Correlation between a phenotypic assay and three bioinformatic tools for determining HIV co-receptor use.
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.
Poveda
Eva
E
Department of Infectious Diseases, Hospital Carlos III, Madrid, Spain.
Briz
Verónica
V
Roulet
Vanessa
V
Del Mar González
María
M
Faudon
Jean-Louis
JL
Skrabal
Katharina
K
Soriano
Vincent
V
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
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