HIV-1 coreceptor usage determination in clinical isolates using clonal and population-based genotypic and phenotypic assays

Orally bioavailable CXCR4 and CCR5 coreceptor antagonists are being developed for the treatment of HIV-1 infection. A new tropism-testing platform, which offers various options depending on the needs, was established. Each option has specific characteristics in terms of sensitivity, information, throughput and cost. The platform consists of four assays, all based on a one-step RT-PCR of the main part of the HIV envelope glycoprotein gp120 (called 'NH2-V4'). Population-based sequencing of gp120's V3 loop is generally cheap and easy to run, and was chosen as the first test in the platform's cascade. Given its drawbacks such as limited sensitivity, additional tests were developed. A sensitive assay using NH2-V4 gp120 clonal sequencing and tropism prediction enabled us to demonstrate the quasispecies diversity present in 13 patient samples. For phenotyping, an eGFP-containing HIV backbone deleted for NH2-V4 was constructed and used for clonal and population tropism determination. As expected, clonal NH2-V4 gp120 phenotyping demonstrated significant correlation between prediction algorithms and phenotype-based classification. The absence of the N-linked glycosylation motif in V3 was associated with CXCR4 usage. Finally, population NH2-V4 gp120 phenotypic tropism determination appeared to be a promising tool for the detection of minority species present in the amplified envelope fragments.