Sequence heterogeneity in human immunodeficiency virus type 1 nef in patients presenting with rapid progression and delayed progression to AIDS

Abstract

Genetic heterogeneity in the nef genes from human immunodeficiency virus type 1 (HIV-1)-infected rapid progressors (RPs) and long-term nonprogressors (LTNPs) was analyzed to identify various amino acid substitutions responsible for the discernible difference in disease progression. It was found that the majority of the strains characterized belonged to subtype C, followed by several BC recombinants and subtype A1. Complete nef subtype C sequences from 33 RPs and seven LTNPs were compared, and it was observed that, in the majority of the sequences from both groups, highly conserved functional motifs showed subtle changes. However, drastic changes were observed in two isolates from LTNPs where the arginine cluster was deleted, while in one of them, additionally, acidic residues were replaced by basic residues (EEEEE→RK(R)KKE). The deletion of the arginine cluster and the mutation of acidic residues to basic residues are predicted to delay disease development by abolishing CD4 downmodulation and causing diminution of major histocompatibility complex class I (MHC-I) downregulation, respectively. Nonetheless, this is an exclusive finding in these LTNPs, which necessitates their analysis at the functional level. The synonymous-to-nonsynonymous substitution ratio was greater than one in both of the groups, suggesting amino acid sequence conservation and functional robustness. Interpatient nucleotide distance within the group and between the two groups showed very little variation, confirming genetic relatedness among isolates.

Comparative genetic variability in HIV‐1 subtype C nef gene in early age groups of infants

“…The motif known as FPD has been reported to play a role in down modulation of CD4 and MHC1, was found to be conserved in both the age groups, however, preceeding to FPD motif, we found substitution of Y121F in 6 and 10 sequences of acute and early age groups, respectively, that has been suggested to play a role in enhancing disease progression. Similar substitution pattern has also been reported in earlier studies in patients with rapid progression to AIDS . Another substitution of I/V 134 in the GPG(I/V) motif by analogue threonine in four and nine sequences of acute and early age groups, respectively, might result in distorted β‐turn resulting in impaired nef protein that has been reported by others too .…”

“…The acidic cluster, compared to other motifs, was found to be highly variable showing insertion, deletion, and charge reversal in both the age groups. The high variability in this cluster has been reported in one of our study earlier also . Deletions and charge reversals observed in this cluster may weaken the signal strength affecting the process of down modulation of MHC1, which may lead to delay in disease progression .…”

“…Full length nef gene with amplicon size 620 bp was amplified through nested PCR as described earlier . Amplification was carried out using the Green Master Mix PCR kit (Promega, Madison) according to the manufacturer's instructions.…”

“…Full length nef gene with amplicon size 620 bp was amplified through nested PCR as described earlier. 11,12…”

HIV-1 Nef: a master manipulator of the membrane trafficking machinery mediating immune evasion

“…Recently, a study from Kuang et al [84] revealed that untreated patients in early stages of HIV-1 infection that maintained a low viral load were more likely to be infected with HIV-1 viruses encoding Nef alleles significantly less efficient at downregulating MHC-I than alleles from patients that did not maintain low viral loads [84]. An additional cohort of 4244 HIV-1 infected individuals in India demonstrated that the frequency of mutations in the PxxP 75 motif of Nef, which is essential for MHC-I downregulation, was greater in patients that progress more slowly, if at all, to AIDS [85]. Interestingly, while other studies have not observed a correlation between rate of progression to AIDS and MHC-I downregulation [86][87][88], these studies were limited by small sample size, with less than a dozen patients per experimental group and likely under-powered to detect significant differences, suggesting further analysis with larger cohorts of HIV-1 infected individuals is warranted.…”