Use of a High Resolution Melting Assay to Analyze HIV Diversity in HIV-infected Ugandan Children
ABSTRACT BACKGROUND:: We used a novel high resolution melting (HRM) diversity assay to analyze HIV diversity in Ugandan children (age 0.6-12.4 years) who were enrolled in an observational study of antiretroviral treatment (ART). Children were maintained on ART if they were clinically and immunologically stable. METHODS:: HIV diversity was measured before ART (baseline) in 76 children and after 48 or 96 weeks of ART in 14 children who were not virally suppressed. HIV diversity (expressed as HRM scores) was measured in 6 regions of the HIV genome (2 in gag, 1 in pol, 3 in env). RESULTS:: Higher baseline HRM scores were significantly associated with older age (≥2 years, P ≤ 0.001 for all 6 regions). HRM scores from different regions were weakly correlated. Higher baseline HRM scores in 3 regions (1 in gag, 2 in env) were associated with ART failure. HIV diversity was lower in 4 regions (2 in gag, 1 in pol, 1 in env) after 48-96 weeks of nonsuppressive ART compared with baseline. CONCLUSIONS:: Higher levels of HIV diversity were observed in older children before ART, and higher levels of diversity in some regions of the HIV genome were associated with ART failure. Prolonged exposure to nonsuppressive ART was associated with a significant decrease in viral diversity in selected regions of the HIV genome.
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ABSTRACT: In HIV-infected children, viral diversity tends to increase with age in the absence of antiretroviral treatment (ART). We measured HIV diversity in African children (ages 6-36 months) enrolled in a randomized clinical trial comparing two ART regimens (Cohort I of the P1060 trial). Children in this cohort were exposed to single dose nevirapine (sdNVP) at birth. HIV diversity was measured retrospectively using a high resolution melting (HRM) diversity assay. Samples were obtained from 139 children at the enrollment visit prior to ART initiation. Six regions of the HIV genome were analyzed: two in gag, one in pol, and three in env. A single numeric HRM score that reflects HIV diversity was generated for each region; composite HRM scores were also calculated (mean and median for all six regions). In multivariable median regression models using backwards selection that started with demographic and clinical variables, older age was associated with higher HRM scores (higher HIV diversity) in pol (P = 0.005) and with higher mean (P = 0.014) and median (P<0.001) HRM scores. In multivariable models adjusted for age, pre-treatment HIV viral load, pre-treatment CD4%, and randomized treatment regimen, higher HRM scores in pol were associated with shorter time to virologic suppression (P = 0.016) and longer time to study endpoints (virologic failure [VF], VF/death, and VF/off study treatment; P<0.001 for all measures). In this cohort of sdNVP-exposed, ART-naïve African children, higher levels of HIV diversity in the HIV pol region prior to ART initiation were associated with better treatment outcomes.PLoS ONE 12/2013; 8(11):e81213. DOI:10.1371/journal.pone.0081213 · 3.53 Impact Factor
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ABSTRACT: Multi-assay algorithms (MAAs) can be used to estimate HIV incidence in cross-sectional surveys. We compared the performance of two MAAs that use HIV diversity as one of four biomarkers for analysis of HIV incidence.PLoS ONE 06/2014; 9(6):e101043. DOI:10.1371/journal.pone.0101043 · 3.53 Impact Factor
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ABSTRACT: Multi-assay algorithms (MAAs) can be used for cross-sectional HIV incidence estimation. We previously identified a robust MAA that includes the BED capture immunoassay (BED-CEIA), the BioRad-Avidity assay, viral load, and CD4 cell count. In this report, we evaluated MAAs that include a high resolution melting (HRM) diversity assay that does not require sequencing. HRM scores were determined for eight regions of the HIV genome (2 in gag, 1 in pol, and 5 in env). MAAs were evaluated that included the BED capture immunoassay (BED-CEIA), the BioRad-Avidity assay, viral load, and HRM score, using HRM scores from different regions and a range of region-specific HRM diversity assay cutoffs. Performance characteristics based on the proportion of samples classified as MAA positive by duration of infection were determined for each MAA, including the mean window period. Cross-sectional incidence estimates obtained using optimized MAAs were compared to longitudinal incidence estimates for three cohorts in the United States. The performance of the HRM-based MAA was nearly identical to that of the MAA that included CD4 cell count. The HRM-based MAA had a mean window period of 154 days and provided cross-sectional incidence estimates that were similar to those based on cohort follow-up._HIV diversity is a useful biomarker for HIV incidence estimation. MAAs that include the HRM diversity assay can provide accurate HIV incidence estimates using stored plasma or serum samples, without the need for CD4 cell counts.Journal of clinical microbiology 10/2013; 52(1). DOI:10.1128/JCM.02040-13 · 4.23 Impact Factor