{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T04:43:55Z","timestamp":1789533835948,"version":"build-2803163510"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"suppl_9","funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000030","name":"Centers for Disease Control and Prevention","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000030","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,12,1]]},"DOI":"10.1093\/infdis\/jix397","type":"journal-article","created":{"date-parts":[[2017,8,4]],"date-time":"2017-08-04T15:11:28Z","timestamp":1501859488000},"page":"S829-S833","source":"Crossref","is-referenced-by-count":52,"title":["Next-Generation Human Immunodeficiency Virus Sequencing for Patient Management and Drug Resistance Surveillance"],"prefix":"10.1093","volume":"216","author":[{"given":"Marc","family":"Noguera-Julian","sequence":"first","affiliation":[{"name":"IrsiCaixa AIDS Research Institute"},{"name":"Universitat Aut\u00f2noma de Barcelona"},{"name":"Universitat de Vic-Universitat Central de Catalunya, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dianna","family":"Edgil","sequence":"additional","affiliation":[{"name":"United States Agency for International Development"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"P Richard","family":"Harrigan","sequence":"additional","affiliation":[{"name":"British Columbia Centre for Excellence in HIV\/AIDS, University of British Columbia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Sandstrom","sequence":"additional","affiliation":[{"name":"National HIV and Retrovirology Laboratory, JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine","family":"Godfrey","sequence":"additional","affiliation":[{"name":"Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roger","family":"Paredes","sequence":"additional","affiliation":[{"name":"IrsiCaixa AIDS Research Institute"},{"name":"Universitat Aut\u00f2noma de Barcelona"},{"name":"Universitat de Vic-Universitat Central de Catalunya, Spain"},{"name":"Infectious Diseases Unit, Hospital Universitari Germans Trias i Pujol, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,9,15]]},"reference":[{"key":"key\n\t\t\t\t20180328152222_CIT0001","volume-title":"HIV drug resistance. Global report on early warning indicators of HIV drug resistance","author":"World Health Organization","year":"2016"},{"key":"key\n\t\t\t\t20180328152222_CIT0002","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1016\/j.meegid.2016.08.031","article-title":"HIV-1 drug resistance and resistance testing","volume":"46","author":"Clutter","year":"2016","journal-title":"Infect Genet Evol"},{"key":"key\n\t\t\t\t20180328152222_CIT0003","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1093\/jac\/dkw445","article-title":"Pretreatment HIV-1 drug resistance in Argentina: results from a surveillance study performed according to WHO-proposed new methodology in 2014\u201315","volume":"72","author":"Bissio","year":"2017","journal-title":"J Antimicrob Chemother"},{"key":"key\n\t\t\t\t20180328152222_CIT0004","doi-asserted-by":"crossref","first-page":"e579","DOI":"10.1016\/S2352-3018(16)30119-9","article-title":"Pretreatment HIV-drug resistance in Mexico and its impact on the effectiveness of first-line antiretroviral therapy: a nationally representative 2015 WHO survey","volume":"3","author":"\u00c1vila-R\u00edos","year":"2016","journal-title":"Lancet HIV"},{"key":"key\n\t\t\t\t20180328152222_CIT0005","doi-asserted-by":"crossref","first-page":"1137","DOI":"10.1097\/QAD.0000000000001033","article-title":"Treatment options after virological failure of first-line tenofovir-based regimens in South Africa: an analysis by deep sequencing","volume":"30","author":"Casadell\u00e0","year":"2016","journal-title":"AIDS"},{"key":"key\n\t\t\t\t20180328152222_CIT0006","volume-title":"Guidelines on the public health response to pretreatment HIV drug resistance","author":"World Health Organization","year":"2017"},{"key":"key\n\t\t\t\t20180328152222_CIT0007","article-title":"Deep sequencing for HIV-1 clinical management","author":"Casadell\u00e0","year":"2016","journal-title":"Virus Res"},{"key":"key\n\t\t\t\t20180328152222_CIT0008","doi-asserted-by":"crossref","first-page":"e267","DOI":"10.1016\/S1473-3099(16)30118-9","article-title":"Affordable HIV drug-resistance testing for monitoring of antiretroviral therapy in sub-Saharan Africa","volume":"16","author":"Inzaule","year":"2016","journal-title":"Lancet Infect Dis"},{"key":"key\n\t\t\t\t20180328152222_CIT0009","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1093\/cid\/cis887","article-title":"The clinical and economic impact of genotype testing at first-line antiretroviral therapy failure for HIV-infected patients in South Africa","volume":"56","author":"Levison","year":"2013","journal-title":"Clin Infect Dis"},{"key":"key\n\t\t\t\t20180328152222_CIT0010","doi-asserted-by":"crossref","first-page":"6824","DOI":"10.1128\/AAC.01490-15","article-title":"HIV drug resistance testing by high-multiplex \u201cwide\u201d sequencing on the Illumina MiSeq","volume":"59","author":"Lapointe","year":"2015","journal-title":"Antimicrob Agents Chemother"},{"key":"key\n\t\t\t\t20180328152222_CIT0011","doi-asserted-by":"crossref","first-page":"e36494","DOI":"10.1371\/journal.pone.0036494","article-title":"Low-cost ultra-wide genotyping using Roche\/454 pyrosequencing for surveillance of HIV drug resistance","volume":"7","author":"Dudley","year":"2012","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t20180328152222_CIT0012","doi-asserted-by":"crossref","first-page":"3349","DOI":"10.1093\/jac\/dku278","article-title":"Cost-efficient HIV-1 drug resistance surveillance using multiplexed high-throughput amplicon sequencing: implications for use in low- and middle-income countries","volume":"69","author":"Ekici","year":"2014","journal-title":"J Antimicrob Chemother"},{"key":"key\n\t\t\t\t20180328152222_CIT0013","doi-asserted-by":"crossref","first-page":"930","DOI":"10.1093\/jac\/dku426","article-title":"Low-frequency drug-resistant HIV-1 and risk of virological failure to first-line NNRTI-based ART: a multicohort European case-control study using centralized ultrasensitive 454 pyrosequencing","volume":"70","author":"Cozzi-Lepri","year":"2015","journal-title":"J Antimicrob Chemother"},{"key":"key\n\t\t\t\t20180328152222_CIT0014","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1186\/s12977-014-0122-8","article-title":"Cross-clade simultaneous HIV drug resistance genotyping for reverse transcriptase, protease, and integrase inhibitor mutations by Illumina MiSeq","volume":"11","author":"Dudley","year":"2014","journal-title":"Retrovirology"},{"key":"key\n\t\t\t\t20180328152222_CIT0015","doi-asserted-by":"crossref","first-page":"871","DOI":"10.3851\/IMP1839","article-title":"Next-generation sequencing of dried blood spot specimens: a novel approach to HIV drug-resistance surveillance","volume":"16","author":"Ji","year":"2011","journal-title":"Antivir Ther"},{"key":"key\n\t\t\t\t20180328152222_CIT0016","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1089\/gtmb.2008.0073","article-title":"High-throughput genotyping on archived dried blood spot samples","volume":"13","author":"Hollegaard","year":"2009","journal-title":"Genet Test Mol Biomarkers"},{"key":"key\n\t\t\t\t20180328152222_CIT0017","doi-asserted-by":"crossref","first-page":"129","DOI":"10.20411\/pai.v1i1.116","article-title":"Use of dried blood spots to elucidate full-length transmitted\/founder HIV-1 genomes","volume":"1","author":"Salazar-Gonzalez","year":"2016","journal-title":"Pathog Immun"},{"key":"key\n\t\t\t\t20180328152222_CIT0018","doi-asserted-by":"crossref","first-page":"1361","DOI":"10.1089\/aid.2013.0175","article-title":"Nautilus: a bioinformatics package for the analysis of HIV type 1 targeted deep sequencing data","volume":"29","author":"Kijak","year":"2013","journal-title":"AIDS Res Hum Retroviruses"},{"key":"key\n\t\t\t\t20180328152222_CIT0019","doi-asserted-by":"crossref","first-page":"674","DOI":"10.1186\/1471-2164-14-674","article-title":"V-Phaser 2: variant inference for viral populations","volume":"14","author":"Yang","year":"2013","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t20180328152222_CIT0020","doi-asserted-by":"crossref","first-page":"329","DOI":"10.3389\/fmicb.2012.00329","article-title":"Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data","volume":"3","author":"Beerenwinkel","year":"2012","journal-title":"Front Microbiol"},{"key":"key\n\t\t\t\t20180328152222_CIT0021","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1186\/gb-2011-12-8-125","article-title":"The real cost of sequencing: higher than you think!","volume":"12","author":"Sboner","year":"2011","journal-title":"Genome Biol"},{"key":"key\n\t\t\t\t20180328152222_CIT0022","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1016\/j.ijmedinf.2015.01.005","article-title":"Implementation of a cloud-based electronic medical record for maternal and child health in rural Kenya","volume":"84","author":"Haskew","year":"2015","journal-title":"Int J Med Inform"},{"key":"key\n\t\t\t\t20180328152222_CIT0023","article-title":"Development of bioinformatics infrastructure for genomics research in H3Africa [manuscript published online ahead of print 13 March 2017]","author":"Mulder","year":"2017","journal-title":"Glob Heart"},{"key":"key\n\t\t\t\t20180328152222_CIT0024","volume-title":"Making viral load routine. Successes and challenges in the implementation of routine HIV viral load monitoring. Part 1: programmatic strategies","author":"M\u00e9decins Sans Fronti\u00e8res"},{"key":"key\n\t\t\t\t20180328152222_CIT0025","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1016\/S1473-3099(13)70008-2","article-title":"Advances in tuberculosis diagnostics: the Xpert MTB\/RIF assay and future prospects for a point-of-care test","volume":"13","author":"Lawn","year":"2013","journal-title":"Lancet Infect Dis"},{"key":"key\n\t\t\t\t20180328152222_CIT0026","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1186\/1471-2105-12-119","article-title":"ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data","volume":"12","author":"Osvaldo Zagordi","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180328152222_CIT0027","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1093\/bioinformatics\/btu587","article-title":"VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering","volume":"31","author":"Verbist","year":"2015","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180328152222_CIT0028","article-title":"High-throughput pipeline for de-novo assembly and drug resistance mutations identification from next-generation sequencing viral data of residual diagnostic samples","author":"Cassarino","year":"2016","journal-title":"bioRxiv"},{"key":"key\n\t\t\t\t20180328152222_CIT0029","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1016\/j.jviromet.2016.11.008","article-title":"MinVar: a rapid and versatile tool for HIV-1 drug resistance genotyping by deep sequencing","volume":"240","author":"Huber","year":"2017","journal-title":"J Virol Methods"},{"key":"key\n\t\t\t\t20180328152222_CIT0030","doi-asserted-by":"crossref","first-page":"19752","DOI":"10.7448\/IAS.17.4.19752","article-title":"Analysis of transmitted HIV-1 drug resistance using 454 ultra-deep-sequencing and the DeepChek(\u00ae)-HIV system","volume":"17","author":"Garcia-Diaz","year":"2014","journal-title":"J Int AIDS Soc"}],"container-title":["The Journal of Infectious Diseases"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/jid\/article-pdf\/216\/suppl_9\/S829\/24264660\/jix397.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,3,28]],"date-time":"2018-03-28T17:54:37Z","timestamp":1522259677000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jid\/article\/216\/suppl_9\/S829\/4159381"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,9,15]]},"references-count":30,"journal-issue":{"issue":"suppl_9","published-online":{"date-parts":[[2017,9,15]]},"published-print":{"date-parts":[[2017,12,1]]}},"URL":"https:\/\/doi.org\/10.1093\/infdis\/jix397","relation":{},"ISSN":["0022-1899","1537-6613"],"issn-type":[{"value":"0022-1899","type":"print"},{"value":"1537-6613","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,11,15]]},"published":{"date-parts":[[2017,9,15]]}}}