Figure 1.

Phylogenetic analysis of the human immunodeficiency virus type 1 (HIV-1) envelope sequences obtained from gut and peripheral blood compartments. Two representative patterns are shown for group 1 (patients with HIV RNA levels of <50 copies/mL) (A) and group 2 (patients with HIV RNA levels of ≥50 copies/mL) (B ). C, Phylogenetic analysis of HIV for the 2 subjects who underwent serial colonic biopsies prior to and 3 and 12 months after starting highly active antiretroviral therapy. Phylogenetic relationships among the C2-V3 region of the env gene were estimated using the neighbor-joining method. All the sequences presented in the phylogenetic trees come from independent polymerase chain reaction (PCR) runs that utilized samples obtained by limiting dilution. Bootstrap percentile values from 1,000 replications are shown at nodes defining major groupings of sequences. Statistical support of ≥50% is shown. The charts shown depict the color and shape codes used to identify different genetic materials derived from the colon, terminal ileum, peripheral blood mononuclear cells (PBMCs), and plasma (A, B ) or different sampling time points (C ). Gray symbols in the charts indicate that PCR amplification of the HIV-1 env gene was unsuccessful. An additional phylogenetic tree analysis, which involved the envelope sequences obtained from all 10 patients, revealed that isolates from each patient were well confined within distinct patient-specific clusters that were divergent from each other and from known laboratory strains of HIV-1, confirming the absence of cross-patient contamination (data not shown). HIV-1 U455 was used as an outgroup.