V3 amino acid sequence alignments and matched phenotypes of the 26 subtype D viruses (1a) and of 13 reference subtype B viruses (1b). V3 amino acid sequence alignments were obtained by bulk sequencing env PCR products from the 26 subtype D-infected patients, 10 subtype B-infected patients and 3 reference subtype B viruses. These sequences are shown with the following abbreviations with reference to the consensus sequences: 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 and mutated N-linked glycosylation sites 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. Discordances between the genotypic predictions and the phenotype are boxed.