Correlation between a phenotypic assay and three bioinformatic tools for determining HIV co-receptor use

AIDS. 2007 Jul 11;21(11):1487-90. doi: 10.1097/QAD.0b013e32826fb741.

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.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Computational Biology
  • DNA Primers / genetics
  • Female
  • Genotype
  • HIV Envelope Protein gp120 / genetics*
  • HIV Infections / diagnosis*
  • HIV Infections / genetics
  • HIV-1 / genetics*
  • Humans
  • Male
  • Molecular Sequence Data
  • Peptide Fragments / genetics*
  • Phenotype
  • Receptors, CCR5 / genetics
  • Receptors, CXCR4 / genetics
  • Receptors, HIV / genetics*
  • Sensitivity and Specificity
  • Sequence Analysis, DNA / methods

Substances

  • DNA Primers
  • HIV Envelope Protein gp120
  • HIV envelope protein gp120 (305-321)
  • Peptide Fragments
  • Receptors, CCR5
  • Receptors, CXCR4
  • Receptors, HIV