Fig 1: The dynamic characteristics and functional changes in T cells from lung and intestinal tissues during SARS-CoV-2 infection(A) Subclustering of T cells in all lung tissue samples (n = 6).(B) Quantification of T cell subsets in 3 (n = 1), 7 (n = 1), and 10 (n = 1) dpi in lung. Three healthy animals were regarded as the control. For each T cell cluster, the average fraction of cells is shown at different infection time points.(C) Subclustering of T cells in the small intestine (n = 8).(D) The histogram represents the quantification of T cell cluster frequency at different infection time points (3, 7, and 10 dpi) in the small intestine.(E) The differential expression levels of the genes CD38, CD69, GZMB, CD74, IFI27, and IFNG at 3 (n = 1), 7 (n = 2), and 10 (n = 2) dpi in the small intestine. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, Wilcoxon test.(F) Analysis of the expression of T cell activation-related factors by a confocal immunofluorescence assay. Top: T cells were detected by an anti-CD3 antibody followed by Alexa Fluor 488 dye-conjugated secondary antibody. The T cell activation-related molecules CD38 and CD69 were detected with anti-CD38 and anti-CD69 primary antibodies, followed by secondary antibodies conjugated with Alexa Fluor 555 and Alexa Fluor 647 dyes, respectively. Bottom: T cells were detected by an anti-CD3 antibody followed by Alexa Fluor 488 dye-conjugated secondary antibody. The T cell activation-related granzyme B and molecules CD74 were detected with anti-granzyme B and anti-CD74 primary antibodies, followed by secondary antibodies conjugated with Alexa Fluor 555 and Alexa Fluor 647 dyes, respectively. Nuclei were stained with DAPI (magnification, 630×). Scale bar, 100 µm. Control, normal tissues.(G) Percentage of CD3+CD38+, CD3+CD69+, CD3+CD74+, and CD3+GZMB+ cells were computed in total intestine cells (number of cells from three randomly selected fields captured by confocal fluorescence microscope) for normal controls and COVID-19 intestine samples.(H) Genes clustered by their expression pattern during the progression of SARS-CoV-2 infection (3, 7, 10 dpi). GO term analysis revealed the top five enriched biological processes in nine clusters from the lung.(I) Genes clustered by their expression pattern during the progression of SARS-CoV-2 infection (3, 7, 10 dpi). GO term analysis revealed the top five enriched biological processes in nine clusters from the small intestine. Cluster 4 does not contained a significantly enriched term of biological process, so it is not shown.(J) Signature scores of the GO term “regulatory T cell differentiation” genes in T cell subsets (Trm, Teff, and Naive_T or _Tcm) in the lung by Ucell package.(K) Signature scores of the GO term “response to virus” gene module in major immune cells, including B cells, DC cells, macrophages, NK cells, and T cells of the small intestine by Ucell package.*p < 0.05, ***p < 0.001, ****p < 0.0001, Wilcoxon test.See also Figure S2.