{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T20:52:30Z","timestamp":1790110350673,"version":"4.0.1"},"reference-count":29,"publisher":"SAGE Publications","issue":"6","license":[{"start":{"date-parts":[[2011,8,1]],"date-time":"2011-08-01T00:00:00Z","timestamp":1312156800000},"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":["Antiviral Therapy"],"published-print":{"date-parts":[[2011,8]]},"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>HIV drug-resistance (DR) surveillance in resource-limited settings can be performed using dried blood spots (DBS) because of ease of collection, transportation and storage. Analysis of pooled specimens on next-generation sequencing (NGS)-based platforms, such as the 454 pyrosequencing, is an efficient sequencing method for determining HIV DR rates. In this study, we conducted HIV DR surveillance on DBS using NGS and identified minority variants in individual patients.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>A total of 48 extracts of DBS from an HIV DR surveillance study in Mexico City were re-amplified using primers tagged with multiplex identifiers, pooled and pyrosequenced. Consensus sequences were generated for each specimen with mixtures identified at positions where &gt;20% of the reads contained a variant. Individual consensus sequences were then analysed for DR mutations and compared with those derived from Sanger sequencing.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>DBS analysed with tagged pooled pyrosequencing (TPP) were highly concordant with Sanger sequencing genotypes from matching plasma and DBS (99.21% and 99.51%, respectively). An exception was an M184I mutation only detected with TPP of DBS at a frequency of 20.4%. Multiple specimens had minority variant reads below the 20% mixture threshold.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>TPP using DBS is an effective method for HIV DR surveillance. TPP for genotyping results in cost savings of 40% over conventional in-house methods. The effect of low-abundance DR mutations, undetectable by conventional methods, remains to be determined. This technology might be applied to any HIV specimen (plasma\/ serum) and can also be used for other diagnostic assays where DNA sequencing is required.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3851\/imp1839","type":"journal-article","created":{"date-parts":[[2011,6,30]],"date-time":"2011-06-30T10:01:52Z","timestamp":1309428112000},"page":"871-878","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":32,"title":["Next-Generation Sequencing of Dried Blood Spot Specimens: A Novel Approach to HIV Drug-Resistance Surveillance"],"prefix":"10.1177","volume":"16","author":[{"given":"Hezhao","family":"Ji","sequence":"first","affiliation":[{"name":"National HIV & Retrovirology Laboratories, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, ON, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Li","sequence":"additional","affiliation":[{"name":"National HIV & Retrovirology Laboratories, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, ON, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Morag","family":"Graham","sequence":"additional","affiliation":[{"name":"Genomics Core Facility, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada"},{"name":"Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ben Binhua","family":"Liang","sequence":"additional","affiliation":[{"name":"Bioinformatics Core, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard","family":"Pilon","sequence":"additional","affiliation":[{"name":"National HIV & Retrovirology Laboratories, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, ON, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shari","family":"Tyson","sequence":"additional","affiliation":[{"name":"Genomics Core Facility, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Geoff","family":"Peters","sequence":"additional","affiliation":[{"name":"Genomics Core Facility, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaun","family":"Tyler","sequence":"additional","affiliation":[{"name":"Genomics Core Facility, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harriet","family":"Merks","sequence":"additional","affiliation":[{"name":"National HIV & Retrovirology Laboratories, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, ON, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silvia","family":"Bertagnolio","sequence":"additional","affiliation":[{"name":"World Health Organization, Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luis","family":"Soto-Ramirez","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n, Mexico City, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Sandstrom","sequence":"additional","affiliation":[{"name":"National HIV & Retrovirology Laboratories, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, ON, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Brooks","sequence":"additional","affiliation":[{"name":"National HIV & Retrovirology Laboratories, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, ON, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"179","published-online":{"date-parts":[[2011,8,1]]},"reference":[{"key":"bibr1-IMP1839","unstructured":"UNAIDS. AIDS epidemic update \u2013 December 2009. (Updated December 2009. Accessed 30 June 2010.) Available from http:\/\/data.unaids.org\/pub\/Report\/2009\/JC1700_Epi_Update_2009_en.pdf."},{"issue":"2","key":"bibr2-IMP1839","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1177\/135965350801302S03","volume":"13","author":"Bennett D.E.","year":"2008","journal-title":"Antivir Ther"},{"issue":"2","key":"bibr3-IMP1839","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1177\/135965350801302S05","volume":"13","author":"Bertagnolio S.","year":"2008","journal-title":"Antivir Ther"},{"key":"bibr4-IMP1839","doi-asserted-by":"publisher","DOI":"10.1177\/135965350801302S04"},{"key":"bibr5-IMP1839","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1177\/135965350701200114","volume":"12","author":"Bertagnolio S.","year":"2007","journal-title":"Antivir Ther"},{"key":"bibr6-IMP1839","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1177\/135965350901400513","volume":"14","author":"Hamers R.L.","year":"2009","journal-title":"Antivir Ther"},{"key":"bibr7-IMP1839","doi-asserted-by":"publisher","DOI":"10.2174\/157016210790442740"},{"key":"bibr8-IMP1839","doi-asserted-by":"publisher","DOI":"10.3851\/IMP1660"},{"key":"bibr9-IMP1839","doi-asserted-by":"publisher","DOI":"10.1007\/s00705-010-0696-y"},{"key":"bibr10-IMP1839","doi-asserted-by":"publisher","DOI":"10.1097\/QAD.0b013e3281c618db"},{"key":"bibr11-IMP1839","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkn100"},{"key":"bibr12-IMP1839","doi-asserted-by":"publisher","DOI":"10.1038\/nature03959"},{"key":"bibr13-IMP1839","doi-asserted-by":"publisher","DOI":"10.1038\/nbt1486"},{"key":"bibr14-IMP1839","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0812600106"},{"key":"bibr15-IMP1839","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0002836"},{"key":"bibr16-IMP1839","doi-asserted-by":"publisher","DOI":"10.1086\/596736"},{"key":"bibr17-IMP1839","doi-asserted-by":"publisher","DOI":"10.1101\/gr.6468307"},{"key":"bibr18-IMP1839","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm435"},{"key":"bibr19-IMP1839","doi-asserted-by":"publisher","DOI":"10.1186\/1742-4690-6-15"},{"key":"bibr20-IMP1839","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0009263"},{"key":"bibr21-IMP1839","unstructured":"Roche. 454 Sequencing Technical Bulletin. Amplicon fusion primer design guidelines for GS FLX Titanium Series Lib-A chemistry. No 013-2009. (Updated August 2009. Accessed November 2009.) Available from http:\/\/www.igsb.org\/uploads\/pdf\/TCB-09013_AmpliconFusionPrimerDesignGuidelines.pdf."},{"key":"bibr22-IMP1839","unstructured":"Roche. 454 Sequencing Technical Bulletin. Using multiplex identifier (MID) adaptors for the GS FLX Titanium chemistry \u2013 extended MID set. No. 005-2009. (Updated April 2009. Accessed November 2009.) Available from http:\/\/www.eurofinsdna.com\/fileadmin\/PDFs\/product_services\/TB-0905_Technical_Bulletin_Roche_MID_Adaptors.pdf."},{"key":"bibr23-IMP1839","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msm092"},{"key":"bibr24-IMP1839","doi-asserted-by":"publisher","DOI":"10.1002\/0471715816.ch3"},{"key":"bibr25-IMP1839","doi-asserted-by":"publisher","DOI":"10.1097\/01.qai.0000174656.71276.d6"},{"key":"bibr26-IMP1839","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pmed.0050158"},{"key":"bibr27-IMP1839","first-page":"662","volume":"201","author":"Paredes R.","year":"2010","journal-title":"J Infect Dis"},{"key":"bibr28-IMP1839","first-page":"672","volume":"201","author":"Halvas E.K.","year":"2010","journal-title":"J Infect Dis"},{"key":"bibr29-IMP1839","doi-asserted-by":"publisher","DOI":"10.1086\/595703"}],"container-title":["Antiviral Therapy"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.3851\/IMP1839","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.3851\/IMP1839","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T12:50:14Z","timestamp":1777380614000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.sagepub.com\/doi\/10.3851\/IMP1839"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,8]]},"references-count":29,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2011,8]]}},"alternative-id":["10.3851\/IMP1839"],"URL":"https:\/\/doi.org\/10.3851\/imp1839","relation":{},"ISSN":["1359-6535","2040-2058"],"issn-type":[{"value":"1359-6535","type":"print"},{"value":"2040-2058","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,8]]}}}