Pharmacological management of COVID-19 patients with ARDS (CARDS): A narrative review

Coronavirus disease 2019 (COVID-19) is highly infectious. It has been highlighted that if not expertly and individually managed with consideration of the vasocentric features, a COVID-19 patient with an acute respiratory distress syndrome (CARDS) may eventually develop multiorgan failure. Unfortunately, there is still no definite drug for CARDS that is capable of reducing either short-term or long-term mortality and no specific treatments for COVID-19 exist right now. In this narrative review, based on a selective literature search in EMBASE, MEDLINE, Scopus, The Cochrane Library, Web of Science, and Google Scholar and ClinicalTrials.gov, we have examined the emerging evidence on the possible treatment of CARDS. Although numerous pharmacologic therapies to improve clinical outcomes in CARDS have been studied also in clinical trials, none have shown efficacy and there is great uncertainty about their effectiveness. There is still no recommendation for the therapeutic use of any specific agent to treat CARDS because no drugs are validated to have significant efficacy in clinical treatment of COVID-19 patients in large-scale trials. However, there exist a number of drugs that may be useful at least in some patients. The real challenge now is to link the right patient to the right treatment

Innate immune evasion and interferon antagonism by porcine epidemic diarrhea virus

Porcine epidemic diarrhea (PED) is a highly contagious and acute enteric disease of swine featured by vomiting, watery diarrhea, and severe dehydration causing high mortality in piglets. In the U.S., PED emerged for the first time in 2013 and severely affected most pig-producing states. The causative agent is PED virus (PEDV), which is an enveloped, positive-sense, single-strand RNA virus in the genus Alphacoronavirus of the family Coronaviridae in the order Nidovirales. The innate immune system is the first line of host defense in response to viral infections. Type I interferons (IFN-α/β) are the major components of the innate immune system, and in turn many viruses have evolved to modulate the host interferon responses. In the present study, the PEDV IFN antagonism was investigated. We found that IFN-β production was significantly suppressed during PEDV infection, and of 16 PEDV nonstructural proteins (nsps), nsp1, nsp3, nsp7, nsp14, nsp15, and nsp16 were found to inhibit the IFN-β and IRF3 promoter activities. The sole accessory protein ORF3 and the envelope (E), membrane (M), and nucleocapsid (N) proteins were also determined to inhibit such activities. Since nsp1 is the first viral protein synthesized during PEDV infection and appears to be the most potent IFN antagonist, nsp1 was further investigated for its action. PEDV nsp1 did not interfere the IRF3 phosphorylation and nuclear translocation upon stimulation but interrupted the enhanceosome assembly of IRF3 and CREB-binding protein (CBP) by degrading CBP. The CBP degradation by nsp1 was proteasome-dependent. We further showed that PEDV inhibited both NF-κB and proinflammatory cytokine production in porcine epithelial cells. PEDV blocked the p65 activation in infected cells and suppressed the PRD II-mediated NF-κB activity. Nine proteins were identified as NF-κB antagonists, and nsp1 was the most potent suppressor of proinflammatory cytokines. Nsp1 interfered the phosphorylation and degradation of IκBα, and thus blocked the p65 activation. Mutational studies demonstrated the essential requirements of the conserved residues of nsp1 for NF-κB suppression. Recent reports showed that type III interferons (IFN-λs) play a vital role to maintain the antiviral state of the mucosal epithelial surface in the gut. The intestinal epithelial cells selectively produce and respond to type III IFNs. To study the type III IFN response to PEDV, a line of porcine intestinal epithelial cells was developed as a cell model for PEDV replication. Recombinant proteins IFN-λ1 and IFN-λ3 inhibited PEDV replication, indicating the anti-PEDV activity of type III IFNs. Of the total of 21 PEDV proteins, nsp1, nsp3, nsp5, nsp8, nsp14, nsp15, nsp16, ORF3, E, M, and N were found to suppress the type III IFN response. PEDV specifically inhibited IRF1 nuclear translocation. Peroxisomes are the innate antiviral signaling platforms for activation of IRF1-mediated IFN-λ production, and they were found to decrease in number in PEDV-infected cells. PEDV nsp1 blocked the nuclear translocation of IRF1 and reduces the number of the peroxisomes to suppress the IRF1-mediated type III IFN production. The conserved residues of nsp1 were crucial for IRF1-mediated IFN-λ suppression. Taken together, these studies provide the evidence that PEDV and its nsp1 protein, a potent multifunctional IFN antagonist, evade both type I and type III IFN responses and the molecular basis for this antagonism

Immune Predictors of Mortality After Ribonucleic Acid Virus Infection

Background Virus infections result in a range of clinical outcomes for the host, from asymptomatic to severe or even lethal disease. Despite global efforts to prevent and treat virus infections to limit morbidity and mortality, the continued emergence and re-emergence of new outbreaks as well as common infections such as influenza persist as a health threat. Challenges to the prevention of severe disease after virus infection include both a paucity of protective vaccines as well as the early identification of individuals with the highest risk that may require supportive treatment. Methods We completed a screen of mice from the Collaborative Cross (CC) that we infected with influenza, severe acute respiratory syndrome-coronavirus, and West Nile virus. Results The CC mice exhibited a range of disease manifestations upon infections, and we used this natural variation to identify strains with mortality after infection and strains exhibiting no mortality. We then used comprehensive preinfection immunophenotyping to identify global baseline immune correlates of protection from mortality to virus infection. Conclusions These data suggest that immune phenotypes might be leveraged to identify humans at highest risk of adverse clinical outcomes upon infection, who may most benefit from intensive clinical interventions, in addition to providing insight for rational vaccine design

MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape

Convergent evolution dictates that diverse groups of viruses will target both similar and distinct host pathways to manipulate the immune response and improve infection. In this study, we sought to leverage this uneven viral antagonism to identify critical host factors that govern disease outcome. Utilizing a systems-based approach, we examined differential regulation of IFN-γ–dependent genes following infection with robust respiratory viruses including influenza viruses [A/influenza/Vietnam/1203/2004 (H5N1-VN1203) and A/influenza/California/04/2009 (H1N1-CA04)] and coronaviruses [severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome CoV (MERS-CoV)]. Categorizing by function, we observed down-regulation of gene expression associated with antigen presentation following both H5N1-VN1203 and MERS-CoV infection. Further examination revealed global down-regulation of antigen-presentation gene expression, which was confirmed by proteomics for both H5N1-VN1203 and MERS-CoV infection. Importantly, epigenetic analysis suggested that DNA methylation, rather than histone modification, plays a crucial role in MERS-CoV–mediated antagonism of antigen-presentation gene expression; in contrast, H5N1-VN1203 likely utilizes a combination of epigenetic mechanisms to target antigen presentation. Together, the results indicate a common mechanism utilized by H5N1-VN1203 and MERS-CoV to modulate antigen presentation and the host adaptive immune response

Surveying Host Innate Immune Responses To Interferon Antagonist-Deficient Murine Coronaviruses

Two coronaviruses (CoVs)—severe acute respiratory syndrome (SARS) virus and Middle East respiratory syndrome (MERS) virus—have emerged in the 21st century from animal reservoirs into the human population, each causing an epidemic associated with significant disease and mortality. CoV epidemics are currently only controllable by rigorous public health measures; no targeted therapeutics or vaccines exist to treat or prevent any human CoV infection. One method of generating attenuated CoV strains to be studied as vaccine candidates involves specifically disrupting CoV-encoded interferon (IFN) antagonists, thereby rendering the virus vulnerable to host innate antiviral immunity. Deubiquitinating (DUB) activity encoded within CoV nonstructural protein (nsp) 3 and endoribonuclease (EndoU) activity encoded within nsp15 are both reported to suppress IFN-mediated antiviral immunity during infection. Using murine hepatitis virus (MHV) as a model CoV, we generated viruses that encode enzymatically-deficient forms of these proteins and have shown that EndoU-mutant- and DUB-mutant-MHV elicit significantly increased type I IFN responses relative to the parental wild type (WT) strain. However, despite similar patterns of IFN induction by both mutant viruses, we previously found that only the EndoU-mut virus is attenuated and does not cause detectable disease in mice, whereas DUB-mut-MHV is not attenuated in vivo and causes disease similar to WT-MHV. The purpose of this project was to investigate the host transcriptional response to infection with EndoU-mut-, DUB-mut-, and WT-MHV in primary murine macrophages using RNA-sequencing (RNA-seq) technology to examine the cellular dynamics that underlie the remarkably distinct phenotypes of EndoU-mut- and DUB-mut-MHV infections in mice. The results of our RNA-seq experiments and subsequent bioinformatic analyses demonstrate that WT-MHV infection led to profound transcriptional dysregulation of thousands of host genes, many of which encode proteins that are involved in inflammation, antiviral defense, signaling pathways, and transcription regulation. Similarly, DUB-mut-MHV elicited a statistically indistinguishable transcriptional response of all but a select few genes relative to WT-MHV. In stark contrast, EndoU-mut-MHV-infected cells exhibited markedly diminished transcription of the vast majority of genes that were induced by DUB-mut- and WT-MHV, leading to a profoundly distinct transcriptional response overall. Both EndoU-mut- and DUB-mut-MHV induced significantly higher expression of type I IFN isoforms relative to the WT virus, with the EndoU-mut strain prompting a dramatically higher IFN response than even the DUB-mut virus. Together, the results of this work suggest that the induction of IFN alone is not a sufficient marker for mutant CoV attenuation or of widespread dysregulation of host gene expression in the context of studying interferon antagonist-deficient coronavirus strains; rather, the magnitude and timing of IFN expression are critical. We conclude that there is a threshold of interferon expression that must be crossed before a host macrophage mounts a differential response to an IFN antagonist-deficient coronavirus that is capable of limiting the infection. Furthermore, we propose that MHV encodes a hierarchy of IFN antagonists that suppress and/or evade the host immune response in different ways and to different degrees. The results of this project advance what is known about how coronavirus-encoded interferon antagonists fine-tune the host response to viral infection and we hope that this work will guide future studies involving interferon antagonist-deficient coronaviruses being evaluated as vaccine candidates

High levels of immunosuppression are related to unfavourable outcomes in hospitalised patients with rheumatic diseases and COVID-19 : first results of ReumaCoV Brasil registry

Objectives To evaluate risk factors associated with unfavourable outcomes: emergency care, hospitalisation, admission to intensive care unit (ICU), mechanical ventilation and death in patients with immune-mediated rheumatic disease (IMRD) and COVID-19. Methods Analysis of the first 8 weeks of observational multicentre prospective cohort study (ReumaCoV Brasil register). Patients with IMRD and COVID-19 according to the Ministry of Health criteria were classified as eligible for the study. Results 334 participants were enrolled, a majority of them women, with a median age of 45 years; systemic lupus erythematosus (32.9%) was the most frequent IMRD. Emergency care was required in 160 patients, 33.0% were hospitalised, 15.0% were admitted to the ICU and 10.5% underwent mechanical ventilation; 28 patients (8.4%) died. In the multivariate adjustment model for emergency care, diabetes (prevalence ratio, PR 1.38; 95% CI 1.11 to 1.73; p=0.004), kidney disease (PR 1.36; 95% CI 1.05 to 1.77; p=0.020), oral glucocorticoids (GC) (PR 1.49; 95% CI 1.21 to 1.85; p50 years (PR 1.89; 95% CI 1.26 to 2.85; p=0.002), no use of tumour necrosis factor inhibitor (TNFi) (PR 2.51;95% CI 1.16 to 5.45; p=0.004) and methylprednisolone pulse therapy (PR 2.50; 95% CI 1.59 to 3.92; p<0.001); for ICU admission, oral GC (PR 2.24; 95% CI 1.36 to 3.71; p<0.001) and pulse therapy with methylprednisolone (PR 1.65; 95% CI 1.00 to 2.68; p<0.043); the two variables associated with death were pulse therapy with methylprednisolone or cyclophosphamide (PR 2.86; 95% CI 1.59 to 5.14; p<0.018). Conclusions Age >50 years and immunosuppression with GC and cyclophosphamide were associated with unfavourable outcomes of COVID-19. Treatment with TNFi may have been protective, perhaps leading to the COVID-19 inflammatory process

Hypergraph models of biological networks to identify genes critical to pathogenic viral response

BACKGROUND: Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capture the multi-way relationships present among genes and proteins in biological systems. Hypergraphs are generalizations of graphs that naturally model multi-way relationships and have shown promise in modeling systems such as protein complexes and metabolic reactions. In this paper we seek to understand how hypergraphs can more faithfully identify, and potentially predict, important genes based on complex relationships inferred from genomic expression data sets. RESULTS: We compiled a novel data set of transcriptional host response to pathogenic viral infections and formulated relationships between genes as a hypergraph where hyperedges represent significantly perturbed genes, and vertices represent individual biological samples with specific experimental conditions. We find that hypergraph betweenness centrality is a superior method for identification of genes important to viral response when compared with graph centrality. CONCLUSIONS: Our results demonstrate the utility of using hypergraphs to represent complex biological systems and highlight central important responses in common to a variety of highly pathogenic viruses

Hypergraph models of biological networks to identify genes critical to pathogenic viral response

Background: Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capture the multi-way relationships present among genes and proteins in biological systems. Hypergraphs are generalizations of graphs that naturally model multi-way relationships and have shown promise in modeling systems such as protein complexes and metabolic reactions. In this paper we seek to understand how hypergraphs can more faithfully identify, and potentially predict, important genes based on complex relationships inferred from genomic expression data sets. Results: We compiled a novel data set of transcriptional host response to pathogenic viral infections and formulated relationships between genes as a hypergraph where hyperedges represent significantly perturbed genes, and vertices represent individual biological samples with specific experimental conditions. We find that hypergraph betweenness centrality is a superior method for identification of genes important to viral response when compared with graph centrality. Conclusions: Our results demonstrate the utility of using hypergraphs to represent complex biological systems and highlight central important responses in common to a variety of highly pathogenic viruses

GENERATION AND CHARACTERIZATION OF HUMAN MONOCLONAL ANTIBODIES WITH NEUTRALIZING ACTIVITY FOR DENGUE VIRUS

Ph.DDOCTOR OF PHILOSOPH