Extended Data Fig. 11: Longitudinal tracking of day 5 stem-like and effector CD8⁺ T cells from acute viral infection following transfer into chronically infected mice.

a, 2 × 10³ TCF7-YFP reporter P14 CD8⁺ T cells (CD45.1⁻CD45.2⁺) were transferred into congenically distinct naïve mice (CD45.1⁺CD45.2⁻) before i.v. infection with 2 × 10⁶ PFU of LCMV Armstrong (acute). On day 5 p.i. stem-like (TCF7-YFP+ Tim-3−) and effector (TCF7-YFP⁻Tim-3⁺ (effect.) P14 T cells were isolated from the spleen via FACS and transferred into separate groups of day 5 LCMV clone 13-infected recipients (CD45.1⁺CD45.2⁻), which had been transiently depleted of CD4⁺ T cells before infection. b, Flow plots showing stem and effector subsets pre- and post-sort with purity indicated. c, Frequencies of stem-like and effector P14 donor cells recovered from the spleens, livers, and lungs, of chronic LCMV recipient mice at indicated times post-transfer. Data represent one independent experiment. d, Expression of TCF-1 and Tim-3 on stem-like P14 donor cells pre-transfer (spleen, day 5 p.i., acute) and at indicated times post-transfer in the livers and lungs of chronically infected recipients. Data represent one independent experiment. e, UMAP plot showing scRNA-seq analysis of stem donor P14 cells on day 15 post-transfer (right) and endogenous GP33⁺CD8⁺ T cells from stem donor P14 recipient mice (left). UMAPs represent 1 independent experiment.