ACCUMULATION OF DEFECTIVE VIRAL GENOMES IN PERIPHERAL-BLOOD MONONUCLEAR-CELLS OF HUMAN-IMMUNODEFICIENCY-VIRUS TYPE 1-INFECTED INDIVIDUALS

Human immunodeficiency virus type 1 (HIV-1) genomes present in periphe ral blood mononuclear cells (PBMCs) of infected persons or in lymphocy tes infected in vitro were studied by long-distance PCR (LD-PCR) using primers localized in the HIV-1 long terminal repeats. The full-length 9-kb DNA was the only LD-PCR product obtained in peripheral and cord blood lymphocytes from seronegative donors infected in vitro. However, a high proportion (27% to 66%) of distinct populations of extensively deleted HIV-1 genomes of variable size was detected in PBMCs of 15 of 16 HIV-1-infected persons. Physical mapping of defective genomes show ed that the frequency of deletions is proportional to their proximity to the central part of HIV-1 genome, which is consistent with a deleti on mechanism involving a single polymerase jump during reverse transcr iption. Sequencing of deletion junctions revealed the presence of shor t direct repeats of three or four nucleotides, The number of defective HIV-1 genomes decreased after in vitro activation of PBMCs. Persisten ce of full-length and deleted genomes in in vitro activated PBMCs corr elated with isolation of an infectious virus, Our results represent th e first quantitative assessment of intragenomic rearrangements in HIV- 1 genomes in PBMCs of infected persons and demonstrate that, in contra st to in vitro infection, defective genomes accumulate in PBMCs of inf ected persons.