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Table 4 Comparison of genotypic prediction of HIV tropism and the observed phenotype on a GenBank data set of HIV-1 subtype D viruses

From: Genotypic prediction of HIV-1 subtype D tropism

   Phenotype Concordance Genotypic Prediction
Genotypic tool   R5 R5X4/X4   Sena Speb
Geno2pheno10 R5 21 1 67% 96% 50%
  X4 21 24 κ = 0.40 (p < 0.001)   
Combined 11/25 and net charge rules R5 26 5 69% 80% 62%
  X4 16 20 κ = 0.38 (p < 0.001)   
Combined 11/25 and net charge rules for subtype D R5 40 8 85% 68% 95%
  X4 2 17 κ = 0.63 (p < 0.0001)   
  1. aSen: sensitivity for predicting CXCR4-using viruses
  2. bSpe: specificity for predicting CXCR4-using viruses
  3. κ: kappa coefficient.