Fig. 1: Illustration of the experimental setup and the patient cohort used in this study.

a, Schematic representation of the experimental workflow. Depicted are the sampling sites (left) and the 3′ scRNA-seq library preparation using 10X Genomics (middle) followed by data analysis revealing cell type identity (right). b, Overview of the patient cohort. Given are age, sex and COVID-19 severity as well as onset of symptoms, hospitalization duration and sampling time points in days after onset of symptoms, with all patients being temporally aligned to the day of positive SARS-CoV-2 test. Admission to the ICU is also depicted if applicable. One patient required ECMO. We obtained NSs from all patients and, in addition, PSBs and BLs from patients BIH-CoV-01 and BIH-CoV-04 (marked with *). The sampling day relative to the onset of symptoms is given as a number in a square or triangle.