ABSTRACT
Spike proteins of coronaviruses are highly glycosylated and responsible for host recognition and viral entry. The glycans provide a camouflaging shield to help coronaviruses evade host immunity and, in some cases, modulate functional domain structures and dynamics pertinent to host recognition. However, the glycans are chemically and conformationally heterogeneous, making it challenging to determine the chemical compositions and conformations quantitatively. Combining cryo-electron microscopy, mass spectrometry, and molecular modeling, we systematically characterize a panel of spike protein variants of human and animal coronaviruses, including those of the variants of concern of SARS-CoV-2. We have established a robust workflow to quantify the heterogeneity of individual N-glycans by mass spectrometry. We also demonstrated the ability to visualize long glycan structures directly in regions where the dynamics are restricted. In places where the N-glycans are too dynamic, their structural information is generally lost after extended cryo-EM data processing that aims to achieve high resolution. To address this issue, we developed a computational tool called GlycoSHIELD to generate ensembles of glycan conformers to recapitulate the fuzzy structures that are in quantitative agreement with the experimental cryo-EM data. The ability to generate fully glycosylated spike protein models enables the prediction of hitherto unknown receptor and antibody binding sites. This work was supported by Academia Sinica intramural fund, an Academia Sinica Career Development Award, Academia Sinica to STDH (AS-CDA-109- L08), an Infectious Disease Research Supporting Grant to STDH (AS-IDR- 110-08), and the Ministry of Science and Technology (MOST), Taiwan (MOST 109-3114-Y-001-001, MOST 110-2113-M-001- 050-MY3 and MOST 110-2311-B-001-013-MY3) to STDH.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.
ABSTRACT
Four copper (II) complexes bearing tris-(2-pyridyl)-pyrazolyl borate (Tppy) ligand with corresponding chloride (Cu-1), aqua (Cu-2), azide (Cu-3), and thiocyanide (Cu-4) substitutions were synthesized and characterized by spectroscopic and analytical methods. Spectroscopic and molecular docking studies were employed to investigate the interactions of these complexes with calf thymus (CT) DNA and bovine serum albumin (BSA). The results inferred intercalation binding mode of the complexes with DNA. All the complexes exhibited good binding with BSA as well. In addition, the binding efficacy of the Cu (II) complexes with SARS-Cov-2 was tested in silico. Further, in vitro anticancer activity of the complexes was investigated against the HeLa-cervical, HepG2-liver and A549-lung cancer, and one normal (L929-fibroblast) cell line. IC50 values unveiled that the complexes were more active than cisplatin against all three cancer cells. It was understood that complex Cu-3 containing azide substitution displayed the highest activity on the HeLa cell line (IC50 = 6.3 μM). More importantly, TppyCu (II) complexes were not active against the normal cell line. Lastly, the acridine orange/ethidium bromide (AO/EB) and 4′,6-diamidino-2-phenylindole staining assays indicated that Cu-3 induced cell death in HeLa cells at the late apoptotic stage. This complex also efficiently generated ROS in HeLa cells promoting apoptosis as understood from the DCFH-DA assay. © 2023 John Wiley & Sons, Ltd.
ABSTRACT
BACKGROUND: Barriers to rapid return of sequencing results can affect the utility of sequence data for infection prevention and control decisions. AIM: To undertake a mixed-methods analysis to identify challenges that sites faced in achieving a rapid turnaround time (TAT) in the COVID-19 Genomics UK Hospital-Onset COVID-19 Infection (COG-UK HOCI) study. METHODS: For the quantitative analysis, timepoints relating to different stages of the sequencing process were extracted from both the COG-UK HOCI study dataset and surveys of study sites. Qualitative data relating to the barriers and facilitators to achieving rapid TATs were included from thematic analysis. FINDINGS: The overall TAT, from sample collection to receipt of sequence report by infection control teams, varied between sites (median 5.1 days, range 3.0-29.0 days). Most variation was seen between reporting of a positive COVID-19 polymerase chain reaction (PCR) result to sequence report generation (median 4.0 days, range 2.3-27.0 days). On deeper analysis, most of this variability was accounted for by differences in the delay between the COVID-19 PCR result and arrival of the sample at the sequencing laboratory (median 20.8 h, range 16.0-88.7 h). Qualitative analyses suggest that closer proximity of sequencing laboratories to diagnostic laboratories, increased staff flexibility and regular transport times facilitated a shorter TAT. CONCLUSION: Integration of pathogen sequencing into diagnostic laboratories may help to improve sequencing TAT to allow sequence data to be of tangible value to infection control practice. Adding a quality control step upstream to increase capacity further down the workflow may also optimize TAT if lower quality samples are removed at an earlier stage.
ABSTRACT
Background: Student-pharmacists forced into remote-learning by the COVID-19 pandemic participated in a Virtual Mock Trial (VMT). Objective(s): Feasibility of VMTs was assessed by evaluating student VMT performance, student perceptions on technology and overall experiences. Method(s): The VMT was implemented via video conferencing technology in April 2020. Faculty-judges and student-jurors observed/rated student performance using pre-established rubrics. A post-VMT survey was administered electronically. Descriptive analyses were performed, and Wilcoxon-Mann-Whitney tests were conducted to compare programmes. Result(s): Forty-six students from Programme A (East Coast, USA) and 89 from Programme B (West Coast, USA) participated in the VMTs. The faculty-judges' evaluation scores for student performance ranged from 85.0% to 96.7%, while the student-jurors' evaluation scores ranged from 68.3% to 100%. Student perceptions on the four categories regarding technology use all had means > 5 on a 7-Point Likert Scale. More than 79.0% of students rated their VMT experience positively (i.e. 6 or 7). Conclusion(s): VMT is feasible for the current pandemic remote-learning environment, and it could be replicated in other pharmacy or healthcare programmes to enrich students' active learning in virtual education. Copyright © 2021 FIP.
ABSTRACT
To evaluate the difference in hazardous air pollutants in PM2.5 between reference method (National Institute of Environmental Analysis;NIEAA205) and high-volume air sampler (European standard:EN14907 and Japan method), we set up a sampling station on the campus of National Yang-Ming Chiao Tung University, northern Taiwan, during 2014-2015. Both vapor and solid phases of dioxins were collected using high-volume samplers, according to EN14907 and Japan method. The flow rate was set at 500 L min(-1) and 1000 L min(-1), respectively. To compare the difference with the high-volume air sampler, we simultaneously used the reference air sampler based on Taiwan NIEA A205.11C, at the flow rate of 16.7 L min(-1) (BGI PQ200-FRM). The mass concentrations of PM2.5 measured with NIEA A205, EN14907, and Japan method were 20.2 +/- 8.79, 25.4 +/- 10.5 and 28.6 +/- 13.9 mu g m(-3), respectively. The difference of the mass concentration of PM2.5 obtained from two different methods was lower than 3.9%. Moreover, the concentrations of PCDD/F between solid and vapor phases were 56.9-1,090 and 38.6-67.1 fg m(-3) via EN14907 and 51.1-1,150 and 18.4-81.8 fg m(-3) via Japan method, respectively. Obviously, there is no significant difference between these two samplers. Compared to the method of NIEA, high volume air sampling method not only provided equivalently good quality data but offer a higher sample quantity for analyzing the trace level chemical component of hazardous air pollutants and the toxicity in different areas.
ABSTRACT
Background: The COVID-19 pandemic is a global health crisis with a likely long-term psychological impact on healthcare workers (HCWs). As the pandemic moves towards endemic status, little knowledge exists on how it has affected HCWs in the Kingdom of Bahrain. This study aims to evaluate the psychological impact and related factors of HCWs during the COVID-19 pandemic. Factors were assessed at two time periods: 1- July 2020 (T1: 6 months after the pandemic started in Bahrain) and 2- 6-month follow-up during January 2021 (T2: 12 months).
ABSTRACT
Background: Coronavirus disease 2019 (COVID-19) can cause acute respiratory failure and acute respiratory distress syndrome (ARDS). The prone position (PP) is widely used in patients with severe hypoxemia due to ARDS as it improves oxygenation. The aim of this study was to investigate whether improvements in gas exchange and lung mechanics with the PP were associated with survival in ventilated COVID-19 patients. Methods: Fourteen ventilated patients who were placed in the PP were included from May to June 2021. Clinical manifestations and lung mechanics parameters were collected. Results: The overall intensive care unit (ICU) mortality rate was 42.9%. Nonsurvivors were older (p = 0.014) and had higher Charlson comorbidity index (2.1 +/- 1.5 vs. 4.8 +/- 2.4, p = 0.035) and Sepsis-related Organ Failure Assessment (SOFA) (3.3 +/- 1.0 vs. 7.3 +/- 3.5, p = 0.019) scores compared to survivors. There was no difference in PaO2/FiO(2) (P/F ratio) at baseline between the survivors and nonsurvivors. The improvement in P/F ratio (p = 0.0037) and reduction in driving pressure (Pdrive) (p = 0.046) on the second day after first PP were correlated with lower mortality. Significant predictors of successfully stopping prone treatment included a reduction in Pdrive at the first hour, lower tidal volume (Vt) at the fourth hour, and P/F ratio improvement on the second day after PP. Conclusion: Improvement in P/F ratio and reduction in driving pressure on the second day after PP were correlated with reduced mortality. Three parameters could predict successful resumption of the supine position. Copyright (c) 2022, Taiwan Society of Geriatric Emergency & Critical Care Medicine.
ABSTRACT
Vaccine development is among the critical issues for ceasing the COVID-19 pandemic. This review discusses the current usage of biomaterials in vaccine development and provides brief descriptions of the vaccine types and their working mechanisms. New types of vaccine platforms (next-generation vaccines and DNA- or mRNA-based vaccines) are discussed in detail. The mRNA vaccine encoding the spike protein viral antigen can be produced in a cell-free system, suggesting that mRNA vaccines are safer than “classic vaccines” using live or inactivated virus. The mRNA vaccine efficacy is typically high at approximately 95%. However, most mRNA vaccines need to be maintained at −20 or −70 degrees for storage for long periods (half a year) and their transportation because of mRNA vaccine instability in general, although mRNA vaccines with unmodified and self-amplifying RNA (ARCT-154, Arcturus), which have a lyophilized form, have recently been reported to be kept at room temperature. mRNA vaccines are typically entrapped in lipid nanoparticles composed of ionizable lipids, polyethylene glycol (PEG)-lipids, phospholipids, and cholesterol. These components and their composition affect mRNA vaccine stability and efficacy and the size of the mRNA vaccine. The development of an improved mRNA vaccine entrapped in sophisticated biomaterials, such as novel lipid nanoparticles, using new types of biopolymers or lipids is necessary for high efficacy, safe transportation and long-term storage of the next generation of mRNA vaccines under mild conditions. © 2022 Taylor & Francis Group, LLC.
ABSTRACT
On analyzing the results of cell-based assays, we have previously shown that perilla (Perilla frutescens) leaf extract (PLE), a food supplement and orally deliverable traditional Chinese medicine approved by the Taiwan Food and Drug Administration, effectively inhibits SARS-CoV-2 by directly targeting virions. PLE was also found to modulate virus-induced cytokine expression levels. In this study, we explored the anti-SARS-CoV-2 activity of PLE in a hamster model by examining viral loads and virus-induced immunopathology in lung tissues. Experimental animals were intranasally challenged with different SARS-CoV-2 doses. Jugular blood samples and lung tissue specimens were obtained in the acute disease stage (3-4 post-infection days). As expected, SARS-CoV-2 induced lung inflammation and hemorrhagic effusions in the alveoli and perivascular areas;additionally, it increased the expression of several immune markers of lung injury - including lung Ki67-positive cells, Iba-1-positive macrophages, and myeloperoxidase-positive neutrophils. Virus-induced lung alterations were significantly attenuated by orally administered PLE. In addition, pretreatment of hamsters with PLE significantly reduced viral loads and immune marker expression. A purified active fraction of PLE was found to confer higher antiviral protection. Notably, PLE prevented SARS-CoV-2-induced increase in serum markers of liver and kidney function as well as the decrease in serum high-density lipoprotein and total cholesterol levels in a dose-dependent fashion. Differently from lung pathology, monitoring of serum biomarkers in Syrian hamsters may allow a more humane assessment of the novel drugs with potential anti-SARS-CoV-2 activity. Our results expand prior research by confirming that PLE may exert an in vivo therapeutic activity against SARS-CoV-2 by attenuating viral loads and lung tissue inflammation, which may pave the way for future clinical applications.
ABSTRACT
The insufficiency of continued nonpharmaceutical interventions (NPIs) and ongoing vaccination programs continues to pose challenges in recovering from the COVID-19 pandemic. Before herd immunity, controlling at-risk and vulnerable groups in combination with vaccination plans is strongly recommended. The construction industry is especially vulnerable to the negative impacts of COVID-19 as illustrated by frequent relevant clusters globally and given the manual labor performed by construction workers in close physical proximity, which increases the likelihood of exposure. To gain insights into the transmission dynamics of COVID-19 to inform the establishment of effective and targeted NPIs in the construction industry, a dual-community model was developed that includes the susceptible-exposed-infectious/asymptomatic-hospitalized-recovered-pathogen (SEI/AHR-P) model for construction workers and the susceptible-exposed-infectious/asymptomatic-hospitalized-recovered (SEI/AHR) model for their close contacts. The results of our sensitivity analysis corroborate previous findings that close contacts are significant participants in the spread of the infection. However, the contributions of indirect transmission pathways at a construction site were found to be weak, suggesting the need for further study given conflicting results in other research. Based on the parameters identified as significant in the sensitivity analyses, 28 NPI scenarios were devised to analyze the total attack rate (TAR) and duration of an outbreak (DO). The scenario in which exposed individuals are controlled in terms of close contacts performs best, reducing the TAR with 25% absolute efficiency (AE) and decreasing the DO in the whole population by 1.8 days. In addition to NPIs, both construction workers and their close contacts are suggested to get vaccinated. Vaccination of all construction workers would lead to a lower TAR compared to vaccination of only 15% of both construction workers and their close contacts. Vaccination of all construction workers along with at least 67% of their close contacts can extinguish an ongoing wave. © 2022 American Society of Civil Engineers.
ABSTRACT
Purpose This study deals with attenuating the risk of relying on a single export market, which was heightened by the outbreak of the COVID-19 pandemic. It focuses on Taiwanese atemoya (a fruit with short storage life) and the adoption of active controlled atmosphere (CA) containers, a new technology which lengthens storage time for other export markets. This study looks at the financial feasibility of the technology's first ever use in atemoya exports. Design/methodology/approach Apart from the standard financial assessment tools-like net present value (NPV), internal rate of return (IRR), benefit-cost ratio (BCR) and payback period (PBP)-this study calibrated five different scenarios based on data gathered from relevant market agents including suppliers, exporters, customs brokers and technology developer. Findings Due to the high profit margin and low investment cost, the use of active CA containers for long-haul exports of this highly perishable fruit is found both technically and financially feasible, despite the generally higher operational cost during the pandemic. Research limitations/implications This study looked at three specific export markets: Malaysia, Dubai and Canada. Results here may lack generalizability in other markets, although it is believed that slight deviations would not invalidate the conclusions of this research because short, medium and long distances were all covered therein. Originality/value This paper studies the first time that active CA is used for export of atemoyas to expand existing markets.
ABSTRACT
Purpose : Coronavirus disease 2019 (COVID-19) has impacted individuals seeking preventative, follow-up, and emergent ophthalmic care. In this retrospective study, we assessed the impact of COVID-19 on inpatient and emergency department (ED) ophthalmology care at a large tertiary academic hospital in the United States. Methods : We analyzed 570 ED and inpatient ophthalmology consults from March 13 to May 15 in 2020 and over the same period in 2019. Our primary endpoints were the number of consults and the percentage of consults that were 'vision-threatening' between the time periods. Our secondary endpoints were the demographics of the patients, relation to trauma, relation to an exacerbation of a chronic ocular condition, if the consult required surgical intervention, and time to surgery. Results : The total number of ED and inpatient consults decreased by 35.2% in 2020 compared to 2019. The total number of visually threatening diagnoses decreased, 97 in 2019 to 83 in 2020. The proportion of presentations with visually threatening diagnosis increased from 28.0% to 37.1% (p=0.0237). In 2020, there were a higher proportion of consults related to trauma (31.7% compared to 23.4%, p=0.0289), and consults requiring surgical intervention (19.6% compared to 12.4%, p=0.0192). The time to surgery was similar between time periods studied (p=0.902). There was not a significant difference in proportion of consults resulting from exacerbations of chronic ocular conditions (p=0.554). Conclusions : The volume of ophthalmic consults to our tertiary eye center and ED declined during the COVID-19 pandemic. There was an increase in the proportion of visually threatening diseases indicating a higher overall acuity seen by the consulting service. There was a total decrease in visually threatening diseases (despite an increase in numbers of consults from trauma), suggesting that some patients may have avoided urgent ophthalmic care due to fear of COVID-19 and the lockdown. Further research is needed to characterize the effect of COVID-19 and the regional stay-at-home order on emergent ophthalmic care delivery so we can better prepare for later stages of the pandemic and also for future pandemics.
ABSTRACT
Rationale: Growing literature on the coronavirus disease 2019 (COVID-19) suggests that obesity (BMI > 30 kg/m2) is a strong risk factor for increasing disease severity, hospitalization and admission to the intensive care unit (ICU). In such critically ill patients with acute respiratory distress syndrome (ARDS), the use of extracorporeal membrane oxygenation (ECMO) can serve as salvage therapy. The Extracorporeal Life Support Organization (ELSO) COVID-19 ECMO registry reports that 49% of its patients were classified as obese as of 12/01/2020. However, the morbidity and mortality outcomes of this subgroup remains unclear. As such, this high-risk population merits further examination. Methods: We identified adult COVID-19 ARDS patients who were candidates for either veno-venous ECMO or veno-arterial ECMO between March 13, 2020 and August 31, 2020. The eligibility for ECMO was selected based on our institutional algorithm and the EOLIA Trial criteria (except for high BMI cutoff). Patients were divided into two groups, obese (BMI > 30 kg/m2) and non-obese (BMI < 29.9 kg/m2). We compared the pre-cannulation characteristics including time elapsed between admission to ECMO, intubation to ECMO and respiratory indices. We then examined length on ECMO, ICU or hospital length of stay and disposition. Fisher's exact and Mann-Whitney U tests were used to analyze categorical and continuous data. Results: We identified a total of 41 patients, 33 (80.5%) were obese and 8 (19.5%) were non-obese [Table 1]. The average age of the obese and non-obese groups was 47.8 years and 55.5 years respectively. The median BMI was 39.85 kg/m2 (IQR: 35.63, 43.00) in the obese group and 29.05 kg/m2 (IQR: 25.35, 29.39) in the non-obese group (p <0.00001). There was no difference in precannulation characteristics between the groups. In terms of timelines, the obese group was borderline significant with regards to more time elapsed between admission to ECMO (p = 0.058), however, no other significant changes were noted. The ICU length of stay was lower in the obese group with median runtime of 22 days versus 35.5 days (p = 0.029). There was no statistically significant difference in mortality (p = 0.43) or dispositions between the two groups. Conclusion: In our study, the obesity group did not have worse outcomes than the non-obese group. This should encourage consideration of ECMO in carefully selected obese patients with severe ARDS from COVID-19.
ABSTRACT
Purpose There is increasing evidence of adverse cardiovascular morbidity associated with SARS-CoV-2 (COVID-19). Pro-B-type natriuretic peptide (proBNP) is a biomarker of myocardial stress associated with outcomes in various respiratory and cardiac diseases. We hypothesized that proBNP level would be associated with mortality and clinical outcomes in hospitalized COVID-19 patients. Methods We performed a retrospective analysis of hospitalized COVID-19 patients (n=1232) using adjusted logistic and linear regression to assess the association of admission proBNP (analyzed by both categorical cutoff >125 pg/mL and continuous log transformed proBNP) with clinical outcomes. Covariates included age, sex, race, body mass index (BMI), hypertension, coronary artery disease (CAD), diabetes, smoking history, and chronic kidney disease stage (Model 1), with Troponin I added in Model 2. We performed survival analysis by a multivariate Cox proportional hazard model, incorporating log transformed proBNP. We additionally treated BMI, a strong potential confounder of both proBNP levels and COVID-19 outcomes, as an ordinal variable ordered across tertiles. Results Patients were mean age 62.9±17.6, 53.8% male, and 35.9% Black. Preadmission comorbidities were hypertension (57.1%), diabetes (31.6%), CAD (9.0%) and heart failure (HF, 10.6%). In Model 1 and 2, higher proBNP level was significantly associated with death, new HF, length of stay, ICU duration and need for ventilation among hospitalized COVID-19 patients. This significance persisted after ordinal compression of BMI across tertiles. The adjusted hazard ratio of death for log[proBNP] was 1.56 (95% CI: 1.23-1.97;P<0.0001). Conclusion Using a relatively large and racially diverse hospitalized COVID-19 patient cohort, we find that proBNP is associated with adverse clinical outcomes, including mortality and new HF in COVID-19. Further prospective investigation is warranted on the utility of proBNP for clinical prognostication in COVID-19.