Background Inborn errors of immunity (IEI) and autoantibodies to type I interferons (IFNs) underlie critical COVID-19 pneumonia in at least 15% of the patients, while the causes of multisystem inflammatory syndrome in children (MIS-C) remain elusive. Objectives To detect causal genetic variants in very rare cases with concomitant critical COVID-19 pneumonia and MIS-C. Methods Whole exome sequencing was performed, and the impact of candidate gene variants was investigated. Plasma levels of cytokines, specific antibodies against the virus, and autoantibodies against type I IFNs were also measured. Results We report a 3-year-old child who died on day 56 of SARS-CoV-2 infection with an unusual clinical presentation, combining both critical COVID-19 pneumonia and MIS-C. We identified a large, homozygous loss-of-function deletion in IFNAR1, underlying autosomal recessive IFNAR1 deficiency. Conclusions Our findings confirm that impaired type I IFN immunity can underlie critical COVID-19 pneumonia, while suggesting that it can also unexpectedly underlie concomitant MIS-C. Our report further raises the possibility that inherited or acquired dysregulation of type I IFN immunity might contribute to MIS-C in other patients.

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Human inborn errors of IFN-γ underlie mycobacterial disease, due to insufficient IFN-γ production by lymphoid cells, impaired myeloid cell responses to this cytokine, or both. We report four patients from two unrelated kindreds with intermittent monocytosis and mycobacterial disease, including bacillus Calmette–Guérin-osis and disseminated tuberculosis, and without any known inborn error of IFN-γ. The patients are homozygous for ZNFX1 variants (p.S959* and p.E1606Rfs*10) predicted to be loss of function (pLOF). There are no subjects homozygous for pLOF variants in public databases. ZNFX1 is a conserved and broadly expressed helicase, but its biology remains largely unknown. It is thought to act as a viral double-stranded RNA sensor in mice, but these patients do not suffer from severe viral illnesses. We analyze its subcellular localization upon overexpression in A549 and HeLa cell lines and upon stimulation of THP1 and fibroblastic cell lines. We find that this cytoplasmic protein can be recruited to or even induce stress granules. The endogenous ZNFX1 protein in cell lines of the patient homozygous for the p.E1606Rfs*10 variant is truncated, whereas ZNFX1 expression is abolished in cell lines from the patients with the p.S959* variant. Lymphocyte subsets are present at normal frequencies in these patients and produce IFN-γ normally. The hematopoietic and nonhematopoietic cells of the patients tested respond normally to IFN-γ. Our results indicate that human ZNFX1 is associated with stress granules and essential for both monocyte homeostasis and protective immunity to mycobacteria.

19Four endemic human coronaviruses (HCoVs) are commonly associated with acute respiratory 20 infection in humans but immune responses to these "common cold" viruses remain 21 incompletely understood. Moreover, there is evidence emerging from independent studies 22 which suggests that endemic HCoVs can induce broadly cross-reactive T cell responses and 23 may thereby affect clinical outcomes of acute infections with the phylogenetically related 24 epidemic viruses, namely MERS-CoV and SARS-CoV-2. Here we report a comprehensive 25 retrospective analysis of CoV-specific antibody specificities in a large number of samples from 26 children and adults using Phage-Immunoprecipitation Sequencing (PhIP-Seq). We estimate 27 the seroprevalence for endemic HCoVs to range from ~4% to ~27% depending on species and 28 cohort. Most importantly, we identified a large number of novel linear B cell epitopes of HCoV 29 proteins and demonstrate that antibody repertoires against endemic HCoVs are qualitatively 30 different in children in comparison to the general adult population and healthy adult blood 31 bank donors. We show that anti-HCoV IgG specificities more frequently found among children 32 target functionally important and structurally conserved regions of the HCoV spike and 33 nucleocapsid proteins and some antibody specificities are broadly cross-reactive with 34 peptides of epidemic human and non-human coronavirus isolates. Our findings shed light on 35 the humoral immune responses to natural infection with endemic HCoVs and may have 36 important implications for understanding of the highly variable clinical outcomes of human 37 coronavirus infections, for the development of prophylactic or therapeutic monoclonal 38 antibodies and vaccine design. 39 parainfluenza viruses (HPIVs), albeit with differences in seasonality and prevalence of the 48 viruses depending on the species [5-7]. In addition to the four endemic HCoV, three epidemic 49 coronaviruses (CoVs) have emerged in humans over the last two decades, including Severe 50 Acute Respiratory Syndrome-associated CoV (SARS-CoV) [8], Middle East Respiratory 51

Four endemic human coronaviruses (HCoVs) are commonly associated with acute respiratory infection in humans. B cell responses to these “common cold” viruses remain incompletely understood. Here we report a comprehensive analysis of CoV-specific antibody repertoires in 231 children and 1168 adults using phage immunoprecipitation sequencing. Seroprevalence of antibodies against endemic HCoVs ranged between approximately 4% and 27% depending on the species and cohort. We identified at least 136 novel linear B cell epitopes. Antibody repertoires against endemic HCoVs were qualitatively different between children and adults in that anti-HCoV IgG specificities more frequently found among children targeted functionally important and structurally conserved regions of the spike, nucleocapsid, and matrix proteins. Moreover, antibody specificities targeting the highly conserved fusion peptide region and S2′ cleavage site of the spike protein were broadly cross-reactive with peptides of epidemic human and nonhuman coronaviruses. In contrast, an acidic tandem repeat in the N-terminal region of the Nsp3 subdomain of the HCoV-HKU1 polyprotein was the predominant target of antibody responses in adult donors. Our findings shed light on the dominant species-specific and pan-CoV target sites of human antibody responses to coronavirus infection, thereby providing important insights for the development of prophylactic or therapeutic monoclonal antibodies and vaccine design.