Extended Data Fig. 6: Cell types/states throughout the upper (NS) and lower (PBS, BL) respiratory tract in the two critical COVID-19 patients BIH-CoV-01 and BIH-CoV-04.

a, UMAP depicting all identified cell types across the upper (NS) and lower (PSB, BL) respiratory tract of the two critical patients BIH-CoV-01 and BIH-CoV-04 (sampling days +17 and +13 after onset of symptoms, respectively). Please note that the majority of cell types correspond to the cell types identified in the upper respiratory tract (cf. Figure 2). For identification and description of the additional cell types including secretory LYPD2, ciliated IFN, basophil, NK and hybrid cells please refer to Methods. b, UMAPs depicting the cell types in the NS (left), PSB (middle) or BL (right) of patients BIH-CoV-01 and BIH-CoV-04. c, UMAP depicting ACE2⁺ cells and virus⁺ cells across NS, PBS, or BL samples. d, Viral RNA reads within aggregated pseudo-bulks for patient BIH-CoV-01 and BIH-CoV-04 in counts per million (CPM) detected in either NS, PSB or BL. e. Viral genome equivalents/ml of patient BIH-CoV-01 cell-free sample as measured by quantitative RT-PCR. NS: nasopharyngeal swab, PSB: protected specimen brush, BL: bronchial lavage.