Circuits between infected alveolar macrophages and T cells in severe COVID-19

Samples were collected as part of the Successful Clinical Response in Pneumonia Therapy (SCRIPT) Systems Biology Center, an observational study of patients with severe pneumonia, defined as those requiring mechanical ventilation. We collected bronchoalveolar lavage fluid samples from 88 patients with SARS-CoV-2-induced respiratory failure and 211 patients with known or suspected pneumonia from other pathogens and subjected them to flow cytometry and bulk transcriptomic profiling. In the majority of patients with SARS-CoV-2 infection, the alveolar space was persistently enriched in T cells and monocytes. Alveolar macrophages demonstrated interferon-response signature in samples from patients with COVID-19.