Genotypic determination of HIV-1 tropism in the clinical setting

HIV enters cells via the CD4 receptor and a coreceptor, generally CCR5 or CXCR4. The specific coreceptor used by a patient’s virus is referred to as its tropism. Tropism testing is necessary prior to treatment with CCR5 antagonist medication to rule out the presence of CXCR4-using (X4) virus, with the phenotypic Trofile™ assay being the most commonly used test for HIV coreceptor usage. Genotypic tropism testing may offer some practical advantages to phenotypic tropism testing and Trofile. Genotypic tropism assays are typically based on sequencing the V3 loop of HIV env and analysis using bioinformatic algorithms to infer the likely coreceptor usage of the virus. Genotypic methods have been refined and improved over the years and have recently been used as retrospective (and occasionally prospective) screening tools for treatment with CCR5 antagonist medication, such as maraviroc. Alternative approaches to genotypic tropism testing include heteroduplex tracking assays, ‘deep’ V3 sequencing and testing of c...