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 peripheral blood mononuclear cells (PBMCs) of infected persons or in lymphocytes 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 showed that the frequency of deletions is proportional to their proximity to the central part of HIV-1 genome, which is consistent with a deletion mechanism involving a single polymerase jump during reverse transcription. Sequencing of deletion junctions revealed the presence of short direct repeats of three or four nucleotides. The number of defective HIV-1 genomes decreased after in vitro activation of PBMCs. Persistence of full-length and deleted genomes in in vitro activated PBMCs correlated with isolation of an infectious virus. Our results represent the first quantitative assessment of intragenomic rearrangements in HIV-1 genomes in PBMCs of infected persons and demonstrate that, in contrast to in vitro infection, defective genomes accumulate in PBMCs of infected persons.
Sanchez
G
G
INSERM U322, Unité de Recherches sur les Rétrovirus et Maladies Associées, Parc Scientifique et Technologique de Luminy, Marseille, France.
Xu
X
X
Chermann
J C
JC
Hirsch
I
I
D000328:Adult; D000368:Aged; D002461:Cell Line, Transformed; D002478:Cells, Cultured; D004279:DNA, Viral; D003673:Defective Viruses / Q000235:genetics* / Q000302:isolation & purification; D005260:Female; D016679:Genome, Viral; D006679:HIV Seropositivity / Q000097:blood / Q000821:virology*; D015497:HIV-1 / Q000235:genetics* / Q000302:isolation & purification; D019073:HT29 Cells; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000166:cytology / Q000821:virology*; D008213:Lymphocyte Activation; D008297:Male; D008875:Middle Aged; D016133:Polymerase Chain Reaction; D012091:Repetitive Sequences, Nucleic Acid; D017384:Sequence Deletion
D004279:DNA, Viral