Extended Data Fig. 3: (matched to Fig. 4).

a. t-distributed stochastic neighbor embedding (t-SNE) plot with clustering results of single cell RNA sequencing of mouse cells from lungs at 4dpi. Single cell suspensions from whole infected lung at 4dpi were processed and sequenced. There were 731 cells identified as mouse cells. b. Dot plot of cluster identifying genes for mouse cell clusters described in S4A. c. Cluster distribution and expression profile of mouse inflammatory cytokines for clusters described in 4B. d. Normalized expression of human IFNB measured by qPCR in homogenized lung tissue of uninfected and infected (2,4,7,14,28dpi) mice. Expression was normalized to human HPRT1. Unpaired t-test, one-tailed since the distribution is expected to be one-sided. Uninfected n=3, 2dpi n=3, 4dpi n=6, 7dpi n=7, 14dpi n=10, 28dpi n=2 biologically independent mice examined over at least 3 independent experiments. Individual values for each mouse and means are presented. P-values<0.05 are plotted. e. IFNA levels measured by ELISA in serum and BAL of uninfected or infected mice. Serum: Uninfected n=6, 4dpi n=3, 7dpi n=2, 14dpi n=5, 28dpi n=3; BAL: Uninfected n=3, 14dpi n=4 biologically independent mice examined over at least 2 independent experiments for all time points. Individual values (average of duplicates) for each mouse and means are plotted. f. Type I interferon levels (IFNA6 and IFNB) per cell measured by qPCR in sorted human immune cells (human CD45+): plasmacytoid dendritic cells (PDCs; CD123^hi CD11B-), macrophages and monocytes (CD11B+) and rest of human immune cells (CD123-CD11B-CD45+). Expression was normalized to human ACTB. Individual values and means are plotted. n=3 biologically independent mice examined over 2 independent experiments. Individual values with means are plotted. g. Normalized expression of human IFNG measured by qPCR in homogenized lung tissue of uninfected and infected (2,4,7,14,28dpi) mice. Expression was normalized to human HPRT1. Unpaired t-test, one tailed since distribution is expected to be one-sided. Uninfected n=10, 2dpi n=3, 4dpi n=8, 7dpi n=3, 14dpi n=15, 28dpi n=5 biologically independent mice examined over at least 3 independent experiments for all time points. h. Heat map of normalized counts for bystander activated memory T cell signature genes⁶⁴ (based on Low et al., JEM 2020) in lungs of MISTRG6-hACE2 mice infected with SARS-CoV-2. Row min and max of transformed values, calculated by subtracting row mean and diving by STD for each gene across all samples, are visualized. Uninfected n=5, 2dpi n=4, 4dpi n=7, 7dpi n=3, 14dpi n=2, 28dpi n=2 biologically independent mice examined over at least 2 independent experiments for all time points. i. Volcano plot showing foldchange and adjusted p-values (by Wald test using DESeq2) of differentially regulated genes at 28dpi compared to uninfected lungs. Genes with FC(Log2)>1 and p value<0.05 are highlighted in red. Replicates of at least 2 mice. Uninfected n=5, 28dpi n=2 biologically independent mice examined over 2 independent experiments. j. Heatmap of normalized counts for genes that are induced in B cells of patients with moderate or severe COVID-19 in comparison with healthy controls. Normalized counts in lungs of uninfected or infected MISTRG6-hACE2 were plotted over the course of infection. Row min and max of transformed values, calculated by subtracting row mean and diving by STD for each gene across all samples, are visualized. Uninfected n=5, 2dpi n=4, 4dpi n=7, 7dpi n=3, 14dpi n=2, 28dpi n=2 biologically independent mice examined over at least 2 independent experiments for all time points. k. Heatmap of normalized counts for bystander activated memory B cell signature genes⁶⁵ (based on Horns et al., 2020) in lungs of MISTRG6-hACE2 mice infected with SARS-CoV-2. Row min and max of transformed values, calculated by subtracting row mean and diving by STD for each gene across all samples, are visualized. Uninfected n=5, 2dpi n=4, 4dpi n=7, 7dpi n=3, 14dpi n=2, 28dpi n=2 biologically independent mice examined over at least 2 independent experiments for all time points.