Genotypic prediction of HIV‐1 subtype CRF01‐AE tropism

Abstract

Purpose of the studyDetermination of HIV‐1 coreceptor usage is crucial for the clinical management of HIV‐infected patients and for optimizing patient selection prior to coreceptor antagonist use. HIV‐1 subtype CRF01‐AE predominates in south and south‐east Asia and has spread all around the world. As for other subtypes, the HIV‐1 subtype CRF01‐AE tropism must be assessed before CCR5 antagonists’ usage. Genotypic methods would be useful for tropism determination but their correlation with the phenotypic approach has not been assessed.MethodsWe determined the HIV‐1 coreceptor usage in 44 subjects infected with subtype CRF01‐AE by both a recombinant phenotypic entry assay and sequencing of the V3 region to determine the correlation between them.Summary of resultsWe first used genotypic algorithms currently used for subtype B HIV‐1. The sensitivity of the Geno2pheno10 genotypic algorithm was 75% but the specificity was poor (46%). In contrast, the sensitivity of the combined 11/25 and net charge rule was poor (50%) but the specificity was 96%. We used a GenBank clonal data set of 69 CRF01‐AE V3 sequences of viruses with known phenotype to identify subtype CRF01‐AE determinants in the V3 region associated with CXCR4 use and built a new simple genotypic rule for optimizing the genotypic prediction of CRF01‐AE tropism. The data showed that loss of the N‐linked glycosylation site at the beginning of V3 was an independent determinant of CXCR4 use by the CRF01‐AE virus clones. The new genotypic tool based on the 11/25, net charge and glycosylation site mutation criteria was 96% concordant with the phenotype on the GenBank clonal data set. Lastly, this algorithm has been validated using our patients’ data set in which the sensitivity was 70% and the specificity was 96% for predicting CXCR4 use.ConclusionsThe concordance between genotype and phenotype was 84% when using the CRF01‐AE genotypic tool, approaching the concordance obtained for the tropism prediction of HIV‐1 subtype B. The genotypic prediction of HIV‐1 subtype CRF01‐AE coreceptor usage requires an optimized genotypic tool for a safely use of CCR5 antagonists.