Fig 2: Orthogonal validation of phenotypic signatures of HIV-1 reservoir cells using fluorescence-activated cell sorting of patient-derived memory CD4+ T lymphocytes.(A): Representative flow cytometry dot plots demonstrating the gating strategy for mCD4+ T cell populations isolated from peripheral blood; gates used for sorting (G1-G4) are indicated. (B): Flow cytometry plots for displaying expression of indicated markers on non-CD4+ T cells are shown for comparative purposes. (C): Frequencies of intact proviruses, sequence-identical clonal proviruses (including both intact and defective proviruses) and non-clonal defective proviruses in indicated, sorted mCD4+ T cell subpopulations, determined by near full-length proviral sequencing (FLIP-seq). (D): Phylogenetic tree of all intact proviruses retrieved from sorted mCD4+ T cell subpopulations. Note that in study participant D, the majority of intact proviruses were detected within mCD4+ T cells that were negative for PD-1, TIGIT, HVEM and PVR but positive for BTLA/KLRG-1 and/or HLA-E/PD-L1.

Fig 3: Orthogonal validation of phenotypic signatures of HIV-1 reservoir cells using fluorescence-activated cell sorting of patient-derived memory CD4+ T lymphocytes.(A): Representative flow cytometry dot plots demonstrating the gating strategy for memory CD4+ T cell populations isolated from peripheral blood; gates used for sorting (G1-G4) are indicated. (B): Flow cytometry plots for displaying expression of indicated markers on non-CD4+ T cells are shown for comparative purposes. (C): Frequencies of intact proviruses, sequence-identical clonal proviruses (including both intact and defective proviruses) and non-clonal defective proviruses in indicated, sorted memory CD4+ T cell subpopulations, determined by near full-length proviral sequencing (FLIP-seq). (D): Phylogenetic tree of all intact proviruses retrieved from sorted mCD4+ T cell subpopulations. Note that in study participant D, the majority of intact proviruses were detected within memory CD4+ T cells that were negative for PD-1, TIGIT, HVEM and PVR but positive for BTLA/KLRG-1 and/or HLA-E/PD-L1.