Effect of VPA and intensified ART on resting cell infection and low-level viremia.

<p>*All results represent pooled assays at entry/week −4, and week 12/16. Baseline ART assays for patients 6, 9, and 12 represent pooled assays from entry/week −4 and 2 prior time points. Weeks 32, 48, 96 are assays from only those time points.</p><p>**Simultaneous Amplicor assays at all SCA time points were <50 copies, except for patient 3 at day of study entry when Amplicor = 58 and SCA>1000.</p><p>†Declined VPA dose escalation.</p><p>††Intermittent non-adherence to study medication.</p><p>§Early study discontinuation.</p

Lower pre-ART intra-participant HIV-1 <i>pol</i> diversity may not be associated with virologic failure in adults

<div><p>Background</p><p>Identifying pre-ART factors associated with the emergence of HIV-1 drug resistance is critical for optimizing strategies to prevent virologic failure. A previous study reported that lower pre-ART HIV-1 <i>pol</i> diversity was associated with higher risk of virologic failure in HIV-1-infected children. To investigate this association in adults, we measured HIV-1 diversity with deep sequencing in pre-ART samples from adults with well-characterized virologic outcomes in a study (A5142) of initial ART conducted by the AIDS Clinical Trials Group (ACTG).</p><p>Methods</p><p>We identified 22 cases in ACTG A5142 who experienced virologic failure with drug resistance mutations in RT and 44 matched controls who did not experience virologic failure. cDNA was synthesized from plasma HIV-1 RNA. Each cDNA molecule was tagged with a unique primer ID and RT codons 41–103 were amplified and deep sequenced. Sequences with the same tag were aligned and a consensus was generated to reduce PCR and sequencing errors. Diversity was calculated by measuring average pairwise distance (APD) of the consensus sequences. An exact conditional logistic regression model with percent APD as the risk factor estimated the odds ratio for VF and the corresponding 95% confidence interval.</p><p>Results</p><p>Consensus single-genome sequences and diversity estimates of <i>pol</i> were obtained for pre-ART samples from 21 cases and 42 controls. The median (IQR) pre-ART percent APD was 0.71 (0.31–1.13) in cases and 0.58 (0.32–0.94) in controls. A possible trend was found for higher diversity being associated with greater risk of virologic failure in adults (OR = 2.2 per one percent APD increase, 95% CI = [0.8, 7.2]; p = 0.15).</p><p>Conclusions</p><p>This study in adults suggests there is a positive association between higher pre-ART <i>pol</i> diversity and the risk of virologic failure in adults rather than an inverse relationship reported in children.</p></div

Pre-ART participants characteristics used for matching.

<p>Pre-ART participants characteristics used for matching.</p

Percent Average Pairwise Distance (%APD) for each cut off.

<p>Percent Average Pairwise Distance (%APD) for each cut off.</p

Neighbor-joining tree of 25 consensus sequences from each pre-ART participant sample using a requirement of 5 sequences containing the same primer ID to generate the consensus.

<p>Bootstrap values are shown for each branch. Cases are shown in blue and controls in black. The width of each triangle is indicative of the APD of HIV sequences in each participant.</p

Univariate analysis of Baseline T and NK Cell Populations and Immune Activation Markers with in Participants with and without detectable HIV-1 RNA after Regimen Simplification.

<p>The significant p-values for univariate comparisons are in bold.</p

Univariate and Multivariate Regression Analysis of Baseline T and NK Cell Populations and Immune Activation Markers and the Risk of Detectable Plasma HIV-1 RNA.

<p>Cox regression analyses included all variables with p-values ≤0.1 in the univariate analyses, and age, race and CD4 nadir prior to starting ART. Odds ratio above 1.0 are associated with increased risk of virologic failure.</p

Comparison of NK cells and T cell populations based on HIV-1 viremia below and above 50 copies/mL.

<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095524#pone-0095524-g003" target="_blank">Figure 3</a> demonstrates that the population percentage of CD3-CD56+CD16+ cells (panel 1) and CD4-CD45RO+CCR7+CD27- cells (panel 2) were decreased in samples with HIV-1 RNA levels of 50–99 copies/mL as compared to samples obtained with HIV-1 RNA below 50 copies/mL with p-values of 0.036 and 0.018, respectively. The median level for each cell population is indicated by the line in the scatterplot for each group.</p

Proportions with HIV-1 RNA < 50 copies/ml after regimen simplification by baseline NK cell levels.

<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095524#pone-0095524-g002" target="_blank">Figure 2</a> shows a Kaplan-Meier plot for the survival with HIV-1 RNA level above 50 copies/mL during the A5201 study based on the participant's NK cell level at study entry. The p-value is 0.023 by Kaplan-Meier analyses for the difference at 54 weeks between the groups above and below the median NK cell level.</p

Baseline NK Cell percentages by HIV-1 RNA Outcome following Regimen Simplification.

<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095524#pone-0095524-g001" target="_blank">Figure 1</a> compares the baseline NK cell levels, defined by CD3-CD56+CD16+ cells, and virologic outcome (HIV-1 RNA below or above 50 copies/mL, throughout the study). The circles represent each study participant with either sustained HIV-1 RNA suppression during the trial and those participants who developed detectable viremia following treatment simplification. The difference in the median NK cell levels between the groups with detectable and suppressed viremia was statistically significant with a p-value of 0.002. The median level is noted by the line in the scatterplot for each group.</p