Extended Data Fig. 8: In vivo expansion of pre-existing SARS-CoV-2-reactive T cells post-infection or post-exposure.
From: Pre-existing polymerase-specific T cells expand in abortive seronegative SARS-CoV-2
a, Change in magnitude of T cell response between pre-pandemic and post-infection (upper panel: all proteins, lower panel: NSP12) in seropositive close contacts of cases. b, Summary data for paired pre-pandemic and post-exposure NSP12 and Flu/EBV/CMV (FEC) responses in seronegative close contacts of infections. Below; example ELISpot well images from a seronegative close contact (NSP12-4: pre-pandemic 45 and post-exposure 95 SFCs per 106 PBMCs). c, Change in magnitude of T cell response between pre-pandemic and post-exposure samples (upper panel: all proteins, lower panel: NSP12) from seronegative close contacts of cases. d, Summary data for NSP12 and FEC responses in SN-HCW (sub-group with the top RTC response at wk16, n=19, Extended Data Fig. 4a). e, Summary data and f, change in magnitude of T cell responses for individual HCW to NSP7 (15 peptide pool) or a single subpool from NSP12 and NSP13 between baseline and post-exposure in SN-HCW (wk16-26, 29 responses from 13 SN-HCW). g, Change in magnitude of T cell response to individual 9-15mer peptides pre- and post-exposure in SN-HCW (wk16-26, 11 responses from 9 SN-HCW). h, Example plots of CTVlo IFNγ+ SARS-CoV-2-specific T cells after 10day expansion of PBMC from baseline and wk16 with peptide #166 (YVYLPYPDPSRILGA) or unstimulated in an HLA-B*51+ SN-HCW (gated on CD8+, percentage of CD8+ shown, gating strategy Extended Data Fig. 3a). i, Proportion of SN-HCW with NP1 + NP2-reactive T cells grouped by those with and without newly detected or expanded NSP12 responses at wk16, Fig. 4b. j, Correlation between the fold-change in NSP12 between recruitment and wk16 and total response to RTC or structural proteins at wk16 in SN-HCWs. Dotted line at 2-fold increase. k, The breadth of the NSP12-specific T cell response (number of subpools recognized, pre-pandemic or wk16). l Change in magnitude of the T cell response to NSP12 between baseline (open circles) and wk16 (closed circles) in SN-HCW and HCW with laboratory-confirmed infection. Percentage of responders shown below. m, Change in magnitude of NSP12-specific T cell response between pre-pandemic and post-infection in HCW with laboratory-confirmed infection. a,c,f-g,m, Expanded, >2-fold increase or >35 SFCs per 106 PBMCs increase. a, Red line mean, d-e,I, Red line/bars, geomean. k, red line, median. b,d,e Wilcoxon test. l, Mann-Whitney (unpaired) and Wilcoxon (paired) tests. k, Kruskal-Wallis with Dunn’s correction. j, Spearman r. a-c, Contact cohort, Extended Data Table 5. d-m, COVIDsortium cohort Extended Data Table 1.
