Independent divergences in the CD4 binding site and V3 loop encoded in two seroprevalent Ugandan HIV-1 clinical isolates

Two major epitopes expressed in HIV-1 have been recently shown to play a central role in virus neutralization. One of these important specificities is a type-specific or group-specific, principal neutralizing determinant (PND) located in the V3 loop of gp120. The other is a more broadly neutralizing determinant associated with the CD4 binding site. Structural and serological studies of the variation in these epitopes have become important in vaccine research. This report describes the analysis of the DNA clones encoding a region of gp120 that overlaps the V3 loop and the putative CD4 recognition site in two new African isolates, UG06c and UG23c. Phylogenetic analyses of the DNA sequences showed that the new African isolates clustered with two very distinct subtypes of HIV-1. UG06c was grouped with U455, D687, and Z321, previously classified as "HIV-1 subtype A" in the AIDS and human retroviruses database; and UG23c was grouped with MAL, JY1, NDK, ELI, and Z2Z6 classified as "HIV-1 subtype D." Considerable variation was apparent in the V3 loop. The divergence included the presence of the hexapeptides GP-GRSF and GLGQAL at the cap of the loop in UG06c and UG23c, respectively. The GPGR tetrapeptide in UG06c formed a beta-turn configuration similar to that of MN or IIIB. The beta-turn was not found to be a likely conformation for GLGQ. The amino acids previously implicated in CD4 binding and the associated neutralizing activity were relatively conserved. To assess a possible impact of the sequence and conformational variations on serological reactivity, UG06c and UG23c were subjected to neutralization assay.