Clade-specific differences between human immunodeficiency virus type 1 clades B and C: Diversity and correlations in C3-V4 regions of gp120

Current knowledge of human immunodeficiency virus type 1 envelope (Env) glycoprotein structure and function is based on studies of clade B viruses. We present evidence of sequence and structural differences in viral glycoprotein gp120 between clades B and C. In clade C, the C3 region alpha 2-helix exhibits high sequence entropy at the polar face but maintains its amphipathicity, whereas in clade B it accommodates hydrophobic residues. The V4 hypervariable domain in clade C is shorter than that in clade B. Generally, shorter V4 loops are incompatible with a glycine occurring in the alpha 2-helix in clade C, an intriguing association that could be exploited to inform Env immunogen design.