title: Correlation between a phenotypic assay and three bioinformatic tools for determining HIV co-receptor use.
abstract: The predictive value of three genotypic methods to determine HIV-1 co-receptor usage was assessed in 83 plasma specimens taking as reference the results obtained using a recombinant phenotypic assay (Phenoscript). The best concordance was found for webPSSM, followed by geno2pheno and wetcat (85.9, 71.8 and 70.5%, respectively). Less than 5.1% of phenotypic X4 viruses were missed by genotypic tools. The genotypic prediction of HIV-1 co-receptor usage can thus assist therapeutic decisions for using CCR5 antagonists.
authors.affiliation: Department of Infectious Diseases, Hospital Carlos III, Madrid, Spain.
authors.forename: Eva
authors.initials: E
authors.lastname: Poveda
authors.forename: Verónica
authors.initials: V
authors.lastname: Briz
authors.forename: Vanessa
authors.initials: V
authors.lastname: Roulet
authors.forename: María
authors.initials: M
authors.lastname: Del Mar González
authors.forename: Jean-Louis
authors.initials: JL
authors.lastname: Faudon
authors.forename: Katharina
authors.initials: K
authors.lastname: Skrabal
authors.forename: Vincent
authors.initials: V
authors.lastname: Soriano
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D019295:Computational Biology; D017931:DNA Primers / Q000235:genetics; D005260:Female; D005838:Genotype; D015699:HIV Envelope Protein gp120 / Q000235:genetics*; D015658:HIV Infections / Q000175:diagnosis* / Q000235:genetics; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000235:genetics*; D010641:Phenotype; D019713:Receptors, CCR5 / Q000235:genetics; D019718:Receptors, CXCR4 / Q000235:genetics; D015728:Receptors, HIV / Q000235:genetics*; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D017931:DNA Primers; D015699:HIV Envelope Protein gp120; C059762:HIV envelope protein gp120 (305-321); D010446:Peptide Fragments; D019713:Receptors, CCR5; D019718:Receptors, CXCR4; D015728:Receptors, HIV