Extended Data Table 2 HIV-1 reservoir analyses
- HIV-1 reservoir was assessed in peripheral blood, bone marrow, lymph node and gut tissue. For quantification of HIV-1 DNA in peripheral T cell subsets and tissue-derived cells, HIV-1 LTR ddPCR was applied. In 119 negative controls (n = 83 no template controls and n = 36 donor PBMC controls) used in 20 experiments for the LTR ddPCR assays of the peripheral blood, only one positive droplet was detected in a no-template control. Additionally, ddPCR with gag primers and qPCR approaches were used at certain time points. In gut- and lymph node-derived tissue sections, in situ hybridization was used to detect HIV-1 DNA and RNA. Quantitative and two different murine viral outgrowth assays were performed to exclude replication-competent virus isolates. For individual time points, ultrasensitive residual HIV-1 RNA in plasma was quantified. ATI, analytical treatment interruption; Ct, cycle threshold; ddPCR, droplet digital polymerase chain reaction; HSCT, hematopoietic stem cell transplantation; IHC, immunohistochemistry; IL-2, interleukin-2; IPDA, intact proviral DNA assay; ISH, in situ hybridization; IUPM, infectious units per million; LNMC, lymph node mononuclear cell; LTR, long terminal repeat; mVOA, murine viral outgrowth assay; PBMC, peripheral blood mononuclear cell; PHA, phytohemagglutinin; qPCR, quantitative polymerase chain reaction; qVOA, quantitative viral outgrowth assay; SIMOA, single molecule array; Tn, naive T cell; Tcm, central memory T cell; Ttm, transitional memory T cell; Tem, effector memory T cell; TFH, follicular helper T cell.
