NATURAL VARIATION IN HIV-1 PROTEASE, GAG P7 AND P6, AND PROTEASE CLEAVAGE SITES WITHIN GAG POL POLYPROTEINS - AMINO-ACID SUBSTITUTIONS IN THE ABSENCE OF PROTEASE INHIBITORS IN MOTHERS AND CHILDREN INFECTED BY HUMAN-IMMUNODEFICIENCY-VIRUS TYPE-1/

Reduced sensitivity of human immunodeficiency virus type 1 (HIV-1) to protease inhibitors is associated with multiple amino acid substitutio ns in the virus-encoded protease. The combination of changes that cont ribute to drug resistance is dependent in part upon the amino acid res idues comprising protease alleles prior to drug therapy. We analyzed w ithin peripheral blood mononuclear cells from HIV-1-infected mothers a nd their children viral gag/pol regions, which included p7, transframe p6/p6, and protease coding sequences, as well as six protease cleava ge sites. Sixty protease alleles from 12 individuals differed by at le ast 3 to as many as 10 amino acids from proteases encoded by molecular clones of HIV-1, indicating that there is no prototype or consensus w ild-type HIV-1 protease sequence. Protease variants with a proline at position 63, a substitution associated with resistance to protease inh ibitors, appeared in the absence of antiprotease therapy in 7 patients and were transmitted by 2 mothers to their infants. Gag p7 and p6 reg ions were significantly more variable than protease. The p6/p6 region contained length variants and amino acid repeats in both reading fram es. Five protease cleavage sites (B, D', D, E, and F) contained highly conserved amino acid sequences in individuals infected by epidemiolog ically distinct viruses. In contrast, C cleavage sites, localized betw een Gag p2 and Gag p7, displayed considerable amino acid variability, were unique among groups of infected individuals, and appeared to be r elated to particular protease alleles. Genetic variability in vivo in protease, in cleavage sites, and in proteins upstream of protease prov ides the potential to modulate enzyme activity and susceptibility to p rotease inhibitors. (C) 1996 Academic Press, Inc.