Evaluation of the clinical sensitivities of three viral load assays with plasma samples from a pediatric population predominantly infected with human immunodeficiency virus type 1 subtype G and BG recombinant forms

Abstract

The viral load assays AMPLICOR HIV-1 Monitor Test 1.5, Nuclisens HIV-1 QT, and Quantiplex HIV RNA 3.0 (bDNA) were evaluated for their abilities to quantify human immunodeficiency virus type 1 (HIV-1) RNA in 64 plasma samples from 21 children infected in Portugal. The children were infected with HIV-1 subtypes A1, B, F1, G, and BG recombinant virus. AMPLICOR v1.5 and Quantiplex v3.0 detected all samples, and there was a good correlation of results between the two kits. Thirty-eight specimens containing HIV-1 subtype B, G, or recombinant BG, could not be detected by Nuclisens HIV-1 QT. We also evaluated the new Retina HIV-1 assay on 21 samples that were HIV-1 positive; Retina HIV-1 failed to detect 5 of 11 subtype G specimens. AMPLICOR v1.5 and Quantiplex v3.0 assays may be used for HIV-1 RNA quantification in Portugal, whereas an improvement in sensitivity for subtype G and recombinant BG is required for Nuclisens HIV-1 QT and Retina HIV-1.

FIG. 1.

Genetic subtypes and evolutionary relationships of the virus sequenced in this study based on neighbor-joining phylogenetic trees of partial gag (A) sequences (p17) and partial env (B) sequences (C2-V3). The phylogenetic trees were constructed with reference sequences from all HIV-1 subtypes and subsubtypes as well as with the Portuguese (PT) sequences (shown in boldface type). The bootstrap values supporting each of the internal branches defining a subtype or subsubtype are shown. Bootstrap values of 70% or greater provide reasonable confidence for assignment of an individual segment to one or the other genotype. The scale represents genetic distance.

FIG. 1.

Genetic subtypes and evolutionary relationships of the virus sequenced in this study based on neighbor-joining phylogenetic trees of partial gag (A) sequences (p17) and partial env (B) sequences (C2-V3). The phylogenetic trees were constructed with reference sequences from all HIV-1 subtypes and subsubtypes as well as with the Portuguese (PT) sequences (shown in boldface type). The bootstrap values supporting each of the internal branches defining a subtype or subsubtype are shown. Bootstrap values of 70% or greater provide reasonable confidence for assignment of an individual segment to one or the other genotype. The scale represents genetic distance.

FIG. 2.

HIV-1 RNA levels (log₁₀ copies/ml) for subtypes A1, B, G, F1, and BG recombinant forms. The box extends from the 25th percentile to the 75th percentile, with a line at the median (50th percentile). The tabs extend above and below the boxes to show the highest and lowest values. Only data for samples that were positive were included in the figure. Due to the low number of cases, individual data points are shown for subtypes A1 and F1. V, version. Subtype B graphic includes B/B, −/B, and B/− samples. Recombinant B/G and G/B samples are included in the recombinant BG graphic.