Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia. Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia

Some patients infected with Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) develop severe pneumonia and the acute respiratory distress syndrome (ARDS). Distinct clinical features in these patients have led to speculation that the immune response to virus in the SARS-CoV-2-infected alveolus differs from other types of pneumonia. 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. We performed single-cell RNA-seq on 10 bronchoalveolar lavage fluid samples collected from patients with severe COVID-19 within 48 hours of intubation. In the majority of patients with SARS-CoV-2 infection, the alveolar space was persistently enriched in T cells and monocytes. Bulk and single-cell transcriptomic profiling suggested that SARS-CoV-2 infects alveolar macrophages, which in turn respond by producing T cell chemoattractants. These T cells produce interferon-gamma to induce inflammatory cytokine release from alveolar macrophages and further promote T cell activation. Collectively, our results suggest that SARS-CoV-2 causes a slowly-unfolding, spatially-limited alveolitis in which alveolar macrophages harboring SARS-CoV-2 and T cells form a positive feedback loop that drives persistent alveolar inflammation. Overall design: Bronchoalveolar lavage (BAL) fluid from 12 patients (10 COVID-19 positive, 1 COVID-19 negative with bacterial pneumonia secondary to infection with Pseudomonas aeruginosa and Acinetobacter baumannii, 1 COVID-19 negative, intubated for airway protection to facilitate endoscopy for severe gastrointestinal bleeding without pneumonia) was obtained within 48 hours of intubation at Northwestern Memorial ICU. BAL fluid was flow-sorted for macrophages and T cells and single-cell libraries were prepared with 10x 5' gene expression kit. Libraries were sequenced on Illumina NovaSeq 6000. Gene expression matrices were generated with 10x cellranger v3.1.0 software. Matrices were combined together and processed with scanpy to create an integrated object with COVID-19-only samples (main.h5ad; 10 COVID-19-positive patients) and a supplemental object with all samples (supplement.h5ad; 10 COVID-19-positive patients and 2 COVID-19-negative patients). [contributor] The NU SCRIPT Study Investigators Please note that the following files have been corrected on July 17, 2023: main-metadata.csv.gz main.h5ad.gz supplement-metadata.csv.gz supplement.h5ad.gz ***Due to patient privacy concerns, the submitter declares that patient data will be submitted to dbGaP.***