Factors Associated With the Control of Viral Replication and Virologic Breakthrough in a Recently Infected HIV-1 Controller

Abstract

HIV-1 controllers are patients who control HIV-1 viral replication without antiretroviral therapy. Control is achieved very early in the course of infection, but the mechanisms through which viral replication is restricted are not fully understood. We describe a patient who presented with acute HIV-1 infection and was found to have an HIV-1 RNA level of <100copies/mL. She did not have any known protective HLA alleles, but significant immune activation of CD8+ T cells and natural killer (NK) cells was present, and both cell types inhibited viral replication. Virus cultured from this patient replicated as well in vitro as virus isolated from her partner, a patient with AIDS who was the source of transmission. Virologic breakthrough occurred 9months after her initial presentation and was associated with an increase in CD4+ T cell activation levels and a significant decrease in NK cell inhibitory capacity. Remarkably, CD8+ T cell inhibitory capacity was preserved and there were no new escape mutations in targeted Gag epitopes. These findings suggest that fully replication-competent virus can be controlled in acute HIV-1 infection in some patients without protective HLA alleles and that NK cell responses may contribute to this early control of viral replication.

Keywords: CD8+ T cells; HIV controllers; HIV-1; NK cells; Transmission pair.

Fig. 1

Clinical history of AC1. CD4 + T cell count (red) and viral load (blue) over time, with day 1 as onset of clinical symptoms.

Fig. 2

HIV-1 proviral and replication-competent Nef sequences. Nef amino acid sequence of replication competent (RC) and proviral (P) sequences from both VP1 and AC1 with time relative to the first clinic visit of AC1 aligned to the Consensus B sequence retrieved from the Los Alamos Database. The AC1 HIV-1 proviral sequence from D335 is post-loss of control. All other sequences of AC1 are pre-loss of control.

Fig. 3

Phylogenetic analysis of viral sequences obtained from AC1 and VP1. Maximum likelihood phylogenetic trees of nef (a) and gag (b) nucleotide sequences are shown. Sequences amplified from replication-competent virus (circles) and provirus (squares) for AC1 (green) and VP1 (blue) are compared to the most homologous clade B sequences (branches without symbols) in the Los Alamos Database. Sequences from clade D (black squares) serve as an outgroup. Bootstrap values of the clades including AC1 and VP1 sequences are indicated.

Fig. 4

Kinetics of replication of AC1 viral isolate compared to isolates from her partner (VP1) and a recently infected patient with a high HIV RNA levels (AP3). Patient viruses isolated from the viral outgrowth assay were used to infect stimulated, primary CD4 + T cells, and p24 production was measured for a week post-infection. The AC1 viral isolate was obtained before loss of control.

Fig. 5

Immune activation of CD4 + T cells, CD8 + T cells, and NK cells. Whole blood incubated at room temperature overnight was stained for HLA-DR and CD38 in the presence of T and NK cell markers. A) CD4 + T cell activation. B) CD8 + T cell activation. C) NK Cell activation. HD = HIV-negative healthy donor (n = 16). CP = chronic progressor (n = 11). ES = elite suppressor (n = 12). AP = acute progressors (3 recently infected patients with high viral loads). AC1c = time points for which AC1 controlled viremia. AC1v = time points for which AC1 had lost control of viremia. Specific day post initial clinic visit is indicated in legend.

Fig. 6

Loss of viral control leads to increased levels of IP-10, IFN-y and MIP1-α in the serum. Serum from five healthy donors (HD), eight chronic progressors (CP), eight elite suppressors (ES), and two acute progressors (AP) were tested. Chronic progressor 1 (VP1) was tested at one time point. Acute controller 1 (AC1) was tested at four time points, two prior to loss of viremic control (AC1c: D50, D160) and two post loss of viremic control (AC1v: D280, D335). All samples were tested using the MSD multiplex and reported as pg/ml, the lower limit of quantification (LLOQ) is indicated as a dotted line for each analyte.

Fig. 7

Gag epitope evolution in AC1. Gag epitopes responded to by AC1 as determined by ELISpot are shown compared to the Consensus B sequence for Gag retrieved from the Los Alamos Database. Proviral or replication-competent determination is indicated next to time post first clinic visit. Replication-competent sequence is from before loss of control, and the proviral sequence is from before (D50) and after (D335) the loss of control.

Fig. 8

CD8 + T cell and NK cell Suppression of HIV-1 Replication. CD8 + T cells (red bars) or NK cells (blue bars) isolated from viremic controllers (VC), elite suppressors (ES), acute progressors (AP) or AC1 (c = control, day 47, v = viremic, day 277, gray box) were co-cultured with autologous CD4 + T cells infected with GFP pseudotyped virus at a 1:1 effector:target ratio (A) or a 1:2 effector:target ratio (B). Suppression was calculated with respect to target only controls.