Fig. 2.

Rapid and transient alterations in CD14⁺ monocytes in PBMCs after SARS-CoV-2 infection. (A) UMAP plot representing the clustering pattern of cells from scRNA-seq data of PBMCs from 4 animals (DGCX, DG3V, DHGF, and DHKM) (left panel). Each dot denotes a cell and is colored based on automated cluster identification. Clusters of cells belonging to a certain cell-type are demarcated and indicated on the plot. Expression levels of cell type defining markers are shown as a dot plot (right panel). Color intensity and dot size represent level of expression and percent of cells in that cluster expressing the gene as defined in the key. (B) UMAP representation of the sub-clustering of the myeloid cells from A. Clusters were annotated with cell-types based on gene expression patterns as shown on the dot plot and are identified with different numbers and colors on the plots. (C) UMAP plots separated by time depict the kinetic of the myeloid cells characterized in B at pre-infection, and day 4, 7, and 10 post-infection. (D) Fraction of cells that comprise each myeloid cell-type for each of the 4 timepoints shown in C is summarized. (E-G). Heatmap represents the hierarchical clustering of normalized expression levels of differentially expressed genes for each cell for three myeloid clusters. The cluster names are indicated on top of the heatmap and the first and second color bars distinguish time point and animal respectively. Genes were considered differentially expressed between timepoints if log fold change ≥ 0.5 and adjusted p-value < 0.01. Biological processes associated with the genes are indicated on the side and the blue box highlights type I IFN-responsive genes up-regulated at day 4.