A genotypic HIV-1 proviral DNA coreceptor tropism assay: Characterization in viremic subjects

Jennifer Brown, Harold Burger, Barbara Weiser, Richard B. Pollard, Xiao Dong Li, Lynell J. Clancy, Russell E. Baumann, Amy A. Rogers, Hasnah B. Hamdan, Rick L. Pesano, Ron M. Kagan

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


Background: HIV-1 coreceptor tropism testing is used to evaluate eligibility for CCR5 antagonist therapy. However, HIV-1 RNA-based tests are not suitable for virologically suppressed patients, therefore the use of proviral DNA tropism testing has been investigated. We describe a novel proviral DNA-based genotypic tropism assay and compare its performance to that of a sensitive HIV-1 RNA-based genotypic test. Methods: Tropism was determined using HIV-1 plasma RNA and proviral DNA from 42 paired samples from patients with plasma viral loads ≥1000 HIV-1 RNA copies/mL. Proviral DNA sample types included whole blood, separated peripheral blood mononuclear cells resuspended in phosphate-buffered saline and peripheral blood mononuclear cells resuspended in spun plasma. The HIV-1 envelope V3 region was PCR-amplified, sequenced in triplicate, and analyzed for tropism with the geno2pheno algorithm using a 10% false-positive rate (FPR). Results: Amplicons were obtained from proviral DNA and plasma RNA in 41/42 samples. Tropism predictions were highly concordant (93%-98%) between proviral DNA and plasma RNA, regardless of the proviral DNA isolation method. Non-R5 proviral DNA results were obtained for 100% of patients with detectable non-R5 plasma HIV-1 RNA results. Geno2pheno FPRs for proviral DNA and plasma RNA were highly correlated (Spearman rho = 0.86). Conclusions: Our findings demonstrate that proviral DNA tropism determinations from whole blood or peripheral blood mononuclear cells were highly concordant with plasma HIV-1 RNA tropism determinations. This assay may be useful for screening virologically suppressed patients for CCR5-antagonist eligibility and for research purposes.

Original languageEnglish (US)
Article number14
JournalAIDS Research and Therapy
Issue number1
StatePublished - May 21 2014


  • HIV-1 diagnostic tests
  • HIV-1 proviral tropism
  • HIV-1 tropism

ASJC Scopus subject areas

  • Virology
  • Molecular Medicine
  • Pharmacology (medical)


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