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

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

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

Pre-ART participants characteristics used for matching.

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

Study population.

<p>Study population.</p

Correlations between pre-ART HIV-1 DNA and CA-RNA levels (A) and between pre-ART HIV-1 DNA and CD4+ T-cell counts (B).

<p>Correlations between pre-ART HIV-1 DNA and CA-RNA levels (A) and between pre-ART HIV-1 DNA and CD4+ T-cell counts (B).</p

No association between HIV-1 DNA and T cell activation or T cell cycling.

<p>Data in this figure are from year 4 of antiretroviral therapy.</p

Longitudinal changes in markers of inflammation after initiation of antiretroviral therapy.

<p>The p-value in each panel is for the change in the log-transformed level of the specified biomarker from pre-ART to year 1.</p

Correlation between pre- and on-ART levels of inflammatory biomarkers.

<p>The figures show the correlation between the levels of the biomarkers before starting ART and the levels at year 4 after starting therapy. The levels at the other on-ART time points (year 1, years 6–15) also correlated with the levels before starting ART (<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006285#ppat.1006285.t002" target="_blank">Table 2</a>).</p

In participants on Antiretroviral Therapy (ART) with suppressed plasma viremia, longitudinal decay in HIV-1 DNA (A), cell-associated RNA (B) and proportion with detectable 2-LTR circles (C) over time.

<p>Between initiation of ART and year 4 of therapy, there was a 15-fold drop in HIV-1 DNA and a 525-fold drop in CA-RNA. After year 4 of ART, HIV-1 DNA decayed at 5% per year (half-life of 13 years); there was no further decay in CA-RNA levels.</p