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Article: Evaluation of an in-house genotyping resistance test for HIV-1 drug resistance interpretation and genotyping

TitleEvaluation of an in-house genotyping resistance test for HIV-1 drug resistance interpretation and genotyping
Authors
Issue Date2007
PublisherElsevier BV. The Journal's web site is located at http://www.elsevier.com/locate/jcv
Citation
Journal Of Clinical Virology, 2007, v. 39 n. 2, p. 125-131 How to Cite?
AbstractIntroduction: The human immunodeficiency virus type 1 (HIV-1) genotyping resistance test (GRT) has been considered essential for HIV-1 drug resistance monitoring. However, it is not commonly used in some developing countries in Asia and Africa due to its high running cost. Objective: This study aims to evaluate a new low-cost in-house GRT for both subtype B and non-B HIV-1. Study design: The in-house GRT sequenced the entire protease and 410 codons of reverse transcriptase (RT) in the pol gene. Its performance on drug resistance interpretation was evaluated against the FDA-approved ViroSeq™ HIV-1 Genotyping System. Particularly, a panel of 235 plasma samples from 205 HIV-1-infected patients in Hong Kong was investigated. The HIV-1 drug resistance-related mutations detected by the two systems were compared. The HIV-1 subtypes were analyzed through the REGA HIV-1 Genotyping Tool and env phylogenetic analysis. Results: Among the 235 samples, 229 (97.4%) were successfully amplified by both in-house and ViroSeq™ systems. All PCR-negative samples harbored viral RNA at <400 copies/mL. The in-house and ViroSeq™ system showed identical drug resistance-related mutation patterns in 216 out of 229 samples (94.3%). The REGA pol genotyping results showed 93.9% (215/229) concordance with the env phylogenetic results including HIV-1 subtype A1, B, C, D, G, CRF01_AE, CRF02_AG, CRF06_cpx, CRF07_BC, CRF08_BC, CRF15_01B and other recombinant strains. The cost of running the in-house GRT is only 25% of that for the commercial system, thus making it suitable for the developing countries in Asia and Africa. Conclusions: Overall, our in-house GRT provided comparable results to those of the commercial ViroSeq™ genotyping system on diversified HIV-1 subtypes at a more affordable price which make it suitable for HIV-1 monitoring in developing countries. © 2007 Elsevier B.V. All rights reserved.
Persistent Identifierhttp://hdl.handle.net/10722/79044
ISSN
2015 Impact Factor: 2.647
2015 SCImago Journal Rankings: 1.503
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorChen, JHKen_HK
dc.contributor.authorWong, KHen_HK
dc.contributor.authorChan, Ken_HK
dc.contributor.authorLam, HYen_HK
dc.contributor.authorLee, SSen_HK
dc.contributor.authorLi, Pen_HK
dc.contributor.authorLee, MPen_HK
dc.contributor.authorTsang, DNen_HK
dc.contributor.authorZheng, BJen_HK
dc.contributor.authorYuen, KYen_HK
dc.contributor.authorYam, WCen_HK
dc.date.accessioned2010-09-06T07:49:54Z-
dc.date.available2010-09-06T07:49:54Z-
dc.date.issued2007en_HK
dc.identifier.citationJournal Of Clinical Virology, 2007, v. 39 n. 2, p. 125-131en_HK
dc.identifier.issn1386-6532en_HK
dc.identifier.urihttp://hdl.handle.net/10722/79044-
dc.description.abstractIntroduction: The human immunodeficiency virus type 1 (HIV-1) genotyping resistance test (GRT) has been considered essential for HIV-1 drug resistance monitoring. However, it is not commonly used in some developing countries in Asia and Africa due to its high running cost. Objective: This study aims to evaluate a new low-cost in-house GRT for both subtype B and non-B HIV-1. Study design: The in-house GRT sequenced the entire protease and 410 codons of reverse transcriptase (RT) in the pol gene. Its performance on drug resistance interpretation was evaluated against the FDA-approved ViroSeq™ HIV-1 Genotyping System. Particularly, a panel of 235 plasma samples from 205 HIV-1-infected patients in Hong Kong was investigated. The HIV-1 drug resistance-related mutations detected by the two systems were compared. The HIV-1 subtypes were analyzed through the REGA HIV-1 Genotyping Tool and env phylogenetic analysis. Results: Among the 235 samples, 229 (97.4%) were successfully amplified by both in-house and ViroSeq™ systems. All PCR-negative samples harbored viral RNA at <400 copies/mL. The in-house and ViroSeq™ system showed identical drug resistance-related mutation patterns in 216 out of 229 samples (94.3%). The REGA pol genotyping results showed 93.9% (215/229) concordance with the env phylogenetic results including HIV-1 subtype A1, B, C, D, G, CRF01_AE, CRF02_AG, CRF06_cpx, CRF07_BC, CRF08_BC, CRF15_01B and other recombinant strains. The cost of running the in-house GRT is only 25% of that for the commercial system, thus making it suitable for the developing countries in Asia and Africa. Conclusions: Overall, our in-house GRT provided comparable results to those of the commercial ViroSeq™ genotyping system on diversified HIV-1 subtypes at a more affordable price which make it suitable for HIV-1 monitoring in developing countries. © 2007 Elsevier B.V. All rights reserved.en_HK
dc.languageengen_HK
dc.publisherElsevier BV. The Journal's web site is located at http://www.elsevier.com/locate/jcven_HK
dc.relation.ispartofJournal of Clinical Virologyen_HK
dc.rightsJournal of Clinical Virology. Copyright © Elsevier BV.en_HK
dc.subject.meshAnti-HIV Agents - pharmacologyen_HK
dc.subject.meshAntiretroviral Therapy, Highly Active - classification - methodsen_HK
dc.subject.meshBase Sequenceen_HK
dc.subject.meshDrug Resistance, Viral - geneticsen_HK
dc.subject.meshGenetic Techniquesen_HK
dc.subject.meshGenotypeen_HK
dc.subject.meshHIV-1 - classification - drug effects - genetics - isolation & purificationen_HK
dc.subject.meshHong Kongen_HK
dc.subject.meshHumansen_HK
dc.subject.meshMicrobial Sensitivity Testsen_HK
dc.subject.meshPolymerase Chain Reactionen_HK
dc.subject.meshSensitivity and Specificityen_HK
dc.titleEvaluation of an in-house genotyping resistance test for HIV-1 drug resistance interpretation and genotypingen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1386-6532&volume=39&issue=2&spage=125&epage=131.&date=2007&atitle=Evaluation+of+an+in-house+genotyping+resistance+test+for+HIV-1+drug+resistance+interpretation+and+genotyping.en_HK
dc.identifier.emailZheng, BJ:bzheng@hkucc.hku.hken_HK
dc.identifier.emailYuen, KY:kyyuen@hkucc.hku.hken_HK
dc.identifier.emailYam, WC:wcyam@hkucc.hku.hken_HK
dc.identifier.authorityZheng, BJ=rp00353en_HK
dc.identifier.authorityYuen, KY=rp00366en_HK
dc.identifier.authorityYam, WC=rp00313en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1016/j.jcv.2007.03.008en_HK
dc.identifier.pmid17449318-
dc.identifier.scopuseid_2-s2.0-34248639310en_HK
dc.identifier.hkuros132259en_HK
dc.identifier.hkuros142137-
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-34248639310&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume39en_HK
dc.identifier.issue2en_HK
dc.identifier.spage125en_HK
dc.identifier.epage131en_HK
dc.identifier.isiWOS:000247509500010-
dc.publisher.placeNetherlandsen_HK
dc.identifier.scopusauthoridChen, JHK=12763271400en_HK
dc.identifier.scopusauthoridWong, KH=7404758411en_HK
dc.identifier.scopusauthoridChan, K=35097079800en_HK
dc.identifier.scopusauthoridLam, HY=35097472400en_HK
dc.identifier.scopusauthoridLee, SS=18042141700en_HK
dc.identifier.scopusauthoridLi, P=36068280500en_HK
dc.identifier.scopusauthoridLee, MP=7409121315en_HK
dc.identifier.scopusauthoridTsang, DN=7005609132en_HK
dc.identifier.scopusauthoridZheng, BJ=7201780588en_HK
dc.identifier.scopusauthoridYuen, KY=36078079100en_HK
dc.identifier.scopusauthoridYam, WC=7004281720en_HK

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