Experimental design for the systems immunology approach (integrated multiomics single-cell assays) to study patients with COVID-19 and identify robust neutrophilia in the lungs. (A) Respiratory samples (sputum or endotracheal aspirates) and matching blood from all subjects were collected for 21-plex Mesoscale analysis, high-dimensional (Hi-D) 30-parameter flow cytometry, and multiomics scRNA-seq. Cells from endotracheal aspirates (ETA) and blood of patients with severe COVID-19 along with blood from healthy individuals were surface-stained with a panel of 89 oligo-conjugated monoclonal antibodies before single-cell encapsulation, and analyses were performed with a custom human reference genome that included the SARS-CoV-2 genome to simultaneously detect viral mRNA transcripts. Integrative multiomics analyses were performed on the resulting datasets. (B) Box plots showing the distribution of leukocytes isolated from endotracheal aspirates (ETA). (C) Box plots showing the distribution of leukocytes isolated from the whole blood of severe patients. For comparisons across the 3 patient groups (ie, healthy, MA, and severe), ordinary one-way ANOVA (if equal variance) or Brown-Forsythe and Welch ANOVA (if unequal variance) tests were performed for data with a normal distribution. Data with a lognormal distribution were analyzed using the Kruskal-Wallis test.