(a) The levels of selected cytokines and chemokines in the BALF were measured by cytometric bead array. Patient S6 was previously in critical condition (S6-1) but improved later (S6-2). S2, S8 and S9 are critical COVID-19 cases cared in ICU with longitudinal BALF samples, as labeled sequentially as S2-(1, 2, 3), S8-(1, 2, 3) and S9-(1, 2). The detailed information of studied subjects was described in Supplementary Tables 1 and 4. (b) The gene expression levels of selected cytokines and chemokines in macrophages from health controls (n = 4), moderate cases (n = 3) and severe/critical cases (n = 6). *P < 0.05, **P < 0.01, ***P < 0.001, P-value adjusted by false discovery rate in MAST. (c) The gene expression levels of indicated cytokines and chemokines in macrophages of each studied COVID-19 patient based on the scRNA-seq data. The horizontal dashed lines separate controls, moderate and severe/critical patients. Some ligand-receptor pairs are indicated by dashed boxes. (d) The gene expression levels of chemokine receptors by various immune cell subsets, including myeloid, B cell, plasma cell, NK cell and T cell subsets based on the scRNA-seq data (n = 13).