The original Trofile phenotypic assay was able to reliably detect 10% minority X4 variants, based on mixtures of R5 and X4 DNA clones.11 When the same clonal experiments were conducted with the enhanced sensitivity assay
(ESTA), 0.3% minority X4 clones could be reliably detected.12 Similarly, the UDS instrument used for Quest Diagnostics genotypic tropism testing can detect 0.5% X4 in mixed clones.7
Biological sensitivity is defined as the ability to reliably detect X4 virus in mixed R5/X4 plasma samples similar to those taken from HIV-1 patients. Unlike clonal analysis, biological sensitivity measures the sensitivity of the entire assay, which may be influenced by the efficiency of nucleic acid extraction and PCR amplification of minor variants, as well as the viral load in the sample.
The biological sensitivity of the Quest Diagnostics UDS assay to detect X4 virus in 90% of dual-mixed samples is 18% X4 at a viral load of 25,000 copies/mL and 6% X4 at a viral load of 100,000 copies/mL.7 The biological sensitivity of the Trofile assay, however, is unpublished. Because the Trofile assay also uses extraction and amplification, its biological sensitivity is likely higher than the published technical sensitivity.
Regardless of these potential differences in sensitivity, the Quest Diagnostics genotype assay and the current Trofile assay appear equal when predicting maraviroc response.7