Identification of novel cell surface markers to identify transitional stem-like CD8 ⁺ T cell states that align with antigen load. (A and B) Surface protein sequencing analysis of P14 cells as described in Fig. 3. (A) Surface expression of CD61 on UMAPs of CD8⁺ T cells. (B) Surface expression of CD55 on UMAPs of CD8⁺ T cells. (C–E) Flow cytometry analysis of P14 cell frequency and numbers at d8 to d14 of acute LCMV, with or without IFNAR blocking at d0–1, or chronic LCMV infection. Data are representative of two independent experiments with three mice per infection setting per time point. Data are the mean ± SEM. Statistical differences were analyzed using a one-way ANOVA test. (C) Overlayed representative flow cytometry plots from d8 to d14 in each experimental group. (D and E) Graphs summarizing the frequencies and total cell numbers of (D) CD61⁺CD55⁻ (T_PEX) and (E) CD61⁻CD55⁺ (T_SCM) cells throughout each infection condition. Each cell population was pre-gated on TCF-1⁺SLAMF6⁺CXCR6⁻CD62L⁺ P14 cells as shown in Fig. S2 F. (F) Graphs summarizing the PFU from viable virus in spleens of mice in each infection condition over the time course. The dashed line indicates viral plaque LOD. (G–K) Isolation, adoptive cell transfer, and analysis of CD61⁺ T_PEX and CD55⁺ T_SCM cell surface marker expression in either antigen-free or antigen-rich host mice. Data are representative of three independent experiments with three to four mice per group. Each dot in F and K represents a single mouse. Data are the mean ± SEM. Statistical differences were analyzed using a one-way ANOVA test. (G) Experimental scheme. CD61⁺ T_PEX and CD55⁺ T_SCM cells were sorted from d8 chronic LCMV– and day 10 acute LCMV–infected mice, respectively. Isolated cells were individually transferred into either recovered (from acute infection, antigen-free) or d1 chronically infected host mice. Mice were maintained for 5 days before subsequent cell surface marker analysis. (H) Flow cytometry plots analyzing the expression of CD61 and CD55 on sorted single-positive cell populations prior to adoptive cell transfer. (I) Representative flow cytometry plots of CD61⁺ and CD55⁺ donor T cells isolated from host mice 5 days following cell transfer. (J) Graphs summarizing the frequencies of CD61⁺CD55⁻ T_PEX, CD61⁺CD55⁺, and CD61⁻CD55⁺ T_SCM cells shown in I. (K) Pie charts summarizing I and J. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. Fig. S2 shows additional supporting data. LOD, limit of detection.