Discovery and evaluation of active compounds from Xuanfei Baidu Formula against COVID-19 via SARS-Cov-2 Mpro (preprint)

Background The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus (SARS-CoV-2) is still a widespread concern. As one of the effective traditional Chinese medicine (TCM) formula, Xuanfei Baidu formula (XFBD) shows significant efficacy for treatment of COVID-19 patients. However, its antiviral compounds and mechanism are still unclear. Purpose: In this study, we explored the bioactive compounds of XFBD and its antiviral mechanism by integrating computational analysis and experimental testing. Methods Aiming at the SARS-CoV-2 main protease (Mpro), as a key target in virus replication, the fluorescence resonance energy transfer (FRET) assay was built to screen out satisfactory natural inhibitors from XFBD. The surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) were undertaken to verify the binding affinity of Mpro-ligand. Omicron BA.1.1 and BA.2 variants were used to evaluate the antiviral activity of the focused compounds in non-cytotoxicity concentrations. For introducing the molecular mechanism, computational modeling and NMR spectra were employed to predict the binding mode and binding site of Mpro-ligand. Results From a library of 83 natural compounds, acteoside, licochalcone B, licochalcone D, linoleic acid, and physcion showed the satisfactory inhibition effect on Mpro with IC50 from 1.93 to 42.96 µM, which were further verified by SPR. Showing the excellent binding affinity, acteoside was witnessed to gain valuable insights into the thermodynamic signatures by ITC and presented antiviral activity on Omicron BA.1.1 and BA.2.3 variants in vitro. The results revealed that acteoside inhibited Mpro via forming the hydrogen bond between 7-H of acteoside and Mpro. Conclusion Acteoside is regarded as a representative active natural compound in XFBD to inhibit replication of SARS-CoV-2, which provides the antiviral evidence and some insight into the identifications of SARS-CoV-2 Mpro natural inhibitors.

Research progress on palmitoylation of SARS-CoV-2 surface proteins and receptor ACE2

It has been more than 2 years since the outbreak of corona virus disease 2019（COVID-19） caused by severe acute respiratory syndrome coronavirus 2（SARS-CoV-2）.SARS-CoV-2 is a member of positive single-stranded RNA viruses and could infect multiple mammals.Palmitoylation is a post-translational lipid modification of protein, which regulates protein localization and trafficking.Spike protein（S）, envelope protein（E） and SARS-CoV-2 receptor ACE2 have been identified of being palmitoylated.This paper reviews the research progress on the palmitoylation of S, E and ACE2, including the sites of palmitoylation of S protein, the enzymes involved in this process, and their functions.Through the integrated review of these contents, which would provide mechanistic insights into the pathogenesis and treatment of COVID-19.

Icon Arrays Reduce Concern Over COVID-19 Vaccine Side Effects: A Randomized Control Study (preprint)

On April 13, 2021, the CDC announced that the administration of Johnson and Johnson’s COVID-19 vaccine would be paused due to a rare blood clotting side effect in ~0.0001% of people given the vaccine. Most people who are hesitant to get a COVID-19 vaccine list potential side effects as their main concern (PEW, 2021); thus, it is likely that this announcement increased vaccine hesitancy among the American public. Two days after the CDC’s announcement, we administered a survey to a group of 2,046 Americans to assess their attitudes toward COVID-19 vaccines. The aim of this study was to investigate best practices for communicating information about the risk of side effects to the public. We found that the use of icon arrays to illustrate the small chance of experiencing the blood clotting side effect greatly decreased reported aversion toward the Johnson and Johnson vaccine as well as all other COVID-19 vaccines.

Persistently Reduced Pulmonary Function and Quality of Life in Patients With Mild COVID-19 One Year After Discharge: a Cohort Study (preprint)

Purpose: The epidemiological and clinical features, pathogenesis, and complications of patients with COVID-19 in the acute phase have been well described, but the long-term prognosis and rehabilitation of the patients remain largely unknown. Methods: 39 COVID-19 patients were followed up at 3, 6, and 12 months after discharge. The mental health, pulmonary function, exercise capacity, and quality of life were assessed by Self-Depression Scale and the Self Anxiety Scale, pulmonary function test, 6MWT, 36-Item Short-Form, respectively. Results: Total 33 survivors completed the assessment, 40.8 ± 0.8 years, body mass index= 22.7 ±1.3 kg/m 2 . The length of hospital stays was 19.6 ± 6.6 d. One year after discharge, the mean scores of SDS and SAS showed decreasing trends from 3-months to 12-months post-discharge. 6 patients (18.2%) had FVC <80% of the predicted value, 12 patients (36.4%) had FEV1 <80% of the predicted value. And 9 (27.3%), 3 (9.1%), and 2 (6.1%) of the patients showed reduced FEF25, FEF50, and FEF75 (<70% expected values), respectively. The mean 6MWD values increased significantly from 397±25.4 m at 3-months to 514±40.8 m at 12-months. Conclusions: the impaired pulmonary function in mild COVID-19 survivors was noted after 12 months discharging from hospital. The exercise capacity, mental status, and health status were lower than those of the normal population.

Circulating Level of Interleukin-6 Correlates With Poor Prognosis in Males With COVID-19: A Systematic Review and Meta-Analysis (preprint)

Coronavirus disease 2019 (COVID-2019), caused by severe acute respiratory syndrome coronavirus 2, has become a worldwide epidemic and claimed millions of lives. Accumulating evidence suggests that males suffer more severe symptoms and higher mortality than females, but the underlying mechanism of this sex predisposition remains unclear. We aimed to explore whether inflammatory cytokines are risk factors correlated with this sex predisposition, especially in terms of the severity and mortality of COVID-19 patients. To clarify whether inflammatory cytokines are related to male sex bias towards increased mortality, we systematically searched PubMed, Embase and Web of Science to identify related studies with the keywords "COVID-19" and "cytokines". We preliminarily screened 13468 studies from the databases. A total of 77 articles with 13468 patients were ultimately included in our study. The expression levels of interleukin-6 (IL-6), interleukin-10 (IL-10), interleukin-2 receptor (IL-2R) and tumour necrosis factor α (TNF-α) were significantly different between males and females. The serum level of IL-6 was much higher in males than in females, which implies that the increased mortality and severity in males was partly due to the higher level of IL-6. Interestingly, we also found that in the severe and non-survivor groups, European patients had elevated levels of IL-6 compared with Asian patients. These large-scale data demonstrated that the circulating level of IL-6 is a potential risk factor for severity and high mortality in COVID-19. The upregulation of IL-6 may be a driving factor for severity and high mortality in males with COVID-19.Funding Information: This work was financially supported by National Key Research and Development Project of China (2020YFA0708003).Declaration of Interests: There is no conflict of interest.

Nosocomial Pseudomonas aeruginosaregulates alginate biosynthesis and Type VI secretion system during adaptive and convergent evolution for coinfection in critically ill COVID-19 patients (preprint)

COVID-19 pandemic has caused millions of death globally and caused huge impact on the health of infected patients. Shift in the lung microbial ecology upon such viral infection often worsens the disease and increases host susceptibility to secondary infections. Recent studies have indicated that bacterial coinfection is an unignorable factor contributing to the aggravation of COVID-19 and posing great challenge to clinical treatments. However, there is still a lack of in-depth investigation on the coinfecting bacteria in COVID-19 patients for better treatment of bacterial coinfection. With the knowledge that Pseudomonas aeruginosa is one of the top coinfecting pathogens, we analyzed the adaptation and convergent evolution of nosocomial Pseudomonas aeruginosa isolated from two critical COVID-19 patients in this study. We sequenced and compared the genomes and transcriptomes of Pseudomonas aeruginosa isolates longitudinally and parallelly for its evolutionary traits. Pseudomonas aeruginosa overexpressed alginate and attenuated Type VI secretion system (T6SS) during coinfection for excessive biofilm formation and suppressed virulence. Results of bacterial competition assay and macrophage cytotoxicity test indicated that Pseudomonas aeruginosa reduced its virulence towards both prokaryotic competitors and eukaryotic host through inhibiting its T6SS during evolution. Pseudomonas aeruginosa T6SS is thus one of the reasons for its advantage to cause coinfection in COVID-19 patients while the attenuation of T6SS could cause a shift in the microecological composition in the lung. Our study will contribute to the development of therapeutic measures and the discovery of novel drug target to eliminate Pseudomonas aeruginosa coinfection in COVID-19 patient.

Altered O-glycosylation Level of SARS-CoV-2 Spike Protein by Host O-glycosyltransferase Strengthens Its Trimeric Structure (preprint)

The trimeric spike protein (S) mediates host-cell entry and membrane fusion of SARS-CoV-2. S protein is highly glycosylated, whereas its O-glycosylation is still poorly understood. Herein, we site-specifically examine the O-glycosylation of S protein through a mass spectrometric approach with HCD-triggered-ETD model. We identify 15 high-confidence O-glycosites and at least 10 distinct O-glycan structures on S protein. Peptide microarray assays prove that human ppGalNAc-T6 actively participates in O-glycosylation of S protein. Importantly, the upregulation of ppGalNAc-T6 expression can profoundly enhance the O-glycosylation level by generating new O-glycosites and increasing both O-glycan heterogeneity and intensities. Further molecular dynamics simulations reveal that the O-glycosylation on the protomer-interface regions, which are mainly modified by ppGalNAc-T6, can potentially stabilize the trimeric S protein structure. Our work provides deep molecular insights of how viral infection harnesses the host O-glycosyltransferases to dynamically regulate the O-glycosylation level of the viral envelope protein responsible for membrane fusion.

Sub10 μm macroporous aramid substrates with a hierarchically structured interface for organic solvent nanofiltration

Compared with traditional methods for elaborately tailoring the active layer of thin-film composite (TFC) membranes, this study focused on building novel substrates for potential applications in developing organic solvent nanofiltration (OSN) membranes. One kind of “three-parts” hierarchically structured interface with nanospheres and macro surface pores was successfully prepared via Michael addition and Schiff's base (M&S) reactions between N-(2-aminoethyl)-3-aminopropyl triethoxysilane (NAE-A) and glycerite (a natural polyphenol) in the aramid substrate. The thickness was reduced to sub10 μm with the aid of the high-speed spin coating process coupling nonsolvent-induced phase separation (HSSC-co-NIPS) method. The composition characterization results demonstrated the introduction of glycerite, and the reactions occurred in/on the substrate. Scanning electron microscopy (SEM) images clearly showed that the sub10 μm substrate contained a “three-level” hierarchically structured interface that included: (1) a “stalk-like” structure;(2) glycerite-NAE-A silane (GNAS) nanospheres;and (3) the substrate surface. These phenomena also resulted in better surface hydrophilicity. All types of organic solvents, including harsh solvents, such as tetrahydrofuran (THF) and N,N-dimethylformamide (DMF), had stable permeability within the substrate, as did apolar n-hexane and isopar™ G. Therefore, the as-prepared TFC OSN membrane, which had an extremely short polymerization time, retained broad-spectrum solvent stability and had the highest solvent permeance in acetonitrile (24.5 ± 0.4 L m−2 h−1·bar−1). In addition, the resultant TFC membrane almost completely rejected the popular macrolide antibiotic azithromycin (AZM, 748.98 g mol−1) in ethanol, which is used to treat COVID-19.

Sub-second heat inactivation of coronavirus (preprint)

Heat treatment denatures viral proteins that comprise the virion, making virus incapable of infecting a host. Coronavirus (CoV) virions contain single-stranded RNA genomes with a lipid envelope and 4 proteins, 3 of which are associated with the lipid envelope and thus are thought to be easily denatured by heat or surfactant-type chemicals. Prior studies have shown that a temperature of as low as 75 oC and treatment duration of 15 min can effectively inactivate CoV. The applicability of a CoV heat inactivation method greatly depends on the length of time of a heat treatment and the temperature needed to inactivate the virus. With the goal of finding conditions where sub-second heat exposure of CoV can sufficiently inactivate CoV, we designed and developed a simple system that can measure sub-second heat inactivation of CoV. The system is composed of capillary stainless-steel tubing immersed in a temperature-controlled oil bath followed by an ice bath, through which virus solution can be flowed at various speeds. Flowing virus solution at different speeds, along with a real-time temperature monitoring system, allows the virus to be accurately exposed to a desired temperature for various durations of time. Using mouse hepatitis virus (MHV), a beta-coronavirus, as a model system, we identified that 85.2 oC for 0.48 s exposure is sufficient to obtain > 5 Log10 reduction in viral titer (starting titer: 5 x 107 PFU/mL), and that when exposed to 83.4 oC for 0.95 s, the virus was completely inactivated (zero titer, > 6 Log10 reduction).

How Does COVID-19 impact Students with Disabilities/Health Concerns? (preprint)

The impact of COVID-19 on students has been enormous, with an increase in worries about fiscal and physical health, a rapid shift to online learning, and increased isolation. In addition to these changes, students with disabilities/health concerns may face accessibility problems with online learning or communication tools, and their stress may be compounded by additional risks such as financial stress or pre-existing conditions. To our knowledge, no one has looked specifically at the impact of COVID-19 on students with disabilities/health concerns. In this paper, we present data from a survey of 147 students with and without disabilities collected in late March to early April of 2020 to assess the impact of COVID-19 on these students' education and mental health. Our findings show that students with disabilities/health concerns were more concerned about classes going online than their peers without disabilities. In addition, students with disabilities/health concerns also reported that they have experienced more COVID-19 related adversities compared to their peers without disabilities/health concerns. We argue that students with disabilities/health concerns in higher education need confidence in the accessibility of the online learning tools that are becoming increasingly prevalent in higher education not only because of COVID-19 but also more generally. In addition, educational technologies will be more accessible if they consider the learning context, and are designed to provide a supportive, calm, and connecting learning environment.

Analysis of clinical characteristics of SARS-CoV-2 infected cases: a retrospective study of medical records (preprint)

Objectives In order to identify the clinical characteristics of patients with Corona Virus Disease 2019 (COVID-19) and find out the characteristic effects of 2019 New Coronavirus (SARS-CoV-2) infection on changes in clinical and laboratory data. Patients and methods From January 22 to February 13, 2020, we enrolled consecutive patients with acute respiratory tract symptoms admitted to a hospital (Ezhou, Hubei, China). For different data types t-test, the variables associated with the diagnosis of COVID-19 were compared by chi-square test and u-test, the statistically significant variables (P-value<0.05) were selected into the final logistic regression model. Results 62 (77.5%) confirmed cases and 18 (22.5%) negative cases were confirmed by SARS-CoV-2 nucleic acid test. Epidemiological investigation and statistical analysis were carried out on the clinical and laboratory data of all suspected cases of COVID-19, the specific indicators were found, and the clinical characteristics of COVID-19 were described. Compared with the patients with negative nucleic acid test, the patients with positive nucleic acid test showed shorter time of onset of symptoms, higher plasma CO2 level, lower eosinophil ratio, lower platelet count and hematocrit, lower serum sodium level, higher serum creatinine, higher blood urea and plasma albumin levels (all P<0.05). Conclusions we argue that the SARS-CoV-2 infection can cause multiple organ damage to the heart, liver, kidney and bone marrow other than lung injury.

Analysis of clinical characteristics of SARS-CoV-2 infected cases: a retrospective study of medical records (preprint)

In order to identify the clinical characteristics of patients with Corona Virus Disease 2019 (COVID-19) and find out the characteristic effects of 2019 New Coronavirus (SARS-CoV-2) infection on changes in clinical and laboratory data, we analyzed the medical records of 80 suspected cases who admitted in the national designated hospital due to the relevant clinical manifestations of SARS-CoV-2 infection from January 22 to February 13, 2020. 62 (77.5%) confirmed cases and 18 (22.5%) negative cases were confirmed by SARS-CoV-2 nucleic acid test. Epidemiological investigation and statistical analysis were carried out on the clinical and laboratory data of all suspected cases of COVID-19, the specific indicators were found, and the clinical characteristics of COVID-19 were described. Compared with the patients with negative nucleic acid test, the patients with positive nucleic acid test showed shorter time of onset of symptoms, higher plasma CO2 level, lower eosinophil ratio, lower platelet count and hematocrit, lower serum sodium level, higher serum creatinine, higher blood urea and plasma albumin levels (all P<0.05). Our results might provide some suggestions in diagnosis, clinical treatment and prevention for COVID-19.