title: Concordance between two phenotypic assays and ultradeep pyrosequencing for determining HIV-1 tropism.
abstract: There have been few studies on the concordance between phenotypic assays for predicting human immunodeficiency virus type 1 (HIV-1) coreceptor usage. The sensitivity of ultradeep pyrosequencing combined with genotyping tools is similar to that of phenotypic assays for detecting minor CXCR4-using variants. We evaluated the agreement between two phenotypic assays, the Toulouse tropism test (TTT) and the Trofile assay, and ultradeep pyrosequencing for determining the tropism of HIV-1 quasispecies. The concordance between the TTT and Trofile assays was assessed for 181 samples successfully phenotyped by both assays. The TTT was 86% concordant with the standard Trofile assay and 91.7% with its enhanced-sensitivity version. The concordance between phenotypic characterization of HIV-1 tropism and ultradeep pyrosequencing genotypic prediction was further studied in selected samples. The HIV-1 tropism inferred from ultradeep pyrosequencing of 11 samples phenotyped as X4 and dualtropic and 12 phenotyped as R5-tropic agreed closely with the results of phenotyping. However, ultradeep pyrosequencing detected minor CXCR4-using variants in 3 of 12 samples phenotyped as R5-tropic. Ultradeep pyrosequencing also detected minor CXCR4-using variants that had been missed by direct sequencing in 6 of 9 samples phenotyped as X4-tropic but genotyped as R5-tropic by direct sequencing. Ultradeep pyrosequencing was 87% concordant with the Trofile and TTT phenotypic assays and was in the same range of sensitivity (0.4%) than these two phenotypic assays (0.3 to 0.5%) for detecting minor CXCR4-using variants. Ultradeep pyrosequencing provides a new way to improve the performance of genotypic prediction of HIV-1 tropism to match that of the phenotypic assays.
authors.affiliation: INSERM, UMR1043, Toulouse F-31300, France.
authors.forename: Adrien
authors.initials: A
authors.lastname: Saliou
authors.forename: Pierre
authors.initials: P
authors.lastname: Delobel
authors.forename: Martine
authors.initials: M
authors.lastname: Dubois
authors.forename: Florence
authors.initials: F
authors.lastname: Nicot
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Raymond
authors.forename: Vincent
authors.initials: V
authors.lastname: Calvez
authors.forename: Bernard
authors.initials: B
authors.lastname: Masquelier
authors.forename: Jacques
authors.initials: J
authors.lastname: Izopet
mesh_terms: D000328:Adult; D065100:CCR5 Receptor Antagonists; D015497:HIV-1 / Q000235:genetics / Q000502:physiology*; D006801:Humans; D008875:Middle Aged; D010641:Phenotype; D019718:Receptors, CXCR4 / Q000502:physiology; D017422:Sequence Analysis, DNA; D056189:Viral Tropism
chemical_list: D065100:CCR5 Receptor Antagonists; C527276:CXCR4 protein, human; D019718:Receptors, CXCR4