Grossly Defective<i>nef</i>Gene Sequences in a Human Immunodeficiency Virus Type 1-Seropositive Long-Term Nonprogressor

TLDR

The patient has remained a long‑term nonprogressor since 1985, maintaining CD4 counts above 1,000 cells/µl without AIDS‑related illness, and previous studies have linked nef gene defects to such durable control. The study aimed to characterize the molecular composition of the HIV‑1 quasispecies infecting this individual. The authors amplified the 5′LTR/gag leader and nef regions from fresh, uncultured peripheral blood mononuclear cells, performed length‑polymorphism analysis across 1994–1996 samples, and sequenced the nef gene from a 1996 specimen. Analysis revealed that all proviruses carried nef deletions, with sequencing confirming multiple deletions in nef and the nef/U3 overlap, while 5′LTR/gag leader analysis identified two quasispecies populations, demonstrating that nef defects are associated with long‑term nonprogression even after sexual transmission.

Abstract

ABSTRACT We have been investigating a long-term nonprogressor who was found to be human immunodeficiency virus type 1 (HIV-1) seropositive in 1985 and has survived with stable CD4 + T-cell counts (&gt;1,000 CD4 cells/μl) without any AIDS-related illness. We have previously reported that repeated attempts to measure HIV-1 RNA in the peripheral mononuclear cells obtained from this subject have invariably failed. In the present study, we have analyzed the molecular nature of the HIV-1 quasispecies infecting this patient by PCR amplification of two proviral regions, the 5′ long terminal repeat (5′LTR)/ gag leader and the nef gene, directly from fresh uncultured peripheral mononuclear cells, followed by length polymorphism analysis (with 1994, 1995, and 1996 samples) and sequencing (with a 1996 sample). Only proviral forms with nef deletions were revealed by length polymorphism analysis in samples from all three time points. Sequence analysis of the nef gene from the 1996 sample confirmed the presence of similar proviral quasispecies characterized by the presence of several deletions located in the nef -alone and the nef /U3 overlapping regions. Length polymorphism analysis of the 5′LTR/ gag leader region suggested the existence of two major quasispecies populations, one characterized by the presence of forms carrying deletions in the U3 region and the other showing a completely intact, full-length 5′LTR. Evidence of the role of nef gene defects in long-term survival of HIV-1-infected patients has been provided so far in two independent investigations involving patients infected with HIV through blood transfusion. Here we show the existence of a similar condition in a subject who acquired HIV-1 seropositivity through the sexual route.