ITGAE and COVID-19: Genes from the last 2 sets were expressed at the end of the trajectory and consisted of cytotoxic or increased effector function genes (set 4: GZMA, GZMB, FASLG, CXCR3, CCL5), pro-inflammatory and auto-regulatory genes (set 5: ITGA1, TNF, XCL2, CD7 and LGALS3, SLAMF1, S100A4) and genes marking resident-memory formation (ZNF683, ITGAE).21,22 In mild COVID-19, TRM-cells mainly expressed set 3–5 genes, indicating increased (but balanced) effector function (Supplementary information, Fig. S2g, h), while in critical COVID-19 TRM-cells expressed set 1–2 genes, indicating a more naïve state.