A sensitive phenotypic assay for the determination of human immunodeficiency virus type 1 tropism

J Antimicrob Chemother. 2010 Dec;65(12):2493-501. doi: 10.1093/jac/dkq379. Epub 2010 Oct 14.


Objectives: To develop a sensitive phenotypic assay based on recombinant viruses (RVs) for characterizing HIV-1 tropism.

Methods: Viral tropism was assessed in 159 plasma samples. The env gene was amplified and ligated into pNL-lacZ/env-Ren, which carries a luciferase reporter gene. Resulting constructs were transfected into HEK293T cells to generate RVs. To assess co-receptor tropism, U87.CD4.CXCR4/CCR5 cells were infected and luciferase activity was measured.

Results: RVs containing env from different HIV-1 subtypes were replication competent. Minor variants were detectable in 1% of the viral population. Tropism was determined in 65% of samples with a viral load of <1000 copies/mL. The phenotypic assay described here was validated with the Trofile™ and Trofile™ES assays. Considering the Trofile™ assay as a reference, the sensitivity for R5 and R5X4/X4 detection was 90% and 77%, and the specificity was 77% and 90%, respectively. Our assay was 86% concordant with Trofile™ (90% for R5 and 77% for R5X4/X4). When our system was compared with Trofile™ES, the concordance was 89% (86% for R5 and 92% for R5X4/X4), the sensitivity for R5 was 86% and for R5X4/X4 was 92%, and the specificity for R5 was 92% and for R5X4/X4 was 86%. The phenotypic results were compared with those obtained using the following V3 genotypic prediction tools: position-specific scoring matrix; geno2pheno[coreceptor]; C4.5; C4.5 using positions 8 and 12; PART; support vector machines; and the charge rule.

Conclusions: We describe a system to assess co-receptor tropism based on the generation of chimeric replication-competent viruses with high sensitivity in the detection of minor populations. A good correlation of our results with Trofile™ assays was found.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line, Tumor
  • Genes, Reporter
  • HEK293 Cells
  • HIV-1 / genetics
  • HIV-1 / metabolism
  • HIV-1 / physiology*
  • Humans
  • Luciferases / genetics
  • Luciferases / metabolism
  • Phenotype
  • Receptors, CCR5 / metabolism*
  • Receptors, CXCR4 / metabolism*
  • Recombination, Genetic
  • Sensitivity and Specificity
  • Viral Tropism / physiology*
  • env Gene Products, Human Immunodeficiency Virus / genetics
  • env Gene Products, Human Immunodeficiency Virus / metabolism


  • Receptors, CCR5
  • Receptors, CXCR4
  • env Gene Products, Human Immunodeficiency Virus
  • Luciferases