Table 2

Median and range of percent similarity scores between potential vaccine candidates and an alignment of C clade sequences. The similarities are shown for the p24 and gp160 proteins, representative of highly conserved and highly variable proteins. The C-subtype ancestral and consensus (con) sequences, when compared with the set of protein sequences from contemporary subtype C isolates, have comparable distributions of similar- ity scores. The M-group consensus is comparable to C clade isolate sequences. Two representative C clade isolates are shown, DU422 from South Africa and BR025 from Brazil. The last column shows the results of a subtype B strain compared with C sequences (intersubtype) for contrast. Regions with gaps were included, and either a relative insertion or deletion or an amino acid change at any position is considered one difference.

ProteinConsensus sequencesIsolate sequences
C-subtype conC ancestralM-group conC_ZA.DU422C_BR.92BR025B_FR.HXB2R
p2495.4 (97.4–92.8)94.8 (97.7–92.8)93.1 (95.1–91.1)94.8 (97.4–92.1)92.8 (96.4–88.9)88.9 (91.8–86.6)
gp16087.5 (90.6–83.5)86.1 (88.3–81.7)81.4 (84.0–77.1)81.3 (89.3–77.4)83.1 (85.9–79.6)72.1 (73.8–68.0)