Serial whole blood transcriptomic analysis demonstrates activation of neutrophils, platelets and coagulation in severe and critical COVID-19 – submitted

Introduction: A maladaptive inflammatory response has been implicated in the pathogenesis of severe and critical COVID-19. This study aimed to characterize the temporal dynamics of this response and investigate whether critical disease is associated with distinct gene expression patterns. Methods: We performed microarray analysis of serial whole blood RNA samples from 19 patients with critical COVID-19, 15 patients with severe but non-critical disease and 11 healthy controls. We assessed whole blood gene expression patterns by differential gene expression analysis, gene set enrichment, two clustering methods and estimated relative leukocyte abundance using CIBERSORT. Results: Neutrophils, platelets, cytokine signaling, and the coagulation system were activated in COVID-19, and more pronounced in critical vs. non-critical disease. We observed two different trajectories of neutrophil-associated genes, indicating the emergence of a more immature neutrophil phenotype over time. Interferon-associated genes were strongly enriched in early COVID-19 before falling markedly, with modest severity-associated differences in trajectory. Conclusions: Severe COVID-19 is associated with a broad inflammatory response, which is more pronounced in critical disease. Our data suggest a progressively more immature circulating neutrophil phenotype over time. Interferon signaling is enriched in COVID-19 but does not seem to drive critical disease. Between March and May 2020, 135 patients admitted to Akershus University Hospital with COVID-19 confirmed by SARS-CoV-2 RT-PCR were prospectively recruited to the Coronavirus Disease Mechanisms (COVID MECH) observational cohort study. Thirty-six patients (27%) were admitted to the ICU and 8 (6%) died. Inclusion predated the use of corticosteroids in severe COVID-19. This substudy included 19 patients with critical disease, defined as requiring invasive mechanical ventilation, and 15 patients with non-critical disease receiving supplemental O2. Patients were selected based on the availability of sequential whole blood RNA samples, and time from symptom onset to baseline sampling between five and 15 days. RNA samples from 11 healthy volunteers matched to patients by age and gender served as controls.