Full metadata record
DC Field | Value | Language |
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dc.creator | Garrido, C. (Carolina) | - |
dc.creator | Roulet, V. (Vanessa) | - |
dc.creator | Chueca, N. (Natalia) | - |
dc.creator | Poveda, E. (Eva) | - |
dc.creator | Aguilera, A. (Antonio) | - |
dc.creator | Skrabal, K. (Katharina) | - |
dc.creator | Zahonero, N. (Natalia) | - |
dc.creator | Carlos-Chillerón, S. (Silvia) | - |
dc.creator | Garcia, F. (Federico) | - |
dc.creator | Faudon, J. L. (Jean Louis) | - |
dc.creator | Soriano, V. (Vincent) | - |
dc.creator | Mendoza, C. (Carmen) de | - |
dc.date.accessioned | 2017-03-29T07:52:51Z | - |
dc.date.available | 2017-03-29T07:52:51Z | - |
dc.date.issued | 2008 | - |
dc.identifier.citation | Garrido, C., Roulet, V., Chueca, N., Poveda, E., Aguilera, A., Skrabal, K., et al. Evaluation of eight different bioinformatics tools to predict viral tropism in different human immunodeficiency virus type 1 subtypes. J Clin Microbiol. 2008 Mar;46(3):887-891. | es_ES |
dc.identifier.issn | 0095-1137 | - |
dc.identifier.uri | https://hdl.handle.net/10171/43161 | - |
dc.description.abstract | Human immunodeficiency virus type 1 (HIV-1) tropism can be assessed using phenotypic assays, but this is quite laborious, expensive, and time-consuming and can be made only in sophisticated laboratories. More accessible albeit reliable tools for testing of HIV-1 tropism are needed in view of the prompt introduction of CCR5 antagonists in clinical practice. Bioinformatics tools based on V3 sequences might help to predict HIV-1 tropism; however, most of these methods have been designed by taking only genetic information derived from HIV-1 subtype B into consideration. The aim of this study was to evaluate the performances of several genotypic tools to predict HIV-1 tropism in non-B subtypes, as data on this issue are scarce. Plasma samples were tested using a new phenotypic tropism assay (Phenoscript-tropism; Eurofins), and results were compared with estimates of coreceptor usage using eight different genotypic predictor softwares (Support Vector Machine [SVM], C4.5, C4.5 with positions 8 to 12 only, PART, Charge Rule, geno2pheno coreceptor, Position-Specific Scoring Matrix X4R5 [PSSMX4R5], and PSSMsinsi). A total of 150 samples were tested, with 115 belonging to patients infected with non-B subtypes and 35 drawn from subtype B-infected patients, which were taken as controls. When non-B subtypes were tested, the concordances between the results obtained using the phenotypic assay and distinct genotypic tools were as follows: 78.8% for SVM, 77.5% for C4.5, 82.5% for C4.5 with positions 8 to 12 only, 82.5% for PART, 82.5% for Charge Rule, 82.5% for PSSMX4R5, 83.8% for PSSMsinsi, and 71.3% for geno2pheno. When clade B viruses were tested, the best concordances were seen for PSSMX4R5 (91.4%), PSSMsinsi (88.6%), and geno2pheno (88.6%). The sensitivity for detecting X4 variants was lower for non-B than for B viruses, especially in the case of PSSMsinsi (38.4% versus 100%, respectively), SVMwetcat (46% versus 100%, respectively), and PART (30% versus 90%, respectively). In summary, while inferences of HIV-1 coreceptor usage using genotypic tools seem to be reliable for clade B viruses, their performances are poor for non-B subtypes, in which they particularly fail to detect X4 variants. | es_ES |
dc.language.iso | eng | es_ES |
dc.publisher | American Society for Microbiology | es_ES |
dc.rights | info:eu-repo/semantics/openAccess | es_ES |
dc.subject | Materias Investigacion::Ciencias de la Salud::Microbiología y biología molecular | es_ES |
dc.title | Evaluation of eight different bioinformatics tools to predict viral tropism in different human immunodeficiency virus type 1 subtypes | es_ES |
dc.type | info:eu-repo/semantics/article | es_ES |
dc.identifier.doi | http://dx.doi.org/10.1128/JCM.01611-07 | es_ES |
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