Evolution of HIV-1 quasispecies and coreceptor use in cell reservoirs of patients on suppressive antiretroviral therapy

To track changes in the V3 env region of HIV-1 quasispecies and determine virus coreceptor use in cell reservoirs of patients on long-term suppressive antiretroviral therapy (ART). Ten patients whose plasma viraemia had been suppressed for a median of 5.5 years were followed for 5 years. The V3 env regions of viruses in peripheral blood mononuclear cells were analysed by ultra-deep sequencing (UDS). HIV-1 tropism was predicted using the geno2pheno 5.75 algorithm and a phenotypic assay. The UDS and phenotypic assay data were concordant for predicting HIV-1 tropism. CXCR4-using viruses detected by UDS accounted for 14.7%-76.5% of the virus populations in samples from five patients at enrolment. Five patients harboured pure R5 virus populations and no X4 viruses emerged during the 5 years. The selection pressures estimated by the dN/dS ratio were acting on the V3 region to produce diversification of the quasispecies in CXCR4-infected patients and purification of the quasispecies in R5-infected patients on effective ART. UDS showed that the virus quasispecies in cell reservoirs of patients on long-term suppressive ART continued to evolve. CXCR4-using variants became more diversified. Analysis of the selection pressures on the virus quasispecies could provide a clearer picture of virus persistence in patients on effective ART.