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These data identify a host pathway by which VPS29 and associated factors control the endosomal environment in a manner that influences susceptibility to viral infection. This pathway could serve as a pharmaceutical target for intervention in zoonotic viral diseases, including those caused by coronaviruses, influenza viruses, and filoviruses, all of which are pandemic threats. Emerging zoonotic viral pathogens threaten global health, and there is an urgent need to discover host and viral determinants influencing infection. We performed a loss-of-function genome-wide CRISPR screen in a human lung cell line using HCoV-OC43, a human betacoronavirus. One candidate gene, VPS29, a component of the retromer complex, was required for infection by HCoV-OC43, SARS-CoV-2, other endemic- and pandemic-threat coronaviruses, as well as ebolavirus. Notably, we observed a heightened requirement for VPS29 by the recently described Omicron variant of SARS-CoV-2 compared to the ancestral variant. However, VPS29 deficiency had no effect on certain other viruses that enter cells via endosomes and had an opposing, enhancing effect on influenza A virus infection. Deficiency in VPS29 or other retromer components caused changes in endosome morphology and acidity and attenuated the activity of endosomal proteases. These changes in endosome properties caused incoming coronavirus, but not influenza virus particles, to become entrapped therein. Overall, these data show how host regulation of endosome characteristics can influence cellular susceptibility to viral infection and identify a host pathway that could serve as a pharmaceutical target for intervention in zoonotic viral diseases. IMPORTANCE These data identify a host pathway by which VPS29 and associated factors control the endosomal environment in a manner that influences susceptibility to viral infection. This pathway could serve as a pharmaceutical target for intervention in zoonotic viral diseases, including those caused by coronaviruses, influenza viruses, and filoviruses, all of which are pandemic threats. Our findings show how host regulation of endosome characteristics can influence viral susceptibility in both a positive and negative manner.

Serum antibodies from prior immune responses regulate B cell activation and germinal center (GC) access upon recall immunization. However, how antibodies produced by an ongoing immune response influence the outcomes of contemporaneous GCs is less clear. To explore this, we developed mouse models enabling the targeted ablation of plasma cells and antibodies produced by an immune response of interest, without affecting those produced homeostatically or by prior antigen encounters. Our findings show that, whereas antibody-mediated feedback is not required for affinity maturation, it can influence competition between B cells with different epitope specificities, specifically by reducing the abundance of clones that recognize the same epitopes as circulating antibodies. This modality of feedback represents a mechanism by which antibody responses can influence epitope specificity in ongoing GCs. These findings may therefore have implications for vaccination strategies aimed at steering clonal selection towards desired epitopes on complex antigens.

Re-exposure to an antigen generates serum antibody responses that greatly exceed in magnitude those elicited by primary antigen encounter, while simultaneously driving the formation of recall germinal centers (GCs). Although recall GCs in mice are composed almost entirely of naïve B cells, recall antibody titers derive overwhelmingly from memory B cells, suggesting a division between cellular and serum compartments. Here, we show that this schism is at least partly explained by a marked decrease in the ability of recall GC B cells to detectably bind antigen. Variant priming and plasmablast ablation experiments show that this decrease is largely due to suppression by pre-existing antibody, whereas hapten-carrier experiments reveal a role for memory T cell help in allowing B cells with undetectable antigen binding to access GCs. We propose a model in which antibody-mediated feedback steers recall GC B cells away from previously targeted epitopes, thus enabling specific targeting of variant epitopes.Re-exposure to an antigen generates serum antibody responses that greatly exceed in magnitude those elicited by primary antigen encounter, while simultaneously driving the formation of recall germinal centers (GCs). Although recall GCs in mice are composed almost entirely of naïve B cells, recall antibody titers derive overwhelmingly from memory B cells, suggesting a division between cellular and serum compartments. Here, we show that this schism is at least partly explained by a marked decrease in the ability of recall GC B cells to detectably bind antigen. Variant priming and plasmablast ablation experiments show that this decrease is largely due to suppression by pre-existing antibody, whereas hapten-carrier experiments reveal a role for memory T cell help in allowing B cells with undetectable antigen binding to access GCs. We propose a model in which antibody-mediated feedback steers recall GC B cells away from previously targeted epitopes, thus enabling specific targeting of variant epitopes.

Emerging zoonotic viral pathogens threaten global health and there is an urgent need to discover host and viral determinants influencing infection. We performed a loss-of-function genome-wide CRISPR screen in a human lung cell line using HCoV-OC43, a human betacoronavirus. One candidate gene, VPS29, was required for infection by HCoV-OC43, SARS-CoV-2, other endemic and pandemic threat coronaviruses as well as ebolavirus. However, VPS29 deficiency had no effect on certain other viruses that enter cells via endosomes and had an opposing, enhancing effect on influenza A virus infection. VPS29 deficiency caused changes endosome morphology, and acidity and attenuated the activity of endosomal proteases. These changes in endosome properties caused incoming coronavirus, but not influenza virus particles, to become entrapped therein. Overall, these data show how host regulation of endosome characteristics can influence viral susceptibility and identify a host pathway that could serve as a pharmaceutical target for intervention in zoonotic viral diseases.

This report describes the epidemiology and clinical course of patients younger than 21 years of age from 26 states who had multisystem inflammatory syndrome. Many were infected with SARS-CoV-2 at least 1 to 2 weeks before syndrome onset. The median age of the patients was 8.3 years, and 73% were previously healthy.

Background The Causes And MEchanisms foR non-atopic Asthma in children (CAMERA) study was designed to investigate risk factors and mechanisms of non-atopic asthma in children and young adults in Brazil, Ecuador, Uganda, and New Zealand. Initial epidemiological analyses using existing datasets identified and compared risk factors for both atopic and non-atopic asthma. The focus of this paper is the protocol for sample collection and analysis of clinical data on possible non-atopic mechanisms. Methods In each of the four centres, the CAMERA study will enroll 160 participants aged 10–28 years, equally distributed among atopic asthmatics (AA), non-atopic asthmatics (NAA), atopic non-asthmatics and non-atopic non-asthmatics. Participants will be new recruits or returning World ASthma Phenotypes (WASP) study participants. Phase I consists of skin prick tests to define atopy, a general CAMERA questionnaire that covers respiratory and general health to identify asthma cases, followed by an asthma control questionnaire for asthmatics only. Phase II consists of a stress questionnaire and the following clinical assessments: lung function, nasal cytology, blood sampling, in vitro whole blood stimulation to assess IFN-γ production, hair cortisol concentration, dry air and capsaicin challenges, plus in a subset, cold air challenges. Analyses will compare inflammatory, physiological and clinical parameters across the four groups overall and by country. Discussion Here, we present the protocol for the CAMERA study, to provide relevant methodological details for CAMERA publications and to allow other centres globally to conduct similar analyses. The findings of this mechanistic multi-centre study will inform new and phenotype-specific prevention and treatment approaches. Clinical trial number Not applicable.