Evolution of the HIV-1 nef gene in HLA-B*57 positive elite suppressors

Abstract

Elite controllers or suppressors (ES) are HIV-1 infected patients who maintain viral loads of < 50 copies/ml without antiretroviral therapy. CD8+ T cells are thought to play a key role in the control of viral replication and exert selective pressure on gag and nef in HLA-B*57 positive ES. We previously showed evolution in the gag gene of ES which surprisingly was mostly due to synonymous mutations rather than non-synonymous mutation in targeted CTL epitopes. This finding could be the result of structural constraints on Gag, and we therefore examined the less conserved nef gene. We found slow evolution of nef in plasma virus in some ES. This evolution is mostly due to synonymous mutations and occurs at a rate similar to that seen in the gag gene in the same patients. The results provide further evidence of ongoing viral replication in ES and suggest that the nef and gag genes in these patients respond similarly to selective pressure from the host.

Figure 1

Relevant sequence regions from clonal, nef amplified from plasma or from resting CD4+T cells. The date of sample acquisition and number of clones that are identical to the displayed sequences are noted. The HLA-B*57-restricted epitope YT9 (Nef 120-128) and the undefined epitope KG15 (nef 105-119) in ES3 are denoted by empty boxes outlined in blue and yellow respectively. The HLA-B*57-restricted epitopes KF9 (Nef 82-90), and HW9 (Nef 116-124), are denoted by boxes shaded in green and pink respectively. Sequences from 2004 and 2005 for ES3, ES7, ES8, and ES9 have been previously reported and are shown for comparative purposes only.

Figure 2

Phylogenetic analysis of nef in the 4 elite suppressor patients. Phylogenies were estimated by using a "classical" approach, functioning under maximum-likeluhood (ML) optimality criterion. All sequences are clonal, and APOBEC-mediated hypermutated sequences were removed from analysis. Colors indicate time, with the scale below in years. Triangles represent clonal plasma sequences, circles represent proviral sequences from CD4+ resting T cells.

Figure 3

Analysis of synonymous and non-synonymous mutation in the plasma virus and proviral compartments. Shown are p-distance values for plasma (A) and proviral (B) sequences as determined by comparing early and late samples for each patient utilizing the Nei-Gojobori method. The numbers of differences also were calculated for plasma (C) and proviral (D) sequences using the Nei-Gojobori method.

Figure 4

Comparison of synonymous and non-synonymous mutations in nef and gag for plasma (top panel) and proviral (bottom panel) clones. P-distance values were calculated for each patient utilizing the Nei-Gojobori method.