Background:  The gut is a major reservoir for HIV persistence in patients receiving ART. Distinct immune environments within the gut may support varying levels of HIV. To test this hypothesis, we systematically measured levels of HIV RNA, DNA, and T cell activation throughout the gut and in peripheral blood mononuclear cells.

Methods:  In 8 HIV⁺ patients on ART with CD4 >200 and plasma RNA <40 for 2.8 to 12 years, we obtained plasma, peripheral blood mononuclear cells (PBMC), and endoscopic biopsies from the duodenum, terminal ileum, right colon, and rectum. T cell subsets and activation markers (CD38, HLA-DR) were measured in PBMC and gut cells using flow cytometry. Measures of HIV included:  plasma HIV RNA (modified Abbott assay); HIV DNA in peripheral blood mononuclear cells and gut cells (real time PCR); unspliced and multiply spliced HIV RNA in peripheral blood mononuclear cells and gut cells (real-time PCR); and RNA in intact gut biopsies (in situ hybridization). Sites were compared using the paired Wilcoxon signed-rank test, while outcomes were correlated using the Pearson and Spearman tests.

Results:  Plasma RNA was detectable in all patients (median 2.3 copies/mL). Unspliced HIV RNA was detectable in each gut site in the majority (63 to 88%) of patients using RT PCR but was undetectable by in situ hybridization (LOD of 10⁴/g). HIV DNA increased from the duodenum to the rectum, and the HIV DNA per CD4⁺ T cell was higher in all 4 gut sites relative to the peripheral blood mononuclear cell (ratio = 2.8, 6.5, 6.3, 9.1 for duodenum, ileum, colon, rectum; P = NS, 0.016, 0.008, 0.008). The median unspliced HIV RNA (copies/CD4) was also higher in all gut sites compared to peripheral blood mononuclear cells and peaked in the ileum (ratio=10.2; P = 0.02). HIV DNA correlated positively with T cell activation markers in the peripheral blood mononuclear cell (max r = 0.88), but negatively with T cell activation in the gut (min r = –0.98). The ratio of unspliced HIV RNA to HIV DNA (transcriptional activity per infected cell) decreased from small to large bowel. Multiply spliced RNA was infrequently detected in gut (0 to 16.7%) relative to peripheral blood mononuclear cells (50%), and RNA/DNA ratios were lower in the colon (median 0.01) and rectum (0.01) relative to peripheral blood mononuclear cells (0.06), reflecting paradoxically low HIV transcription given the higher level of T cell activation in the gut.

Conclusions:  HIV DNA and RNA are both concentrated in the gut relative to blood, but HIV RNA is highest in the ileum whereas HIV DNA is highest in the rectum. The inverse relationship between HIV DNA and T cell activation in the gut and the paradoxically low levels of HIV expression in the large bowel suggest that different processes drive HIV persistence in the blood and gut.