Longitudinal characterization of circulating neutrophils uncovers phenotypes associated with severity in hospitalized COVID-19 patients

Mechanisms of neutrophil involvement in severe COVID-19 remain incompletely understood. Here we collect longitudinal blood samples from 306 hospitalized COVID-19+ patients and 86 controls, and perform bulk RNA-sequencing of enriched neutrophils, plasma proteomics, and high-throughput antibody profiling to investigate relationships between neutrophil states and disease severity. We identify dynamic switches between 6 distinct neutrophil subtypes. At days 3 and 7 post-hospitalization, patients with severe disease display a granulocytic myeloid-derived suppressor cell-like gene expression signature, while patients with resolving disease show a neutrophil progenitor-like signature. Humoral responses are identified as potential drivers of neutrophil effector functions, with elevated SARS-CoV-2-specific IgG1-to-IgA1 ratios in plasma of severe patients who survived. In vitro experiments confirm that while patient-derived IgG antibodies induce phagocytosis in healthy donor neutrophils, IgA antibodies predominantly induce neutrophil cell death. Overall, our study demonstrates a dysregulated myelopoietic response in severe COVID-19 and a potential role for IgA-dominant responses contributing to mortality. Neutrophil Bulk RNA-seq: Longitudinal gene expression profiling analysis using bulk RNA-seq data of neutrophils enriched from fresh whole blood of 306 hospitalized COVID-19+ patients, 78 symptomatic controls, and 8 healthy controls for a total of 781 samples. Blood samples were drawn on D0, D3, and D7 (days post-hospitalization) if the patient remained hospitalized, and some patients had an event-driven draw (DE) which corresponds to a change in patient status (e.g. intubation, removal from ventilator). Please note that 'COVID-19 status' simply refers to whether the patient is COVID+ or COVID-. COVID- includes both negative symptomatic controls and healthy controls. The healthy controls have an H in their sample name, and also in the time point, and the disease severity characteristics. Any other sample which is COVID- is a symptomatic control. NOTE: The data for the study were collected at the very beginning of the COVID-19 pandemic, and as such, a waiver of informed consent was approved by the governing institutional review board at Massachusetts General Hospital, in compliance with the Code of Federal Regulation (45CFR 46, 2018 Common Rule). To protect the identity of individual subjects, public posting of raw sequencing data from the patients has not been approved; Therefore, raw data is not provided.