title: Concordance of HIV type 1 tropism phenotype to predictions using web-based analysis of V3 sequences: composite algorithms may be needed to properly assess viral tropism.
abstract: Genotypic prediction of HIV-1 tropism has been considered a practical surrogate for phenotypic tests and recently an European Consensus has set up recommendations for its use in clinical practice. Twenty-five antiretroviral-experienced patients, all heavily treated cases with a median of 16 years of antiretroviral therapy, had viral tropism determined by the Trofile assay and predicted by HIV-1 sequencing of partial env, followed by interpretation using web-based tools. Trofile determined 17/24 (71%) as X4 tropic or dual/mixed viruses, with one nonreportable result. The use of European consensus recommendations for single sequences (geno2pheno false-positive rates 20% cutoff) would lead to 4/24 (16.7%) misclassifications, whereas a composite algorithm misclassified 1/24 (4%). The use of the geno2pheno clinical option using CD4 T cell counts at collection was useful in resolving some discrepancies. Applying the European recommendations followed by additional web-based tools for cases around the recommended cutoff would resolve most misclassifications.
authors.affiliation: Adolfo Lutz Institute, Virology Center, Retrovirus Laboratory, São Paulo, Brazil.
authors.forename: Gabriela Bastos
authors.initials: GB
authors.lastname: Cabral
authors.forename: João Leandro de Paula
authors.initials: JL
authors.lastname: Ferreira
authors.forename: Luana Portes Osório
authors.initials: LP
authors.lastname: Coelho
authors.forename: Mylva
authors.initials: M
authors.lastname: Fonsi
authors.forename: Denise Lotufo
authors.initials: DL
authors.lastname: Estevam
authors.forename: Jaqueline Souza
authors.initials: JS
authors.lastname: Cavalcanti
authors.forename: Luis Fernando de Macedo
authors.initials: LF
authors.lastname: Brígido
mesh_terms: D000293:Adolescent; D000328:Adult; D000465:Algorithms; D015496:CD4-Positive T-Lymphocytes; D004279:DNA, Viral; D005260:Female; D015699:HIV Envelope Protein gp120 / Q000235:genetics*; D006679:HIV Seropositivity / Q000235:genetics* / Q000276:immunology; D015497:HIV-1 / Q000235:genetics* / Q000502:physiology; D006801:Humans; D020407:Internet; D008297:Male; D008875:Middle Aged; D010641:Phenotype; D011237:Predictive Value of Tests; D019713:Receptors, CCR5 / Q000235:genetics*; D015728:Receptors, HIV / Q000235:genetics*; D056189:Viral Tropism / Q000235:genetics*; D055815:Young Adult
chemical_list: D004279:DNA, Viral; D015699:HIV Envelope Protein gp120; D019713:Receptors, CCR5; D015728:Receptors, HIV