Distinctive features of SARS-CoV-2-specific T cells predict recovery from severe COVID-19
Data files
Jan 25, 2021 version files 1.18 GB
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Baseline_Conv_4100_CD4T_Survivor.fcs
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Baseline_Conv_4100_CD8T_Survivor.fcs
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Baseline_Conv_4102_CD4T_Survivor.fcs
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Baseline_Conv_4102_CD8T_Survivor.fcs
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Baseline_Conv_4103_CD4T_Survivor.fcs
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Baseline_Conv_4103_CD8T_Survivor.fcs
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Baseline_Conv_4104_CD4T_Survivor.fcs
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Baseline_Conv_4104_CD8T_Survivor.fcs
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Baseline_Conv_4106_CD4T_Survivor.fcs
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Baseline_Conv_4106_CD8T_Survivor.fcs
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Baseline_Conv_4112_CD4T_Survivor.fcs
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Baseline_Conv_4112_CD8T_Survivor.fcs
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Baseline_Conv_4114_CD4T_Survivor.fcs
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Baseline_Conv_4114_CD8T_Survivor.fcs
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Baseline_Conv_4122_CD4T_Survivor.fcs
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Baseline_Conv_4122_CD8T_Survivor.fcs
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Baseline_Conv_4123_CD4T_Survivor.fcs
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Baseline_Conv_4123_CD8T_Survivor.fcs
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Baseline_Moderate_16_CD4T_Survivor.fcs
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Baseline_Moderate_16_CD8T_Survivor.fcs
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Baseline_Moderate_21_CD4T_Survivor.fcs
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Baseline_Moderate_21_CD8T_Survivor.fcs
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Baseline_Moderate_25_CD4T_Survivor.fcs
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Baseline_Moderate_25_CD8T_Survivor.fcs
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Baseline_Moderate_26_CD4T_Survivor.fcs
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Baseline_Moderate_26_CD8T_Survivor.fcs
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Baseline_Severe_01_CD4T_Nonsurvivor.fcs
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Baseline_Severe_01_CD8T_Nonsurvivor.fcs
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Baseline_Severe_02_CD4T_Nonsurvivor.fcs
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Baseline_Severe_02_CD8T_Nonsurvivor.fcs
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Baseline_Severe_03_CD4T_Survivor.fcs
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Baseline_Severe_03_CD8T_Survivor.fcs
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Baseline_Severe_04_CD4T_Survivor.fcs
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Baseline_Severe_04_CD8T_Survivor.fcs
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Baseline_Severe_05_CD4T_Survivor.fcs
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Baseline_Severe_05_CD8T_Survivor.fcs
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Baseline_Severe_08_CD4T_Survivor.fcs
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Baseline_Severe_08_CD8T_Survivor.fcs
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Baseline_Severe_10_CD4T_Nonsurvivor.fcs
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Baseline_Severe_10_CD8T_Nonsurvivor.fcs
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Baseline_Severe_11_CD4T_Survivor.fcs
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Baseline_Severe_11_CD8T_Survivor.fcs
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Baseline_Severe_12_CD4T_Survivor.fcs
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Baseline_Severe_12_CD8T_Survivor.fcs
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Baseline_Severe_13_CD4T_Survivor.fcs
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Baseline_Severe_13_CD8T_Survivor.fcs
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Baseline_Severe_14_CD4T_Survivor.fcs
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Baseline_Severe_14_CD8T_Survivor.fcs
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Baseline_Severe_15_CD4T_Nonsurvivor.fcs
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Baseline_Severe_15_CD8T_Nonsurvivor.fcs
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Baseline_Severe_17_CD4T_Survivor.fcs
7.65 MB
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Baseline_Severe_17_CD8T_Survivor.fcs
2.06 MB
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Baseline_Severe_18_CD4T_Nonsurvivor.fcs
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Baseline_Severe_18_CD8T_Nonsurvivor.fcs
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Baseline_Severe_19_CD4T.fcs
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Baseline_Severe_19_CD8T.fcs
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Baseline_Severe_20_CD4T_Survivor.fcs
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Baseline_Severe_20_CD8T_Survivor.fcs
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Baseline_Severe_22_CD4T_Nonsurvivor.fcs
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Baseline_Severe_22_CD8T_Nonsurvivor.fcs
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Baseline_Severe_24_CD4T_Nonsurvivor.fcs
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Baseline_Severe_24_CD8T_Nonsurvivor.fcs
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Baseline_Severe_31_CD4T_Survivor.fcs
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Baseline_Severe_31_CD8T_Survivor.fcs
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Baseline_Severe_37_CD4T.fcs
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Baseline_Severe_37_CD8T.fcs
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Baseline_Severe_38_CD4T_Survivor.fcs
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Baseline_Severe_38_CD8T_Survivor.fcs
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Baseline_Severe_39_CD4T_Nonsurvivor.fcs
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Baseline_Severe_39_CD8T_Nonsurvivor.fcs
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Baseline_Severe_42_CD4T_Survivor.fcs
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Baseline_Severe_42_CD8T_Survivor.fcs
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Baseline_Severe_45_CD4T_Nonsurvivor.fcs
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Baseline_Severe_45_CD8T_Nonsurvivor.fcs
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Baseline_Severe_46_CD4T_Survivor.fcs
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Baseline_Severe_46_CD8T_Survivor.fcs
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Baseline_Severe_47_CD4T_Survivor.fcs
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Baseline_Severe_47_CD8T_Survivor.fcs
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Baseline_Severe_53b_CD4T_Survivor.fcs
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Baseline_Severe_53b_CD8T_Survivor.fcs
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Baseline_Severe_61_CD4T_Survivor.fcs
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Baseline_Severe_61_CD8T_Survivor.fcs
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Baseline_Severe_62_CD4T_Nonsurvivor.fcs
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Baseline_Severe_62_CD8T_Nonsurvivor.fcs
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Baseline_Severe_69_CD4T_Survivor.fcs
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Baseline_Severe_69_CD8T_Survivor.fcs
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Baseline_Severe_74_CD4T_Survivor.fcs
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Baseline_Severe_74_CD8T_Survivor.fcs
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Baseline_Severe_80_CD4T_Survivor.fcs
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Baseline_Severe_80_CD8T_Survivor.fcs
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Baseline_Severe_86_CD4T_Survivor.fcs
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Baseline_Severe_86_CD8T_Survivor.fcs
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Bystander_Conv_4100__CD4T_Survivor.fcs
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Bystander_Conv_4100__CD8T_Survivor.fcs
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Bystander_Conv_4102__CD4T_Survivor.fcs
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Bystander_Conv_4102__CD8T_Survivor.fcs
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Bystander_Conv_4103__CD4T_Survivor.fcs
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Bystander_Conv_4103__CD8T_Survivor.fcs
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Bystander_Conv_4104__CD4T_Survivor.fcs
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Bystander_Conv_4104__CD8T_Survivor.fcs
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Bystander_Conv_4106__CD4T_Survivor.fcs
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Bystander_Conv_4106__CD8T_Survivor.fcs
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Bystander_Conv_4112__CD4T_Survivor.fcs
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Bystander_Conv_4112__CD8T_Survivor.fcs
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Bystander_Conv_4114__CD4T_Survivor.fcs
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Bystander_Conv_4114__CD8T_Survivor.fcs
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Bystander_Conv_4122__CD4T_Survivor.fcs
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Bystander_Conv_4122__CD8T_Survivor.fcs
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Bystander_Conv_4123__CD4T_Survivor.fcs
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Bystander_Conv_4123__CD8T_Survivor.fcs
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Bystander_Moderate_06__CD4T_Survivor.fcs
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Bystander_Moderate_06__CD8T_Survivor.fcs
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Bystander_Moderate_07__CD4T_Survivor.fcs
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Bystander_Moderate_07__CD8T_Survivor.fcs
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Bystander_Moderate_16__CD4T_Survivor.fcs
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Bystander_Moderate_16__CD8T_Survivor.fcs
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Bystander_Moderate_21__CD4T_Survivor.fcs
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Bystander_Moderate_21__CD8T_Survivor.fcs
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Bystander_Moderate_25__CD4T_Survivor.fcs
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Bystander_Moderate_25__CD8T_Survivor.fcs
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Bystander_Moderate_26__CD4T_Survivor.fcs
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Bystander_Moderate_26__CD8T_Survivor.fcs
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Bystander_Severe_01__CD4T_Nonsurvivor.fcs
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Bystander_Severe_01__CD8T_Nonsurvivor.fcs
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Bystander_Severe_02__CD4T_Nonsurvivor.fcs
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Bystander_Severe_02__CD8T_Nonsurvivor.fcs
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Bystander_Severe_03__CD4T_Survivor.fcs
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Bystander_Severe_03__CD8T_Survivor.fcs
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Bystander_Severe_04__CD4T_Survivor.fcs
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Bystander_Severe_04__CD8T_Survivor.fcs
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Bystander_Severe_05__CD4T_Survivor.fcs
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Bystander_Severe_05__CD8T_Survivor.fcs
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Bystander_Severe_08__CD4T_Survivor.fcs
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Bystander_Severe_08__CD8T_Survivor.fcs
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Bystander_Severe_10__CD4T_Nonsurvivor.fcs
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Bystander_Severe_10__CD8T_Nonsurvivor.fcs
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Bystander_Severe_11__CD4T_Survivor.fcs
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Bystander_Severe_12__CD4T_Survivor.fcs
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Bystander_Severe_13__CD8T_Survivor.fcs
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Bystander_Severe_14__CD4T_Survivor.fcs
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Bystander_Severe_14__CD8T_Survivor.fcs
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Bystander_Severe_15__CD4T_Nonsurvivor.fcs
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Bystander_Severe_15__CD8T_Nonsurvivor.fcs
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Bystander_Severe_17__CD4T_Survivor.fcs
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Bystander_Severe_17__CD8T_Survivor.fcs
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Bystander_Severe_18__CD4T_Nonsurvivor.fcs
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Bystander_Severe_19__CD4T.fcs
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Bystander_Severe_20__CD4T_Survivor.fcs
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Bystander_Severe_20__CD8T_Survivor.fcs
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Bystander_Severe_22__CD4T_Nonsurvivor.fcs
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Bystander_Severe_24__CD4T_Nonsurvivor.fcs
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Bystander_Severe_24__CD8T_Nonsurvivor.fcs
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Bystander_Severe_31__CD4T_Survivor.fcs
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Bystander_Severe_31__CD8T_Survivor.fcs
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Bystander_Severe_37__CD4T.fcs
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Bystander_Severe_37__CD8T.fcs
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Bystander_Severe_38__CD4T_Survivor.fcs
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Bystander_Severe_38__CD8T_Survivor.fcs
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Bystander_Severe_39__CD4T_Nonsurvivor.fcs
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Bystander_Severe_39__CD8T_Nonsurvivor.fcs
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Bystander_Severe_42__CD4T_Survivor.fcs
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Bystander_Severe_42__CD8T_Survivor.fcs
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Bystander_Severe_45__CD4T_Nonsurvivor.fcs
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Bystander_Severe_45__CD8T_Nonsurvivor.fcs
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Bystander_Severe_46__CD4T_Survivor.fcs
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Bystander_Severe_47__CD8T_Survivor.fcs
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Bystander_Severe_53b__CD4T_Survivor.fcs
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Bystander_Severe_53b__CD8T_Survivor.fcs
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Bystander_Severe_61__CD4T_Survivor.fcs
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Bystander_Severe_61__CD8T_Survivor.fcs
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Bystander_Severe_62__CD4T_Nonsurvivor.fcs
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Bystander_Severe_86__CD8T_Survivor.fcs
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READ_ME_FILE.docx
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Responder_Conv_4100__CD4T__Survivor.fcs
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Responder_Conv_4100__CD8T__Survivor.fcs
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Responder_Conv_4123__CD4T__Survivor.fcs
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Responder_Conv_4123__CD8T__Survivor.fcs
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Responder_Moderate_21__CD8T_Survivor.fcs
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Responder_Moderate_25__CD4T_Survivor.fcs
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Responder_Severe_01__CD8T_Nonsurvivor.fcs
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Responder_Severe_03__CD4T__Survivor.fcs
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Responder_Severe_14__CD8T__Survivor.fcs
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Responder_Severe_15__CD4T__Nonsurvivor.fcs
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Responder_Severe_15__CD8T__Nonsurvivor.fcs
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Responder_Severe_17__CD8T__Survivor.fcs
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Responder_Severe_18__CD4T__Nonsurvivor.fcs
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Responder_Severe_19__CD4T_.fcs
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Responder_Severe_39__CD8T_Nonsurvivor.fcs
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Abstract
Although T cells are recognized as likely important players in SARS-CoV-2 immunity, little is known about the phenotypic features of SARS-CoV-2-specific T cells associated with recovery from COVID-19. We analyzed total and SARS-CoV-2-specific T cells from longitudinal specimens of 34 COVID-19 cases with severities ranging from mild (outpatient) to critical (ICU) culminating in death. The subset distribution of SARS-CoV-2-specific T cells differed in mild vs. severe ICU cases. Longitudinal analyses of severe ICU cases revealed that while those that survived infection mounted an increasing SARS-CoV-2-specific T cell response over time, those that succumbed to infection did not, in a manner associated with antigen-independent T cell activation. Relative to severe cases that culminated in death, individuals that recovered from severe COVID-19 harbored elevated levels of SARS-CoV-2-specific T cells capable of homeostatic proliferation. In the fatal COVID-19 cases, SARS-CoV-2-specific regulatory T cells were elevated and antigen-independent activated CXCR4+ T cells increased over time. Together with the demonstration of elevated proportions of inflammatory CXCR4+ T cells in the lungs of severe COVID-19 patients, these results support a model whereby T cells activated through bystander effects contribute to immunopathology by being non-specifically recruited to the inflamed lung. Overall, these findings suggest that a robust, non-suppressive SARS-CoV-2-specific T cell response is important for limiting immunopathology and recovery from severe COVID-19.