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

MOESM2 of Well-mixed plasma and tissue viral populations in RT-SHIV-infected macaques implies a lack of viral replication in the tissues during antiretroviral therapy

Additional file 2: Figure S2. Phylogenetic relationships between single-genome proviral env sequences obtained from various anatomical compartments 30 weeks post-infection from the untreated animal 6760. The env sequence populations in the tissues (open colored circles) were not significantly different from each other indicating that the virus is well circulated across compartments, consistent with the results from the pol analyses. Highly divergent sequences are G to A hypermutants

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

Neighbor-joining trees of single-genome plasma sequences from rebound viremia in patients in Group 3.

<p>Phylogenetic analyses reveal populations of identical plasma sequences in rebound viremia after interrupting long-term cART.</p

Allele frequency during cART.

a<p>Analysis includes only patients who had sampling during viral RNA decay on cART.</p

Measurements of the probability of panmixia before and after cART in (A) Group 1 - short-term cART (B) Group 2 - long-term cART (C) Group 3 - cART with treatment interruptions.

<p>We considered a panmixia p value of <0.001 to be statistically significant according to the original publication of the method (1). Significance reveals a shift in population over time on cART and was found primarily in patients on long-term cART.</p

HIV-1 plasma RNA copy numbers and diversity as calculated by APD in longitudinal samples prior to and during cART in selected patients on (A) short-term cART (Group 1) (B) long-term cART (Group 2) and (C) cART with treatment interruptions (Group 3).

<p>We found no relationship between HIV-1 RNA copy number and viral diversity in the plasma.</p

Evolutionary distances of each single-genome sequence from pre-cART and during and after cART compared to the consensus subtype B HIV-1 sequence and plotted over (A) short-term cART (B) long-term cART (C) long-term cART with brief treatment interruptions and (D) rebound viremia.

<p>Positive slopes indicate the emergence of new variants and on-going replication during cART. Only one patient (PID 1) showed a positive slope and evidence of molecular evolution during cART.</p