"11","license":[{"start":{"date-parts":[[2020,11,1]],"date-time":"2020-11-01T00:00:00Z","timestamp":1604188800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["AIDS Research and Human Retroviruses"],"published-print":{"date-parts":[[2020,11]]},"abstract":"<jats:p>The prevalence of HIV-1 drug resistance is increasing worldwide and monitoring its emergence is important for the successful management of populations receiving combination antiretroviral therapy. It is likely that pre-existing drug resistance mutations linked on the same viral genomes are predictive of treatment failure. Because of the large number of sequences generated by ultrasensitive single-genome sequencing (uSGS) and other similar next-generation sequencing methods, it is difficult to assess each sequence individually for linked drug resistance mutations. Several software\/programs exist to report the frequencies of individual mutations in large data sets, but they provide no information on linkage of resistance mutations. In this study, we report the HIV-DRLink program, a research tool that provides resistance mutation frequencies as well as their genetic linkage by parsing and summarizing the Sierra output from the Stanford HIV Database. The HIV-DRLink program should only be used on data sets generated by methods that eliminate artifacts due to polymerase chain reaction recombination, for example, standard single-genome sequencing or uSGS. HIV-DRLink is exclusively a research tool and is not intended to inform clinical decisions.<\/jats:p>","DOI":"10.1089\/aid.2020.0109","type":"journal-article","created":{"date-parts":[[2020,7,20]],"date-time":"2020-07-20T01:02:05Z","timestamp":1595206925000},"page":"942-947","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":7,"title":["Short Communication: HIV-DRLink: A Tool for Reporting Linked HIV-1 Drug Resistance Mutations in Large Single-Genome Data Sets Using the Stanford HIV Database"],"prefix":"10.1177","volume":"36","author":[{"given":"Wei","family":"Shao","sequence":"first","affiliation":[{"name":"Advanced Biomedical Computing Science, Frederick National Laboratory for Cancer Research (FNLCR) sponsored by the National Cancer Institute, Frederick, Maryland, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valerie F.","family":"Boltz","sequence":"additional","affiliation":[{"name":"HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, Maryland, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junko","family":"Hattori","sequence":"additional","affiliation":[{"name":"HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, Maryland, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael J.","family":"Bale","sequence":"additional","affiliation":[{"name":"HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, Maryland, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frank","family":"Maldarelli","sequence":"additional","affiliation":[{"name":"HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, Maryland, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John M.","family":"Coffin","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mary F.","family":"Kearney","sequence":"additional","affiliation":[{"name":"HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, Maryland, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"179","published-online":{"date-parts":[[2020,11,6]]},"reference":[{"key":"e_1_3_5_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(13)62230-8"},{"key":"e_1_3_5_3_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.7824947"},{"key":"e_1_3_5_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(17)30702-8"},{"key":"e_1_3_5_5_2","doi-asserted-by":"publisher","DOI":"10.1111\/hiv.12522"},{"key":"e_1_3_5_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/S2352-3018(14)70021-9"},{"key":"e_1_3_5_7_2","unstructured":"WHO: 2019. 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