The SARS-CoV-2 papain-like protease suppresses type I interferon responses by deubiquitinating STING.

The SARS-CoV-2 papain-like protease (PLpro), which has deubiquitinating activity, suppresses the type I interferon (IFN-I) antiviral response. We investigated the mechanism by which PLpro antagonizes cellular antiviral responses. In HEK392T cells, PLpro removed K63-linked polyubiquitin chains from Lys289 of the stimulator of interferon genes (STING). PLpro-mediated deubiquitination of STING disrupted the STING-IKKε-IRF3 complex that induces the production of IFN-ß and IFN-stimulated cytokines and chemokines. In human airway cells infected with SARS-CoV-2, the combined treatment with the STING agonist diABZi and the PLpro inhibitor GRL0617 resulted in the synergistic inhibition of SARS-CoV-2 replication and increased IFN-I responses. The PLpros of seven human coronaviruses (SARS-CoV-2, SARS-CoV, MERS-CoV, HCoV-229E, HCoV-HKU1, HCoV-OC43, and HCoV-NL63) and four SARS-CoV-2 variants of concern (α, ß, γ, and δ) all bound to STING and suppressed STING-stimulated IFN-I responses in HEK293T cells. These findings reveal how SARS-CoV-2 PLpro inhibits IFN-I signaling through STING deubiquitination and a general mechanism used by seven human coronaviral PLpros to dysregulate STING and to facilitate viral innate immune evasion. We also identified simultaneous pharmacological STING activation and PLpro inhibition as a potentially effective strategy for antiviral therapy against SARS-CoV-2.

Identification of priority pathogens for aetiological diagnosis in adults with community-acquired pneumonia in China: a multicentre prospective study.

BACKGROUND: Community-acquired pneumonia (CAP) is a major public health challenge worldwide. However, the aetiological and disease severity-related pathogens associated with CAP in adults in China are not well established based on the detection of both viral and bacterial agents. METHODS: A multicentre, prospective study was conducted involving 10 hospitals located in nine geographical regions in China from 2014 to 2019. Sputum or bronchoalveolar lavage fluid (BALF) samples were collected from each recruited CAP patient. Multiplex real-time PCR and bacteria culture methods were used to detect respiratory pathogens. The association between detected pathogens and CAP severity was evaluated. RESULTS: Among the 3,403 recruited eligible patients, 462 (13.58%) had severe CAP, and the in-hospital mortality rate was 1.94% (66/3,403). At least one pathogen was detected in 2,054 (60.36%) patients, with two or more pathogens were co-detected in 725 patients. The ten major pathogens detected were Mycoplasma pneumoniae (11.05%), Haemophilus influenzae (10.67%), Klebsiella pneumoniae (10.43%), influenza A virus (9.49%), human rhinovirus (9.02%), Streptococcus pneumoniae (7.43%), Staphylococcus aureus (4.50%), adenovirus (2.94%), respiratory syncytial viruses (2.35%), and Legionella pneumophila (1.03%), which accounted for 76.06-92.52% of all positive detection results across sampling sites. Klebsiella pneumoniae (p < 0.001) and influenza viruses (p = 0.005) were more frequently detected in older patients, whereas Mycoplasma pneumoniae was more frequently detected in younger patients (p < 0.001). Infections with Klebsiella pneumoniae, Staphylococcus aureus, influenza viruses and respiratory syncytial viruses were risk factors for severe CAP. CONCLUSIONS: The major respiratory pathogens causing CAP in adults in China were different from those in USA and European countries, which were consistent across different geographical regions over study years. Given the detection rate of pathogens and their association with severe CAP, we propose to include the ten major pathogens as priorities for clinical pathogen screening in China.

COVID-19 Metabolomic-Guided Amino Acid Therapy Protects from Inflammation and Disease Sequelae.

The outbreak of coronavirus disease 2019 (COVID-19) has caused a worldwide pandemic since 2019. A metabolic disorder is a contributing factor to deaths from COVID-19. However, the underlying mechanism of metabolic dysfunction in COVID-19 patients and the potential interventions are not elucidated. Here targeted plasma metabolomic is performed, and the metabolite profiles among healthy controls, and asymptomatic, moderate, and severe COVID-19 patients are compared. Among the altered metabolites, arachidonic acid and linolenic acid pathway metabolites are profoundly up-regulated in COVID-19 patients. Arginine biosynthesis, alanine, aspartate, and glutamate metabolism pathways are significantly disturbed in asymptomatic patients. In the comparison of metabolite variances among the groups, higher levels of l-citrulline and l-glutamine are found in asymptomatic carriers and moderate or severe patients at the remission stage. Furthermore, l-citrulline and l-glutamine combination therapy is demonstrated to effectively protect mice from coronavirus infection and endotoxin-induced sepsis, and is observed to efficiently prevent the occurrence of pulmonary fibrosis and central nervous system damage. Collectively, the data reveal the metabolite profile of asymptomatic COVID-19 patients and propose a potential strategy for COVID-19 treatment.

Baricitinib inhibits type I IFN-signaling during SARS-CoV-2 infection in vitro

Objective: To explore the antiviral effect of baricitinib in the SARS-CoV-2 infection and influence on cytokine levels.

Treating patients infected with the SARS-CoV-2 Omicron variant with a traditional Chinese medicine, Shufeng Jiedu capsule.

Patients infected with the Omicron variant of SARS-CoV-2 mainly develop mild COVID-19, manifesting as upper respiratory symptoms, fatigue, and fever. Shufeng Jiedu capsule (SFJDC), a traditional Chinese medicine indicated for treatment of upper respiratory infections in China, was tested for its efficacy and safety in treatment of an Omicron infection at a mobile cabin hospital in response to an outbreak of COVID-19 in Shanghai, China in April 2022. In this open-label, randomized controlled trial, patients in the control group received best supportive care, while those in the test group received additional SFJDC therapy for 7 days. SFJDC markedly alleviated patients' symptoms including a sore throat, coughing, fatigue, and a fever after 7 days of treatment. The virus negative time was significantly shorter in the SFJDC treatment group, but there were no obvious differences in the virus negative rate between the two groups at the end of the 7-day follow-up. These results suggest that patients with the Omicron infection may benefit from SFJDC treatment. Double-blind, randomized controlled trials are warranted to comprehensively evaluate the efficacy and safety of SFJDC in a large cohort study in the future.

The Adverse Reactions of Lianhua Qingwen Capsule/Granule Compared With Conventional Drug in Clinical Application: A Meta-Analysis.

Objectives: Lianhua Qingwen capsule/granule (LHQW) is an innovative patented traditional Chinese medicine with potential curative effects on respiratory diseases. However, no consensus has been reached on the security of LHQW to date. The current meta-analysis was performed to evaluate the safety profile of LHQW in relation to conventional drugs (PROSPERO CRD-42020224180). Methods: Comprehensive document retrieval was performed from both English and Chinese databases. Results were reported as risk ratio (RR) with 95% confidence interval (CI). Subgroup, sensitivity and meta-regression analyses were conducted to explore the possible sources of heterogeneity across eligible studies. Results: In total, 217 experimental studies were included. For pooled studies, the incidence of adverse reactions was lower in the LHQW group than the conventional drug group (RR = 0.63, 95% CI = 0.58-0.69, p < 0.001). In the evaluation of treating disease, significant reduced incidence of adverse reactions during treatment of influenza A (H1N1) and influenza were detected in the LHQW group. In the evaluation of security indexes, LHQW group has a reduced incidence of respiratory system damage, skin and its appendages injury, nervous system damage and gastrointestinal system damage, along with other adverse reactions. Subgroup analysis additionally revealed a reduced incidence of some adverse reactions in the LHQW group compared to the conventional drug group (Rash of skin and its appendage damage, dizziness or headache owing to nervous system damage, nausea or vomiting from gastrointestinal system damage and resurgence of disease from other adverse reactions). Conclusion: The current study provides potential a reference for the security of LHQW. Further long-term high-quality studies are essential to validate our conclusions. Systematic Review Registration: https://clinicaltrials.gov/, CRD-42020224180.

Antiviral drugs arbidol and interferon alpha-1b contribute to reducing the severity of COVID-19 patients: a retrospective cohort study.

OBJECTIVES: The aim of this study was to evaluate the role of antiviral drugs in reducing the risk of developing severe illness in patients with moderate COVID-19 pneumonia. METHODS: This retrospective cohort study included 403 adult patients with moderate COVID-19 pneumonia who were admitted to Shenzhen Third People's Hospital, China. The antiviral drugs arbidol, interferon alpha-1b, lopinavir-ritonavir and ribavirin were distributed to the patients for treatment. The primary endpoint of this study was the time to develop severe illness. RESULTS: Of the 462 patients admitted, 403 had moderate COVID-19 symptoms at hospital admission and were included in this study. 90 of the 403 (22.3%) patients progressed to severe illness. The use of arbidol was associated with a lower severity rate 3.5% compared to control group 30.5%, p-value < 0.0001; the adjusted hazard ratio was 0.28 (95% CI: 0.084-0.90, p = 0.033). The use of interferon alpha-1b was associated with a lower severity rate 15.5% compared to control group 29.3%, with p-value < 0.0001; the adjusted hazard ratio was 0.30 (95% CI: 0.15-0.58, p =  0.0005). The use of lopinavir-itonavir and ribavirin did not show significant differences in adjusted regression models. Early use of arbidol within 7 days of symptom onset was significantly associated with a reduced recovery time of - 5.2 days (IQR - 3.0 to - 7.5, p = 4e-06) compared with the control group. CONCLUSION: Treatment with arbidol and interferon alpha-1b contributes to reducing the severity of illness in patients with moderate COVID-19 pneumonia. Early use of arbidol may reduce patients' recovery time.

The complex structure of GRL0617 and SARS-CoV-2 PLpro reveals a hot spot for antiviral drug discovery.

SARS-CoV-2 is the pathogen responsible for the COVID-19 pandemic. The SARS-CoV-2 papain-like cysteine protease (PLpro) has been implicated in playing important roles in virus maturation, dysregulation of host inflammation, and antiviral immune responses. The multiple functions of PLpro render it a promising drug target. Therefore, we screened a library of approved drugs and also examined available inhibitors against PLpro. Inhibitor GRL0617 showed a promising in vitro IC50 of 2.1 µM and an effective antiviral inhibition in cell-based assays. The co-crystal structure of SARS-CoV-2 PLproC111S in complex with GRL0617 indicates that GRL0617 is a non-covalent inhibitor and it resides in the ubiquitin-specific proteases (USP) domain of PLpro. NMR data indicate that GRL0617 blocks the binding of ISG15 C-terminus to PLpro. Using truncated ISG15 mutants, we show that the C-terminus of ISG15 plays a dominant role in binding PLpro. Structural analysis reveals that the ISG15 C-terminus binding pocket in PLpro contributes a disproportionately large portion of binding energy, thus this pocket is a hot spot for antiviral drug discovery targeting PLpro.

Emerging biosensing technologies for improved diagnostics of COVID-19 and future pandemics.

Diagnostic tools play significant roles in the fight against COVID-19 and other pandemics. Existing tests, such as RT-qPCR, have limitations including long assay time, low throughput, inadequate sensitivity, and suboptimal portability. Emerging biosensing technologies hold the promise to develop tests that are rapid, highly sensitive, and suitable for point-of-care testing, which could significantly facilitate the testing of COVID-19. Despite that, practical applications of such biosensors in pandemics have yet to be achieved. In this review, we consolidate the newly developed diagnostic tools for COVID-19 using emerging biosensing technologies and discuss their application promise. In particular, we present nucleic acid tests and antibody tests of COVID-19 based on both conventional and emerging biosensing methods. We then provide perspectives on the existing challenges and potential solutions.

Genomic Diversity of Severe Acute Respiratory Syndrome-Coronavirus 2 in Patients With Coronavirus Disease 2019.

BACKGROUND: A novel coronavirus (CoV), severe acute respiratory syndrome (SARS)-CoV-2, has infected >75 000 individuals and spread to >20 countries. It is still unclear how fast the virus evolved and how it interacts with other microorganisms in the lung. METHODS: We have conducted metatranscriptome sequencing for bronchoalveolar lavage fluid samples from 8 patients with SARS-CoV-2, and also analyzed data from 25 patients with community-acquired pneumonia (CAP), and 20 healthy controls for comparison. RESULTS: The median number of intrahost variants was 1-4 in SARS-CoV-2-infected patients, ranged from 0 to 51 in different samples. The distribution of variants on genes was similar to those observed in the population data. However, very few intrahost variants were observed in the population as polymorphisms, implying either a bottleneck or purifying selection involved in the transmission of the virus, or a consequence of the limited diversity represented in the current polymorphism data. Although current evidence did not support the transmission of intrahost variants in a possible person-to-person spread, the risk should not be overlooked. Microbiotas in SARS-CoV-2-infected patients were similar to those in CAP, either dominated by the pathogens or with elevated levels of oral and upper respiratory commensal bacteria. CONCLUSION: SARS-CoV-2 evolves in vivo after infection, which may affect its virulence, infectivity, and transmissibility. Although how the intrahost variant spreads in the population is still elusive, it is necessary to strengthen the surveillance of the viral evolution in the population and associated clinical changes.

Clinical characteristics of cardiac injury in patients with COVID-19

Objective: To analyze the clinical characteristics, cardiac injury characteristics and early warning indexes of severe type in patients with COVID-19, so as to provide data for the evaluation, clinical treatment and prognosis of COVID-19 patients.

Efficacy of Lianhua Qingwen Compared with Conventional Drugs in the Treatment of Common Pneumonia and COVID-19 Pneumonia: A Meta-Analysis.

METHODS: Seven English and Chinese databases were used to search for qualified experimental studies as of July 27, 2020. All data were extracted directly from the included studies, and no special conversion formula was used. The weighted mean difference (WMD), 95% confidence interval (CI), and odds ratio (OR) were used for evaluation. RESULTS: Forty-two studies involving 3793 subjects met the qualification criteria. For common pneumonia, a short duration of flu-like symptoms (WMD = -1.81, 95% CI = -2.12 to -1.50, P < 0.001), sputum (WMD = -1.10, 95% CI = -1.50 to -0.70, P < 0.001), pulmonary rale (WMD = -2.03, 95% CI = -2.74 to -1.31, P < 0.001), pulmonary imaging improvement (WMD = -1.88, 95% CI = -2.28 to -1.47, P < 0.001), curative effect (OR = 3.65, 95% CI = 2.81 to 4.76, P < 0.001), and healing period (WMD = -1.68, 95% CI = -2.62 to -0.74, P < 0.001) were associated with the Lianhua Qingwen group; subgroup analysis based on flu-like symptoms showed statistically significant improvements in fever and cough. For COVID-19 pneumonia, improvements in flu-like symptoms (OR = 3.18, 95% CI = 2.36 to 4.29, P < 0.001), shortness of breath (OR = 10.62, 95% CI = 3.71 to 30.40, P < 0.001), curative effect (OR = 2.49, 95% CI = 1.76 to 3.53, P < 0.001), healing period (WMD = -2.06, 95% CI = -3.36 to -0.75, P = 0.002), and conversion of severe cases (OR = 0.46, 95% CI = 0.27 to 0.77, P = 0.003) were associated with the Lianhua Qingwen group; subgroup analysis indicated statistically significant improvements of fever, cough, fatigue, and muscle pain in the Lianhua Qingwen group compared to the conventional drug group. Regarding adverse reactions, no significant difference was detected for common pneumonia (OR = 0.75, 95% CI = 0.54 to 1.05, P = 0.097). CONCLUSIONS: Lianhua Qingwen combined with conventional drugs may be a promising therapy for treating common pneumonia and COVID-19 pneumonia.

Comparative Analysis of Early-Stage Clinical Features Between COVID-19 and Influenza A H1N1 Virus Pneumonia.

Introduction: Influenza virus pneumonia and COVID-19 are two different types of respiratory viral pneumonia but with very similar clinical manifestations. The aim of the present study was to help clinicians gain a better understanding about differences between Influenza virus pneumonia and COVID-19 by comparative analysis of the early-stage clinical features. Methods: Clinical data of patients with confirmed diagnosis of COVID-19 and influenza A pneumonia identified in our hospital were collected and analyzed retrospectively to identify the clinical features that could differentiate between the two types of viral pneumonia. Results: The two types of viral pneumonia mainly affected adults, especially people over 50 years, with no gender difference between them. Fever, cough, sputum and muscle soreness were the most common symptoms of COVID-19. Some patients with COVID-19 may also exhibit digestive tract symptoms. Elevation of C-reactive protein (CRP) was a more common phenomenon in patients with COVID-19 than that in patients with influenza A H1N1 virus pneumonia. In addition, eosinophil count was decreased and the monocyte percentage was increased in COVID-19 patients. The grid-form shadow was a typical presentation of COVID-19 on the lung CT image, and the disease usually progressed quickly within a week. Conclusion: Influenza pneumonia and COVID-19 are two different types of respiratory viral pneumonia with very similar clinical manifestations. The percentage of monocytes is increased and the eosinophil count is decreased in COVID-19. Glass-ground density exudation shadow located peripherally is the typical sign of COVID-19 on the lung CT image, and the shadow often with grid-form sign. These features may not be typically observed in patients with influenza pneumonia. Chest CT scan combined with nucleic acid detection is an effective and accurate method for diagnosing COVID-19. Blood routine test has a limited diagnostic value in differentiating the two forms of pneumonia.

The epidemiologic and clinical features of suspected and confirmed cases of imported 2019 novel coronavirus pneumonia in north Shanghai, China.

BACKGROUND: A recent cluster of pneumonia cases in Wuhan (China) is known to be caused by a novel beta-coronavirus named the corona virus disease 2019 (COVID-19) and can be spread through human-to-human transmission. METHODS: Data of 21 patients with laboratory-confirmed COVID-19 and 84 patients with suspected COVID-19 were analyzed by RT-PCR. The epidemiologic and clinical features as well as clinical outcomes were compared between the confirmed and suspected cases. RESULTS: Altogether 105 patients had been enrolled in this study by February 15, 2020 in north Shanghai, including 21 confirmed cases and 84 suspected cases of COVID-19. The incubation period of these confirmed patients with imported COVID-19 was 17.6 days (IQR 5-34 days) and the median time from symptom onset to diagnosis was 145.64 h (IQR 21-441 h). More than 50% of the confirmed patients were older than 51 (range, 51-60) years. Fifty (59.5%) of the 84 probably patients were younger than 40 years, including 27 (32%) patients younger than 30 years. Most confirmed patients were men (61.9%, 13/21), and less than 50% of them had underlying diseases, including diabetes (9.5%, 2/21), hypertension (19%, 4/21), COPD (23.8%, 5/21), and CD (23.8%, 5/21). In addition, 10 (47.6%) of the 21 confirmed patients were ordinary employees, and 12 (57.2%) of them had recently been to Wuhan or had close contacts with people from Wuhan. Of the 84 suspected patients, 28 (33.3%) were retired employees; 69 (82.1%) had recently been to supermarkets and groceries or had a history of traveling abroad or to other cities of China. The common onset symptoms of the patients in both groups were fever and cough. The symptom of Sputum production was more pronounced in probably patients (40.5%, 34/84) than that in confirmed patients (9.5%, 2/21). More than 50% imported patients (53.3%, 56/105) had one and two affected lobes. Twenty-nine (27.6%) of the 105 imported patients had been discharged, no patient had died, and all the other patients are still in hospital. CONCLUSIONS: The overall incubation period in this cohort of imported confirmed COVID-19 patients was longer than that in Wuhan, mostly infecting older men. The disease onset of imported COVID-19 infection was occult, and the clinical symptoms were usually mild, mostly presenting as low fever, fatigue, light cough, and mild dyspnea.

Renin-angiotensin system inhibitors improve the clinical outcomes of COVID-19 patients with hypertension.

The dysfunction of the renin-angiotensin system (RAS) has been observed in coronavirus infection disease (COVID-19) patients, but whether RAS inhibitors, such as angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin II type 1 receptor blockers (ARBs), are associated with clinical outcomes remains unknown. COVID-19 patients with hypertension were enrolled to evaluate the effect of RAS inhibitors. We observed that patients receiving ACEI or ARB therapy had a lower rate of severe diseases and a trend toward a lower level of IL-6 in peripheral blood. In addition, ACEI or ARB therapy increased CD3 and CD8 T cell counts in peripheral blood and decreased the peak viral load compared to other antihypertensive drugs. This evidence supports the benefit of using ACEIs or ARBs to potentially contribute to the improvement of clinical outcomes of COVID-19 patients with hypertension.