Summary SARS-CoV-2 Spike protein is critical for virus infection via engagement of ACE2 1 , and is a major antibody target. Here we report chronic SARS-CoV-2 with reduced sensitivity to neutralising antibodies in an immune suppressed individual treated with convalescent plasma, generating whole genome ultradeep sequences over 23 time points spanning 101 days. Little change was observed in the overall viral population structure following two courses of remdesivir over the first 57 days. However, following convalescent plasma therapy we observed large, dynamic virus population shifts, with the emergence of a dominant viral strain bearing D796H in S2 and ΔH69/ΔV70 in the S1 N-terminal domain NTD of the Spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype diminished in frequency, before returning during a final, unsuccessful course of convalescent plasma. In vitro , the Spike escape double mutant bearing ΔH69/ΔV70 and D796H conferred modestly decreased sensitivity to convalescent plasma, whilst maintaining infectivity similar to wild type. D796H appeared to be the main contributor to decreased susceptibility but incurred an infectivity defect. The ΔH69/ΔV70 single mutant had two-fold higher infectivity compared to wild type, possibly compensating for the reduced infectivity of D796H. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy associated with emergence of viral variants with evidence of reduced susceptibility to neutralising antibodies.

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Inflammasome complexes function as key innate immune effectors that trigger inflammation in response to pathogen- and danger-associated signals. Here, we report that germline mutations in the inflammasome sensor NLRP1 cause two overlapping skin disorders: multiple self-healing palmoplantar carcinoma (MSPC) and familial keratosis lichenoides chronica (FKLC). We find that NLRP1 is the most prominent inflammasome sensor in human skin, and all pathogenic NLRP1 mutations are gain-of-function alleles that predispose to inflammasome activation. Mechanistically, NLRP1 mutations lead to increased self-oligomerization by disrupting the PYD and LRR domains, which are essential in maintaining NLRP1 as an inactive monomer. Primary keratinocytes from patients experience spontaneous inflammasome activation and paracrine IL-1 signaling, which is sufficient to cause skin inflammation and epidermal hyperplasia. Our findings establish a group of non-fever inflammasome disorders, uncover an unexpected auto-inhibitory function for the pyrin domain, and provide the first genetic evidence linking NLRP1 to skin inflammatory syndromes and skin cancer predisposition.

Pyrin responds to pathogen signals and loss of cellular homeostasis by forming an inflammasome complex that drives the cleavage and secretion of IL-1β. We studied a family with dominantly inherited autoinflammatory disease characterised by childhood-onset recurrent episodes of neutrophilic dermatosis, fever, elevated acute-phase reactants, arthralgia, and myalgia/myositis. Disease was caused by a mutation in MEFV, the gene encoding pyrin (S242R). The clinical distinction from FMF, also caused by MEFV mutation, was due to loss of a 14-3-3 binding motif at phosphorylated S242. This interaction represents a guard regulating pyrin activation, which is downstream of bacterial effectors that trigger the pyrin inflammasome. S242R mutation recapitulated the effect of pathogen sensing, triggering inflammasome activation and IL-1β production. Successful therapy targeting IL-1β has been initiated in one patient, resolving Pyrin-Associated Autoinflammation with Neutrophilic Dermatosis (PAAND). This unique disease provides evidence that a guard mechanism, originally identified in plant innate immunity, also exists in humans.3 Main textAutoinflammatory diseases are characterized by recurrent episodes of fever with systemic and organ-specific inflammation, as well as uncontrolled activation of the innate immune response in the apparent absence of an infectious trigger(1). Familial Mediterranean fever (FMF, OMIM ID: 249100) is the most common of these monogenic diseases, characterized by short (24-72 h) episodes of fever associated with serositis, progressing to amyloidosis if untreated(2). FMF is an autosomal recessive disease caused by mutations in both alleles of the MEFV (MEditerranean FeVer) locus, which encodes the protein pyrin(3). Normally, pyrin functions as a link between intracellular pathogen sensing and activation of the inflammasome, allowing the production of inflammatory mediators during infection. As a potent checkpoint for the initiation of inflammation, the mechanisms of pyrin regulation are critical, and yet still poorly understood.We studied a three-generation Belgian family of 22 individuals, of whom 12 developed autoinflammatory disease (Figure 1a). The disease was characterized by neutrophilic dermatosis, childhood-onset recurrent episodes of fever lasting several weeks, increased levels of acute-phase reactants, arthralgia and myalgia/myositis (Figure 1b). The neutrophilic dermatosis comprised a spectrum of clinical manifestations including severe acne, sterile skin abscesses, pyoderma gangrenosum and neutrophilic small vessel vasculitis (Figure 1c,d).Pathological examination of affected skin showed a dense, predominantly neutrophilic, vascular, perivascular and interstitial infiltrate (Figure 1d). Serum cytokine analysis revealed elevated inflammatory mediators such as IL-1β, IL-6 and TNFα, and cytokines induced by inflammation such as IL-1Ra (Figure 1e, Figure S1a unlike some of the more typical FMF variants, that naturally occur in other species(7). Despite the association of MEFV mutations w...