Clonal analysis of the virus populations of three patients whose genotypic prediction and phenotype were discordant. Clonal composition of the HIV-1 quasispecies of three patients harboring R5 phenotyped viruses mispredicted X4 by the genotypic algorithms built for subtype B viruses. V3 amino acid sequence alignments were obtained by sequencing molecular clones of env PCR products. Theses sequences are shown with the following abbreviations with reference to the direct sequence: dot, identity with amino acid baseline sequence; dash, gap inserted to maintain alignment; slash, amino acid position related to dual virus population. Replacements are indicated by the appropriate code letters. Residues at positions 11 and 25 are boxed to highlight the substitutions noted. The V3 net charge (calculated by subtracting the number of negatively charged amino acids [D and E] from the number of positively charged ones [K and R]); the number of amino acids in V3; the genotype predicted by the combined 11/25 and net charge rules built for subtype B viruses and the Geno2pheno are shown, together with the observed phenotype.