There is an urgent need to better understand the pathophysiology of Coronavirus disease 2019 (COVID-19), the global pandemic caused by SARS-CoV-2, which has infected more than three million people worldwide 1 . Approximately 20% of patients with COVID-19 develop severe disease and 5% of patients require intensive care 2 . Severe disease has been associated with changes in peripheral immune activity, including increased levels of pro-inflammatory cytokines 3,4 that may be produced by a subset of inflammatory monocytes 5,6 , lymphopenia 7,8 and T cell exhaustion 9,10 . To elucidate pathways in peripheral immune cells that might lead to immunopathology or protective immunity in severe COVID-19, we applied single-cell RNA sequencing (scRNA-seq) to profile peripheral blood mononuclear cells (PBMCs) from seven patients hospitalized for COVID-19, four of whom had acute respiratory distress syndrome, and six healthy controls. We identify reconfiguration of peripheral immune cell phenotype in COVID-19, including a heterogeneous interferon-stimulated gene signature, HLA class II downregulation and a developing neutrophil population that appears closely related to plasmablasts appearing in patients with acute respiratory failure requiring mechanical ventilation. Importantly, we found that peripheral monocytes and lymphocytes do not express substantial amounts of pro-inflammatory cytokines. Collectively, we provide a cell atlas of the peripheral immune response to severe COVID-19.To profile the peripheral immune response to severe COVID-19, we performed Seq-Well-based 11,12 massively parallel single-cell RNA sequencing (scRNA-seq) on eight peripheral blood samples from seven hospitalized patients with polymerase chain reaction with reverse transcription (RT-PCR)-confirmed SARS-CoV-2 infection and six healthy controls. The demographics and clinical features of these patients are listed in Fig. 1a. The seven patients profiled were male, aged 20 to >80 years. We collected samples between 2 and 16 days following symptom onset; healthy controls were asymptomatic, four male and two female, and aged 30-50 years (Fig. 1a and Extended Data Fig. 1). Four of eight COVID-19 samples were collected from ventilated patients who were diagnosed with acute respiratory distress syndrome (ARDS; Fig. 1a). One patient (C1) was sampled twice: at nine days post-symptom onset while only requiring supplemental oxygen and at 11 days post-symptom onset following intubation. Three patients received azithromycin, which

The coronavirus disease 2019 (COVID-19) pandemic caused by SARS-CoV-2 has had devastating global impacts and will continue to have dramatic effects on public health for years to come. A better understanding of the immune response to SARS-CoV-2 will be critical for the application and development of therapeutics. The degree to which the innate immune response confers protection or induces pathogenesis through a dysregulated immune response remains unclear. In this review, we discuss what is known about the role of the innate immune system during SARS-CoV-2 infection, suggest directions for future studies, and evaluate proposed COVID-19 immunomodulating therapeutics.

Our understanding of protective versus pathological immune responses to SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is limited by inadequate profiling of patients at the extremes of the disease severity spectrum. Here, we performed multi-omic single-cell immune profiling of 64 COVID-19 patients across the full range of disease severity, from outpatients with mild disease to fatal cases. Our transcriptomic, epigenomic, and proteomic analyses revealed widespread dysfunction of peripheral innate immunity in severe and fatal COVID-19, including prominent hyperactivation signatures in neutrophils and NK cells. We also identified chromatin accessibility changes at NF-κB binding sites within cytokine gene loci as a potential mechanism for the striking lack of pro-inflammatory cytokine production observed in monocytes in severe and fatal COVID-19. We further demonstrated that emergency myelopoiesis is a prominent feature of fatal COVID-19. Collectively, our results reveal disease severity–associated immune phenotypes in COVID-19 and identify pathogenesis-associated pathways that are potential targets for therapeutic intervention.

Reagents for detecting post-translational modifications in the context of their protein scaffold are powerful tools, but are challenging to develop for glycosylated epitopes. We describe a strategy for detecting protein-specific glycosylation through the use of cyclooctyne-aptamer conjugates. These molecules selectively ligate to azidosugar-labeled glycans exclusively on a target protein on live cells. We characterized aptamer conjugates against two different cell surface glycoproteins and show that these reagents are amenable to detecting protein sialoforms by mass spectrometry, Western blotting, and flow cytometry. Given the abundance of aptamers that bind cell surface targets, we expect this technology will be a useful platform for investigating the roles of protein-specific glycosylation in various cellular contexts.