Background
Elite controllers maintain undetectable levels of HIV replication in the absence of antiretroviral treatment and are considered as a model for a cure of HIV infection. Recent studies suggest distinct viral reservoir characteristics in blood in such persons, however, viral reservoirs in lymphoid tissues from elite controllers remain largely unexplored.
Methods
Paired samples of mononuclear cells from blood (PBMC) and from lymph nodes (LNMC) from two elite controllers (MP032 and MP083) who maintained undetectable viremia for over ten years were studied. Viral reservoir cells were evaluated using full-length individual proviral sequencing (FLIP-Seq) and matched integration site and proviral sequencing (MIP-Seq). Integration site loop amplification (ISLA) was performed to determine proviral integration sites.
Results
MP032 had a viral reservoir of 17.36 HIV copies per million PBMC versus 5.91 copies per million LNMC, and MP083 had a reservoir of 11.49 HIV copies per million PBMC versus 5.90 HIV copies per million LNMC. In MP032, a major clone of genome-intact proviruses was found in both the PBMC and the LNMC samples. This clone was integrated in the pericentromeric area of chromosome 10 and made up 67.9% of all intact sequences. In addition, two other intact clones were found in the PBMC, one in the pericentromeric region of chromosome X and the other in a gene desert in chromosome X. MP083 also had one major intact clone that was found in both the PBMC and LNMC samples in a non-genic pericentromeric area of chromosome 12. A smaller clone of intact proviruses was found in a gene desert of chromosome 22, and an additional intact sequence was integrated into the centromeric area of chromosome 19; both of these subdominant clones were detected in PBMC only. Despite this overlap between clonal sequences from PBMC and LNMC, we found that not every proviral sequence was found in both sample types; the majority of un-shared clones of intact proviruses were found in the PBMC, and very few LNMC-only intact viral sequences were detected.
Conclusions
Lymph node viral reservoir cells from elite controllers displayed an increased propensity for viral integration into heterochromatin regions of the human genome. Transcriptional repression of intact proviruses in heterochromatin regions in lymphoid tissues is likely to contribute to spontaneous viral control.