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. 2022 Mar 3;185(5):916–938.e58. doi: 10.1016/j.cell.2022.01.012

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© 2022 The Author

This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

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Figure S6 — Dynamic changes in lymphocyte populations associated with COVID-19 severity, related to Figure 4

(A) Frequency of activated CD4 and CD8 T cells assayed by single cell mass cytometry. (B-D) Multicolor flow cytometry analysis of PBMC. (B,C) Boxplots, dotplots and heatmap describing the phenotype and frequency of subsets of memory CD4 T cell subsets defined based on the expression of CCR4, CCR6 and CXCR3. (D) Frequency of TIM3⁺CD38⁺HLADR⁺ CD8⁺ T cells. (E) Frequency of CLA⁺ HLADR⁺ NK cells assayed by single cell mass cytometry. (F-H) CITE-seq profiling CD4⁺ CD8⁺ T and NK cell clusters. (F) Frequency between comparator groups. (G) Principal Components Analysis (PCA) and correlation with clinical covariates and severity measures for gene expression in acute hospitalized cases (mild, severe, critical) in activated NK cells. (H) scRNA-seq MSigDB hallmark gene set enrichment for T cell populations. (I) Single cell mass cytometry composition analysis of B and plasmablast cell populations comparing study groups. (J) CITE-seq compositional differential abundance analysis of B and plasmablast cell clusters. All boxplots show median, first and third quartiles; whiskers show 1.5x interquartile range. Abbreviations for CITE-seq (panels F-H,J). B: B cell; cDC: classical dendritic cell; cyc: cycling; DN: CD4/CD8 double negative; DP: CD4/CD8: double positive; hi: high; IFN, interferon; int: intermediate; mito, mitochondrial; NK: natural killer cell; PB: plasmablast; PBMC: peripheral blood mononuclear cell; resp: responsive; TCM, T central memory; TEM(RA): T effector memory (CD45RA re-expressing); Th, T helper; TREG: T regulatory cell. Comparator group abbreviations. HV: healthy volunteer; CM: COVID-19 in-patient mild; CS: COVID-19 in-patient severe; CC: COVID-19 in-patient critical; CComm: COVID-19 community case in the recovery phase (never admitted to hospital); CConv: COVID-19 convalescence (survivors from 28 days after discharge); Flu: influenza in-patient critical; Sepsis: in-patient severe and critical sepsis; SeConv: sepsis convalescence.