Defective accessory genes in a human immunodeficiency virus type 1-infected long-term survivor lacking recoverable virus

Abstract

We have been studying a patient who acquired human immunodeficiency virus (HIV) infection via a blood transfusion 13 years ago. She has remained asymptomatic since that time. The blood donor and two other recipients have all died of AIDS. Although this patient has shown persistently strong seroreactivity to HIV type 1 (HIV-1) antigens by Western blot (immunoblot), she has been continually HIV culture negative in results from multiple laboratories over the last 6 years and has a very low viral burden. Her CD4 ؉ T-cell count has fluctuated around a mean of 399 cells per l, with little change in lymphocyte subset percentages. Strong cellular immune responses to HIV-1 epitopes by this patient have been demonstrated. We now report the results of an intensive molecular genetic analysis of the HIV-1 proviral quasispecies from this patient sampled over 5 years. Long terminal repeat region sequences supported the argument for normal basal and Tatmediated promoter activities. Sequential sequencing of the nef gene revealed a low frequency (8.3%) of defective genes and a striking lack of sequence evolution. Functional analysis of predominant nef genes by both a cell surface CD4 downregulation and a viral infectivity complementation assay showed wild-type function. In contrast, sequential analysis of an amplicon containing the vif, vpr, vpu, tat1, and rev1 genes revealed the presence of inactivating mutations in 64% of the clones. These data suggest that this patient, initially infected with a virulent swarm of HIV-1, is presently infected with a more-attenuated viral quasispecies as a result of effective host immunity.

Analysis of the HIV-1 nef gene in five intravenous drug users with long-term nonprogressive HIV-1 infection in Italy

“…A 2-aa or 4-aa deletion was present in the highly polymorphic region in three of the five LTNPs (L1, L2, L3) but in none of the five rapid progressors. Deletions in this same region have been documented previously in some LTNPs and occasionally in rapid progressors [Huang et al, 1995;Michael et al, 1995;]. A 4-aa insertion at codon 23 in the variable region was found in Patients L2 and R1.…”

“…A longer (10 aa) insertion at the same codon was detected in Patient L1. Different insertion at this position have been reported in infected patients independently of the rate of disease progression [Huang et al, 1995;Michael et al, 1995;Blaak et al, 1998;Vallejo et al, 1999]. Nef from Patient L1 only additionally had a 2-aa deletion nine codons upstream the cleavage site.…”

“…The viral nef accessory gene has been associated with pathogenesis in vivo in the simian immunodeficiency virus (SIV) [Kestler et al, 1991], SCID-human [Jamieson et al, 1994] and transgenic mouse [Hanna et al, 1998] models and has been found to be defective in several human LTNPs [Huang et al 1995;Deacon et al, 1995;Kirchhoff et al, 1995;Mariani et al, 1996, Michael et al, 1995Premkumar et al, 1996;Salvi et al, 1998]. A number of functions have been consistently attributed in vitro to wild type nef alleles including down-regulation of the cell surface CD4 receptor and MHC-I molecules [Mangasarian et al, 1999;Greenberg et al, 1998;Hua et al, 1997], modulation of cellular activation and signal transduction pathways [Sawai et al, 1994;Baur et al, 1997], and enhancement of viral infectivity [Guatelli, 1997].…”

“…Although at least some of the in vitro functions of Nef are expected to influence HIV-1 replication in vivo, their relative contribution toward AIDS pathogenesis have not yet been defined. Most data on nef structure in LTNPs have been obtained from patients infected by blood product transfusion and sexual contacts [Deacon et al, 1995;Huang et al 1995;Kirchhoff et al, 1995;Michael et al, 1995;Mariani et al, 1996, Premkumar et al, 1996Salvi et al, 1998;Vallejo et al, 1999]. To contribute additional data on the possible association between Nef variants and the rate of disease progression, we have directly isolated and analyzed nef alleles from clinical specimens of LTNP and rapid progressor drug addicts by nested PCR and DNA population sequencing.…”

Prolonged survival of rat liver allograft with adenoviral gene transfection of human immunodeficiency virus type 1 nef

“…11 The human and simian immune deficiency viruses (HIV and SIV) encode three signatory retroviral genes (gag, pol, and env) and seven regulatory genes (tat, rev, tev, vup, vpr, vif, and nef) that may be associated with the pathogenesis of the virus infection. 12 The nef of HIV-1, HIV-2, and SIV seems to be a substantial virulence factor and is critical for the development of AIDS. 13 Although its function in vivo still remains unclear, in vitro studies have well established that it has great implication in cell function.…”