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<title>22 September, 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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<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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<h1 data-aos="fade-right" id="from-preprints">From Preprints</h1>
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<li><strong>Information Delivered by a Chatbot Has a Positive Impact on COVID-19 Vaccines Attitudes and Intentions</strong> -
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The COVID-19 vaccines will not end the pandemic if they stay in freezers. In many countries, such as France, COVID-19 vaccines hesitancy is high. It is crucial that governments make it as easy as possible for people who want to be vaccinated to do so, but also that they devise communication strategies to address the concerns of vaccine hesitant individuals. We introduce and test on 701 French participants a novel messaging strategy: a chatbot that answers people’s questions about COVID-19 vaccines. We find that interacting with this chatbot for a few minutes significantly increases people’s intentions to get vaccinated (ß = 0.12) and has a positive impact on their attitudes towards COVID-19 vaccination (ß = 0.23). Our results suggest that a properly scripted and regularly updated chatbot could offer a powerful resource to help fight hesitancy towards COVID-19 vaccines.
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🖺 Full Text HTML: <a href="https://psyarxiv.com/eb2gt/" target="_blank">Information Delivered by a Chatbot Has a Positive Impact on COVID-19 Vaccines Attitudes and Intentions</a>
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<li><strong>PepGM: A probabilistic graphical model for taxonomic inference of viral proteome samples with associated confidence scores</strong> -
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Motivation: Inferring taxonomy in mass spectrometry-based shotgun proteomics is a complex task. In multi-species or viral samples of unknown taxonomic origin, the presence of proteins and corresponding taxa must be inferred from a list of identified peptides which is often complicated by protein homology: many proteins do not only share peptides within a taxon but also between taxa. However, correct taxonomic identification is crucial when identifying different viral strains with high sequence homology, considering, e.g., the different epidemiological characteristics of the various strains of SARS-CoV-2. Additionally, many viruses mutate frequently, further complicating the correct assignment of virus proteomic samples. Results: We present PepGM, a probabilistic graphical for the taxonomic assignment of virus proteomic samples with strain-level resolution and associated confidence scores. PepGM combines the results of a standard proteomic database search algorithm with belief propagation to calculate the marginal distributions, and thus confidence score, for potential taxonomic assignments. We demonstrate the performance of PepGM using several publicly available virus proteomic datasets, showing its strain level resolution performance. In two out of eight cases, the taxonomic assignments were only correct on species level, which PepGM clearly indicates by lower confidence scores. Availability and Implementation: PepGM is written in Python and embedded into a Snakemake workflow. Its is available at https://github.com/BAMeScience/PepGM .
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🖺 Full Text HTML: <a href="https://www.biorxiv.org/content/10.1101/2022.09.21.508832v1" target="_blank">PepGM: A probabilistic graphical model for taxonomic inference of viral proteome samples with associated confidence scores</a>
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<li><strong>Prediction of RNA secondary structures in SARS-CoV-2 and comparison with contemporary predictions</strong> -
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SARS-CoV-2, the causative agent of covid-19, is known to exhibit secondary structure in its 5’ and 3’ untranslated regions, along with the frameshifting stimulatory element situated between ORF1a and 1b. To identify further regions containing conserved structure, multiple sequence alignment with related coronaviruses was used as a starting point from which to apply a modified computational pipeline developed to identify non-coding RNA elements in vertebrate eukaryotes. Three different RNA structural prediction approaches were employed in this modified pipeline. Forty genomic regions deemed likely to harbour structure were identified, ten of which exhibited three-way consensus substructure predictions amongst our predictive utilities. Intracomparison of the pipeline’s predictive utilities, along with intercomparison with three previously published SARS-CoV-2 structural datasets, were performed. Limited agreement as to precise structure was observed, although different approaches appear to agree upon regions likely to contain structure in the viral genome.
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🖺 Full Text HTML: <a href="https://www.biorxiv.org/content/10.1101/2022.09.20.508790v1" target="_blank">Prediction of RNA secondary structures in SARS-CoV-2 and comparison with contemporary predictions</a>
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<li><strong>Prevalence of SARS-CoV-2 Antibodies after the Omicron Surge, Kingston, Jamaica, 2022</strong> -
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A cross-sectional SARS-CoV-2 serosurvey was conducted after the Omicron surge in Jamaica using 1,540 samples collected during March - May 2022 from persons attending antenatal, STI and non-communicable diseases clinics in Kingston, Jamaica. SARS-CoV-2 spike receptor binding domain (RBD) and/or nucleocapsid IgG antibodies were detected for 88.4% of the study population, with 77.0% showing evidence of previous SARS-CoV-2 infection. Of persons previously infected with SARS-CoV-2 and/or with COVID-19 vaccination, 9.6% were negative for spike RBD IgG, most of which were unvaccinated previously infected persons. Amongst unvaccinated previously infected people, age was associated with testing spike RBD IgG negative. When considering all samples, median spike RBD IgG levels were 131.6 BAU/mL for unvaccinated persons with serological evidence of past infection, 90.3 BAU/mL for vaccinated persons without serological evidence of past infection, and 896.1 BAU/mL for vaccinated persons with serological evidence of past infection. Our study of the first reported SARS-CoV-2 serosurvey in Jamaica shows extensive SARS-CoV-2 population immunity, identifies a substantial portion of the population lacking spike RBD IgG, and provides additional evidence for increasing COVID-19 vaccine coverage in Jamaica.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.09.20.22280173v1" target="_blank">Prevalence of SARS-CoV-2 Antibodies after the Omicron Surge, Kingston, Jamaica, 2022</a>
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<li><strong>Food Insecurity During the First Year of COVID-19: An Analysis of Employment and Sociodemographic Factors Among a Longitudinal Cohort (CHASING COVID)</strong> -
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Objectives While much has been reported about the impact of COVID-19 on U.S. food insecurity, longitudinal data and the variability experienced by people working in different industries are limited. This study aims to further characterize individuals experiencing food insecurity during the pandemic in terms of employment and sociodemographic characteristics and degree of food insecurity. Methods The study sample consisted of people enrolled in a U.S. prospective cohort study (CHASING COVID) who completed all food insecurity questionnaires from Visit 1 (April-July 2020) through Visit 7 (May-June 2021). Descriptive statistics and logistic regression models were used to determine employment and sociodemographic correlates of food insecurity (using a screening question from the USDA HFSS). Patterns of food insecurity and utilization of food benefit programs were also examined. Results Thirty-one percent (1251/4019) of the sample were food insecure. Black and Hispanic respondents, households with children, and those with lower income and education levels had a higher odds of food insecurity. People employed in construction, leisure/hospitality and trade/transportation industries had the highest burden of both food insecurity and income loss. Among those reporting food insecurity, 40% were persistently food insecure (≥4 consecutive visits), and 46% did not utilize any food benefit programs. Conclusions The pandemic resulted in widespread food insecurity in our cohort, much of which was persistent. In addition to addressing sociodemographic disparities, future policies should focus on the needs of those working in vulnerable industries and ensure those experiencing food insecurity can easily participate in food benefit programs for which they are eligible.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.09.20.22280094v1" target="_blank">Food Insecurity During the First Year of COVID-19: An Analysis of Employment and Sociodemographic Factors Among a Longitudinal Cohort (CHASING COVID)</a>
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<li><strong>Safety, Immunogenicity and Efficacy of NVX-CoV2373 in Adolescents in PREVENT-19: A Randomized, Phase 3 Trial</strong> -
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BACKGROUND Over 20% of cases and 0.4% of deaths from Covid-19 occur in children. Following demonstration of safety and efficacy of the adjuvanted, recombinant spike protein vaccine NVX-CoV2373 in adults, the PREVENT-19 trial enrolled adolescents. METHODS Safety, immunogenicity, and efficacy of NVX-CoV2373 were evaluated in adolescents aged 12 to <18 years in an expansion of PREVENT-19, a phase 3, randomized, observer-blinded, placebo-controlled trial in the United States. Participants were randomized 2:1 to two doses of NVX-CoV2373 or placebo 21 days apart, and followed for a median of 2 months after second vaccination. Primary end points were serologic non-inferiority of neutralizing antibody (NA) responses compared with young adults (18 to <26 years) in PREVENT-19, protective efficacy against laboratory-confirmed Covid-19, and assessment of reactogenicity/safety. RESULTS Among 2,247 participants randomized between April-June 2021, 1,491 were allocated to NVX-CoV2373 and 756 to placebo. Post-vaccination, the ratio of NA geometric mean titers in adolescents compared to young adults was 1.5 (95% confidence interval [CI] 1.3 to 1.7). Twenty Covid-19 cases (all mild) occurred: 6 among NVX-CoV2373 and 14 among placebo recipients (vaccine efficacy [VE]: 79.5%, 95% CI, 46.8 to 92.1). All sequenced viral genomes (11/20) were identified as Delta variant (Delta variant VE: 82.0% [95% CI: 32.4 to 95.2]). Reactogenicity was largely mild-to-moderate, transient, and more frequent in NVX-CoV2373 recipients and after the second dose. Serious adverse events were rare and evenly distributed between treatments. CONCLUSIONS NVX-CoV2373 was safe, immunogenic, and efficacious in the prevention of Covid-19 and those cases caused by the Delta variant in adolescents. (Funded by the Office of the Assistant Secretary for Preparedness and Response, Biomedical Advanced Research and Development Authority and the National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health; PREVENT-19 ClinicalTrials.gov number, NCT04611802).
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.09.20.22279903v1" target="_blank">Safety, Immunogenicity and Efficacy of NVX-CoV2373 in Adolescents in PREVENT-19: A Randomized, Phase 3 Trial</a>
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<li><strong>Comprehensive analysis of immune responses in CLL patients after heterologous COVID-19 vaccination</strong> -
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Patients with chronic lymphocytic leukemia (CLL) treated with B-cell pathway inhibitors and anti-CD20 antibodies exhibit low humoral response rate (RR) following SARS-CoV-2 vaccination. To investigate the relationship between the initial transcriptional response to vaccination with ensuing B and T cell immune responses, we performed a comprehensive immune transcriptome analysis flanked by antibody and T cell assays in peripheral blood prospectively collected from 15 CLL/SLL patients vaccinated with heterologous BNT162b2/ChAdOx1 with follow up at a single institution. The two-dose antibody RR was 40% increasing to 53% after booster. Patients on BTKi, venetoclax and/or anti-CD20 antibody within 12 months of vaccination responded less well than those under BTKi alone. The two-dose T cell RR was 80% increasing to 93% after booster. Transcriptome studies revealed that seven patients showed interferon-mediated signaling activation within 2 days and one at 7 days after vaccination. Increasing counts of COVID-19 specific IGHV genes correlated with B-cell reconstitution and improved humoral RR. T cell responses in CLL patients appeared after vaccination regardless of treatment status. A higher humoral RR was associated with BTKi treatment and B-cell reconstitution. Boosting was particularly effective when intrinsic immune status was improved by CLL-treatment.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.09.21.22280205v1" target="_blank">Comprehensive analysis of immune responses in CLL patients after heterologous COVID-19 vaccination</a>
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<li><strong>Exploring the relationship between job characteristics and infection: Application of a COVID-19 Job Exposure Matrix to SARS-CoV-2 infection data in the United Kingdom</strong> -
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Objectives To assess whether workplace exposures as estimated via a COVID-19 Job Exposure Matrix (JEM) are associated with SARS-CoV-2. Methods Data on 244,470 participants were available from the ONS Coronavirus Infection Survey (CIS) and 16,801 participants from the Virus Watch Cohort, restricted to workers aged 20 to 64. Analysis used logistic regression models with SARS-CoV-2 as the dependent variable for eight individual JEM domains (number of workers, nature of contacts, contact via surfaces, indoor or outdoor location, ability to social distance, use of face covering, job insecurity, migrant workers) with adjustment for age, sex, ethnicity, Index of Multiple Deprivation (IMD), region, household size, urban vs rural area, and health conditions. Analyses were repeated for three time periods (i) February 2020 (Virus Watch)/April 2020 (CIS) to May 2021), (ii)June 2021 to November 2021, (iii) December 2021 to January 2022. Results Overall, higher risk classifications for the first six domains tended to be associated with an increased risk of infection, with little evidence of a relationship for domains relating to proportion of workers with job insecurity or migrant workers. By time there was a clear exposure-response relationship for these domains in the first period only. Results were largely consistent across the two cohorts. Conclusions An exposure-response relationship exists in the early phase of the COVID-19 pandemic for number of contacts, nature of contacts, contacts via surfaces, indoor or outdoor location, ability to social distance and use of face coverings. These associations appear to have diminished over time.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.09.21.22280191v1" target="_blank">Exploring the relationship between job characteristics and infection: Application of a COVID-19 Job Exposure Matrix to SARS-CoV-2 infection data in the United Kingdom</a>
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<li><strong>Reconstructing the SARS-CoV-2 epidemic in eastern Uganda through longitudinal serosurveillance in a malaria cohort</strong> -
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ABSTRACT Importance: Estimating the true burden of SARS-CoV-2 infection has been difficult in sub-Saharan Africa due to asymptomatic infections and inadequate testing capacity. Antibody responses from serologic surveys can provide an estimate of SARS-CoV-2 exposure at the population level. Objective: To estimate SARS-CoV-2 seroprevalence, attack rates, and re-infection in eastern Uganda using serologic surveillance from 2020 to early 2022. Design: Plasma samples from participants in the Program for Resistance, Immunology, Surveillance, and Modeling of Malaria in Uganda (PRISM) Border Cohort were obtained at four sampling intervals: October-November 2020; March-April 2021; August-September 2021; and February-March 2022. Setting: Tororo and Busia districts, Uganda. Participants: 1,483 samples from 441 participants living in 76 households were tested. Each participant contributed up to 4 time points for SARS-CoV-2 serology, with almost half of all participants contributing at all 4 time points, and almost 90% contributing at 3 or 4 time points. Information on SARS-CoV-2 vaccination status was collected from participants, with the earliest reported vaccinations in the cohort occurring in May 2021. Main Outcome(s) and Measure(s): The main outcomes of this study were antibody responses to the SARS-CoV-2 spike protein as measured with a bead-based serologic assay. Individual-level outcomes were aggregated to population-level SARS-CoV-2 seroprevalence, attack rates, and boosting rates. Estimates were weighted by the local age distribution based on census data. Results: By the end of the Delta wave and before widespread vaccination, nearly 70% of the study population had experienced SARS-CoV-2 infection. During the subsequent Omicron wave, 85% of unvaccinated, previously seronegative individuals were infected for the first time, and ~50% or more of unvaccinated, already seropositive individuals were likely re-infected, leading to an overall 96% seropositivity in this population. Our results suggest a lower probability of re-infection in individuals with higher pre-existing antibody levels. We found evidence of household clustering of SARS-CoV-2 seroconversion. We found no significant associations between SARS-CoV-2 seroconversion and gender, household size, or recent Plasmodium falciparum malaria exposure. Conclusions and Relevance: Findings from this study are consistent with very high infection rates and re-infection rates for SARS-CoV-2 in a rural population from eastern Uganda throughout the pandemic.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.09.20.22280170v1" target="_blank">Reconstructing the SARS-CoV-2 epidemic in eastern Uganda through longitudinal serosurveillance in a malaria cohort</a>
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<li><strong>Comparative epidemic expansion of SARS-CoV-2 variants Delta and Omicron in Amazonas, a Brazilian setting with high levels of hybrid immunity</strong> -
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The SARS-CoV-2 variants of concern (VOCs) Delta and Omicron spread globally during mid and late 2021, respectively, with variable impact according to the immune population landscape. In this study, we compare the dissemination dynamics of these VOCs in the Amazonas state, one of Brazil9s most heavily affected regions. We sequenced the virus genome from 4,128 patients collected in Amazonas between July 1st, 2021 and January 31st, 2022 and investigated the lineage replacement dynamics using a phylodynamic approach. The VOCs Delta and Omicron displayed similar patterns of phylogeographic spread but significantly different epidemic dynamics. The Delta and Omicron epidemics were fueled by multiple introduction events, followed by the successful establishment of a few local transmission lineages of considerable size that mainly arose in the Capital, Manaus. The VOC Omicron spread and became dominant much faster than the VOC Delta. We estimate that under the same epidemiological conditions, the average Re of Omicron was ~3.3 times higher than that of Delta and the average Re of the Delta was ~1.3 times higher than that of Gamma. Furthermore, the gradual replacement of Gamma by Delta occurred without an upsurge of COVID-19 cases, while the rise of Omicron fueled a sharp increase in SARS-CoV-2 infection. The Omicron wave displayed a shorter duration and a clear decoupling between the number of SARS-CoV-2 cases and deaths compared with previous (B.1.* and Gamma) waves in the Amazonas state. These findings suggest that the high level of hybrid immunity (infection plus vaccination) acquired by the Amazonian population by mid-2021 was able to limit the spread of the VOC Delta and was also probably crucial to curb the number of severe cases, although not the number of VOC Omicron new infections.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.09.21.22280193v1" target="_blank">Comparative epidemic expansion of SARS-CoV-2 variants Delta and Omicron in Amazonas, a Brazilian setting with high levels of hybrid immunity</a>
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<li><strong>Bayesian Prediction of Severe Outcomes in the LabMarCS: Laboratory Markers of COVID-19 Severity - Bristol Cohort</strong> -
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<b>Objectives:</b> To develop cross-validated prediction models for severe outcomes in COVID-19 using blood biomarker and demographic data; Demonstrate best practices for clinical data curation and statistical modelling decisions, with an emphasis on Bayesian methods. <b>Design:</b> Retrospective observational cohort study. <b>Setting:</b> Multicentre across National Health Service (NHS) trusts in Southwest region, England, UK. <b>Participants:</b> Hospitalised adult patients with a positive SARS-CoV 2 by PCR during the first wave (March - October 2020). 843 COVID-19 patients (mean age 71, 45% female, 32% died or needed ICU stay) split into training (n=590) and validation groups (n=253) along with observations on demographics, coinfections, and 30 laboratory blood biomarkers. <b>Primary outcome measures:</b> ICU admission or death within 28-days of admission to hospital for COVID-19 or a positive PCR result if already admitted. <b>Results:</b> Predictive regression models were fit to predict primary outcomes using demographic data and initial results from biomarker tests collected within 3 days of admission or testing positive if already admitted. Using all variables, a standard logistic regression yielded an internal validation median AUC of 0.7 (95% Interval [0.64,0.81]), and an external validation AUC of 0.67 [0.61, 0.71], a Bayesian logistic regression using a horseshoe prior yielded an internal validation median AUC of 0.78 [0.71, 0.85], and an external validation median AUC of 0.70 [0.68, 0.71]. Variable selection performed using Bayesian predictive projection determined a four variable model using Age, Urea, Prothrombin time and Neutrophil-Lymphocyte ratio, with a median AUC of 0.74 [0.67, 0.82], and external validation AUC of 0.70 [0.69, 0.71]. <b>Conclusions:</b> Our study reiterates the predictive value of previously identified biomarkers for COVID-19 severity assessment. Given the small data set, the full and reduced models have decent performance, but would require improved external validation for clinical application. The study highlights a variety of challenges present in complex medical data sets while maintaining best statistical practices with an emphasis on showcasing recent Bayesian methods.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.09.16.22279985v2" target="_blank">Bayesian Prediction of Severe Outcomes in the LabMarCS: Laboratory Markers of COVID-19 Severity - Bristol Cohort</a>
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<li><strong>Guillain-Barré Syndrome: A Case Report of Post Covid-19 Vaccination in the Philippines</strong> -
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Guillain-Barré Syndrome (GBS) is a complex autoimmune disorder where a person’s own immune system damages the nerve and is usually characterized by ascending symmetrical weakness of the upper and lower extremities (Wijdicks & Klein, 2017). It is a rare condition and the worldwide frequency of GBS is only 2 in 100,000 adult individuals (McGrogan et al., 2009). Studies have shown its association with different vaccines but in these pandemic times, there is a lack of literature on post-COVID-19 vaccination-associated GBS. We report a case of a 68-year-old male from Caloocan City with an initial complaint of febrile illness followed by distal lower extremity weakness which started seven (7) days after the patient received his first Sinovac-CoronaVac vaccine. We report a case of GBS that is related to the Sinovac-CoronaVac vaccine which adds to the body of literature that is currently available and may reflect a possible link.
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🖺 Full Text HTML: <a href="https://osf.io/zsvmf/" target="_blank">Guillain-Barré Syndrome: A Case Report of Post Covid-19 Vaccination in the Philippines</a>
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<li><strong>Government in the Money View: Sovereign Debt, Liquidity Preference, and the Fiscal-Monetary Nexus</strong> -
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In times of financial crisis, we expect monetary authorities to provide liquidity support to banks at risk of failure. However, governments often provide monetary support to banks at risk of failure through guarantees and direct lending to financial institutions, often in tandem with monetary authorities. At the same time, governments may require liquidity support in moments of crisis, when cyclical deficits rise, and bond market activity constrains access to funding. This paper introduces governments’ activity into both the Post-Keynesian theory of endogenous money as well as Mehrling’s ‘Money View’ of the economy. It demonstrates how government activity becomes more important during periods of heightened liquidity preference through its support of financial institutions, while governments may simultaneously become more vulnerable to private bondholders increased liquidity preference. Some governments are likely to face greater obstacles in providing liquidity and accessing funding in times of economic uncertainty, while others may find their ability to provide liquidity is bolstered by popular perceptions of their credit worthiness. Recent experiences during the Global Financial Crisis, the Eurozone Crisis, and the COVID-19 Crisis illustrate the importance of understanding the monetary and financial factors that may constrain governments’ abilities to fund deficits, especially given the importance of fiscal expenditure as a stabilizing economic force, or as a potential driver of economic development.
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🖺 Full Text HTML: <a href="https://osf.io/preprints/socarxiv/nmcp5/" target="_blank">Government in the Money View: Sovereign Debt, Liquidity Preference, and the Fiscal-Monetary Nexus</a>
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<li><strong>Recommendation for dual peer-reviewing in science journals supported by two interpretations of Jacques Derrida’s critical thinking and not so-tiring queries of Michel Foucault</strong> -
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Abstract A short u-tube presentation on discovering a new allotrope of carbon, subsequently published in the journal Science is the motivation to recommend dual peer-reviewing in science journals. Journals have anonymous and non-anonymous submissions. The non-anonymous submission with authors and affiliations is recommended for a single-blind oral peer review by technology preceded by the popular double-blind peer review of the anonymous submission. This paper has two parts. Part 1 describes the procedure for single-blind oral peer review. Jacques Derrida’s exclusivity in writing is used as an analogy for the exclusion of data points. Two interpretations of Derrida’s critical thinking and not-so-tiring queries of Michel Foucault are invoked in part 2 to bring out the effectiveness of the single-blind oral peer review. Foucault lists queries describing them as “No longer the tiresome repetitions” in his seminal essay “What is an author?” However, two queries are relevant to retracted papers on hydroxychloroquine for COVID-19, with one significant to non-native speakers of English for the single-blind oral peer review. Paying peer reviewers, communicated in the journal “Lancet,” is discussed considering the enormous profits made by publishers. The reported nomenclature “actual investigator” alongside ‘principal investigator’ is recommended since it presents a better equity balance than author for journal publications. If dual peer reviewing is feasible, will it clear the chinks in metrics and result in new metrics?
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🖺 Full Text HTML: <a href="https://osf.io/preprints/socarxiv/f3bgc/" target="_blank">Recommendation for dual peer-reviewing in science journals supported by two interpretations of Jacques Derrida’s critical thinking and not so-tiring queries of Michel Foucault</a>
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<li><strong>Predicting COVID-19 mortality in Zambia - an Application of Machine Learning</strong> -
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Background: The Corona virus, has caused havoc all over the world, it has left no country untouched resulting in millions of cases and deaths. In an effort to fight back, scientist and public health professionals have used every form of advancing technology to curb the spread, predict the unforeseen adverse events, improve preparedness, and bring the world under control once more. Objective: The objective of this study was to predict mortality in hospitalized COVID-19 patients in Zambia using ML methods from a number of predictors that have been shown to be predictive of mortality. Methods: This research used powerful ML models in predicting COVID-19 mortality in 1,433 hospitalized patients in Zambia. The feature importance analysis helped in identification of important factors. The ML models GB, RF, SVM, DT, LR, and NB were used the performance metrics checked for each model were accuracy, recall, specificity, precision, F1 Score, ROC-AUC, and PRC-AUC. Results: The feature importance analysis found that hospital length of stay (LOS) and white blood cell count were the most influential features, other factors arranged in order of reducing importance included: age, wave, diabetes, hypertension, and sex. The GB achieved accuracy of 91.5%, recall of 93.6%, F1 Score of 91.7%, and ROC-AUC of 96.9%. The RF achieved accuracy of 90.9%, recall of 93.8%, F1 Score of 91.2%, and ROC-AUC of 96.8%. The SVM achieved accuracy of 87.8%, recall of 91.2%, F1 Score of 88.2%, and ROC-AUC of 94.1%. The accuracy and ROC-AUC of other models were 88.2% and 90.7% respectively for DT, 81.9% and 90.1% respectively for LR, and 79.2% and 86.9% respectively for NB. Conclusion: The study successfully derived and validated multiple ML models that predicted mortality effectively with reasonably high performance in stated metrics. The GB was the best suited for the data in our study. GB was thus recommended for similar studies with RF as best alternative. Knowledge of underlying health conditions about patients (length of hospitalization (LOS), white blood cell count, age, sex, hypertension, diabetes, and other factors) can help healthcare providers offer lifesaving services on time, improve preparedness and decongest health facilities.
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🖺 Full Text HTML: <a href="https://thesiscommons.org/b5a6n/" target="_blank">Predicting COVID-19 mortality in Zambia - an Application of Machine Learning</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>Association Between Smell Training and Quality of Life in Patients With Impaired Sense of Smell Following COVID-19</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Other: Olfactory training with essential oils; Other: Olfactory training with fragrance-free oils<br/><b>Sponsor</b>: Ditte Gertz Mogensen<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>COVID-19 Fourth Dose Study in Australia</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Biological: Tozinameran; Biological: Elasomeran; Biological: Bivalent Pfizer-BioNTech; Biological: Bivalent Moderna<br/><b>Sponsors</b>: Murdoch Childrens Research Institute; 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>Trial of 2nd Booster Dose of COVID-19 Vaccine</strong> - <b>Condition</b>: COVID-19<br/><b>Intervention</b>: Other: Invitation to get a 2nd booster dose of COVID-19 vaccine<br/><b>Sponsor</b>: Norwegian Institute of Public Health<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>SCALE-UP Utah II: Community-Academic Partnership to Address COVID-19 Text Message Study</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Behavioral: Text-Messaging (TM); Behavioral: Patient Navigation (PN)<br/><b>Sponsors</b>: University of Utah; Utah Department of Health; Association for Utah Community Health; National Institutes of Health (NIH); National Institute on Minority Health and Health Disparities (NIMHD)<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>SCALE-UP Utah II: Community-Academic Partnership to Address COVID-19 Conversational Agent Study</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Behavioral: Text-Messaging (TM); Behavioral: Conversational Agent (CA); Behavioral: Patient Navigation (PN)<br/><b>Sponsors</b>: University of Utah; Utah Department of Health; Association for Utah Community Health; National Institutes of Health (NIH); National Institute on Minority Health and Health Disparities (NIMHD)<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>PBI-0451 Phase 2 Study in Nonhospitalized Symptomatic Adults With COVID-19</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Drug: PBI-0451; Drug: Placebo<br/><b>Sponsor</b>: Pardes Biosciences, Inc.<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>Evaluating the Safety and Efficacy of AD17002 Intranasal Spray in Treating Participants With Mild to Moderate COVID-19</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Biological: AD17002 + Formulation buffer; Biological: Placebo<br/><b>Sponsors</b>: Advagene Biopharma Co. Ltd.; Gadjah Mada University<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>Community-Based Health Education Programs for the Early Detection of, and Vaccination Against, COVID-19 and the Adoption of Self-Protective Measures of Hong Kong Residents</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Behavioral: Community-based Health Education based on core intervention package; Behavioral: Health Information Sharing Group<br/><b>Sponsors</b>: The Hong Kong Polytechnic University; Food and Health Bureau, Hong Kong<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>Efficacy and Safety Evaluation of Paxlovid for COVID-19: a Real-world Case-control Study</strong> - <b>Condition</b>: COVID-19 Pneumonia<br/><b>Interventions</b>: Drug: standard-of-care plus Paxlovid; Drug: standard-of-care<br/><b>Sponsor</b>: Ruijin 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>Multidisciplinary Day-hospital Versus Waiting List Management of Post-COVID-19 Persistent Symptoms (ECHAP-COVID)</strong> - <b>Condition</b>: Post COVID-19 Condition<br/><b>Intervention</b>: Behavioral: Personalized multidisciplinary day-hospital intervention<br/><b>Sponsor</b>: Assistance Publique - Hôpitaux de Paris<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>Safety and Effects of an Investigational COVID-19 Vaccine as a Booster in Healthy People</strong> - <b>Conditions</b>: SARS-CoV-2 Infection; COVID-19<br/><b>Interventions</b>: Biological: BNT162b5 Bivalent or BNT162b2 Bivalent 30 µg; Biological: BNT162b4 5 µg; Biological: BNT162b4 10 µg; Biological: BNT162b4 15 µg<br/><b>Sponsors</b>: BioNTech SE; 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>Simvastatin Nasal Rinses for the Treatment of COVID-19 Mediated Dysomsia</strong> - <b>Conditions</b>: Olfactory Disorder; COVID-19<br/><b>Intervention</b>: Drug: Simvastatin<br/><b>Sponsors</b>: Washington University School of Medicine; Duke University<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>Engaging Church Health Ministries to Decrease Coronavirus Disease-19 Vaccine Hesitancy in Underserved Populations</strong> - <b>Condition</b>: COVID-19<br/><b>Intervention</b>: Behavioral: Active Intervention Group<br/><b>Sponsor</b>: Pennington Biomedical Research Center<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>Cardiopulmonary Rehabilitation in Post-acute COVID-19 Syndrome</strong> - <b>Condition</b>: Post Acute COVID-19 Syndrome<br/><b>Interventions</b>: Other: Cardiopulmonary rehabilitation; Other: Health education<br/><b>Sponsor</b>: Taipei Medical University Shuang Ho 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>Motivation, Syringe Exchange, and COVID-19</strong> - <b>Condition</b>: COVID-19 Pandemic<br/><b>Intervention</b>: Behavioral: Connect2Test<br/><b>Sponsors</b>: University of Oregon; National Institute on Drug Abuse (NIDA)<br/><b>Recruiting</b></p></li>
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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>PD-1/PD-L1 blockade abrogates a dysfunctional innate-adaptive immune axis in critical β-coronavirus disease</strong> - Severe COVID-19 is associated with hyperinflammation and weak T cell responses against SARS-CoV-2. However, the links between those processes remain partially characterized. Moreover, whether and how therapeutically manipulating T cells may benefit patients are unknown. Our genetic and pharmacological evidence demonstrates that the ion channel TMEM176B inhibited inflammasome activation triggered by SARS-CoV-2 and SARS-CoV-2-related murine β-coronavirus. Tmem176b^(-/-) mice infected with murine…</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>MERS-CoV ORF4b is a virulence factor involved in the inflammatory pathology induced in the lungs of mice</strong> - No vaccines or specific antiviral drugs are authorized against Middle East respiratory syndrome coronavirus (MERS-CoV) despite its high mortality rate and prevalence in dromedary camels. Since 2012, MERS-CoV has been causing sporadic zoonotic infections in humans, which poses a risk of genetic evolution to become a pandemic virus. MERS-CoV genome encodes five accessory proteins, 3, 4a, 4b, 5 and 8b for which limited information is available in the context of infection. This work describes 4b as…</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>Contribution of <em>Trp63<sup>CreERT2</sup></em> labeled cells to alveolar regeneration is independent of tuft cells</strong> - Viral infection often causes severe damage to the lungs, leading to the appearance of ectopic basal cells (EBCs) and tuft cells in the lung parenchyma. Thus far the roles of these ectopic epithelial cells in alveolar regeneration remain controversial. Here, we confirm that the ectopic tuft cells are originated from EBCs in mouse models and COVID-19 lungs. The differentiation of tuft cells from EBCs is promoted by Wnt inhibition while suppressed by Notch inhibition. Although progenitor functions…</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>Anti-breast cancer drugs targeting cell-surface glucose-regulated protein 78: a drug repositioning <em>in silico</em> study</strong> - Breast cancer (BC) is prevalent worldwide and is a leading cause of death among women. However, cell-surface glucose-regulated protein 78 (cs-GRP78) is overexpressed in several types of cancer and during pathogen infections. This study examines two well-known BC drugs approved by the FDA as BC treatments to GRP78. The first type consists of inhibitors of cyclin-based kinases 4/6, including abemaciclib, palbociclib, ribociclib, and dinaciclib. In addition, tunicamycin, and doxorubicin, which 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>Estimating the binding energetics of reversible covalent inhibitors of the SARS-CoV-2 main protease: an <em>in silico</em> study</strong> - The main protease (M^(pro)) of the SARS-CoV-2 virus is an attractive therapeutic target for developing antivirals to combat COVID-19. M^(pro) is essential for the replication cycle of the SARS-CoV-2 virus, so inhibiting M^(pro) blocks a vital piece of the cell replication machinery of the virus. A promising strategy to disrupt the viral replication cycle is to design inhibitors that bind to the active site cysteine (Cys145) of the M^(pro). Cysteine targeted covalent inhibitors are gaining…</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>The Impact of Colchicine on COVID-19 patients: A Clinical Trial Study</strong> - CONCLUSION: Colchicine can be effective in amelioration of systemic symptoms and duration of hospitalisation probably by inhibition of inflammatory biomarkers in COVID-19 patients.</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>Rational Design of an anti-cancer Peptide inhibiting CD147 / Cyp A interaction</strong> - The CD147 / Cyp A interaction is a critical pathway in cancer types and an essential factor in entering the COVID-19 virus into the host cell. Melittin acts as an inhibitory peptide in cancer types by blocking the CD147/ Cyp A interaction. The clinical application of Melittin is limited due to weak penetration into cancer cells. TAT is an arginine-rich peptide with high penetration ability into cells widely used in drug delivery systems. This study aimed to design a hybrid peptide derived from…</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 computational study of metal-organic frameworks (MOFs) as potential nanostructures to combat SARS-CoV-2</strong> - The COVID-19 causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has a critical surface protein called spike protein (S protein), which is the target of many vaccines and drugs developments. Among non-structural proteins of SARS-CoV-2, main protease (M^(pro)) has drawn much attention to itself for designing antiviral drugs since it is very crucial for the virus replication in host cells. In the first part of the present study, the application of metal-organic…</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>Molecular Mechanism of the Non-Covalent Orally Targeted SARS-CoV-2 M<sup>pro</sup> Inhibitor S-217622 and Computational Assessment of Its Effectiveness against Mainstream Variants</strong> - Convenient and efficient therapeutic agents are urgently needed to block the continued spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, the mechanism for the novel orally targeted SARS-CoV-2 main protease (M^(pro)) inhibitor S-217622 is revealed through a molecular dynamics simulation. The difference in the movement modes of the S-217622-M^(pro) complex and apo-M^(pro) suggested S-217622 could inhibit the motility intensity of M^(pro), thus maintaining their stable…</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>SARS-CoV-2 Diverges from Other Betacoronaviruses in Only Partially Activating the IRE1α/XBP1 Endoplasmic Reticulum Stress Pathway in Human Lung-Derived Cells</strong> - Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has killed over 6 million individuals worldwide and continues to spread in countries where vaccines are not yet widely available or its citizens are hesitant to become vaccinated. Therefore, it is critical to unravel the molecular mechanisms that allow SARS-CoV-2 and other coronaviruses to infect and overtake the host machinery of human cells. Coronavirus replication triggers endoplasmic reticulum (ER) stress and activation of 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>An insight into the neuroprotective effects and molecular targets of pomegranate (<em>Punica granatum</em>) against Alzheimer’s disease</strong> - Alzheimer’s disease (AD) is a progressive neurodegenerative disease that still has no permanent cure. The drugs prescribed in the present days are only for symptomatic relief for the patients. Many studies correlating the reduction in the incidence of AD with the diet consumed have been published. These studies showed that a diet rich in polyphenols is associated with a decrease in the incidence of AD. The present review is focused on the ability of pomegranate and its bioactive components to…</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><em>In silico</em> approach identified benzoylguanidines as SARS-CoV-2 main protease (M<sup>pro</sup>) potential inhibitors</strong> - The coronavirus disease-2019 (COVID-19) pandemic, caused by the novel coronavirus severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), became the highest public health crisis nowadays. Although the use of approved vaccines for emergency immunization and the reuse of FDA-approved drugs remains at the forefront, the search for new, more selective, and potent drug candidates from synthetic compounds is also a viable alternative to combat this viral disease. In this context, the present…</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>Single-cell transcriptome atlas reveals protective characteristics of COVID-19 mRNA vaccine</strong> - mRNA vaccines are promising alternatives to conventional vaccines in many aspects. We previously developed a lipopolyplex (LPP)-based mRNA vaccine (SW0123) that demonstrated robust immunogenicity and strong protective capacity against SARS-CoV-2 infection in mice and rhesus macaques. However, the immune profiles and mechanisms of pulmonary protection induced by SW0123 remain unclear. Through high-resolution single-cell analysis, we found that SW0123 vaccination effectively suppressed…</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>Identification and characterization of a novel cell binding and cross-reactive region on spike protein of SARS-CoV-2</strong> - Given that COVID-19 continues to wreak havoc around the world, it is imperative to search for a conserved region involved in viral infection so that effective vaccines can be developed to prevent the virus from rapid mutations. We have established a twelve-fragment library of recombinant proteins covering the entire region of spike protein of both SARS-CoV-2 and SARS-CoV from Escherichia coli. IgGs from murine antisera specifically against 6 spike protein fragments of SARS-CoV-2 were produced,…</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>Nanomolar inhibition of SARS-CoV-2 infection by an unmodified peptide targeting the prehairpin intermediate of the spike protein</strong> - Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge currently available coronavirus disease 2019 vaccines and monoclonal antibody therapies through epitope change on the receptor binding domain of the viral spike glycoprotein. Hence, there is a specific urgent need for alternative antivirals that target processes less likely to be affected by mutation, such as the membrane fusion step of viral entry into the host cell. One such antiviral class includes peptide…</p></li>
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<h1 data-aos="fade-right" id="from-patent-search">From Patent Search</h1>
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