The human immunodeficiency virus (HIV-1) gp120 envelope glycoprotein mediates host cell entry via interactions with the CD4 receptor and a chemokine coreceptor. The CCR5 chemokine coreceptor is associated with transmitted viruses and is often retained throughout all disease stages. Major determinants for CCR5 usage are found in the third variable region (V3), which is maintained despite sequence variation in terms of amino acid substitutions and length differences. We investigated this functional conservation by the V3 by focusing on a representative of the subtype D, which has been associated with more divergent envelope sequence and more rapid disease progression, in comparison with the extensively-studied subtype B. Our analyses of V3 length revealed that HIV-1D V3 sequences are mostly 34 residues in length, while HIV-1B V3 sequences are mostly 35.

We investigated the consequence of amino acid substitution through alanine scanning mutagenesis of V3 residues. The study revealed that coreceptor binding by the V3 of the HIV-1D isolate 94UG114 is highly sensitive to mutations, contrary to what we observed for the HIV-1B isolate JRFL. Sequence context has a significant impact on the ability of an envelope to accommodate mutations. Length variation was studied by insertion or deletion of a single glycine residue observed to account for a significant portion of intersubtype differences. Our data suggest there is conservation of functional structure dependent upon the length of the stem, regardless of amino acid sequence. Nevertheless, the impact of length variation appears to vary with envelope context.

As soluble gp120 binding assays were used in these studies, we addressed concerns about assay discrepancies when compared against the fusion assay by demonstrating that function of oligomeric envelope in the fusion assay can reflect the capacity of soluble gp120 to bind CCR5. The binding assay remains a valuable tool for understanding a critical stage in viral entry, especially with the availability of CCR5 binding inhibitors for clinical use. Our results also suggest a mechanism by which V3 mutations may mediate resistance to CCR5 binding inhibitors among R5 escape viruses.