Swine acute diarrhoea syndrome coronavirus (SADS-CoV) Nsp5 antagonizes type I interferon signaling by cleaving DCP1A.

Swine acute diarrhoea syndrome coronavirus (SADS-CoV), which is a recently discovered enteric coronavirus, is the major aetiological agent that causes severe clinical diarrhoea and intestinal pathological damage in pigs, and it has caused significant economic losses to the swine industry. Nonstructural protein 5, also called 3C-like protease, cleaves viral polypeptides and host immune-related molecules to facilitate viral replication and immune evasion. Here, we demonstrated that SADS-CoV nsp5 significantly inhibits the Sendai virus (SEV)-induced production of IFN-ß and inflammatory cytokines. SADS-CoV nsp5 targets and cleaves mRNA-decapping enzyme 1a (DCP1A) via its protease activity to inhibit the IRF3 and NF-κB signaling pathways in order to decrease IFN-ß and inflammatory cytokine production. We found that the histidine 41 and cystine 144 residues of SADS-CoV nsp5 are critical for its cleavage activity. Additionally, a form of DCP1A with a mutation in the glutamine 343 residue is resistant to nsp5-mediated cleavage and has a stronger ability to inhibit SADS-CoV infection than wild-type DCP1A. In conclusion, our findings reveal that SADS-CoV nsp5 is an important interferon antagonist and enhance the understanding of immune evasion by alpha coronaviruses.

cGAS-STING PATHWAY LIMITS SARS-CoV-2 REPLICATION IN ACE2+ AIRWAY CELL LINES

Background: We previously screened 10 human lung and upper airway cell lines expressing variable levels of endogenous ACE2/TMPRSS2. We found that H522 human lung adenocarcinoma cells supported SARS-CoV-2 replication independent of ACE2, whereas the ACE2 positive cell lines were not permissive to infection. Type I/III interferons (IFNs) potently restrict SARS-CoV-2 replication through the actions of hundreds of interferon-stimulated genes (ISGs) that are upregulated upon IFN signaling. Here we report that a number of ACE2 positive airway cell lines are unable to support SARS-CoV-2 replication due to basal activation of the cGAS-STING DNA sensing pathway and subsequent upregulation of IFNs and ISGs which restrict SARS-CoV-2 replication. Method(s): SARS-CoV-2 WT strain 2019-nCoV/USA-WA1/2020 viral replication was detected through analysis of cell associated RNA. RNA sequencing was used to study the basal level of genes in the type-I IFN pathway in the 10 cell lines, which was further validated by western blotting and qRT-PCR. A panel of 5 cell lines, with varying expression levels of ACE2 and TMPRSS2, were pre-treated with Ruxolitinib, a JAK1/2 inhibitor. A siRNA-mediated screen was used to determine the molecular basis of basally high expression of ISGs in cell lines. CRISPR knockout of IFN-alpha receptor and cGAS-STING pathway components was conducted in parallel Results: Here we show that higher basal levels of IFN pathway activity underlie the inability of ACE2+ cell lines to support virus replication. Importantly, this IFN-induced block can be overcome by chemical inhibition and genetic disruption of the IFN signaling pathway or by ACE2 overexpression, suggesting that one or more saturable ISGs underlie the lack of permissivity of these cells. Ruxolitinib treatment increased SARS-CoV-2 RNA levels by nearly 3 logs in OE21 and SCC25. Furthermore, the baseline activation of the STING-cGAS pathway accounts for the high ISG levels and genetic disruption of the cGAS-STING pathway enhances levels by nearly 2 and 3 logs of virus replication in the two separate ACE2+ cell line models respectively. Conclusion(s): Our findings demonstrate that cGAS-STING-dependent activation of IFN-mediated innate immunity underlies the inability of ACE2+ airway cell lines to support SARS-CoV-2 replication. Our study highlights that in addition to ACE2, basal activation of cGAS-STING pathway, IFNs and ISGs may play a key role in defining SARS-CoV-2 cellular tropism and may explain the complex SARS-CoV- 2 pathogenesis in vivo.

Immune and ionic mechanisms mediating the effect of dexamethasone in severe COVID-19.

Introduction: Severe COVID-19 is characterized by cytokine storm, an excessive production of proinflammatory cytokines that contributes to acute lung damage and death. Dexamethasone is routinely used to treat severe COVID-19 and has been shown to reduce patient mortality. However, the mechanisms underlying the beneficial effects of dexamethasone are poorly understood. Methods: We conducted transcriptomic analysis of peripheral blood mononuclear cells (PBMCs) from COVID-19 patients with mild disease, and patients with severe COVID-19 with and without dexamethasone treatment. We then treated healthy donor PBMCs in vitro with dexamethasone and investigated the effects of dexamethasone treatment ion channel abundance (by RT-qPCR and flow cytometry) and function (by electrophysiology, Ca2+ influx measurements and cytokine release) in T cells. Results: We observed that dexamethasone treatment in severe COVID-19 inhibited pro-inflammatory and immune exhaustion pathways, circulating cytotoxic and Th1 cells, interferon (IFN) signaling, genes involved in cytokine storm, and Ca2+ signaling. Ca2+ influx is regulated by Kv1.3 potassium channels, but their role in COVID-19 pathogenesis remains elusive. Kv1.3 mRNA was increased in PBMCs of severe COVID-19 patients, and was significantly reduced in the dexamethasone-treated group. In agreement with these findings, in vitro treatment of healthy donor PBMCs with dexamethasone reduced Kv1.3 abundance in T cells and CD56dimNK cells. Furthermore, functional studies showed that dexamethasone treatment significantly reduced Kv1.3 activity, Ca2+ influx and IFN-g production in T cells. Conclusion: Our findings suggest that dexamethasone attenuates inflammatory cytokine release via Kv1.3 suppression, and this mechanism contributes to dexamethasone-mediated immunosuppression in severe COVID-19.

The "Janus-like" RNA-editing machinery in innate antiviral immunity

Our innate immune systems are evolved to provide the first line of immune defense against microbial infections. A key effector component is the adenosine deaminase acting on the RNA-1 (ADAR-1)/ interferon (IFN) pathway of the innate cytoplasmic immunity that mounts rapid responses to many viral pathogens. As an RNA-editing enzyme, ADAR-1 targets viral RNA intermediates in the cytoplasmic compartment to interfere with the infection. However, ADAR-1 may also edit characteristic RNA structures of certain host genes, notably, the 5-hydroxytryptamine (serotonin) receptor 2C (5HT2CR). Dysfunction of 5-HT2CR has been linked to the pathology of several human mental conditions, such as Schizophrenia, anxiety, bipolar disorder, major depression, and the mental illnesses of substance use disorders (SUD). Thus, the ADAR-1mediated RNA editing may be either beneficial or harmful;these effects need to be tightly modulated to sustain innate antiviral immunity while restricting undesired off-target self-reactivity. In this communication, we discuss ideas and tools to identify the orphan drug candidates, including small molecules and biologics that may serve as effective modulators of the ADAR-1/IFN innate immunity and are thereby promising for use in treating or preventing SUD-and/or viral infection-associated mental illnesses.Copyright © 2023, Research Trends (P) LTD.. All rights reserved.

Antagonism and Evasion of Cellular Innate Immunity by SARS-CoV-2

The replication cycle of severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) shares many features with other human Coronaviruses such as SARS-CoV and Middle East respiratory syndrome Coronavirus (MERS-CoV). Recent studies have elucidated the viral strategies of antagonizing the host immune response, including a multitude of mechanisms by which SARS-CoV-2 can dampen the interferon-mediated innate immunity. Furthermore, an imbalance and delay in interferon production, and exaggerated secretion of pro-inflammatory cytokines contribute to the severe immunopathology of Coronavirus disease 2019 (COVID-19). This chapter summarizes our current understanding of the intimate relationship between SARS-CoV-2 and the host innate and adaptive immune responses. The strategies that the virus utilizes to exploit cellular resources and to evade the innate immune system are described. The chapter provides a detailed discussion of interferonmediated innate immunity, interferon evasion and antagonism by SARSCoV- 2 and human Coronaviruses. © 2023 by World Scientific Publishing Co. Pte. Ltd.

Longitudinal profiling of the peripheral blood transcriptome identifies risk of Major Cardiac Events after Hospitalization for COVID-19

Introduction: SARS-CoV-2 infection has profound effects on endothelial and immune cell function and coagulation, and better understanding of these events in COVID-19 would allow for targeted cardiovascular treatment and followup. Method(s): Longitudinal observational study of patients with PCR-confirmed SARS-CoV-2 infection admitted to hospital at two UK sites. Patients were enrolled within 96 hours of admission, with sampling up to day 29. RNAstabilised whole blood was processed for mRNA sequencing. Gene expression levels were compared between patients who did and did not suffer a major cardiac event (MACE) from admission to 1-year post-hospitalization. Result(s): At day 1, in acute COVID-19, no differences in gene expression were observed between those with (n=23) and without (n=140) a MACE. However, 93 significant differentially expressed genes (DEGs;adjusted pvalue<0.05;Wald test with Benjamini-Hochberg correction) were identified at day 29 between patients who suffered a MACE (n=16) or not (n=85) post-hospitalization. Neutrophil elastase (ELANE), tissue factor pathways inhibitor (TFPI) and integrin subunit alpha-2 (ITGA2B) were significantly elevated in patients who suffered a MACE. Significantly enriched pathways associated with cardiovascular events included type I interferon signalling and neutrophil chemotaxis. Conclusion(s): COVID-19 patients who experienced a MACE demonstrated significant changes in peripheral blood transcriptome 29 days after hospital admission. Significant DEGs were related to neutrophil activity, coagulation and interferon signalling, suggesting a relationship between these pathways and increased cardiovascular risk.

Type I interferon signaling in SARS-CoV-2 associated neurocognitive disorder (SAND): Mapping host-virus interactions to an etiopathogenesis.

Epidemiological, clinical, and radiological studies have provided insights into the phenomenology and biological basis of cognitive impairment in COVID-19 survivors. Furthermore, its association with biomarkers associated with neuroinflammation and neurodegeneration supports the notion that it is a distinct aspect of LongCOVID syndrome with specific underlying biology. Accounting for the latter, translational studies on SARS-CoV-2's interactions with its hosts have provided evidence on type I interferon dysregulation, which is seen in neuroinflammatory and neurodegenerative diseases. To date, studies attempting to describe this overlap have only described common mechanisms. In this manuscript, we attempt to propose a mechanistic model based on the host-virus interaction hypothesis. We discuss the molecular basis for a SARS-CoV-2-associated neurocognitive disorder (SAND) focusing on specific genes and pathways with potential mechanistic implications, several of which have been predicted by Vavougios and their research group. Furthermore, our hypothesis links translational evidence on interferon-responsive gene perturbations introduced by SARS-CoV-2 and known dysregulated pathways in dementia. Discussion emphasizes the crosstalk between central and peripheral immunity via danger-associated molecular patterns in inducing SAND's emergence in the absence of neuroinfection. Finally, we outline approaches to identifying targets that are both testable and druggable, and could serve in the design of future clinical and translational studies.

Delineating the SARS-CoV-2 Induced Interplay between the Host Immune System and the DNA Damage Response Network.

COVID-19 is an infectious disease caused by the SARS-CoV-2 coronavirus and characterized by an extremely variable disease course, ranging from asymptomatic cases to severe illness. Although all individuals may be infected by SARS-CoV-2, some people, including those of older age and/or with certain health conditions, including cardiovascular disease, diabetes, cancer, and chronic respiratory disease, are at higher risk of getting seriously ill. For cancer patients, there are both direct consequences of the COVID-19 pandemic, including that they are more likely to be infected by SARS-CoV-2 and more prone to develop severe complications, as well as indirect effects, such as delayed cancer diagnosis or treatment and deferred tests. Accumulating data suggest that aberrant SARS-CoV-2 immune response can be attributed to impaired interferon signaling, hyper-inflammation, and delayed adaptive immune responses. Interestingly, the SARS-CoV-2-induced immunological abnormalities, DNA damage induction, generation of micronuclei, and the virus-induced telomere shortening can abnormally activate the DNA damage response (DDR) network that plays a critical role in genome diversity and stability. We present a review of the current literature regarding the molecular mechanisms that are implicated in the abnormal interplay of the immune system and the DDR network, possibly contributing to some of the COVID-19 complications.

Stromal Antigen 2 Deficiency Induces Interferon Responses and Restricts Porcine Deltacoronavirus Infection.

Porcine deltacoronavirus (PDCoV) is a recently discovered enteropathogenic coronavirus and has caused significant economic impacts on the pork industry. Although studies have partly uncovered the molecular mechanism of PDCoV-host interaction, it requires further research. In this study, we explored the roles of Stromal Antigen 2 (STAG2) in PDCoV infection. We found that STAG2-deficient cells inhibited infection with vesicular stomatitis virus (VSV) and PDCoV, whereas restoration of STAG2 expression in STAG2-depleted (STAG2-/-) IPEC-J2 cells line restored PDCoV infection, suggesting that STAG2 is involved in the PDCoV replication. Furthermore, we found that STAG2 deficiency results in robust interferon (IFN) expression. Subsequently, we found that STAG2 deficiency results in the activation of JAK-STAT signaling and the expression of IFN stimulated gene (ISG), which establish an antiviral state. Taken together, the depletion of STAG2 activates the JAK-STAT signaling and induces the expression of ISG, thereby inhibiting PDCoV replication. Our study provides new insights and potential therapeutic targets for unraveling the mechanism of PDCoV replication.

Angiotensin-Converting Enzyme 2 Potentiates SARS-CoV-2 Infection by Antagonizing Type I Interferon Induction and Its Down-Stream Signaling Pathway.

The innate interferon (IFN) response constitutes the first line of host defense against viral infections. It has been shown that IFN-I/III treatment could effectively contain severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication in vitro. However, how SARS-CoV-2 survives through the innate antiviral mechanism remains to be explored. Our study uncovered that human angiotensin-converting enzyme 2 (ACE2), identified as a primary receptor for SARS-CoV-2 entry, can disturb the IFN-I signaling pathway during SARS-CoV-2 infection in human lung cells. We identified that ACE2 was significantly upregulated by SARS-CoV-2 and Sendai virus (SeV) infection, and exogenous expression of ACE2 suppressed IFN-I production in a dose-dependent manner. Mechanistically, ACE2 disrupted poly (I:C)-mediated inhibition of SARS-CoV2 replication by antagonizing IFN-I production by blocking IRF3 phosphorylation and nuclear translocation. Moreover, ACE2 quenched the IFN-mediated antiviral immune response by degrading endogenous STAT2 protein, inhibiting STAT2 phosphorylation and nuclear translocation. Interestingly, IFN-inducible short ACE2 (dACE2 or MIRb-ACE2) can also be induced by virus infection and inhibits the IFN signaling. Thus, our findings provide mechanistic insight into the distinctive role of ACE2 in promoting SARS-CoV-2 infection and enlighten us that the development of interventional strategies might be further optimized to interrupt ACE2-mediated suppression of IFN-I and its signaling pathway. IMPORTANCE Efficient antiviral immune responses against SARS-CoV-2 infection play a key role in controlling the coronavirus diseases 2019 (COVID-19) caused by this virus. Although SARS-CoV-2 has developed strategies to counteract the IFN-I signaling through the virus-derived proteins, our knowledge of how SARS-CoV-2 survives through the innate antiviral mechanism remains poor. We herein discovered the distinctive role of ACE2 as a restraining factor of the IFN-I signaling in facilitating SARS-CoV-2 infection in human lung cells. Both full-length ACE2 and truncated dACE2 can antagonize IFN-mediated antiviral response. These findings are key to understanding the counteraction between SARS-CoV-2 pathogenicity and the host antiviral defenses.

Type I IFN Signaling Controls Damage and Clearance During Pulmonary Aspergillus Fumigatus Infection

RATIONALE: Recently, there has been an increased incidence of invasive pulmonary aspergillosis (IPA), caused by the human fungal pathogen Aspergillus fumigatus (Af), occurring in patients infected with influenza or SARS-CoV-2. Along with the recently described involvement of type I interferon (IFN) signaling in increased Af susceptibility during viral infection in mice, this strongly indicates that anti-viral immune responses, such as type I IFNs, create an environment permissive to fungal infection. Supporting this, we found that type I IFN signaling, via the type I IFN receptor 2 (IFNAR2) of IFNAR1/2, contributes to regulation of susceptibility to and damage from influenza in mice, while others have found that IFNAR2 expression correlates with SARS-CoV-2 infection severity. As clinical outcome to Af is associated with host tissue damage, this suggests that IFNAR2's regulation of damage response during pulmonary infection may control the immune status of the lung, via tissue damage, allowing for fungal infection to occur. METHODS: We are utilizing a murine pulmonary infection model, to identify distinct roles for IFNAR2 and IFNAR1 and type I IFN signaling in regulating both damage and clearance during IPA. We employed proteomic, histological, and molecular approaches to determine the components and extent of the damage response. RESULTS: We found that absence of IFNAR2 (Ifnar2-/- mice) resulted in increased damage, weight loss, and morbidity early during Af infection compared to WT and Ifnar1-/- mice. Additionally, we also found that both WT and Ifnar1-/- mice had decreased Af clearance early during infection compared to Ifnar2-/- mice and that this difference in killing of Af required in vivo interactions/signaling. However, as Af infection progressed we found that although Ifnar2-/- mice cleared Af early, this did not prevent invasive hyphal growth from occurring. This invasive growth in the Ifnar2-/- mice was found to be associated with increased damage and cell death in the Af lesions within the lung. Importantly, our results suggest that this IFNAR2 damage response is being mediated by distinct type I IFNs, specifically IFNβ. CONCLUSIONS: Together, our results begin to establish a role for IFNAR2 in regulation of the host damage response to Af and suggests that the type of type I IFN signaling may contribute to a permissive environment allowing for Af infection to occur. Understanding the mechanisms involved in IFNAR regulation of damage and anti-fungal immunity could inform design of better treatments aimed at minimizing damage in patients with IPA or controlling pulmonary tissue damage.

SYSTEMATIC ANALYSIS of INNATE IMMUNE ANTAGONISM of SARS-CoV-2 and ITS EVOLUTION

Background: The innate immune system is a powerful anti-viral defense mechanism, which includes the interferon (IFN) system and autophagy. Thus, successful pathogens like SARS-CoV-2 need to counteract or evade these defenses to establish an infection. However, due to its ongoing, worldwide spread in the human population SARS-CoV-2 is evolving and in the meantime four variants with selection advantages (variants of concern) emerged. Methods: Using expression constructs for 29 SARS-CoV-2 proteins we evaluated the impact of individual viral proteins on induction of cytokines (IFNA4, IFNB1, IRF3-signalling, NF-κB-signaling) and cytokine signaling (IFNα2, IFNβ, IFNγ, IFNa;1, IL-1α, TNFα) in luciferase reporter assays, validated by endogenous transcription factor phosphorylation analysis. We assessed the influence of SARS-CoV-2 proteins on autophagy using a flow cytometry-based system. Underlying molecular mechanisms were investigated on an endogenous level using Western blot, confocal fluorescence microscopy, and flow cytometry. In addition, we examined the susceptibility of SARS-CoV-2 including all variants of concern towards type-I,-II, and-III interferons. Results: To understand how SARS-CoV-2 efficiently manipulates the host's innate immune defenses, we systematically analyzed the impact of SARS-CoV-2 encoded proteins on induction of various IFNs and pro-inflammatory cytokines, IFN signaling, and autophagy. Our results reveal the range of innate immune antagonists encoded by SARS-CoV-2 and we characterized selected molecular mechanisms employed by Nsp1 and Nsp14 to downregulate the IFN system or ORF3a and ORF7a to prevent autophagic degradation. Interestingly, our assays show that variants of concern of SARS-CoV-2 remain sensitive to type-II interferon signaling but show increased resistance towards type-I and/or type-III interferons. Conclusion: SARS-CoV-2 has evolved to counteract innate immunity using several synergistic approaches but remains relatively sensitive to type-II and-III interferons. However, emerged variants of concern remain sensitive overall but are less susceptible towards IFNα2/β and IFNa;1 than early SARS-CoV-2 isolates.

TYPE-I INTERFERON MODULATION in VIVO BLOCKS SARS-CoV-2 REPLICATION and INFLAMMATION

Background: Systemic and local inflammation following SARS-CoV-2 infection has been widely described and predictive of disease severity and death. However, the exact immune mediators driving inflammation contributing to SARS-CoV-2 host defense vs. those driving immune-mediated pathology in humans have not been fully elucidated. Deficiencies in type-I interferon (IFN-I) responses, including inborn errors to genes in the IFN-I pathway, neutralizing auto-antibodies against all subtypes of IFN-I, or the lack of production of IFN-I, are associated with severe COVID-19 in otherwise healthy individuals. Conversely, sustained IFN-I responses have been shown to contribute to severe COVID-19 by exacerbating inflammation, and prolonged IFN-I signaling has been shown to interfere with lung repair following viral infection and to increase susceptibility to bacterial infections. Thus, it is critical to understand the roles of IFN-I signaling in COVID-19 to design therapeutic strategies. Methods: Here, we modulated IFN-I signaling in rhesus macaques (Macaca mulatta;RMs) from day-1 through day 2 post SARS-CoV-2 infection (dpi) using an IFN-I antagonist (IFNant). Eighteen RMs (9 control and 9 IFNant treated) were infected with SARS-CoV-2 on day 0, with 6 RMs sacrificed at 2, 4, and 7dpi. Nasal and throat swabs were collected for viral load;blood and bronchoalveolar lavage fluid (BAL) for flow cytometry and RNAseq. Results: IFNant treatment prior to infection resulted in a highly significant and consistent reduction in SARS-CoV-2 viral load in the lower airways (>3-log difference;2dpi BAL) and upper airways (nasal and throat swabs). Treatment with IFNant initiated also potently reduced: (i) soluble markers of inflammation in BAL, (ii) expansion of inflammatory monocytes (CD14+CD16+), and (iii) pathogenesis in the lung. Furthermore, Siglec-1 expression, which has been shown to enhance SARS-CoV-2 infection, was rapidly downregulated in the lung and in monocytes of IFNant-treated RMs. Remarkably, RNAseq analysis showed a robust reduction in pathways associated with inflammation and decreased levels of interferon-stimulated genes post-infection in treated RMs. Thus, IFNant treatment prior to infection resulted in limited viral replication, inflammation, and pathogenesis in SARS-CoV-2-infected RMs. Conclusion: These data indicate a vital, early role of IFN-I in regulating COVID-19 progression and emphasize the importance of understanding IFN-I pathways in COVID-19 for the development of targeted therapeutic strategies.

DIFFERENTIALLY EXPRESSED IMMUNOLOGICAL GENES in MILD and SEVERE CASES of COVID-19

Background: Coronavirus disease 2019 (COVID19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has varied clinical presentations from mild subclinical to severe disease with high mortality. Our aim was to determine whether examining immune-related gene expression early in infection could predict progression to severe disease. Methods: In subjects of the All Ireland Infectious Diseases Cohort study, we analysed expression of 579 genes with the NanoString nCounter Immunology panel in peripheral blood mononuclear cells in those with confirmed SARS-CoV-2 infection collected within 5 days of symptom onset and matched SARS-CoV-2 negative controls with respiratory infection. Subsequent maximum COVID19 disease severity was classified as mild or severe. Read counts were normalized using panel housekeeping genes. Expression changes in severity groups were estimated against control baseline. Results: Between April and July of 2020, we recruited 120 subjects, 62 with COVID19 and 58 controls, with average age 59 y.o. (IQR 34-88), 66% males and 69% Caucasian ethnicity. Maximal disease severity was used to separate COVID19 cases into mild (n=31) and severe (n=31). We identified 20 significantly deregulated genes between those with COVID19 and controls (;log2 fold;>0.5, p<0.05, Benjamin-Yekutieli p-adjustment). Function of 12 of these genes related to cytokine signaling, 9 upregulated genes to type I interferon signaling (MX1, IRF7, IFITM1, IFI35, STAT2, IRF4, PML, BST2, STAT1), while 7 downregulated genes mapped to innate immune function (IRF7, ICAM2, SERPING1, IFI16, BST2, FCER1A, PTK2). Expression in the severe group showed downregulation of FCER1A (innate immunity regulation), IL1B and TNF (inflammatory cytokines), and PTGS2 (inflammatory mediator) and greater upregulation of TNFSF4 (cytokine signaling) and PTK2 (innate immunity). Mild cases presented higher upregulation of IFIT2 (type I interferon signaling). Conclusion: Observed early downregulation of regulators and mediators of inflammation in those who developed severe COVID19, suggested dysregulation of inflammation. Specifically, IFIT2 upregulation in mild cases and FCER1A downregulation in severe cases, points to early differences in host responses centered on deregulation of the interferon and inflammation responses. Whether these patterns reflect delayed interferon involvement in pathways to control the infection and contribute to pathological inflammation and cytokine storms observed in severe COVID19 requires further research.

DEAD/H-Box Helicases in Immunity, Inflammation, Cell Differentiation, and Cell Death and Disease.

DEAD/H-box proteins are the largest family of RNA helicases in mammalian genomes, and they are present in all kingdoms of life. Since their discovery in the late 1980s, DEAD/H-box family proteins have been a major focus of study. They have been found to play central roles in RNA metabolism, gene expression, signal transduction, programmed cell death, and the immune response to bacterial and viral infections. Aberrant functions of DEAD/H-box proteins have been implicated in a wide range of human diseases that include cancer, neurodegeneration, and inherited genetic disorders. In this review, we provide a historical context and discuss the molecular functions of DEAD/H-box proteins, highlighting the recent discoveries linking their dysregulation to human diseases. We will also discuss the state of knowledge regarding two specific DEAD/H-box proteins that have critical roles in immune responses and programmed cell death, DDX3X and DDX58, also known as RIG-I. Given their importance in homeostasis and disease, an improved understanding of DEAD/H-box protein biology and protein-protein interactions will be critical for informing strategies to counteract the pathogenesis associated with several human diseases.

Porcine Epidemic Diarrhea Virus nsp7 Inhibits Interferon-Induced JAK-STAT Signaling through Sequestering the Interaction between KPNA1 and STAT1.

Porcine epidemic diarrhea virus (PEDV) is a highly pathogenic enteric coronavirus that causes high mortality in piglets. Interferon (IFN) responses are the primary defense mechanism against viral infection; however, viruses always evolve elaborate strategies to antagonize the antiviral action of IFN. Previous study showed that PEDV nonstructural protein 7 (nsp7), a component of the viral replicase polyprotein, can antagonize ploy(I:C)-induced type I IFN production. Here, we found that PEDV nsp7 also antagonized IFN-α-induced JAK-STAT signaling and the production of IFN-stimulated genes. PEDV nsp7 did not affect the protein and phosphorylation levels of JAK1, Tyk2, STAT1, and STAT2 or the formation of the interferon-stimulated gene factor 3 (ISGF3) complex. However, PEDV nsp7 prevented the nuclear translocation of STAT1 and STAT2. Mechanistically, PEDV nsp7 interacted with the DNA binding domain of STAT1/STAT2, which sequestered the interaction between karyopherin α1 (KPNA1) and STAT1, thereby blocking the nuclear transport of ISGF3. Collectively, these data reveal a new mechanism developed by PEDV to inhibit type I IFN signaling pathway. IMPORTANCE In recent years, an emerging porcine epidemic diarrhea virus (PEDV) variant has gained attention because of serious outbreaks of piglet diarrhea in China and the United States. Coronavirus nonstructural protein 7 (nsp7) has been proposed to act with nsp8 as part of an RNA primase to generate RNA primers for viral RNA synthesis. However, accumulating evidence indicates that coronavirus nsp7 can also antagonize type I IFN production. Our present study extends previous findings and demonstrates that PEDV nsp7 also antagonizes IFN-α-induced IFN signaling by competing with KPNA1 for binding to STAT1, thereby enriching the immune regulation function of coronavirus nsp7.

Genomic variation underlies the severity of COVID19 clinical manifestation in individuals of European descent

Background: The coronavirus disease (COVID-19) caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is characterised by a wide spectrum of clinical phenotypes ranging in acuteness from asymptomatic, symptomatic with mild or moderate manifestation and severe involving pneumonia and respiratory distress. COVID-19 susceptibility, severity and recovery have demonstrated high variability worldwide. Variances in the host genetic architecture may potentially control the inter-individual and population scale differences in COVID-19 presentation. Methods: We performed a genome-wide association study (GWAS) employing the genotyping data from Ancestry DNA COVID-19 host genetic study that included COVID-19 positive patients and healthy individuals who had tested negative for SARS-CoV-2 infection at the time of recruitment. We restricted our analysis only to the individuals of European descents to avoid genetic structure in the dataset, arising due to the presence of people from different ancestries. Further, we uniquely employed the asymptomatic individuals as controls instead of healthy individuals. Results and Discussion: Our data revealed striking genomic differences between COVID-19 asymptomatic and severely symptomatic individuals. We identified 621 genetic variants that were significantly distinct (Multiple-testing corrected P<0.001) between asymptomatic and acutely symptomatic COVID-19 patients. These variants were found to be associated with pathways governing host immunity, such as innate and adaptive immune system, interferon signaling, interleukin signaling, antigen processing by MHC, cytokine signaling and known COVID-19 comorbidities, such as obesity, cholesterol metabolism and smoking. Variants modulating drug responses including to anti-retroviral agents were also found to vary significantly between asymptomatic and severe patient groups.

COVID-19 and DOWN SYNDROME: UNEXPECTED CONNECTIONS and THERAPEUTIC IMPLICATIONS

Triplication of chromosome 21, or trisomy 21, causes the condition known as Down syndrome, the most common human chromosomal abnormality and a leading cause of intellectual and developmental disability. Remarkably, individuals with Down syndrome display a different disease spectrum relative to the general population, being protected from some conditions, such as most solid malignancies, while being predisposed to others, such as Alzheimer's disease, autoimmune disorders, congenital heart disease, and autism. More recently, trisomy 21 was found to confer high risk of severe COVID-19, whereby adults with Down syndrome show >10-fold risk of developing severe symptoms and die upon SARS-CoV-2 infection. In this presentation, Dr. Espinosa will present a large body of work demonstrating that Down syndrome could be understood in good measure as an immune disorder caused by hyperactivity in the interferon signaling pathway, a key aspect of the innate immune system. Dr. Espinosa will discuss results obtained through a large cohort study of individuals with Down syndrome, the Crnic Institute's Human Trisome Project (www.trisome.org), as well as advanced animal models of Down syndrome. These discoveries led to a first-in-kind clinical trial for immune modulation in Down syndrome using JAK inhibitors. Lastly, Dr. Espinosa will discuss how interferon hyperactivity can contribute to COVID-19 pathology and the therapeutic use of JAK inhibitors in COVID-19. He will share results obtained via the COVIDome Project (www.covicome.org) as well as clinical trials for JAK inhibition in COVID-19.

Longitudinal Transcriptional Analysis of Peripheral Blood Leukocytes in COVID Convalescent Donors

Introduction Severe acute respiratory syndrome coronavirus-2 (SARS-CoV2) can induce a strong host immune response. Several groups have investigated the course of antibody responses in patients recovering from SARS-CoV-2 infections but little is known about the recovery of cellular immunity. This study investigated the cellular immune response in people who had recovered from SARS-CoV2 infection. Methods 162 coronavirus disease 2019 (COVID-19) convalescent plasma donors (CCD) and 40 healthy donor (HD) controls were enrolled prospectively in an IRB-approved protocol (Clinical Trials Number: NCT04360278) and provided written informed consent to participate in the study. Using the nCounter platform and host response panel with 785 genes across more than 50 pathways, we compared transcriptomic profiles on RNA samples obtained from the peripheral blood leukocytes of these 162 CCD and 40 HD. Additionally, in 69 of the 162 CCD samples, we evaluated transcriptomic trends at more than one-time point during the convalescent period. Results Age, sex, ethnicity, and body mass index distributions were similar among the CCD and HD. With respect to baseline complete blood counts, hemoglobin, platelets, and absolute basophil and eosinophil counts, all were similar among CCD and HD (Table 1). However, despite sample collections occurring several days after convalescence, mean counts for absolute neutrophil counts, absolute monocyte counts, and absolute lymphocyte counts were significantly higher among CCD compared to HD. 30-90 days after diagnosis, 19 of 773 genes differed (FDR < 0.05) between the average CCD and HD samples. Up-regulated genes included MAFB, CTLA4, PTGS2, and the chemokine signaling genes CXCR4, CXCL5, CXCL2 and CCR4. Down-regulated genes included PTGER2, CASP8, and the interleukins IL36A, IL31, IL20 and IL21 (Figure 1 a,b). Differential gene expression persisted for months. At 90-120 days, 13 genes were differentially regulated, including again MAFB CXCR4, PTGS2, CXCL2 and PTGER2, plus SMAD4. At 120-150 days post-diagnosis, 58 genes were differentially expressed (FDR < 0.05) compared to HD. Pathways with up-regulated genes included Treg differentiation, type III interferon signaling and chemokine signaling. 150-360 days post-diagnosis, 4 genes remained up-regulated on average (FDR < 0.05): PTGS2, PIK3CR, CXCL1 and SMAD4 (Figure 1 c,d). Individual patients varied considerably from the mean trend. Scoring samples by their similarity to the gene expression profile of the mean HD sample, 21 CCD samples from 20 unique patients (12%) were identified as highly perturbed from HD. 84% of these highly perturbed samples were collected > 90 days post-diagnosis. Of these 21 samples, 6 were distinguished by > 2-fold up-regulation of a cluster of interleukin and type-1 interferon genes (Figure 2). Conclusions Overall, our study identified important gene expression trends in CCD compared to HD in the post-acute period. The changes varied with time and among donors. As the expression of T-cell inhibitory molecule CTLA4 fell, the number of differentially expressed increased with the most marked changes occurring 120 to 150 days post-diagnosis in genes in chemokine signaling, type III interferon signaling and Treg pathways. Persistent alterations in inflammatory pathways and T-cell activation/exhaustion markers for months after active infection may help shed light on the pathophysiology of a prolonged post-viral syndrome observed in individuals following recovery from COVID-19 infection. Our data may serve as the basis for risk modification strategies in the period of active infection. Future studies may inform the ability to identify druggable targets involving these pathways to mitigate the long-term effects of COVID-19 infection. [Formula presented] Disclosures: Danaher: NanoString Technologies: Current Employment, Current holder of individual stocks in a privately-held company.