An HIV-1 infected long-term non-progressor (LTNP): molecular analysis of HIV-1 strains in the vpr and nef genes.

We describe a long-term non-progressive injecting drug user (IDU) who was infected with human immunodeficiency virus type-1 (HIV-1) in 1984, and has survived with stable CD4+ T-cell counts (> 800/microliters blood) without any acquired immune deficiency syndrome (AIDS) related illness. With a goal to investigate the molecular nature of HIV-1 strains infecting this patient, we amplified the nef and vpr genes directly from the fresh uncultured peripheral blood mononuclear cells (PBMCs), and carried out co-culture studies. Sequence analysis of the nef gene (from 1994 samples) showed no deletions (as has been previously reported) expected for a 7 base pair duplication at the C-terminus which prematurely terminated the nef reading frame, whereas even after repeated attempts the nef gene could not be amplified from the 1992 PBMC samples. In contrast, the vpr gene (from 1992 and 1994 samples) revealed two distinct quasispecies with no apparent defects. We observed five amino acid substitutions, between residues 83-90, at the C-terminus which has been recently implicated in G2 cell cycle arrest as an early step to HIV-1 infection. In the light of recent evidence on the role of nef gene defects/attenuations in long-term survival of HIV-1 infected patients, it may be that the nef gene defect created by gene duplication, which eliminated the cysteine-206 crucial in disulfide bond formation, may play a role in chronic HIV-1 infection in this patient. These data further suggest that deletions in the nef gene may not be the only reason for long-term non-progression of HIV-1 infection in some individuals, but the gene defects like duplication and subtle mutations in the functional motifs of both nef and vpr genes may confer similar protection in HIV-1 infected patients surviving for longer periods of time with stable CD4 counts.