Figure 3

Characterization of V3 sequences of clones tested in this study. Column “phenotype” indicates syncytium (SI) or non-syncytium (NSI) inducing phenotype as determined on PBMC cells; n.d., not determined. Columns “geno2pheno score” and “11/25 positions” indicate the prediction score of geno2pheno[coreceptor] method [20] and 11 and 25 residues [11, 12], and the tropism predicted based on these two methods, respectively. A false positive rate of 5% was selected as the decision cut-off for geno2pheno prediction. The colour indicates the predicted phenotype: blue– clearly R5, red – clearly X4, magenta – ambiguous. To obtain IC₅₀ values, entry efficiency was determined by bulk analysis in presence of serial dilutions of the respective coreceptor antagonist as described in Methods. Dose response curves were fitted using GraphPad Prism software. Mean values of three independent experiments are depicted. n.d., not determined in our analysis; n.a., not applicable (no dose response curve could be fitted to the data due to lacking inhibition by the respective drug); incomplete, steep dose response curve with reduced maximum inhibition. “Observed phenotype” indicates the clone phenotype observed in our assay based on the sensitivity to AMD and MVC and entry dependency on the two coreceptors.