Identification of HIV-1 genitourinary tract compartmentalization by analyzing the env gene sequences in urine

Abstract

Objective: HIV-1 persists indefinitely in memory CD4 T cells and other long-lived cellular reservoirs despite antiretroviral therapy. Our group had previously demonstrated that HIV-1 can establish a productive infection in renal epithelial cells and that the kidney represents a separate compartment for HIV-1 replication. Here, to better understand the viruses in this unique site, we genetically characterized and compared the viruses in blood and urine specimens from 24 HIV-1 infected patients with detectable viremia.

Design and methods: Blood and urine samples were obtained from 35 HIV-1 positive patients. Single-genome amplification was performed on HIV-1 env RNA and DNA isolated from urine supernatants and urine-derived cell pellets, respectively, as well as from plasma and peripheral blood mononuclear cell from the same individuals. Neighbor-joining trees were constructed under the Kimura 2-parameter model.

Results: We amplified and sequenced the full-length HIV-1 envelope (env) gene from 12 of the 24 individuals, indicating that 50% of the viremic HIV-1-positive patients had viral RNA in their urine. Phylogenetic analysis of the env sequences from four individuals with more than 15 urine-derived env sequences showed that the majority of the sequences from urine formed distinct cluster(s) independent of those peripheral blood mononuclear cell and plasma-derived sequences, consistent with viral compartmentalization in the urine.

Conclusion: Our results suggest the presence of a distinct HIV compartment in the genitourinary tract.

Figure 1. Analysis of HIV-1 RNA in urine reveals viral compartmentalization and the presence of HIV genomes with identical sequences

(a – c) The full-length env sequences were obtained by SGA from PBMC DNA, plasma viral RNA and urine viral RNA from three different subjects. Sequences were aligned by using Clustal W, and neighbor-joining trees were rooted on the HXB2 sequence (subgroup B). Blue triangles: urine RNA; Full red circles: PBMCs; Empty red circles: Plasma RNA.

Figure 2. Neighbor-joining tree for subject 280

from which in addition to PBMC DNA, plasma viral RNA and urine viral RNA, the full-length env sequences were also obtained from urine cell pellet DNA. Blue triangles: urine RNA; Full red circles: PBMCs; Empty red circles: Plasma RNA; Green diamond: urine Cell-associate DNA.