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Performance of a Population-Based HIV-1 Tropism Phenotypic Assay and Correlation With V3 Genotypic Prediction Tools in Recent HIV-1 Seroconverters

de Mendoza, Carmen PhD*; Van Baelen, Kurt PhD; Poveda, Eva PhD*; Rondelez, Evelien PhD; Zahonero, Natalia PhD*; Stuyver, Lieven PhD; Garrido, Carolina PhD*; Villacian, Jorge MD, PhD; Soriano, Vincent MD, PhD*on behalf of the Spanish HIV Seroconverter Study Group

JAIDS Journal of Acquired Immune Deficiency Syndromes: July 1st, 2008 - Volume 48 - Issue 3 - p 241-244
doi: 10.1097/QAI.0b013e3181734f0e
Basic Science

Background: Pure X4 and X4R5 dual-tropic viruses may be recognized in ∼15% of drug-naive HIV-1-positive patients. CCR5 antagonists are active against R5 viruses; therefore, HIV tropism should be known before their prescription.

Patients and Methods: A population-based phenotypic assay was performed in 61 recent HIV-1 seroconverters. The results were compared with those obtained using 8 different predictor software programs (C4.5, C4.5 with 8 and 12, PART, SVM, Charge Rule, PSSMsinsi, PSSMx4r5, and geno2pheno), which are freely available at 3 different Web sites and use V3 sequences derived from patient's viruses.

Results: Phenotypic testing reported X4R5 dual-tropic viruses in 10 (16.4%) patients. CD4 cell counts and viral loads were significantly lower in X4R5 dual-tropic (450 cells/μL and 3.9 log HIV RNA copies/mL) than in R5 viruses (629 cells/μL, 4.5 log HIV RNA copies/mL) (P < 0.05). The overall concordance of genotype and phenotype was relatively good (>80%). Although specificity was >90% using all but 1 genotypic predictor (geno2pheno), however, the sensitivity for the detection of X4 variants was low (<30%), except for SVM and geno2pheno (70%).

Conclusions: The prevalence of X4 and X4/R5 dual-tropic viruses in recent HIV seroconverters is 16%. Current genotypic algorithms need to be improved for the estimation of HIV-1 coreceptor use before moving to the clinic. This information is crucial for the selection of candidates to receive CCR5 antagonists in places where phenotypic tropism assays may not be feasible.

From the *Department of Infectious Diseases, Hospital Carlos III, Madrid, Spain; and †Virco BVBA, Mechelen, Belgium.

Received for publication October 6, 2007; accepted March 11, 2008.

Supported in part by grants from the Fundación Investigación y Educación en SIDA, ISCIII-RETIC RD06/006, Agencia Lain Entralgo, and Fondo de Investigaciones Sanitarias projects CP06/00284 and PI06/1826.

Correspondence to: Carmen de Mendoza, Department of Infectious Diseases, Hospital Carlos III, 28029 Madrid, Spain (e-mail:

© 2008 Lippincott Williams & Wilkins, Inc.