There are conflicting reports on the similarity of the HIV-1 latent reservoir (LR) in the lymph node (LN) compared to the peripheral blood (PB). Characterizing the composition and any possible differences in anatomical compartments remains a crucial step to understanding the barriers to HIV cure.
HIV+ individuals on ART with suppressed viral loads who were undergoing solid organ transplantation consented to have LN removed at the time of transplant, and PB and LN mononuclear cells (MC) were collected and isolated (n=10). CD4+ cells from matched PBMC and LNMC samples were plated in a novel quantitative viral induction assay (QVIA). Sequence data was obtained from positive wells using a validated site-directed next-generation sequencing based assay that amplified the gp41 region of the viral envelope to identify the prominent induced viral variants (>2.5% of amplicons; Illumina Inc.). Subjects who had sequences obtained from >75% of the positive wells in both compartments were used to examine for compartmentalization. Neighbor-joining trees of all prominent patient sequences were inferred (Geneious prime), and identical variants were classified as ‘replicates’. A Bayesian model (IUPMBayes) was used to estimate the relative size of the LR for each participant, as well as the proportion of the LR made up by each variant for their respective compartments. Compartmentalization was assessed on samples using a Hudson based test for panmixia (non-parametric) and a branch length tree correlation coefficient (parametric).
In four individuals with sufficient sequences, a median of 29 induced variants were identified in PB (IQR=54.8-16.0), as compared to 26 in LN (IQR=27.8-21.3). The estimated frequency of latently infected cells was 10.4 induced proviruses per million cells (IPPMC) in PB (IQR=16.5-7.5) and 8.4 IPPMC in LN (IQR=13.2-6.8). Replicant variants and variants with unique sequences were found in both compartments in all patients. The estimated proportion of the LR made up of variants that were replicated in the patient’s matched compartment varied between compartments and between patients [median % LR shared for PB=37.1% (IQR=40.1-20.5%) and LN=42.4% (IQR=57.9-29.8%); Figure]. There was no significant compartmentalization between PB and LN across all patients.
These data provide further evidence of intermingling and limited compartmentalization between the LN and PB, and support previous data that the LR found in the blood can be a good representation of the LR in the lymph node