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. 2021 Apr 20;27(5):904–916. doi: 10.1038/s41591-021-01329-2

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© The Author(s) 2021

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 3 — a, UMAP visualization of 309,617 T cells based on gene expression shown and colored by cell type. Insets show the two-dimensional kernel density estimates of select T cell types in UMAP space. b, Dot plots of gene (top) and surface protein (bottom) expression for populations shown in a. c, Dot plots of gene expression of cytokine genes for populations shown in a. d, Box plots of cell type proportions that are differentially abundant between healthy donors and individuals with COVID-19. Boxes denote the IQR, and the median is shown as horizontal bars. Whiskers extend to 1.5 times the IQR and outliers are shown as individual points (n = 24 healthy, n = 86 COVID-19 biologically independent samples). e, Box plots of the proportion of cell types shown in a. Only cell types showing trends of changes by severity status are shown. Boxes denote IQR with median shown as horizontal bars. Whiskers extend to 1.5 times the IQR, and outliers are shown as individual points (n = 9 asymptomatic, n = 23 mild, n = 30 moderate, n = 13 severe, n = 10 critical biologically independent samples). f, Bar plots show the frequency of clonal T cells. Expanded clones denote clonotypes observed more than once. Asterisks indicate significance after multiple-testing correction (logistic regression using two-sided t-test with Benjamini–Hochberg FDR correction; CD4⁺ T_CM adjusted P = 0.119, CD4⁺ T_EM adjusted P = 0.472, CD4⁺IL-22⁺ adjusted P = 0.01, CD4⁺ prolif. adjusted P = 0.993, CD4⁺ T_H1 adjusted P = 0.993, CD4⁺ T_FH adjusted P = 0.109, T_reg adjusted P = 0.993, CD8⁺ prolif. adjusted P = 0.016, CD8⁺ T_TE adjusted P = 2.49 × 10⁻¹⁵, CD8⁺ T_EM adjusted P = 0.259). g, Box plots of the proportion of clonally expanded CD8⁺ T_EM cells (left), effector CD8⁺ T cells (middle) and the ratio of effector CD8⁺ T cells to CD8⁺ T_EM cells (right). Boxes denote the IQR, and the median is shown as horizontal bars. Whiskers extend to 1.5 times the IQR, and outliers are shown as individual points. Legend is as in e.