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194 lines
53 KiB
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<meta content="width=device-width, initial-scale=1.0, user-scalable=yes" name="viewport"/>
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<title>03 June, 2022</title>
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<title>Covid-19 Sentry</title><meta content="width=device-width, initial-scale=1.0" name="viewport"/><link href="styles/simple.css" rel="stylesheet"/><link href="../styles/simple.css" rel="stylesheet"/><link href="https://unpkg.com/aos@2.3.1/dist/aos.css" rel="stylesheet"/><script src="https://unpkg.com/aos@2.3.1/dist/aos.js"></script></head>
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<h1 data-aos="fade-down" id="covid-19-sentry">Covid-19 Sentry</h1>
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<h1 data-aos="fade-right" data-aos-anchor-placement="top-bottom" id="contents">Contents</h1>
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<ul>
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<li><a href="#from-preprints">From Preprints</a></li>
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<li><a href="#from-clinical-trials">From Clinical Trials</a></li>
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<li><a href="#from-pubmed">From PubMed</a></li>
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<li><a href="#from-patent-search">From Patent Search</a></li>
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</ul>
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<h1 data-aos="fade-right" id="from-preprints">From Preprints</h1>
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<li><strong>Stratification in Parents’ Selection of Developmentally Appropriate Books for Children: Register-based Evidence from Danish Public Libraries</strong> -
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<div>
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This paper studies socioeconomic gradients in selecting developmentally appropriate children’s books from public libraries. I draw on research on developmental gradients in parental inputs to hypothesize that families with high socioeconomic status (SES) are more likely to select books that match children’s developmental stage in order to best improve children’s learning environments. In contrast to previous survey-based research, I use behavioral data on the actual books families have selected from libraries. Based on Danish registry data that cover all books borrowed from public libraries in 2020, I find that highly educated families are more likely to use libraries and borrow more books when they use libraries, but they do not select a larger share of developmentally appropriate books; in fact, they select a slightly lower share. In contrast, I find only a weak positive income gradient for the amount of books borrowed and the share of developmentally appropriate books. The supplementary analyses show that results are robust across families with children of different ages and to account for nonrandom selection into the sample of library users, socioeconomic differences in children’s reading skills, and the impact of library lockdowns due to Covid-19. I conclude that stratification in library book selection is more prominent concerning the voraciousness with which highly educated parents provide reading inputs (more books) than how discriminating they are in terms of selecting developmentally appropriate books.
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🖺 Full Text HTML: <a href="https://osf.io/preprints/socarxiv/8pzv5/" target="_blank">Stratification in Parents’ Selection of Developmentally Appropriate Books for Children: Register-based Evidence from Danish Public Libraries</a>
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</div></li>
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<li><strong>Schema Playground: A tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data</strong> -
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<div>
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Background: Biomedical researchers are strongly encouraged to make their research outputs more Findable, Accessible, Interoperable, and Reusable (FAIR). While many biomedical research outputs are more readily accessible through open data efforts, finding relevant outputs remains a significant challenge. Schema.org is a metadata vocabulary standardization project that enables web content creators to make their content more FAIR. Leveraging schema.org could benefit biomedical research resource providers, but it can be challenging to apply schema.org standards to biomedical research outputs. We created an online browser-based tool that empowers researchers and repository developers to utilize schema.org or other biomedical schema projects. Results: Our browser-based tool includes features which can help address many of the barriers towards schema.org-compliance such as: The ability to easily browse for relevant schema.org classes, the ability to extend and customize a class to be more suitable for biomedical research outputs, the ability to create data validation to ensure adherence of a research output to a customized class, and the ability to register a custom class to our schema registry enabling others to search and re-use it. We demonstrate the use of our tool with the creation of the Outbreak.info schema–a large multi-class schema for harmonizing various COVID-19 related resources. Conclusions: We have created a browser-based tool to empower biomedical research resource providers to leverage schema.org classes to make their research outputs more FAIR.
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🖺 Full Text HTML: <a href="https://www.biorxiv.org/content/10.1101/2021.09.02.458726v2" target="_blank">Schema Playground: A tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data</a>
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</div></li>
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<li><strong>One Million and Counting: Estimates of Deaths in the United States from Ancestral SARS-CoV-2 and Variants</strong> -
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<b>Background:</b> Over one million COVID-19 deaths have been recorded in the United States. Sustained global SARS-CoV-2 transmission has led to the emergence of new variants with increased transmissibility, virulence, and/or immune evasion. The specific burden of mortality from each variant over the course of the U.S. COVID-19 epidemic remains unclear. <b>Methods:</b> We constructed an epidemiologic model using data reported by the CDC on COVID-19 mortality and circulating variant proportions to estimate the number of recorded COVID-19 deaths attributable to each SARS-CoV-2 variant in the U.S. We conducted sensitivity analysis to account for parameter uncertainty. <b>Findings:</b> Of the 1,003,419 COVID-19 deaths recorded as of May 12, 2022, we estimate that 460,124 (46%) were attributable to WHO-designated variants. By U.S. Census Region, the South recorded the most variant deaths per capita (median estimate 158 per 100,000), while the Northeast recorded the fewest (111 per 100,000). Over 40 percent of national COVID-19 deaths were estimated to be caused by the combination of Alpha (median estimate 39,548 deaths), Delta (273,801), and Omicron (117,560). <b>Interpretation:</b> SARS-CoV-2 variants that have emerged around the world have imposed a significant mortality burden in the U.S. In addition to national public health strategies, greater efforts are needed to lower the risk of new variants emerging, including through global COVID-19 vaccination, treatment, and outbreak mitigation.
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</p>
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<div class="article-link article-html-link">
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.05.31.22275835v1" target="_blank">One Million and Counting: Estimates of Deaths in the United States from Ancestral SARS-CoV-2 and Variants</a>
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</div></li>
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<li><strong>Iron status and the risk of sepsis and severe COVID-19: A two-sample Mendelian randomization study</strong> -
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Introduction: Observational studies have indicated an association between iron status and risk of sepsis and severe COVID-19. However, these findings may be affected by residual confounding, reverse causation. Methods: In a two-sample Mendelian randomization study using inverse variance weighted method, we estimated the effect of genetically-predicted iron biomarkers (serum iron, transferrin saturation (TSAT), total iron binding capacity (TIBC) and ferritin) on risk of sepsis and risk of being hospitalized with COVID-19. For the COVID-19 outcomes we additionally conducted sex-stratified analyses. Weighted median, Weighted mode and MR Egger were used as sensitivity analyses. Results: For risk of sepsis, one standard deviation increase in genetically-predicted serum iron was associated with odds ratio (OR) of 1.14 (95% confidence interval (CI) 1.01 to 1.29, P=0.031). The findings were supported in the analyses for transferrin saturation and total iron binding capacity, while the estimate for ferritin was inconclusive. We found a tendency of higher risk of hospitalization with COVID-19 for serum iron; OR 1.29 (CI 0.97-1.72, P=0.08), where sex stratified analyses showed OR 1.63 (CI 0.94-2.86, P=0.09) for women and OR 1.21 (CI 0.92-1.62, P=0.17) for men. Sensitivity analyses supported the main findings and did not suggest bias due to pleiotropy. Conclusions: Our findings suggest a causal effect of genetically-predicted higher iron status and risk of hospitalization due to sepsis and indications of an increased risk of being hospitalized with COVID-19. These findings warrant further studies to assess iron status in relation to severe infections, including the potential of improved management.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.06.02.22275901v1" target="_blank">Iron status and the risk of sepsis and severe COVID-19: A two-sample Mendelian randomization study</a>
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<li><strong>OpenSAFELY NHS Service Restoration Observatory 2: changes in primary care activity across six clinical areas during the COVID-19 pandemic</strong> -
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Background The COVID-19 pandemic has disrupted healthcare activity across a broad range of clinical services. The NHS stopped non-urgent work in March 2020, later recommending services be restored to near-normal levels before winter where possible. Aims Using routinely collected data, our aim was to describe changes in the volume and variation of coded clinical activity in general practice in: (i) cardiovascular disease, (ii) diabetes, (iii) mental health, (iv) female and reproductive health, (v) screening, and (vi) processes related to medication. Design and setting With the approval of NHS England, we conducted a cohort study of 23.8 million patient records in general practice, in-situ using OpenSAFELY. Methods We selected common primary care activity using CTV3 codes and keyword searches from January 2019 - December 2020, presenting median and deciles of code usage across practices per month. Results We identified substantial and widespread changes in clinical activity in primary care since the onset of the COVID-19 pandemic, with generally good recovery by December 2020. A few exceptions showed poor recovery and warrant further investigation, such as mental health, e.g. “Depression interim review” (median across practices in December 2020 -41.6% compared to December 2019). Conclusions Granular NHS GP data at population-scale can be used to monitor disruptions to healthcare services and guide the development of mitigation strategies. The authors are now developing real-time monitoring dashboards for key measures identified here as well as further studies, using primary care data to monitor and mitigate the indirect health impacts of Covid-19 on the NHS.
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</p>
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.06.01.22275674v1" target="_blank">OpenSAFELY NHS Service Restoration Observatory 2: changes in primary care activity across six clinical areas during the COVID-19 pandemic</a>
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<li><strong>Societal COVID-19 epidemic counter measures and activities associated with SARS-CoV-2 infection in an adult unvaccinated population – a case-control study in Denmark, June 2021</strong> -
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Measures to restrict physical inter-personal contact in the community have been widely implemented during the COVID-19 pandemic. We studied determinants for infection with SARS-CoV-2 with the aim of testing the efficiency of such measures. We conducted a national matched case-control study among unvaccinated persons aged 18-49 years. Cases were selected among those testing positive for SARS-CoV-2 by RT-PCR over a five-day period in June 2021. Controls were selected from the national population register and were individually matched on age, sex and municipality of residence and had not previously tested positive. Cases and controls were interviewed via telephone about contact with other persons and exposures in the community. We included 500 cases and 529 controls and determined odds ratios (ORs) and 95% confidence intervals (95%CIs) by conditional logistical regression with adjustment for household size and immigration status. We found having had contact with another individual with a known infection as the main determinant for SARS-CoV-2 infection. Reporting close contact with an infected person who either had or did not have symptoms resulted in ORs of 20 (95%CI:9.8-39) and 8.5 (95%CI 4.5-16) respectively. In contrast, community exposures were generally not associated with disease; several exposures were negatively associated. Exceptions were: attending fitness centers, OR=1.4 (95%CI:1.0-2.0) and consumption of alcohol in restaurants or cafés, OR=2.3 (95%CI:1.3–4.2). For reference, we provide a timeline of non-pharmaceutical interventions in place in Denmark from February 2020 to March 2022. Fitness centers and alcohol consumption were mildly associated with infection, in agreement with findings of our similar study conducted six month earlier (Epidemiology & Infection 2021;150:e9.). Transmission of disease through involvement in community activities appeared to occur only rarely, suggesting that community restrictions in place were efficient. Instead, transmission appeared to primarily take place in a confined space via contact to known persons.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.05.31.22274922v1" target="_blank">Societal COVID-19 epidemic counter measures and activities associated with SARS-CoV-2 infection in an adult unvaccinated population – a case-control study in Denmark, June 2021</a>
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</div></li>
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<li><strong>The spread of infectious diseases from a physics perspective</strong> -
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This paper presents a theoretical investigation of the spread of infectious diseases (including Covid-19) in a population network. The central idea is that a population can actually be considered as a network of interlinked nodes. The nodes represent the members of the population, the edges between the nodes the social contacts linking 2 population members. Infections spread throughout the population along these network edges. The actual spread of infections is described within the framework of the SIR compartmental model. Special emphasis is laid on understanding and on the interpretation of phenomena in terms of concepts borrowed from condensed-matter and statistical physics. To obtain a mathematical framework that deals with the influence of the network structure and topology, the original SIR model by Kermack and McKendrick was augmented, leading to a system of differential equations that is in principle exact, but the solution of which appears to be intractable. Therefore, combined algebraic/numerical solutions are presented for simplified (approximative) cases that nevertheless capture the essentials of the effect of the network details on the spread of an infection. Solutions of this kind were successfully tested against the results of direct statistical simulations based on Monte-Carlo methods, indicating the appropriateness of the model. Expressions for the (basic) reproduction numbers in terms of the model parameters are presented, and justify some mild criticisms on the widely spread interpretation of reproduction numbers as being the number of secondary infections due to a single active infection. Throughout the entire paper, special attention is paid to the concept of herd-immunity, its nature and its definition. The model allows for obtaining an exact (algebraic) criterion for the most relevant form of herd-immunity to occur in unvaccinated populations. Analysis of the effects of vaccination leads to an even more general version of this criterion in terms of not only the model parameters but also the effectiveness of the vaccine(s) and the vaccination rate(s). This general criterion is also exact within the context of the SIR model. Furthermore it is shown that the onset of herd-immunity can be considered as a 2nd-order phase transition of the kind that is known from thermodynamics and statistical physics, thus offering a fundamentally new viewpoint on the phenomenon. The role of percolation is highlighted and extensively investigated. It is shown that the herd-immunity transition is actually related to a percolation transition, and marks therewith the transition from a regime where the cumulative infections grow into a large macroscopic cluster that spans a major part of the population, towards a regime were the cumulative infections only occur in smaller secondary clusters of limited size. It appears that percolation phenomena become particularly important in the case of (strict) lock-downs. It is also demonstrated how a system of differential equations can be obtained that accounts for the presence of such percolation phenomena. The analyses presented in this paper also provide insight in how various measures to prevent an epidemic spread of an infection work, how they can be optimised and what potentially deceptive issues have to be considered when such measures are either implemented or scaled down. Herd-immunity appears to be a particularly tricky concept in this respect. Phenomena such as a saturation of the cumulative infection number or a fade-out of the number of active infections may easily be mistaken for a stable case of herd-immunity setting in, whereas in reality such phenomena may be no more than an artefact of protective or contact-reducing measures taken, without any meaning for the vulnerability of a population at large under normal (social) conditions. On the other hand, the paper also highlights and explains the theoretical possibility of “smothering” an epidemic via very restrictive measures that prevent it from developing out of a limited number of initial seed-infections.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.06.01.22275842v1" target="_blank">The spread of infectious diseases from a physics perspective</a>
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<li><strong>Development and Validation of Multivariable Prediction Models of Serological Response to SARS-CoV-2 Vaccination in Kidney Transplant Recipients</strong> -
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Background Repeated vaccination against SARS-CoV-2 increases serological response in kidney transplant recipients (KTR) with high interindividual variability. No decision support tool exists to predict SARS-CoV-2 vaccination response in KTR. Methods We developed, internally and externally validated five different multivariable prediction models of serological response after the third and fourth vaccine dose against SARS-CoV-2 in KTR. Using 27 candidate predictor variables, we applied statistical and machine learning approaches including logistic regression (LR), LASSO-regularized LR, random forest, and gradient boosted regression trees. For development and internal validation, data from 585 vaccinations were used. External validation was performed in four independent, international validation datasets comprising 191, 184, 254, and 323 vaccinations, respectively. Findings LASSO-regularized LR performed on the whole development dataset yielded a 23- and 11-variable model, respectively. External validation showed AUC-ROC of 0.855, 0.749, 0.828, and 0.787 for the sparser 11-variable model, yielding an overall performance 0.819. Interpretation An 11-variable LASSO-regularized LR model predicts vaccination response in KTR with good overall accuracy. Implemented as an online tool, it can guide decisions when choosing between different immunization strategies to improve protection against COVID-19 in KTR.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.06.02.22275894v1" target="_blank">Development and Validation of Multivariable Prediction Models of Serological Response to SARS-CoV-2 Vaccination in Kidney Transplant Recipients</a>
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<li><strong>Longitudinal profiles of plasma gelsolin, cytokines and antibody expression predict COVID-19 severity and hospitalization outcomes</strong> -
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Background: Prognostic markers for COVID-19 disease outcome are currently lacking. Plasma gelsolin (pGSN) is an actin-binding protein and an innate immune marker involved in disease pathogenesis and viral infections. Here, we demonstrate the utility of pGSN as a prognostic marker for COVID-19 disease outcome; a test performance that is significantly improved when combined with cytokines and antibodies compared to other conventional markers such as CRP and ferritin. Methods: Blood samples were longitudinally collected from hospitalized COVID-19 patients as well as COVID-19 negative controls and the levels of pGSN in ug/mL, cytokines and anti- SARS-CoV-2 spike protein antibodies assayed. Mean values were correlated with clinical parameters to develop a prognostic platform. Results: pGSN levels were significantly reduced in COVID-19 patients compared to healthy individuals. Additionally, pGSN levels combined with plasma IL-6, IP-10 and M-CSF significantly distinguished COVID-19 patients from healthy individuals. While pGSN and anti-spike IgG titers together strongly predict COVID-19 severity and death, the combination of pGSN and IL-6 was a significant predictor of milder disease and favorable outcomes. Conclusion: Taken together, these findings suggest that multi-parameter analysis of pGSN, cytokines and antibodies could predict COVID-19 hospitalization outcomes with greater certainty compared with conventional clinical laboratory markers such as CRP and ferritin. This research will inform and improve clinical management and health system interventions in response to SARS-CoV-2 infection.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.06.01.22275882v1" target="_blank">Longitudinal profiles of plasma gelsolin, cytokines and antibody expression predict COVID-19 severity and hospitalization outcomes</a>
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<li><strong>Income and race-ethnicity disparities for medical care utilization and expenditures in the United States, 2017-2019</strong> -
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Background: The COVID-19 pandemic has focused attention on race and income disparities in SARS-CoV-2 mortality and morbidity. Much less attention has been paid to other socioeconomic factors including income. Objective: The goal of this study was to compare disparities in medical care utilization and related expenditures associated with income to those associated with race and ethnicity in the US for those aged 0 to 64 for four categories of medical services: hospital, emergency room, ambulatory care, and prescription medications. Methods: We used Medical Expenditure Panel Survey data for years 2017 through 2019. For each of the four medical services, there were three measures. First was the percentage of those aged 0-64 with or without utilization and expenditures. Due to statistical issues related to zero values for utilization and expenditures, the second and third measures were average utilization and expenditures only for those with both utilization and expenditures. Disparities by income and race-ethnicity were measured by calculating the percent difference between the group with the lowest utilization or expenditures and the group with the highest utilization or expenditures. Results: For 9 of the 12 separate differences the income differences exceed the corresponding race-ethnicity difference and the income differences are generally much greater in magnitude. Within the income comparisons, those on Medicaid had the greatest utilization in 7 of the 8 comparisons. The High Income group had greatest expenditures for 3 of the 4 medical services. Non-Hispanic Whites had the greatest utilization and expenditures for 9 of the 12 measures and Hispanics had the least utilization and expenditures for 9 of the 12 measures. Conclusions: These results indicate that income inequalities are more strongly associated with medical care utilization and expenditures than race-ethnicity among those aged 0-64. Although more research should focus on income related health disparities in the United States, it is time to recognize that sound health policy must include reducing socioeconomic inequalities, especially those related to income.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.05.31.22275747v1" target="_blank">Income and race-ethnicity disparities for medical care utilization and expenditures in the United States, 2017-2019</a>
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<li><strong>WAVES (Web-based tool for Analysis and Visualization of Environmental Samples) – a web application for visualization of wastewater pathogen sequencing results</strong> -
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Environmental monitoring of pathogens provides an accurate and timely source of information for public health authorities and policymakers. In the last two years, wastewater sequencing proved to be an effective way of detection and quantification of SARS-CoV-2 variants circulating in population. Wastewater sequencing produces substantial amounts of geographical and genomic data. Proper visualization of spatial and temporal patterns in this data is crucial for the assessment of the epidemiological situation and forecasting. Here, we present a web-based dashboard application for visualization and analysis of data obtained from sequencing of environmental samples. The dashboard provides multi-layered visualization of geographical and genomic data. It allows to display frequencies of detected pathogen variants as well as individual mutation frequencies. The features of WAVES for early tracking and detection of novel variants in the wastewater are demonstrated in an example of BA.1 variant and the signature Spike mutation S:E484A. WAVES dashboard is easily customized through the editable configuration file and can be used for different types of pathogens and environmental samples.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.05.31.22275831v1" target="_blank">WAVES (Web-based tool for Analysis and Visualization of Environmental Samples) – a web application for visualization of wastewater pathogen sequencing results</a>
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<li><strong>Validation of a Deep Learning Model to aid in COVID-19 Detection from Digital Chest Radiographs</strong> -
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Introduction: Using artificial intelligence in imaging practice helps ensure study list reprioritization, prompt attention to urgent studies, and reduces the reporting turn-around time. Purpose: We tested a deep learning-based artificial intelligence model that can detect COVID-19 pneumonia patterns from digital chest radiographs. Material and Methods: The deep learning model was built using the enhanced U-Net architecture with Spatial Attention Gate and Xception Encoder. The model was named DxCOVID and was tested on an external clinical dataset. The dataset included 2247 chest radiographs comprising CXRs from 1046 COVID-19 positive patients (positive on RT-PCR) and 1201 COVID-19 negative patients. Results: We compared the performance of the model with three different radiologists by adjusting the model9s sensitivity as per the individual radiologist. The area under the curve (AUC) on the receiver operating characteristic (ROC) of the model was 0.87 [95% CI: 0.85, 0.89]. Conclusion: When compared to the performance of three expert readers, DxCOVID matched the output of two of the three readers. Disease-specific deep learning models using current technology are mature enough to match radiologists9 performance and can be a suitable tool to be incorporated into imaging workflows.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.06.02.22275895v1" target="_blank">Validation of a Deep Learning Model to aid in COVID-19 Detection from Digital Chest Radiographs</a>
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<li><strong>Pregnancy during COVID-19: social contact patterns and vaccine coverage of pregnant women from CoMix in 19 European countries</strong> -
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Background Evidence and advice for pregnant women evolved during the COVID-19 pandemic. We studied social contact behaviour and vaccine uptake in pregnant women between March 2020 and September 2021 in 19 European countries. Methods In each country, repeated online survey data were collected from a panel of nationally-representative participants. We calculated the mean adjusted contacts reported with an individual-level generalized additive mixed model, modelled using the negative binomial distribution and a log link function. Mean proportion of people in isolation or quarantine, and vaccination coverage by pregnancy status and gender were calculated using a clustered bootstrap. Findings We recorded 4,129 observations from 1,041 pregnant women, and 115,359 observations from 29,860 non-pregnant individuals aged 18-49. Pregnant women made slightly fewer contacts (3.6, 95%CI=3.5-3.7) than non-pregnant women (4.0, 95%CI=3.9-4.0), driven by fewer work contacts but marginally more contacts in non-essential social settings. Approximately 15-20% pregnant and 5% of non-pregnant individuals reported to be in isolation and quarantine for large parts of the study period. COVID-19 vaccine coverage was higher in pregnant women than in non-pregnant women between January and April 2021. Since May 2021, vaccination in non-pregnant women began to increase and surpassed that in pregnant women. Interpretation Social contacts and vaccine uptake protect pregnant women and their newborn babies. Recognition of maternal social support need, and efforts to promote the safety and effectiveness of the COVID-19 vaccines during pregnancy are high priorities in this vulnerable group.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.06.01.22275775v1" target="_blank">Pregnancy during COVID-19: social contact patterns and vaccine coverage of pregnant women from CoMix in 19 European countries</a>
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<li><strong>Impact of the Pandemic: Screening for Social Risk Factors in the Intensive Care Unit</strong> -
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Due to limitations in data collected through electronic health records, the social risk factors (SRF) that predate severe illness and restrict access to critical care services are poorly understood. This study explored the feasibility and utility of directly eliciting SRF in the ICU by implementing a screening program. 566 critically ill patients at the medical ICU of Robert Wood Johnson University Hospital from July 1, 2019, to September 31, 2021, were screened for seven SRF. We compared characteristics between those with and without each SRF through Chi-squared tests and Wilcoxon Rank Sum tests. Overall, 39.58% of critically ill patients reported at least one SRF. Age, socioeconomic status, insurance type, and severity score differed significantly depending on the SRF. Most notably, the prevalence of SRF, overall and individually, changed after March 2020 which represented the onset of the COVID-19 pandemic. Our findings indicate that SRF can induce low-risk severe illnesses and restrict access to critical care services.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.06.01.22275889v1" target="_blank">Impact of the Pandemic: Screening for Social Risk Factors in the Intensive Care Unit</a>
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<li><strong>OxoScan-MS: Oxonium ion scanning mass spectrometry facilitates plasma glycoproteomics in large scale</strong> -
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Protein glycosylation is a complex and heterogeneous post-translational modification. Specifically, the human plasma proteome is rich in glycoproteins, and as protein glycosylation is frequently dysregulated in disease, glycoproteomics is considered an underexplored resource for biomarker discovery. Here, we present OxoScan-MS, a data-independent mass spectrometric acquisition technology and data analysis software that facilitates sensitive, fast, and cost-effective glycoproteome profiling of plasma and serum samples in large cohort studies. OxoScan-MS quantifies glycosylated peptide features by exploiting a scanning quadrupole to assign precursors to oxonium ions, glycopeptide-specific fragments. OxoScan-MS reaches a high level of sensitivity and selectivity in untargeted glycopeptide profiling, such that it can be efficiently used with fast microflow chromatography without a need for experimental enrichment of glycopeptides from neat plasma. We apply OxoScan-MS to profile the plasma glycoproteomic in an inpatient cohort hospitalised due to severe COVID-19, and obtain precise quantities for 1,002 glycopeptide features. We reveal that severe COVID-19 induces differential glycosylation in disease-relevant plasma glycoproteins, including IgA, fibrinogen and alpha-1-antitrypsin. Thus, with OxoScan-MS we present a strategy for quantitatively mapping glycoproteomes that scales to hundreds and thousands of samples, and report glycoproteomic changes in severe COVID-19.
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🖺 Full Text HTML: <a href="https://www.biorxiv.org/content/10.1101/2022.06.01.494393v1" target="_blank">OxoScan-MS: Oxonium ion scanning mass spectrometry facilitates plasma glycoproteomics in large scale</a>
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<h1 data-aos="fade-right" id="from-clinical-trials">From Clinical Trials</h1>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>A Safety and Efficacy Study of Hymecromone Tablets for the Treatment of Patients With COVID-19.</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Drug: Hymecromone tablets; Other: Placebo<br/><b>Sponsor</b>: Shanghai Zhongshan Hospital<br/><b>Recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>A Study to Assess the Safety and Immunogenicity of a COVID-19 Vaccine Booster in Healthy Adults</strong> - <b>Condition</b>: COVID-19<br/><b>Intervention</b>: Biological: Prime-2-CoV_Beta<br/><b>Sponsors</b>: University Hospital Tuebingen; FGK Clinical Research GmbH; VisMederi srl; Staburo GmbH; Viedoc Technologies AB<br/><b>Not yet recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Eucalyptus Oil as Adjuvant Therapy for Coronavirus Disease 19 (COVID-19)</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Drug: Eucalyptus Oil; Drug: Standard COVID medication<br/><b>Sponsors</b>: Hasanuddin University; Ministry of Agriculture, Republic of Indonesia<br/><b>Completed</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Study of Oral High/Low-dose Cepharanthine Compared With Placebo in Non Hospitalized Adults With COVID-19</strong> - <b>Condition</b>: Asymptomatic COVID-19<br/><b>Interventions</b>: Drug: Cepharanthine; Drug: Placebo<br/><b>Sponsors</b>: Shanghai Jiao Tong University School of Medicine; YUNNAN BAIYAO GROUP CO.,LTD<br/><b>Not yet recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>A Study to Learn About the Study Medicine (Called Nirmatrelvir/Ritonavir) in Pregnant Women With Mild or Moderate COVID-19.</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Drug: nirmatrelvir; Drug: ritonavir<br/><b>Sponsor</b>: Pfizer<br/><b>Not yet recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Evaluation of COVID-19 Vaccines Given as a Booster in Healthy Adults in Indonesia (MIACoV Indonesia)</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Biological: Pfizer-BioNTech Standard dose; Biological: AstraZeneca Standard dose; Biological: Pfizer-BioNTech Fractional dose; Biological: AstraZeneca Fractional dose; Biological: Moderna Standard dose; Biological: Moderna Fractional dose<br/><b>Sponsors</b>: Murdoch Childrens Research Institute; Universitas Padjadjaran (UNPAD); Universitas Indonesia (UI); Health Development Policy Agency, Ministry of Health Republic of Indonesia; Coalition for Epidemic Preparedness Innovations; The Peter Doherty Institute for Infection and Immunity<br/><b>Not yet recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>α-synuclein Seeding Activity in the Olfactory Mucosa in COVID-19</strong> - <b>Condition</b>: COVID-19<br/><b>Intervention</b>: Other: Real-time Quaking-Induced Conversion (RT-QuIC)<br/><b>Sponsor</b>: Medical University Innsbruck<br/><b>Recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Immunogenicity and Safety of a Third Dose of COVID-19 Vaccine(Vero Cell), Inactivated in the Elderly</strong> - <b>Condition</b>: COVID-19<br/><b>Intervention</b>: Biological: COVID-19 Vaccine (Vero cell), Inactivated<br/><b>Sponsor</b>: Sinovac Research and Development Co., Ltd.<br/><b>Active, not recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Efficacy, Safety and Immunogenicity Study of the Recombinant Two-component COVID-19 Vaccine (CHO Cell)(Recov)</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Biological: Recombinant two-component COVID-19 vaccine (CHO cell); Biological: Placebo<br/><b>Sponsor</b>: Jiangsu Rec-Biotechnology Co., Ltd.<br/><b>Not yet recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>A Phase 1a Trial to Evaluate the Safety and Immunogenicity of a SARS-CoV-2 mRNA Chimera Vaccine Against COVID-19</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Biological: RQ3013; Biological: Comirnaty<br/><b>Sponsors</b>: Walvax Biotechnology Co., Ltd.; Shanghai RNACure Biopharma Co., Ltd.<br/><b>Not yet recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>A Phase 1b Trial to Evaluate the Safety and Immunogenicity of a SARS-CoV-2 mRNA Chimera Vaccine Against COVID-19</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Biological: RQ3013; Biological: Comirnaty<br/><b>Sponsors</b>: Walvax Biotechnology Co., Ltd.; Shanghai RNACure Biopharma Co., Ltd.<br/><b>Not yet recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Paxlovid in the Treatment of COVID-19 Patients With Uremia</strong> - <b>Conditions</b>: COVID-19; Uremia<br/><b>Interventions</b>: Drug: Paxlovid; Drug: standard-of-care<br/><b>Sponsor</b>: Ruijin Hospital<br/><b>Not yet recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Telemedically Assisted Sampling of COVID-19 Patients - Is the Sampling Quality Sufficient</strong> - <b>Conditions</b>: Telemedicine; Pharynx; COVID-19<br/><b>Intervention</b>: Diagnostic Test: telemedically guided oropharyngeal + nasal (OP+N) self-sampling (GSS) and nasopharyngeal (NP) or OP+N sampling performed by health care professionals (HCP)<br/><b>Sponsor</b>: Teststation Praxis Dr. med Bielecki<br/><b>Active, not recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Treatment of COVID-19 Post-acute Cognitive Impairment Sequelae With tDCS</strong> - <b>Conditions</b>: Cognitive Impairment; Post-Acute Sequelae of SARS-CoV-2 Infection; COVID-19<br/><b>Interventions</b>: Procedure: Active tDCS and cognitive training; Procedure: Sham tDCS and cognitive training<br/><b>Sponsors</b>: University of Sao Paulo; Fundação de Amparo à Pesquisa do Estado de São Paulo<br/><b>Not yet recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Improving Pediatric COVID-19 Vaccine Uptake Using an mHealth Tool</strong> - <b>Conditions</b>: COVID-19 Vaccines; Telemedicine; Vaccine Hesitancy; Pediatric ALL<br/><b>Interventions</b>: Behavioral: COVID-19 Vaccine Uptake App; Other: General Health App<br/><b>Sponsors</b>: University of Arkansas; National Institutes of Health (NIH); University of Nebraska; University of Montana<br/><b>Not yet recruiting</b></p></li>
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</ul>
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<h1 data-aos="fade-right" id="from-pubmed">From PubMed</h1>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>A comprehensive review about immune responses and exhaustion during coronavirus disease (COVID-19)</strong> - Coronavirus disease (COVID-19) is a viral infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. The infection was reported in Wuhan, China, in late December 2019 and has become a major global concern due to severe respiratory infections and high transmission rates. Evidence suggests that the strong interaction between SARS-CoV-2 and patients’ immune systems leads to various clinical symptoms of COVID-19. Although the adaptive immune responses are…</p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Cleavage of the selective autophagy receptor SQSTM1/p62 by the SARS-CoV-2 main protease NSP5 prevents the autophagic degradation of viral membrane proteins</strong> - Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the coronavirus disease 2019 (COVID-19) global pandemic. Omicron, a new variant of SARS-CoV-2, has the characteristics of strong transmission and pathogenicity, short incubation period, and rapid onset progression, and has spread rapidly around the world. The high replication rate and intracellular accumulation of SARS-CoV-2 are remarkable, but the underlying molecular mechanisms remain unclear. Autophagy acts as a…</p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>A dimeric proteomimetic prevents SARS-CoV-2 infection by dimerizing the spike protein</strong> - Protein tertiary structure mimetics are valuable tools to target large protein-protein interaction interfaces. Here, we demonstrate a strategy for designing dimeric helix-hairpin motifs from a previously reported three-helix-bundle miniprotein that targets the receptor-binding domain (RBD) of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). Through truncation of the third helix and optimization of the interhelical loop residues of the miniprotein, we developed a thermostable dimeric…</p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Metformin therapy in COVID-19: inhibition of NETosis</strong> - No abstract</p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>What Is an Antibody Test? Characteristics of Antibodies against SARS-CoV-2 and Their Tests</strong> - Antibodies play a major role in immune responses against viruses, which inhibit infection by binding to target viral antigen. Antibodies are induced by viral entry to the body and vaccination that artificially induces immune responses; therefore, antibody tests are used in research for infection history and evaluation of vaccine efficacy. Currently, antibody tests against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) by immunochromatography, enzyme-linked immunosorbent assay…</p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Suite of TMPRSS2 Assays for Screening Drug Repurposing Candidates as Potential Treatments of COVID-19</strong> - SARS-CoV-2 is the causative viral pathogen driving the COVID-19 pandemic that prompted an immediate global response to the development of vaccines and antiviral therapeutics. For antiviral therapeutics, drug repurposing allows for rapid movement of the existing clinical candidates and therapies into human clinical trials to be tested as COVID-19 therapies. One effective antiviral treatment strategy used early in symptom onset is to prevent viral entry. SARS-CoV-2 enters ACE2-expressing cells…</p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Synthetic Heparan Sulfate Mimetic Pixatimod (PG545) Potently Inhibits SARS-CoV-2 by Disrupting the Spike-ACE2 Interaction</strong> - Heparan sulfate (HS) is a cell surface polysaccharide recently identified as a coreceptor with the ACE2 protein for the S1 spike protein on SARS-CoV-2 virus, providing a tractable new therapeutic target. Clinically used heparins demonstrate an inhibitory activity but have an anticoagulant activity and are supply-limited, necessitating alternative solutions. Here, we show that synthetic HS mimetic pixatimod (PG545), a cancer drug candidate, binds and destabilizes the SARS-CoV-2 spike protein…</p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>High-Resolution Magic-Angle Spinning NMR Spectroscopy for Evaluation of Cell Shielding by Virucidal Composites Based on Biogenic Silver Nanoparticles, Flexible Cellulose Nanofibers and Graphene Oxide</strong> - Antiviral and non-toxic effects of silver nanoparticles onto in vitro cells infected with coronavirus were evaluated in this study using High-Resolution Magic-Angle Spinning Nuclear Magnetic Resonance (HR-MAS NMR) spectroscopy. Silver nanoparticles were designed and synthesized using an orange flavonoid-hesperetin (HST)-for reduction of silver(I) and stabilization of as obtained nanoparticles. The bio-inspired process is a simple, clean, and sustainable way to synthesize biogenic silver…</p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Unravelling the Therapeutic Potential of Botanicals Against Chronic Obstructive Pulmonary Disease (COPD): Molecular Insights and Future Perspectives</strong> - Background: COPD (chronic obstructive pulmonary disease) is a serious health problem worldwide. Present treatments are insufficient and have severe side effects. There is a critical shortage of possible alternative treatments. Medicinal herbs are the most traditional and widely used therapy for treating a wide range of human illnesses around the world. In several countries, different plants are used to treat COPD. Purpose: In this review, we have discussed several known cellular and molecular…</p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Binding of SARS-CoV-2 protein ORF9b to mitochondrial translocase TOM70 prevents its interaction with chaperone HSP90</strong> - The emergence of the COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains a great threat to global health. ORF9b, an important accessory protein of SARS-CoV-2, plays a critical role in the viral host interaction, targeting TOM70, a member of the mitochondrial translocase of the outer membrane complex. The assembly between ORF9b and TOM70 is implicated in disrupting mitochondrial antiviral signaling, leading to immune evasion. We describe the…</p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>High-throughput drug screening allowed identification of entry inhibitors specifically targeting different routes of SARS-CoV-2 Delta and Omicron/BA.1</strong> - The Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV-2) has continuously evolved, resulting in the emergence of several variants of concern (VOCs). To study mechanisms of viral entry and potentially identify specific inhibitors, we pseudotyped lentiviral vectors with different SARS-CoV-2 VOC spike variants (D614G, Alpha, Beta, Delta, Omicron/BA.1), responsible for receptor binding and membrane fusion. These SARS-CoV-2 lentiviral pseudoviruses were applied to screen 774 FDA-approved…</p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Exploration of potential inhibitors for SARS-CoV-2 Mpro considering its mutants via structure-based drug design, molecular docking, MD simulations, MM/PBSA and DFT calculations</strong> - The main protease (Mpro) of SARS-COV-2 plays a vital role in the viral life cycle and pathogenicity. Due to its specific attributes, this 3-chymotrypsin like protease (3Cl-P) can be a reliable target for the drug design to combat COVID-19. Since the advent of COVID-19, Mpro has undergone many mutations. Here, the impact of 10 mutations based on their frequency and 5 more based on their proximity to the active site was investigated. For comparison purposes, the docking process was also performed…</p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Performance of nasopharyngeal swab and saliva in detecting Delta and Omicron SARS-CoV-2 variants</strong> - A prospective cohort study was conducted during the Delta and Omicron SARS-CoV-2 epidemic waves from paired nasopharyngeal swab (NPS) and saliva samples taken from 624 participants. The study aimed to assess if any differences among participants from both waves could be observed and if any difference in molecular diagnostic performance could be observed among the two sample types. Samples were transported immediately to the laboratory to ensure the highest possible sample quality without any…</p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>COVID-19 therapies: do we see substantial progress?</strong> - The appearance of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and its spread all over the world is the cause of the coronavirus disease 2019 (COVID-19) pandemic, which has recently resulted in almost 400 million confirmed cases and 6 million deaths, not to mention unknown long-term or persistent side effects in convalescent individuals. In this short review, we discuss approaches to treat COVID-19 that are based on current knowledge of the mechanisms of viral cell receptor…</p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Structural and biochemical mechanism for increased infectivity and immune evasion of Omicron BA.2 variant compared to BA.1 and their possible mouse origins</strong> - The Omicron BA.2 variant has become a dominant infective strain worldwide. Receptor binding studies show that the Omicron BA.2 spike trimer exhibits 11-fold and 2-fold higher potency in binding to human ACE2 than the spike trimer from the wildtype (WT) and Omicron BA.1 strains. The structure of the BA.2 spike trimer complexed with human ACE2 reveals that all three receptor-binding domains (RBDs) in the spike trimer are in open conformation, ready for ACE2 binding, thus providing a basis for the…</p></li>
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<h1 data-aos="fade-right" id="from-patent-search">From Patent Search</h1>
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