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

Enrollment and follow-up of study infants.

<p>HIV-uninfected infants in the Mashi and Mma Bana trials did not receive cotrimoxazole prophylaxis and serve as a comparison group to the new cohort (CTX) that received cotrimoxazole prophylaxis. CTX, cotrimoxazole; 1 mo., one month; FF, formula-fed; BF, breastfed.</p

Schematic of infant exposures in study cohorts.

<p>ZDV, zidovudine; supp., supplementation; CTX, cotrimoxazole; HAART, highly-active antiretroviral therapy; mo., month. ^aHAART became available through a national program in October 2002, subsequently women in Mashi trial with CD4≤200 cells/ µL were offered HAART.^bInfants in the Mma Bana trial received 1 month of ZDV and breastfed infants in the Mashi trial received 6 months of ZDV.^cNineteen mothers (9.1%) in CTX cohort received non-ZDV-containing HAART.</p

Severe infant anemia and severe neutropenia by prophylactic cotrimoxazole exposure.

<p>Analysis restricted to severe anemia or neutropenia (grade 3 or 4) detected at scheduled measurements at 3 and/or 6 months of age in HIV-exposed uninfected infants in the CTX, Mashi, and Mma Bana cohorts.</p><p>Note: 95% CI, 95% confidence interval.</p>a<p>Mantel-Haenszel methodology.</p>b<p>Exact Cochran-Mantel-Haenszel.</p

Cohort characteristics of HIV-exposed uninfected infants alive through 30 days of age.

<p>Note: CTX, cotrimoxazole; IQR, interquartile range.</p

Factors associated with severe anemia and severe neutropenia among HIV-exposed, uninfected infants.

<p>Prophylactic cotrimoxazole, maternal antenatal HAART use, and infant feeding method are included in the multivariable model, as are other significant factors from the univariate analysis.</p><p>OR, odds ratio; aOR, adjusted odds ratio; CI, confidence interval; HAART, highly-active antiretroviral therapy.</p>a<p>Wald chi-square.</p>b<p>To avoid confounding effect of infant feeding method, univariate estimate for effect of cotrimoxazole is restricted to formula-fed infants. Multivariable analysis includes both formula-fed and breastfed infants.</p>c<p>A modest but significant interaction was noted between feeding method and maternal HAART with increased risk of severe neutropenia associated with breastfeeding from a mother receiving HAART. However, in multivariable analysis this interaction was no longer significant.</p

Abstraction, eligibility, and analysis.

<p>Women could have more than one reason for ineligibility for the analysis.</p