High variability of the gag/pol transframe region among HIV-1 isolates

The overlapping region of gag and pol genes of human immunodeficiency virus type 1 (HIV-1) also called transframe region, contains the frameshift locus from gag to pol. This region encodes both the protein p6, the function of which remains unclear, and a putative transframe protein covently linked to the N-terminus of the viral protease within Gag/Pol protein precursor. We have investigated the variability of the transframe region among nine HIV-1 isolates obtained from Congolese AIDS patients. Nucleotide sequences were determined using the polymerase chain reaction and the direct sequencing of amplified products. The sequences of Congolese isolates markedly differed from one another and from other reference HIV-1 strains by both insertion-deletion events and numerous base substitutions. Several putative cleavage sites of precursor polypeptides were modified. When compared to consensus ones the amino acid sequences of p6 protein were very different among divergent HIV-1 isolates, except for a limited group of 10 conserved amino acids.