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. 2022 Feb 3;13:679. doi: 10.1038/s41467-022-28315-7

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© The Author(s) 2022

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. 7 — BAL lymphoid cell dynamics in macaques infected with SARS-CoV-2 by scRNA-seq demonstrate the presence of IFN responsive T cells. A UMAP plot of lymphoid cells from all scRNA-seq samples together, colored according to cluster classification. B UMAP plots with the expression of markers, characterizing main lymphoid populations in macaques. C Cell proportion of each cluster per condition. n = 6 macaques. Data are presented as mean ± standard error of the mean (SEM). Source data are provided as a source data file. D Bubble plot showing the fold change of genes in identified lymphoid cell clusters and the fraction of cells expressing the gene of interest. E Heatmap of key interferon responsive genes at different timepoints in lymphoid sub-clusters. F Multilabel immunofluorescence confocal images validating in vivo expression of MX1 (yellow) in T-cells marked by CD3 (magenta) and nuclei (blue) in Naive as well as SARS CoV-2 infected lungs at 3 dpi and 14–17 dpi. White arrows represent T cells expressing MX1.