Coronavirus disease 2019 (COVID-19) is characterized by distinct patterns of disease progression suggesting diverse host immune responses. We performed an integrated immune analysis on a cohort of 50 COVID-19 patients with various disease severity. A unique phenotype was observed in severe and critical patients, consisting of a highly impaired interferon (IFN) type I response (characterized by no IFN-β and low IFN-α production and activity), associated with a persistent blood viral load and an exacerbated inflammatory response. Inflammation was partially driven by the transcriptional factor NF-κB and characterized by increased tumor necrosis factor (TNF)-α and interleukin (IL)-6 production and signaling. These data suggest that type-I IFN deficiency in the blood could be a hallmark of severe COVID-19 and provide a rationale for combined therapeutic approaches.

Clinical outcome upon infection with SARS-CoV-2 ranges from silent infection to lethal COVID-19. We have found an enrichment in rare variants predicted to be loss-of-function (LOF) at the 13 human loci known to govern TLR3- and IRF7-dependent type I interferon (IFN) immunity to influenza virus, in 659 patients with life-threatening COVID-19 pneumonia, relative to 534 subjects with asymptomatic or benign infection. By testing these and other rare variants at these 13 loci, we experimentally define LOF variants in 23 patients (3.5%), aged 17 to 77 years, underlying autosomal recessive or dominant deficiencies. We show that human fibroblasts with mutations affecting this pathway are vulnerable to SARS-CoV-2. Inborn errors of TLR3- and IRF7-dependent type I IFN immunity can underlie life-threatening COVID-19 pneumonia in patients with no prior severe infection.

Background: Coronavirus disease 2019 (Covid-19) is a major global threat that has already caused more than 100,000 deaths worldwide. It is characterized by distinct patterns of disease progression implying a diverse host immune response. However, the immunological features and molecular mechanisms involved in Covid-19 severity remain so far poorly known.

Highlights d Combination of single-cell RNA sequencing and mass cytometry d Construction of a cell atlas of adult skeletal muscle d Skeletal muscle is composed of 10 mononucleated cell types and myofibers d Skeletal muscle contains interstitial tenocytes and smooth muscle-mesenchymal cells

The recent introduction of mass cytometry, a technique coupling a cell introduction system generating a stream of single cells with mass spectrometry, has greatly increased the number of parameters that can be measured per single cell. As with all new technology there is a need for dissemination of standardization and quality control procedures. Here, we characterize variations in sensitivity observed across the mass range of a mass cytometer, using different lanthanide tags. We observed a five-fold difference in lanthanide detection over the mass range and demonstrated that each instrument has its own sensitivity pattern. Therefore, the selection of lanthanide combinations is a key step in the establishment of a staining panel for mass cytometry-based experiments, particularly for multicenter studies. We propose the sensitivity pattern as the basis for panel design, instrument standardization and future implementation of normalization algorithms. V C 2015 International Society for Advancement of Cytometry Key terms Key terms: mass cytometry; CyTOF; standardization; flow cytometry CYTOMETRY by time-of-flight (CyTOF) is a recently developed technique allowing the simultaneous detection of more than 40 parameters at the single cell level. CyTOF technology is novel in that it makes use of antibodies or other specific probes conjugated with pure metal isotopes to label cells that are finally detected by atomic mass spectrometry (1). CyTOF technology has recently been used to characterize signaling pathways in hematopoietic cells (2,3), to analyze cytokine expression and phenotype in detail in antigen-specific CD8 T cells (4) and to map cell-cycle phases in PBMCs and bone marrow aspirates (5). The advantages of this new technology over conventional fluorescence-based flow cytometry were described in detail in a recent review (6). In short, whereas conventional flow cytometry can be used to measure fluorescence in a maximum of 18 channels, with considerable spectral overlap requiring ad hoc mathematical processing, CyTOF technology makes it possible to measure more than 40 different parameters, with minimal spectral overlap. The fluorochromes used in conventional flow cytometry include small organic molecules, such as FITC, and larger proteins, such as allophycocyanin, which may differ considerably in molecular weight and chemical properties. In addition, each fluorochrome has its own unique excitation and emission spectra and its spillover characteristics are therefore different from those of other fluorochromes. These properties strongly affect the sensitivity of the assay, the performance of which is dependent on the combination