Inclusion of full length human immunodeficiency virus type 1 (HIV-1) gag sequences in viral recombinants applied to drug susceptibility phenotyping

Drug susceptibility phenotyping of recombinant clinical human immunodeficiency virus type 1 (HIV-1) isolates has been used widely to quantitatively assess viral resistance to antiretroviral agents. A novel method is described for HIV-1 drug susceptibility phenotyping. Recombinant virus that contains the entire HIV-1 Gag, protease (PR) and reverse transcriptase (RT) coding regions is generated from plasma of HIV-1 infected subjects, thus allowing the in vitro investigation of effects caused by all protein-coding sequence elements upstream from the drug targets on: (i) drug susceptibility; and (ii) viral replicative capacity. Mutations known to cause retarded viral growth kinetics (RT M184V and PR I50V) were introduced and analyzed in parallel using both the new Five Prime HIV assay (FPH) and a standard recombinant virus assay (RVA). The M184V and I50V mutants produced up to 4.8- and 5.9-fold higher p24 antigen levels, respectively, with the FPH when compared to the cultures containing RVA-derived viruses. The reduced number of homologous recombination events necessary to generate replication-competent provirus with the FPH is the most likely explanation for these findings. Long range RT-PCR products were generated from plasma of HIV-1 infected subjects and HIV-1 LTR sequences were added using one-step PCR-mediated recombination. FPH-recombinants generated from two patients with previous HIV PR and RT inhibitor therapy showed lower drug susceptibilities than mutants established in parallel by RVA, and relative in vitro replication of the FPH recombinant derived from one of these subjects was enhanced compared to the corresponding RVA mutant. Although there were changes from the HIV-1 subtype B consensus sequence in amino acids flanking the Gag p17/p24, p24/p2 or p2/p7 PR cleavage sites, none were within the 10 amino acids immediately flanking the sites. These data suggest that determinants of drug susceptibility may be encoded in Gag upstream of the p7/p1 and p1/p6 regions, and that some phenotyping assays may therefore be underdetermining the reduction of drug susceptibility in some viral isolates.