HIV-1 tropism dynamics and phylogenetic analysis from longitudinal ultra-deep sequencing data of CCR5- and CXCR4-using variants.

Objective: Coreceptor switch from CCR5 to CXCR4 is associated with HIV disease progression. The molecular and evolutionary mechanisms underlying the CCR5 to CXCR4 switch are the focus of intense recent research. We studied the HIV-1 tropism dynamics in relation to coreceptor usage, the nature of quasispecies from ultra deep sequencing (UDPS) data and their phylogenetic relationships.

Longitudinal HIV-1 gp120-C2V3C3 phylogenetic surveillance and tropism evolution in patients under HAART.

This 8-year longitudinal study was aimed to analyze the HIV-1 gp120-C2V3C3 sequence dynamics, their phylogenetic relationships and tropism evolution in patients under HAART. Such viral analysis comprised two compartments: plasma and PBMC. Fifty gp120-C2V3C3 genomic sequences were characterized from 16 patients: 41 from plasma when viremia was measurable and 9 from PBMCs if plasma viral load was undetectable.