Table 4.
Comparison of genotypic prediction of HIV tropism and the observed phenotype on a GenBank data set of HIV-1 subtype D viruses
| 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) | |||
aSen: sensitivity for predicting CXCR4-using viruses
bSpe: specificity for predicting CXCR4-using viruses
κ: kappa coefficient.