PLoS ONE (Jan 2013)

The genotypic false positive rate determined by V3 population sequencing can predict the burden of HIV-1 CXCR4-using species detected by pyrosequencing.

  • Valentina Svicher,
  • Valeria Cento,
  • Gabriella Rozera,
  • Isabella Abbate,
  • Maria Mercedes Santoro,
  • Daniele Armenia,
  • Lavinia Fabeni,
  • Alessandro Bruselles,
  • Alessandra Latini,
  • Guido Palamara,
  • Valeria Micheli,
  • Giuliano Rizzardini,
  • Caterina Gori,
  • Federica Forbici,
  • Giuseppe Ippolito,
  • Massimo Andreoni,
  • Andrea Antinori,
  • Francesca Ceccherini-Silberstein,
  • Maria Rosaria Capobianchi,
  • Carlo Federico Perno

DOI
https://doi.org/10.1371/journal.pone.0053603
Journal volume & issue
Vol. 8, no. 1
p. e53603

Abstract

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ObjectiveThe false-positive rate (FPR) is a percentage-score provided by Geno2Pheno-algorithm indicating the likelihood that a V3-sequence is falsely predicted as CXCR4-using. We evaluated the correlation between FPR obtained by V3 population-sequencing and the burden of CXCR4-using variants detected by V3 ultra-deep sequencing (UDPS) and Enhanced-Sensitivity Trofile assay (ESTA).Methods54 HIV-1 B-subtype infected-patients (all maraviroc-naïve), with viremia >10,000copies/ml, were analyzed. HIV-tropism was assessed by V3 population-sequencing, UDPS (considering variants with >0.5% prevalence), and ESTA.ResultsBy UDPS, CCR5-using variants were detected in 53/54 patients, irrespective of FPR values, and their intra-patient prevalence progressively increased by increasing the FPR obtained by V3 population-sequencing (rho = 0.75, p = 5.0e-8). Conversely, the intra-patient prevalence of CXCR4-using variants in the 54 patients analyzed progressively decreased by increasing the FPR (rho = -0.61; p = 9.3e-6). Indeed, no CXCR4-using variants were detected in 13/13 patients with FPR>60. They were present in 7/18 (38.8%) patients with FPR 20-60 (intra-patient prevalence range: 2.1%-18.4%), in 5/7 (71.4%) with FPR 10-20, in 4/6 (66.7%) with FPR 5-10, and in 10/10(100%) with FPRConclusionsFPR by V3 population-sequencing can predict the burden of CXCR4-using variants. This information can be used to optimize the management of tropism determination in clinical practice. Due to its low cost and short turnaround time, V3 population-sequencing may represent the most feasible test for HIV-1 tropism determination. More sensitive methodologies (as UDPS) might be useful when V3 population-sequencing provides a FPR >20 (particularly in the range 20-60), allowing a more careful identification of patients harboring CXCR4-using variants.