Sequence Analysis of the gp120 Region of the env Gene of Ugandan Human Immunodeficiency Proviruses from a Single Individual

DNA sequences encoding the surface glycoprotein gp120 of the human immunodeficiency virus type 1 (HIV-1) were amplified by the polymerase chain reaction (PCR) from peripheral blood mononuclear cells obtained from a Ugandan AIDS patient. The PCR-amplified DNA was cloned into a phagemid vector and nine clones sequenced. The gp120 sequences of the proviruses were similar to that of the Zairian isolate HIV-JY1 and unlike that of another Ugandan provirus, U455. Six of the clones were closely related to each other (maximum nucleotide sequence divergence 1.9%), and had a V3 amino acid sequence similar to that frequently seen in recent isolates from Uganda. Two others formed a second group that diverged from the first by an average of 6.0% at the nucleotide level, resulting in a 12.5% divergence of amino acid sequence. These divergent clones had extensive amino acid sequence changes not only in the V3 region, which was highly atypical, but also in V1 and V4, and to a lesser extent in V2 and V5. A further proviral clone had a sequence intermediate between those of the other two groups of clones.