A genotypic test for HIV-1 tropism combining Sanger sequencing with ultradeep sequencing predicts virologic response in treatment-experienced patients

PLoS One. 2012;7(9):e46334. doi: 10.1371/journal.pone.0046334. Epub 2012 Sep 27.

Abstract

A tropism test is required prior to initiation of CCR5 antagonist therapy in HIV-1 infected individuals, as these agents are not effective in patients harboring CXCR4 (X4) coreceptor-using viral variants. We developed a clinical laboratory-based genotypic tropism test for detection of CCR5-using (R5) or X4 variants that utilizes triplicate population sequencing (TPS) followed by ultradeep sequencing (UDS) for samples classified as R5. Tropism was inferred using the bioinformatic algorithms geno2pheno([coreceptor]) and PSSM(x4r5). Virologic response as a function of tropism readout was retrospectively assessed using blinded samples from treatment-experienced subjects who received maraviroc (N = 327) in the MOTIVATE and A4001029 clinical trials. MOTIVATE patients were classified as R5 and A4001029 patients were classified as non-R5 by the original Trofile test. Virologic response was compared between the R5 and non-R5 groups determined by TPS, UDS alone, the reflex strategy and the Trofile Enhanced Sensitivity (TF-ES) test. UDS had greater sensitivity than TPS to detect minority non-R5 variants. The median log(10) viral load change at week 8 was -2.4 for R5 subjects, regardless of the method used for classification; for subjects with non-R5 virus, median changes were -1.2 for TF-ES or the Reflex Test and -1.0 for UDS. The differences between R5 and non-R5 groups were highly significant in all 3 cases (p<0.0001). At week 8, the positive predictive value was 66% for TF-ES and 65% for both the Reflex test and UDS. Negative predictive values were 59% for TF-ES, 58% for the Reflex Test and 61% for UDS. In conclusion, genotypic tropism testing using UDS alone or a reflex strategy separated maraviroc responders and non-responders as well as a sensitive phenotypic test, and both assays showed improved performance compared to TPS alone. Genotypic tropism tests may provide an alternative to phenotypic testing with similar discriminating ability.

Publication types

  • Clinical Trial

MeSH terms

  • Adult
  • Aged
  • Algorithms
  • Anti-HIV Agents / metabolism
  • Anti-HIV Agents / pharmacology*
  • Biological Assay
  • Biomarkers, Pharmacological
  • CCR5 Receptor Antagonists*
  • Cyclohexanes / metabolism
  • Cyclohexanes / pharmacology*
  • Female
  • Genotyping Techniques*
  • HIV Infections / drug therapy*
  • HIV Infections / metabolism
  • HIV Infections / virology
  • HIV-1 / drug effects
  • HIV-1 / physiology
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Male
  • Maraviroc
  • Middle Aged
  • Predictive Value of Tests
  • Receptors, CCR5 / metabolism
  • Receptors, CXCR4 / metabolism
  • Retrospective Studies
  • Triazoles / metabolism
  • Triazoles / pharmacology*
  • Viral Tropism*

Substances

  • Anti-HIV Agents
  • Biomarkers, Pharmacological
  • CCR5 Receptor Antagonists
  • CXCR4 protein, human
  • Cyclohexanes
  • Receptors, CCR5
  • Receptors, CXCR4
  • Triazoles
  • Maraviroc

Grant support

The authors have no support or funding to report.