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Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes : Performance evaluation of the new REGA version 3 and seven other tools

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dc.creatorPineda-Peña, Andrea-Clemencia
dc.creatorRodrigues Faria, Nuno
dc.creatorImbrechts, Stijn
dc.creatorLibin, Pieter
dc.creatorBarroso Abecasis, Ana
dc.creatorDeforche, Koen
dc.creatorGómez-López, Arley
dc.creatorCamacho, Ricardo J.
dc.creatorOliveira, Tulio de
dc.creatorVandamme, Anne-Mieke
dc.creator.googlePineda-Peña, Andrea-Clemenciaspa
dc.creator.googleRodrigues Faria, Nunospa
dc.creator.googleImbrechts, Stijnspa
dc.creator.googleLibin, Pieterspa
dc.creator.googleBarroso Abecasis, Anaspa
dc.creator.googleDeforche, Koenspa
dc.creator.googleGómez-López, Arleyspa
dc.creator.googleCamacho, Ricardo J.spa
dc.creator.googleOliveira, Tulio despa
dc.creator.googleVandamme, Anne-Miekespa
dc.date.accessioned2018-11-21T21:01:24Z
dc.date.available2018-11-21T21:01:24Z
dc.date.created2013
dc.date.issued2013
dc.description.abstractBackground: To investigate differences in pathogenesis, diagnosis and resistance pathways between HIV-1 subtypes, an accurate subtyping tool for large datasets is needed. We aimed to evaluate the performance of automated subtyping tools to classify the different subtypes and circulating recombinant forms using pol, the most sequenced region in clinical practice. We also present the upgraded version 3 of the Rega HIV subtyping tool (REGAv3). Methodology: HIV-1 pol sequences (PR. +. RT) for 4674 patients retrieved from the Portuguese HIV Drug Resistance Database, and 1872 pol sequences trimmed from full-length genomes retrieved from the Los Alamos database were classified with statistical-based tools such as COMET, jpHMM and STAR; similarity-based tools such as NCBI and Stanford; and phylogenetic-based tools such as REGA version 2 (REGAv2), REGAv3, and SCUEAL. The performance of these tools, for pol, and for PR and RT separately, was compared in terms of reproducibility, sensitivity and specificity with respect to the gold standard which was manual phylogenetic analysis of the pol region. Results: The sensitivity and specificity for subtypes B and C was more than 96% for seven tools, but was variable for other subtypes such as A, D, F and G. With regard to the most common circulating recombinant forms (CRFs), the sensitivity and specificity for CRF01_AE was ~99% with statistical-based tools, with phylogenetic-based tools and with Stanford, one of the similarity based tools. CRF02_AG was correctly identified for more than 96% by COMET, REGAv3, Stanford and STAR. All the tools reached a specificity of more than 97% for most of the subtypes and the two main CRFs (CRF01_AE and CRF02_AG). Other CRFs were identified only by COMET, REGAv2, REGAv3, and SCUEAL and with variable sensitivity. When analyzing sequences for PR and RT separately, the performance for PR was generally lower and variable between the tools. Similarity and statistical-based tools were 100% reproducible, but this was lower for phylogenetic-based tools such as REGA (~99%) and SCUEAL (~96%). Conclusions: REGAv3 had an improved performance for subtype B and CRF02_AG compared to REGAv2 and is now able to also identify all epidemiologically relevant CRFs. In general the best performing tools, in alphabetical order, were COMET, jpHMM, REGAv3, and SCUEAL when analyzing pure subtypes in the pol region, and COMET and REGAv3 when analyzing most of the CRFs. Based on this study, we recommend to confirm subtyping with 2 well performing tools, and be cautious with the interpretation of short sequences. © 2013 The Authors.eng
dc.format.mimetypeapplication/pdf
dc.identifier.issnISSN 1567-1348
dc.identifier.urihttp://repository.urosario.edu.co/handle/10336/18729
dc.language.isoengspa
dc.relation.citationEndPage348
dc.relation.citationStartPage337
dc.relation.citationTitleInfection, Genetics and Evolution
dc.relation.citationVolumeVol. 19
dc.relation.ispartofInfection, Genetics and Evolution, ISSN: 1567-1348, Vol. 19 (2013) pp. 337-348spa
dc.relation.urihttps://ac.els-cdn.com/S1567134813001810/1-s2.0-S1567134813001810-main.pdf?_tid=246c1373-351b-42fb-ab29-b0c462bdfee0&acdnat=1540057805_2fbfa5e9a5d0c42ce3a95a4525d47330spa
dc.rights.accesRightsinfo:eu-repo/semantics/openAccess
dc.rights.accesoAbierto (Texto Completo)spa
dc.rights.cchttps://creativecommons.org/licenses/by-nc-nd/3.0/spa
dc.source.bibliographicCitationAbecasis, A., Wensing, A.M., Vercauteren, J., Paraskevis, D., Van De Vijver, D., Albert, J., Asjo, B., Vandamme, A.M., (2008), on behalf of the SPREAD-programme, HIV-1 genetic diversity in Europe and its demographic predictors. Demographic determinants of HIV-1 subtype distribution in Europe, 6th European HIV Drug Resistance Workshop, Budapest, Hungaryspa
dc.source.instnameinstname:Universidad del Rosario
dc.source.reponamereponame:Repositorio Institucional EdocUR
dc.subjectCrfspa
dc.subjectHiv-1spa
dc.subjectPhylogenetic Analysisspa
dc.subjectSensitivityspa
dc.subjectSubtypesspa
dc.subjectSubtypingspa
dc.subject.decsHuman Immunodeficiency Virus Proteinasespa
dc.subject.decsRna Directed Dna Polymerasespa
dc.subject.decsArticlespa
dc.subject.decsAutomationspa
dc.subject.decsCladisticsspa
dc.subject.decsComputer Programspa
dc.subject.decsControlled Studyspa
dc.subject.decsGene Sequencespa
dc.subject.decsHuman Immunodeficiency Virus 1spa
dc.subject.decsIntermethod Comparisonspa
dc.subject.decsNonhumanspa
dc.subject.decsPhylogenyspa
dc.subject.decsPriority Journalspa
dc.subject.decsReproducibilityspa
dc.subject.decsSensitivity And Specificityspa
dc.subject.decsStatistical Analysisspa
dc.subject.decsStructural Genespa
dc.subject.decsVirus Genomespa
dc.subject.decsVirus Recombinantspa
dc.subject.decsVirus Typingspa
dc.subject.decsHuman Immunodeficiency Virus 1spa
dc.subject.decsCirculating Recombinant Formsspa
dc.subject.decsCrfspa
dc.subject.decsCrfsspa
dc.subject.decsHiv-1spa
dc.subject.decsLanlspa
dc.subject.decsLos Alamos Datasetspa
dc.subject.decsManual Phylogenetic Analysisspa
dc.subject.decsMphyspa
dc.subject.decsNtsspa
dc.subject.decsNucleotidesspa
dc.subject.decsPhylogenetic Analysisspa
dc.subject.decsPrspa
dc.subject.decsProteasespa
dc.subject.decsRega Hiv Subtyping Tool Version 2spa
dc.subject.decsRega Hiv Subtyping Tool Version 3spa
dc.subject.decsRegav2spa
dc.subject.decsRegav3spa
dc.subject.decsReverse Transcriptasespa
dc.subject.decsRtspa
dc.subject.decsSensitivityspa
dc.subject.decsSubtypesspa
dc.subject.decsSubtypingspa
dc.subject.decsUnique Recombinant Formsspa
dc.subject.decsUrfsspa
dc.subject.decsCluster Analysisspa
dc.subject.decsComputational Biologyspa
dc.subject.decsDatabases, Geneticspa
dc.subject.decsHiv Infectionsspa
dc.subject.decsHiv-1spa
dc.subject.decsHumansspa
dc.subject.decsMolecular Typingspa
dc.subject.decsPhylogenyspa
dc.subject.decsPublic Health Surveillancespa
dc.subject.decsReproducibility Of Resultsspa
dc.subject.decsSensitivity And Specificityspa
dc.subject.lembVIHspa
dc.subject.lembPatogenicidadspa
dc.subject.lembFilogeniaspa
dc.titleAutomated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes : Performance evaluation of the new REGA version 3 and seven other toolsspa
dc.typearticleeng
dc.type.hasVersioninfo:eu-repo/semantics/publishedVersion
dc.type.spaArtículospa
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