NATURALLY-OCCURRING ACCESSORY GENE-MUTATIONS LEAD TO PERSISTENT HUMAN-IMMUNODEFICIENCY-VIRUS TYPE-1 INFECTION OF CD4-POSITIVE T-CELLS

Proviral DNA from cells surviving severe but transient cytopathic effe cts, mediated by infection with recombinant human immunodeficiency vir us type 1 (HIV-1) carrying a single gene mutation at vif, vpr, or vpu, was characterized by use of HIV-1-specific primer pairs in a two-step PCR. Deletion mutations were detected in a region that spanned the vi f and vpr open reading frames. Cloning and sequencing of the amplified DNA from this region revealed frequent large deletions in a limited n umber of nucleotide positions. Analyses of the deletions suggested tha t (i) genetic recombination, (ii) template-primer slippage, and (iii) misalignment of the growing point during reverse transcription of the HIV-1 genome might be the mechanisms that generated the mutations. Apa rt from the large deletions, smaller deletions that gave frameshift mu tations in vif and/or vpr prevailed. In addition, cells infected with a triple mutant defective in vif, vpr, and vpu did not show any cytopa thic effect. Thus, mutations generating multiple accessory gene defect s during HIV-1 replication correlate with viral persistence and loss o f cytopathogenicity.