title: A genotypic HIV-1 proviral DNA coreceptor tropism assay: characterization in viremic subjects.
abstract: 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.
authors.affiliation: Division of Infectious Diseases, Department of Internal Medicine, University of California, Davis Medical Center, 4150 V. Street, PSSB-G500, Sacramento, CA, USA.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Brown
authors.affiliation: University of California, Davis, School of Medicine, Davis, CA, USA.
authors.forename: Harold
authors.initials: H
authors.lastname: Burger
authors.affiliation: University of California, Davis, School of Medicine, Davis, CA, USA.
authors.forename: Barbara
authors.initials: B
authors.lastname: Weiser
authors.affiliation: Division of Infectious Diseases, Department of Internal Medicine, University of California, Davis Medical Center, 4150 V. Street, PSSB-G500, Sacramento, CA, USA.
authors.forename: Richard B
authors.initials: RB
authors.lastname: Pollard
authors.affiliation: University of California, Davis, School of Medicine, Davis, CA, USA.
authors.forename: Xiao-Dong
authors.initials: XD
authors.lastname: Li
authors.affiliation: Division of Infectious Diseases, Department of Internal Medicine, University of California, Davis Medical Center, 4150 V. Street, PSSB-G500, Sacramento, CA, USA.
authors.forename: Lynell J
authors.initials: LJ
authors.lastname: Clancy
authors.affiliation: Department of Infectious Diseases, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA.
authors.forename: Russell E
authors.initials: RE
authors.lastname: Baumann
authors.affiliation: Department of Infectious Diseases, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA.
authors.forename: Amy A
authors.initials: AA
authors.lastname: Rogers
authors.affiliation: Department of Infectious Diseases, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA.
authors.forename: Hasnah B
authors.initials: HB
authors.lastname: Hamdan
authors.affiliation: Department of Infectious Diseases, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA.
authors.forename: Rick L
authors.initials: RL
authors.lastname: Pesano
authors.affiliation: Department of Infectious Diseases, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA.
authors.forename: Ron M
authors.initials: RM
authors.lastname: Kagan
keywords: HIV-1 diagnostic tests; HIV-1 proviral tropism; HIV-1 tropism