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<title>29 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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<h1 data-aos="fade-right" id="from-preprints">From Preprints</h1>
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<li><strong>Coping with ‘Lockdown Babies’: Understanding Postpartum Maternal Experience in London, UK</strong> -
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<div>
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The postpartum/postnatal period is a time where mothers require greater levels of support from multiple formal and informal sources. However, stay-at-home orders commonly known as “lockdown” deployed in some countries to limit COVID-19 transmission likely led to reduced availability of support, which may have implications for maternal wellbeing. In-depth understanding of maternal experience during this period of heightened collective stress may reveal factors which are crucial for maternal wellbeing, which in turn can help services and policy makers prioritise, protect, or address these areas. Here we conduct an online focus group study involving 20 mothers living in London, England, with “lockdown babies,” following up on our earlier survey on social support and maternal wellbeing. We conduct thematic analysis of focus group transcripts, and identify several key themes around Lockdown Experience and Determinants of Lockdown Experience. Participants raised some positives of lockdown, including fostering connections and protection from external expectations, but also raised many negatives, including social isolation, institutional abandonment, and intense relationships within the household. Potential reasons behind variations in lockdown experience include physical environments, timing of birth, and parity. Our results reveal complex experiences of the first national lockdown, both positive and negative. We discuss potential implications for post-lockdown policy and practice to promote postpartum wellbeing, such as facilitating partners to stay at home, and addressing the culture of “maternal surveillance” and “parenting experts.”
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<div class="article-link article-html-link">
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🖺 Full Text HTML: <a href="https://osf.io/r7enw/" target="_blank">Coping with ‘Lockdown Babies’: Understanding Postpartum Maternal Experience in London, UK</a>
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</div></li>
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<li><strong>Social factors and UFO reports: was the SARS-CoV-2 pandemic associated with an increase in UFO reporting?</strong> -
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<div>
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The ongoing SARS-Cov-2 pandemic had many drastic effects upon society beyond the illness and death it caused. Pandemic mitigation measures disrupted and altered behaviors related to social mobility, significantly increasing the time spent at home compared to the pre-pandemic period. Further, it was well documented that social anxiety and stress increased at a population level. Early in the pandemic there was speculation in the popular media that reporting of paranormal phenomena (e.g., UFOs, ghosts, etc.) increased due to factors associated with the pandemic. Past research on UFO/UAP reporting has theorized that increases are triggered by social factors, and so the pandemic provided a natural experiment to test these claims. To measure UFO reports we utilized two public databases of UFO reports for sightings in the United States, provided by the National UFO Reporting Center and the Mutual UFO Network. To estimate the impact of the pandemic we utilized two measures, one for social mobility and one for pandemic/disease severity. Google Community Mobility Reports provided a metric of social mobility for people who use Google Maps on their cellular telephone (i.e., amount of time spent at work compared to home), which we aggregated to a state level to estimate time spent at home. Second, we used new weekly SARS-CoV-2 cases and deaths, both absolute counts and per capita, which can be considered to be an indirect measure of anxiety and stress. We find that UFO reports did increase in 2020 compared to 2019 (p<0.001 for both databases); however, the level of UFO reporting had little to no association with the various pandemic-related measures, offering no support for hypothesized social factors that influence reporting. A complicating factor in UFO reporting is the start in 2019 of Starlink satellite launches. These launches include up to 60 small satellites at once, and so are very distinctive and often easily visible. As a result, many people report these as UFOs. We coded and removed these reports from the sighting databases, and the filtered data similarly have no association with the pandemic-related factors. Further, with Starlink reports removed, there was no increase in sightings in 2020 compared to 2019. Our results contribute to an understanding of large-scale factors that impact the reporting of paranormal events, especially timely given the renewed public and government focus on the UFO phenomenon today.
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</div>
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<div class="article-link article-html-link">
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🖺 Full Text HTML: <a href="https://osf.io/preprints/socarxiv/exm7c/" target="_blank">Social factors and UFO reports: was the SARS-CoV-2 pandemic associated with an increase in UFO reporting?</a>
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</div></li>
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<li><strong>Increasing SARS-CoV2 cases, hospitalizations and deaths among the vaccinated elderly populations during the Omicron (B.1.1.529) variant surge in UK.</strong> -
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BACKGROUND There were increased SARS-CoV2 hospitalizations and deaths noted during Omicron (B.1.1.529) variant surge in UK despite decreased cases, and the reasons are unclear. METHODS In this observational study, we analyzed reported SARS-CoV2 cases, hospitalizations and deaths during the COVID-19 pandemic in the UK. We also analyzed variables that can affect the outcomes. The vaccine effectiveness among those ≥18 years of age (August 16, 2021 to March 27, 2022) was analyzed. RESULTS Of the total cases (n= 22,072,550), hospitalizations (n=848,911) and deaths (n=175,070) due to COVID-19 in UK; 51.3% of cases (n=11,315,793), 28.8% of hospitalizations (n=244,708) and 16.4% of deaths (n=28,659) occurred during Omicron variant surge. When comparing the period of February 28-May 1, 2022 with the prior 12-weeks, we observed a significant increase in the case fatality rate (0.19% vs 0.41%; RR 2.11[ 2.06-2.16], p<0.001) and odds of hospitalization (1.58% vs 3.72%; RR 2.36[2.34-2.38]; p<0.001). During the same period a significant increase in cases (23.7% vs 40.3%; RR1.70 [1.70-1.71]; p<0.001) among ≥50 years of age and hospitalizations (39.3% vs 50.3%;RR1.28 [1.27-1.30]; p<0.001) and deaths (67.89% vs 80.07%;RR1.18 [1.16-1.20]; p<0.001) among ≥75 years of age was observed. The vaccine effectiveness (VE) for the third dose was in negative since December 20, 2021, with a significantly increased proportion of SARS-CoV2 cases hospitalizations and deaths among the vaccinated; and a decreased proportion of cases, hospitalizations, and deaths among the unvaccinated. The pre-existing conditions were present in 95.6% of all COVID-19 deaths, various ethnic, deprivation score and vaccination rate disparities noted that can adversely affect hospitalization and deaths among compared groups. CONCLUSIONS There is no discernable vaccine effectiveness among ≥18 years of age, vaccinated third dose population since the beginning of the Omicron variant surge. Pre-existing conditions, ethnicity, deprivation score, and vaccination rate disparities data need to be adjusted for evaluating VE for hospitalizations and deaths. The increased cases with significantly increased hospitalizations and deaths among the elderly population during the Omicron variant surge underscores the need to prevent infections in the elderly irrespective of vaccination status with uniform screening protocols and protective measures.
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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/10.1101/2022.06.28.22276926v1" target="_blank">Increasing SARS-CoV2 cases, hospitalizations and deaths among the vaccinated elderly populations during the Omicron (B.1.1.529) variant surge in UK.</a>
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<li><strong>Combination therapy with nirmatrelvir and molnupiravir improves the survival of SARS-CoV-2 infected mice</strong> -
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As the SARS-CoV-2 pandemic remains uncontrolled owing to the continuous emergence of variants of concern, there is an immediate need to implement the most effective antiviral treatment strategies, especially for risk groups. Here, we evaluated the therapeutic potency of nirmatrelvir, remdesivir, and molnupiravir and their combinations in SARS-CoV-2-infected K18-hACE2 transgenic mice. Systemic treatment of mice with each drug (20 mg/kg) resulted in slightly enhanced antiviral efficacy and yielded an increased life expectancy of only about 20-40% survival. However, combination therapy with nirmatrelvir (20 mg/kg) and molnupiravir (20 mg/kg) in lethally infected mice showed profound inhibition of SARS-CoV-2 replication in both the lung and brain and synergistically improved survival times up to 80% compared to those with nirmatrelvir (P= 0.0001) and molnupiravir (P= 0.0001) administered alone. This combination therapy effectively reduced clinical severity score, virus-induced tissue damage, and viral distribution compared to those in animals treated with these monotherapies. Furthermore, all these assessments associated with this combination were also significantly higher than that of mice receiving remdesivir monotherapy (P= 0.0001) and the nirmatrelvir (20 mg/kg) and remdesivir (20 mg/kg) combination (P= 0.0001), underscored the clinical significance of this combination. By contrast, the nirmatrelvir and remdesivir combination showed less antiviral efficacy, with lower survival compared to nirmatrelvir monotherapy, demonstrating the inefficient therapeutic effect of this combination. The combination therapy with nirmatrelvir and molnupiravir contributes to alleviated morbidity and mortality, which can serve as a basis for the design of clinical studies of this combination in the treatment of COVID-19 patients.
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🖺 Full Text HTML: <a href="https://www.biorxiv.org/content/10.1101/2022.06.27.497875v1" target="_blank">Combination therapy with nirmatrelvir and molnupiravir improves the survival of SARS-CoV-2 infected mice</a>
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<li><strong>The Staphylococcus aureus iron-regulated surface determinant A (IsdA) increases SARS CoV-2 replication by modulating JAK-STAT signaling</strong> -
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<div>
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The emergence and spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2) and the associated Coronavirus disease (COVID-19) pandemic have affected millions globally. Like other respiratory viruses, a significant complication of COVID-19 infection is secondary bacterial co-infection, which is seen in approximately 25% of severe cases. The most common organism isolated from co-infection is the Gram-positive bacterium Staphylococcus aureus. Here, we developed an in vitro co-infection model where both CoV-2 and S. aureus replication kinetics can be examined. We demonstrate CoV-2 infection does not alter how S. aureus attaches to or grows in host epithelial cells. In contrast, the presence of replicating S. aureus enhances the replication of CoV-2 by 10-15-fold. We identify this pro-viral activity is due to the S. aureus iron-regulated surface determinant A (IsdA) and this effect is mimicked across different SARS CoV-2 permissive cell lines infected with multiple viral variants. Analysis of co-infected cells demonstrated an IsdA dependent modification of host transcription. Using chemical inhibition, we determined S. aureus IsdA modifies host Janus Kinase - Signal Transducer and Activator of Transcription (JAK-STAT) signalling, ultimately leading to increased viral replication. These findings provide key insight into the molecular interactions that occur between host cells, CoV-2 and S. aureus during co-infection.
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<div class="article-link article-html-link">
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🖺 Full Text HTML: <a href="https://www.biorxiv.org/content/10.1101/2022.06.27.497883v1" target="_blank">The Staphylococcus aureus iron-regulated surface determinant A (IsdA) increases SARS CoV-2 replication by modulating JAK-STAT signaling</a>
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<li><strong>Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2</strong> -
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The nonstructural protein 3 (NSP3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contains a conserved macrodomain enzyme (Mac1) that is critical for pathogenesis and lethality. While small molecule inhibitors of Mac1 have great therapeutic potential, few have been described. Here, we report the structure-based development of several chemical scaffolds exhibiting low- to sub-micromolar affinity for Mac1 through iterations of computer-aided design, structural characterization by ultra-high resolution X-ray protein crystallography, and binding evaluation with in-solution assays. Potent scaffolds were designed with in silico linkage of previously obtained fragment hits and ultra-large library docking screens of more than 450 million molecules. In total, 160 hits comprising 119 different scaffolds were discovered and 152 Mac1-ligand complex crystal structures were determined, typically to 1 [A] resolution or better. The structure-activity-relationships emerging from this study may template future drug development against Mac1.
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<div class="article-link article-html-link">
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🖺 Full Text HTML: <a href="https://www.biorxiv.org/content/10.1101/2022.06.27.497816v1" target="_blank">Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2</a>
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<li><strong>Wastewater surveillance of influenza activity: Early detection, surveillance, and subtyping in city and neighbourhood communities</strong> -
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Recurrent epidemics of influenza infection and its pandemic potential present a significant risk to global population health. To mitigate hospitalizations and death, local public health relies on clinical surveillance to locate and monitor influenza-like illnesses and/or influenza cases and outbreaks. At an international level, the global integration of clinical surveillance networks is the only reliable method to report influenza types and subtypes and warn of an emergent pandemic strain. During the COVID-19 pandemic, the demonstrated utility of wastewater surveillance (WWS) in complementing or even replacing clinical surveillance, the latter a resource-intensive enterprise, was predicated on the presence of stable viral fragments in wastewater. We show that influenza virus targets are stable in wastewaters and partitions to the solids fraction. We subsequently quantify, type, and subtype influenza virus in municipal wastewater and primary sludge throughout the course of a community outbreak. This research demonstrates the feasibility of applying influenza virus WWS to city and neighbourhood levels; showing a 17-day lead time in forecasting a citywide flu outbreak and providing population-level viral subtyping in near real-time using minimal resources and infrastructure.
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</p>
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.06.28.22276884v1" target="_blank">Wastewater surveillance of influenza activity: Early detection, surveillance, and subtyping in city and neighbourhood communities</a>
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<li><strong>Evaluating a novel, integrative dashboard for health professionals performance in managing deteriorating patients: quality improvement project</strong> -
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Background: The quality of recording and documentation of deteriorating patient management by health professionals has been challenged at health system level during the COVID-19 pandemic. Non-adherence to monitoring and escalation guidelines and poor documentation increases risk of serious adverse events. Electronic health record (EHR)-integrated dashboards are real-time auditing tools of patients status and clinicians performance, but neither the views nor the performance of health professionals have been assessed, relating to management of deteriorating patients . Objective: To develop and evaluate a real-time dashboard of deteriorating patients assessment, referral, and therapy by examining the perception of the dashboard and the performance of nurses and physicians. Settings: Five academic hospitals in the largest NHS trust in the UK (Barts Health NHS Trust). Intervention: The dashboard was developed from EHR data to investigate patients with NEWS2>5, assessment, and escalation of deteriorating patients. We adopted the Plan, Do, Study, Act model and followed the SQUIRE framework to evaluate the dashboard. Design: Mixed methods: (i) Virtual, face-to-face, key informant interviews and (ii) Retrospective descriptive EHR data analysis to measure performance change over time. Results: We interviewed 3 nurses (2 quality and safety and 1 informatics specialists). Key themes were: (1) participants perceived the dashboard as a facilitator for auditing NEWS2 recording and escalation of care to improve clinicians practice; (2) There is a need for guiding clinicians and adjusting data sources and metrics which could enhance the functionality and usability. From EHR (2019 to 2022) data analysis showed: (1) NEWS2 recording has gradually improved in the implementation and evaluation phases (May 2021 to Apr 2022) from 64% to 83%; (2) Referral and nurses9 assessment forms completion increased (n: 170 to 6800 & 23 to 540, respectively). Conclusion: The deterioration dashboard is an effective real time data- driven method for improving the quality of managing deteriorating patients. Improving the dashboard by integrating multiple health systems, a wider analysis of further NEWS2 and escalation of care metrics, clinicians learning of digital solutions will enhance functionality and experience, potentially boosting its value. There is a need to examine the generalizability of the dashboard through further validation and quality improvement studies.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.06.28.22276946v1" target="_blank">Evaluating a novel, integrative dashboard for health professionals performance in managing deteriorating patients: quality improvement project</a>
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<li><strong>Changing word meanings in biomedical literature reveal pandemics and new technologies</strong> -
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While we often think of words as having a fixed meaning that we use to describe a changing world, words are also dynamic and changing. Scientific research can also be remarkably fast-moving, with new concepts or approaches rapidly gaining mind share. We examined scientific writing, both preprint and pre-publication peer-reviewed text, to identify terms that have changed and examine their use. One particular challenge that we faced was that the shift from closed to open access publishing meant that the size of available corpora changed by over an order of magnitude in the last two decades. We developed an approach to evaluate semantic shift by accounting for both intra- and inter-year variability using multiple integrated models. Using this strategy and examining year-by-year changes revealed thousands of change points in both corpora. We found change points for tokens including ‘cas9’, ‘pandemic’, and ‘sars’ among many others. The consistent change-points between pre-publication peer-reviewed and preprinted text were largely related to the COVID-19 pandemic. We developed a web app for exploration (https://greenelab.github.io/word-lapse/) that enables users to investigate individual terms. To our knowledge, this analysis is the first to examine the semantic shift in biomedical preprints and pre-publication peer-reviewed text, and it lays the foundation for future work to examine how terms acquire new meaning and the extent to which that process is encouraged or discouraged by peer review.
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🖺 Full Text HTML: <a href="https://www.biorxiv.org/content/10.1101/2022.06.27.497742v1" target="_blank">Changing word meanings in biomedical literature reveal pandemics and new technologies</a>
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<li><strong>The Origin of Immunity by Means of Prior Infection and Vaccination with Implications for the Origin of Species</strong> -
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The expectation that vaccines would solve the COVID-19 problem through herd immunity, which followed logical deductions from inflammatory phenomena in which Mechnikov and his contemporaries described immunity as originating from the elimination of pathogens by a system of cells and substances which has since been named the immune system which would prevent onward transmission of the pathogen, has failed to find representation in reality. But upon illustrating the reality in which the immunological phenomena through which immune mechanisms protect us from the pathological manifestations that occur in response to the pathogen, they were found to be brought about by the attenuation of the causative influence of the same pathogen from a prior infection and an entity that is immunologically-linked with the pathogen from vaccination so that the single pathway through which such pathological manifestations are brought in response to these influences are blocked and infection with the pathogen remains asymptomatic for as long as either or both of the conditions that hive rise to different but connected paths to immunity persist. Rather than asymptomatically hosted variants and subvariants to have become masters in the art of escaping the system which we have described as immune for in the absence of knowledge of reality for severe manifestations to occur in both the vaccinated and unvaccinated or to have become more transmissible for surges of COVID-19 hospitalizations and death to occur, it is these protective conditions that give rise to immunity that needs to disappear. And the higher likelihood of one path disappearing in the unvaccinated than both disappearing in the vaccinated explains why the unvaccinated are at greater risk of such unfortunate events. If we will put an end to such deaths which claimed the lives of millions prematurely during this pandemic and prevent those which may decimate our populations if pathological manifestations such as malignancies should appear catastrophically in our species as they did in Tasmanian devils, an understanding of the immunological nature of the pathological effects of the pathogens that are linked with these manifestations, which will enable us to keep both conditions stable in the vaccinated until eradication occurs, must be our topmost research priority now.
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🖺 Full Text HTML: <a href="https://osf.io/py8ju/" target="_blank">The Origin of Immunity by Means of Prior Infection and Vaccination with Implications for the Origin of Species</a>
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<li><strong>The COVID-19 pandemic sparked off a large-scale outbreak of carbapenem-resistant Acinetobacter baumannii from the endemic strains of an Italian hospital</strong> -
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<i>Acinetobacter baumannii</i> is an insidious nosocomial pathogen that poses a serious threat due to the rise of incidence of multidrug resistant (MDR) strains. During the COVID-19 pandemic, MDR <i>A. baumannii</i> clones have caused several outbreaks worldwide. Here we describe a detailed investigation of an MDR <i>A. baumannii</i> outbreak that occurred at Fondazione IRCCS Policlinico San Matteo (Pavia, Italy). A total of 96 <i>A. baumannii</i> strains, isolated between January and July 2020 from 41 inpatients (both SARS-CoV-2 positive and negative) in different wards, were characterized by phenotypic and genomic analyses combining Illumina and Nanopore sequencing. Antibiotic susceptibility testing revealed that all isolates were resistant to carbapenems and the sequence analysis attributed this to the carbapenemase gene <i>bla</i><sub>OXA-23</sub>. Screening of virulence factors unveiled that all strains carried determinants for biofilm formation. A core genome-based phylogeny was inferred to integrate outbreak strain genomes with background genomes from public databases and the local surveillance program. All strains belonged to the globally disseminated ST2 clone and were divided into two main clades. Strains from the outbreak clustered with surveillance isolates from 2019, suggesting that the outbreak was caused by two strains that were already circulating in the hospital before the start of the pandemic. The intensive spread of <i>A. baumannii</i> in the hospital was enhanced by the extreme emergency situation of the first COVID-19 pandemic wave that resulted in minor attention to infection prevention and control practices.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.06.28.22276851v1" target="_blank">The COVID-19 pandemic sparked off a large-scale outbreak of carbapenem-resistant Acinetobacter baumannii from the endemic strains of an Italian hospital</a>
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<li><strong>BNT162b2 effectiveness against Delta & Omicron variants in teens by dosing interval and duration</strong> -
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Background and Objectives Two- and three-dose BNT162b2 (Pfizer-BioNTech) mRNA vaccine effectiveness (VE) against SARS-CoV-2 infection, including Delta and Omicron variants, was assessed among adolescents in two Canadian provinces where first and second doses were spaced longer than the manufacturer-specified 3-week interval. Methods Test-negative design estimated VE against laboratory-confirmed SARS-CoV-2 infection among adolescents 12-17 years old in Quebec and British Columbia, Canada between September 5, 2021 (epi-week 36), and April 30, 2022 (epi-week 17). Delta-dominant and Omicron-dominant periods spanned epi-weeks 36-47 and 51-17, respectively. VE was assessed from 14 days and explored by interval between first and second doses, time since second dose, and with administration of a third dose. Results Median first-second dosing-interval was ~8 weeks and second-third dosing-interval was ~28-31 weeks. Median follow-up post-second-dose was ~10-11 weeks for Delta-dominant and ~21-22 weeks for Omicron-dominant periods, and ~3-9 weeks post-third dose. VE against Delta was ≥90% to at least the 5th month post-second dose. VE against Omicron declined from ~65-75% at 2-3 weeks to ≤50% by the 3rd month post-vaccination, restored to ~60-65% shortly following a third dose. VE exceeded 90% against Delta regardless of dosing-interval but appeared improved against Omicron with ≥8 weeks between first and second doses. Conclusion In adolescents, two BNT162b2 doses provided strong and sustained protection against Delta but reduced and rapidly-waning VE against Omicron. Longer interval between first and second doses and a third dose improved Omicron protection. Updated vaccine antigens, increased doses and/or dosing-intervals may be needed to improve adolescent VE against immunological-escape variants.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.06.27.22276790v1" target="_blank">BNT162b2 effectiveness against Delta &amp; Omicron variants in teens by dosing interval and duration</a>
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<li><strong>Outcomes of laboratory-confirmed SARS-CoV-2 infection during resurgence driven by Omicron lineages BA.4 and BA.5 compared with previous waves in the Western Cape Province, South Africa</strong> -
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Objective: We aimed to compare clinical severity of Omicron BA.4/BA.5 infection with BA.1 and earlier variant infections among laboratory-confirmed SARS-CoV-2 cases in the Western Cape, South Africa, using timing of infection to infer the lineage/variant causing infection. Methods: We included public sector patients aged ≥20 years with laboratory-confirmed COVID-19 between 1-21 May 2022 (BA.4/BA.5 wave) and equivalent prior wave periods. We compared the risk between waves of (i) death and (ii) severe hospitalization/death (all within 21 days of diagnosis) using Cox regression adjusted for demographics, comorbidities, admission pressure, vaccination and prior infection. Results: Among 3,793 patients from the BA.4/BA.5 wave and 190,836 patients from previous waves the risk of severe hospitalization/death was similar in the BA.4/BA.5 and BA.1 waves (adjusted hazard ratio (aHR) 1.01; 95% confidence interval (CI) 0.92; 1.12). Both Omicron waves had lower risk of severe outcomes than previous waves. Prior infection (aHR 0.19, 95% CI 0.16; 0.22) and vaccination (aHR 0.24; 95% CI 0.15; 0.39 for boosted vs. no vaccine) were protective. Conclusion: Disease severity was similar amongst diagnosed COVID-19 cases in the BA.4/BA.5 and BA.1 periods in the context of growing immunity against SARS-CoV-2 due to prior infection and vaccination, both of which were strongly protective.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.06.28.22276983v1" target="_blank">Outcomes of laboratory-confirmed SARS-CoV-2 infection during resurgence driven by Omicron lineages BA.4 and BA.5 compared with previous waves in the Western Cape Province, South Africa</a>
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<li><strong>Impact of COVID-19 on the management and outcomes of ureteric stones in the UK: a multicentre retrospective study</strong> -
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Objectives: To determine if management of ureteric stones in the United Kingdom changed during the COVID-19 pandemic and whether this affected patient outcomes. Patients and methods: We conducted a multicentre retrospective study of adults with CT-proven ureteric stone disease at 39 UK hospitals during a pre-pandemic period (23/3/19 to 22/6/19) and a period during the pandemic (the 3-month period after the first SARS-CoV-2 case at individual sites). The primary outcome was success of primary treatment modality, defined as no further treatment required for the index ureteric stone. Our study protocol was published prior to data collection. Results: A total of 3735 patients were included (pre-pandemic=1956 patients; pandemic=1779 patients). Stone size was similar between groups (p>0.05). During the pandemic, patients had lower hospital admission rates (pre-pandemic=54.0% vs pandemic=46.5%, p<0.001), shorter length of stay (mean=4.1 vs. 3.3 days, p=0.02), and higher rates of use of medical expulsive therapy (17.4% vs. 25.4%, p<0.001). In patients who received interventional management (pre-pandemic n=787 vs. pandemic n=685), rates of ESWL (22.7% vs. 34.1%, p<0.001) and nephrostomy were higher (7.1% vs. 10.5%, p=0.03); and rates of ureteroscopy (57.2% vs. 47.5%, p<0.001), stent insertion (68.4% vs. 54.6%, p<0.001), and general anaesthetic (92.2% vs. 76.2%, p<0.001) were lower. There was no difference in success of primary treatment modality between patient cohorts (pre-pandemic=73.8% vs. pandemic=76.1%, P=0.11), nor when patients were stratified by treatment modality or stone size. Rates of operative complications, 30-day mortality, and readmission and renal function at 6 months did not differ between the data collection periods. Conclusions: During the COVID-19 pandemic, there were lower admission rates and fewer invasive procedures performed. Despite this, there were no differences in treatment success or outcomes. Our findings indicate that clinicians can safely adopt management strategies developed during the pandemic to treat more patients conservatively and in the community.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.06.27.22276955v1" target="_blank">Impact of COVID-19 on the management and outcomes of ureteric stones in the UK: a multicentre retrospective study</a>
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<li><strong>Do Media Objectivity and Frequency of Informing Mediate the Relationship Between Traditionalist Social Attitudes and COVID-19 Conspiracy Beliefs?</strong> -
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In this study, we hypothesized that traditionalist social attitudes (conservatism, religiousness, and authoritarianism) significantly predict COVID-19 conspiracy beliefs (Hiding Information and Harmless Virus), as well as conspiracy mentality in general. We also hypothesized that these relationships are mediated by the objectivity of the media through which individuals inform themselves, and the frequency of informing. The sample consisted of 341 participants from Serbia (mean age 33.51 years), of which 40.5% were women. The results revealed that conservatism predicts both conspiracy belief sets and conspiracy mentality, authoritarianism only COVID-19 conspiracy beliefs, and religiousness only beliefs that the virus is harmless. Media objectivity does not mediate these relationships. The frequency of informing is a significant mediator only of the relationships between authoritarianism, and conspiracy beliefs and conspiracy mentality, indicating that the role of seeking information is in reducing the threat perceived by more authoritarian individuals. The study reveals that media objectivity might not play a role in reducing conspiracy beliefs. An explanation might be found in the importance of the perceived credibility of the media.
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🖺 Full Text HTML: <a href="https://psyarxiv.com/9tq23/" target="_blank">Do Media Objectivity and Frequency of Informing Mediate the Relationship Between Traditionalist Social Attitudes and COVID-19 Conspiracy Beliefs?</a>
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</div></li>
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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>Immunobridging Study of COVID-19 Protein Subunit Recombinant Vaccine</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Biological: COVID-19 Protein Subunit Recombinant Vaccine; Biological: Active Comparator<br/><b>Sponsors</b>: PT Bio Farma; Faculty of Medicine, Universitas Indonesia, Jakarta; Faculty of Medicine, Diponegoro University, Semarang; Faculty of Medicine, Universitas Andalas, Padang; Faculty of Medicine, Universitas Hassanudin, Makassar<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 Evaluate the Safety, Tolerability, and Immunogenicity of SARS-CoV-2 Variant (COVID-19 Omicron) mRNA Vaccine (Phase 1)</strong> - <b>Condition</b>: COVID-19<br/><b>Intervention</b>: Biological: ABO1009-DP<br/><b>Sponsor</b>: Suzhou Abogen Biosciences 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 Evaluate Safety, Tolerability, and Immunogenicity of SARS-CoV-2 Variant (COVID-19) mRNA Vaccines</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Biological: ABO1009-DP; Biological: ABO-CoV.617.2; Other: Placebo<br/><b>Sponsor</b>: Suzhou Abogen Biosciences 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>Discussing COVID-19 Vaccines in Private Facebook Groups</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Behavioral: Gist messages on COVID-19 vaccination; Behavioral: COVID-19 vaccine information<br/><b>Sponsor</b>: George Washington University<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>Immunogenicity and Safety Study of One Booster Dose of Trivalent COVID-19 Vaccine (Vero Cell), Inactivated</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Biological: Trivalent COVID-19 Vaccine (Vero Cell), Inactivated, Prototype Strain, Delta Strain and Omicron Strain; Biological: COVID-19 Vaccine (Vero Cell), Inactivated<br/><b>Sponsors</b>: Sinovac Biotech (Colombia) S.A.S.; Sinovac Life Sciences 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>Home-Based Exercise Tele-Rehabilitation After COVID-19</strong> - <b>Condition</b>: Post SARS-CoV2 (COVID-19)<br/><b>Intervention</b>: Other: Tele-exercise<br/><b>Sponsors</b>: VA Office of Research and Development; Baltimore Veterans Affairs Medical Center; Salem Veterans Affairs Medical 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>IMM-BCP-01 in Mild to Moderate COVID-19</strong> - <b>Conditions</b>: SARS-CoV2 Infection; COVID-19<br/><b>Interventions</b>: Drug: IMM-BCP-01; Drug: Placebo<br/><b>Sponsors</b>: Immunome, Inc.; United States Department of Defense<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>Mesenchymal Stromal Cells for the Treatment of Patients With COVID-19.</strong> - <b>Conditions</b>: COVID-19 Pneumonia; COVID-19<br/><b>Interventions</b>: Biological: Mesenchymal stem cell; Other: Placebo<br/><b>Sponsors</b>: Paulo Brofman; Conselho Nacional de Desenvolvimento Científico e Tecnológico<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>Study of Self-Amplifying Messenger Ribonucleic Acid (samRNA) Vaccines Against COVID-19 in Healthy Adults and People Living With Human Immunodeficiency Virus (HIV)</strong> - <b>Conditions</b>: COVID-19; SARS-CoV-2<br/><b>Interventions</b>: Drug: GRT-R912, samRNA-Spikebeta-TCE11; Drug: GRT-R914, samRNA-Spikebeta-TCE9; Drug: GRT-R918, samRNA-SpikeOmicron-N-TCE11<br/><b>Sponsor</b>: Gritstone bio, 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>ACE2 Chewing Gum on SARS-CoV-2 Viral Load (COVID 19)</strong> - <b>Condition</b>: SARS-CoV-2<br/><b>Interventions</b>: Drug: ACE2 Chewing Gum; Other: Placebo Chewing Gum<br/><b>Sponsor</b>: University of Pennsylvania<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>Olfactory Training in COVID-19 Associated Loss of Smell</strong> - <b>Conditions</b>: COVID-19; Hyposmia<br/><b>Intervention</b>: Device: Sniffin’ sticks Duftquartett<br/><b>Sponsor</b>: Medical University Innsbruck<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>Psychological Impact of Medical Evacuations on Families of Patients Admitted to Intensive Care Unit for Severe COVID-19</strong> - <b>Conditions</b>: COVID-19; Stress Disorders, Post-Traumatic<br/><b>Interventions</b>: Other: Revised Impact of Event Scale; Other: Hospital Anxiety and Depression scale; Other: 36-Item Short Form Survey; Other: satisfaction survey; Other: semi-directed interview with trusted person on the general experience of the patient’s medical evacuation; Other: semi-directed interview with trusted person on the general experience of hospitalization in intensive care<br/><b>Sponsor</b>: Centre Hospitalier Metropole Savoie<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>Effect of COVID-19 on Platelet Mitochondrial Bioenergetic, Antioxidants and Oxidative Stress in Infertile Men.</strong> - <b>Conditions</b>: Infertility, Male; COVID-19<br/><b>Intervention</b>: Other: diagnostic test and sperm analysis<br/><b>Sponsors</b>: Comenius University; GYN-FIV<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>Clinical Trial of SARS-CoV-2 mRNA Vaccine(LVRNA009) as Heterologous Booster in Islamabad</strong> - <b>Condition</b>: SARS-CoV-2<br/><b>Interventions</b>: Biological: LVRNA009; Biological: CoronaVac®<br/><b>Sponsor</b>: AIM Vaccine 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 Evaluate Immunogenicity and Safety of MVC-COV1901 Vaccine Compared With AZD1222</strong> - <b>Condition</b>: COVID-19 Vaccine<br/><b>Interventions</b>: Biological: MVC-COV1901; Biological: AZD1222<br/><b>Sponsor</b>: Medigen Vaccine Biologics Corp.<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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<ul>
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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>Electrospun nanofibrous membrane with antibacterial and antiviral properties decorated with Myoporum bontioides extract and silver-doped carbon nitride nanoparticles for medical masks application</strong> - Public health safety issues have been plaguing the world since the pandemic outbreak of coronavirus disease (COVID-19). However, most personal protective equipments (PPE) do not have antibacterial and anti- toxicity effects. In this work, we designed and prepared a reusable, antibacterial and anti-toxicity Polyacrylonitrile (PAN) based nanofibrous membrane cooperated with Ag/g-C(3)N(4) (Ag-CN), Myoporum.bontioides (M.bontioides) plant extracts and Ag nanoparticles (NPs) by an…</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 ORF10 antagonizes STING-dependent interferon activation and autophagy</strong> - A characteristic feature of COVID-19, the disease caused by SARS-CoV-2 infection, is the dysregulated immune response with impaired type I and III interferon (IFN) expression and an overwhelming inflammatory cytokine storm. RIG-I-like receptors (RLRs) and cGAS-STING signaling pathways are responsible for sensing viral infection and inducing IFN production to combat invading viruses. Multiple proteins of SARS-CoV-2 have been reported to modulate the RLR signaling pathways to achieve immune…</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>Exploring antiviral and anti-inflammatory effects of thiol drugs in COVID-19</strong> - The redox status of the cysteine-rich SARS-CoV-2 spike glycoprotein (SARS-2-S) is important for binding of SARS-2-S to ACE2, suggesting that drugs with a functional thiol group (“thiol drugs”) may cleave cystines to disrupt SARS-CoV-2 cell entry. In addition, neutrophil-induced oxidative stress is a mechanism of COVID-19 lung injury, and the antioxidant and anti-inflammatory properties of thiol drugs, especially cysteamine, may limit this injury. To first explore antiviral effects of thiol drugs…</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>Targeting and Modulation of the Natriuretic Peptide System in Covid-19: A single or double-edged effect?</strong> - Natriuretic peptide system [NPS] is a group of peptide hormones or paracrine factors, including atrial natriuretic peptide [ANP], brain natriuretic peptide [BNP], and natriuretic peptide precursor C [NPC], that are structurally related. The physiological effects of NPS include natriuresis, increased glomerular filtration rate, inhibition release of renin, vasopressin, and aldosterone, sympathetic inhibition, vasodilatations, and prevents cardiac hypertrophy and remodeling. ANP has immunological…</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>Analysis of Interaction between odorant receptors and flexible spike of SARS CoV-2- key to loss of smell</strong> - The vaccine development for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is primarily focused on structure of the spike (S) protein. The heavy glycosylation of S with flexible hinges at stalk shields from antibodies. The flexible nature of hinges may be one of the important factors which are responsible for binding the odorant receptor of those neurons which are responsible for the loss of smell in patients with COVID-19 infection. In this study strong and stable bond formation…</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>Ongoing positive selection drives the evolution of SARS-CoV-2 genomes</strong> - SARS-CoV-2 is a new RNA virus affecting humans and spreads extensively through world populations since its first outbreak in December, 2019. Whether the transmissibility and pathogenicity of SARS-CoV-2 in humans after zoonotic transfer are actively evolving, and driven by adaptation to the new host and environments is still under debate. Understanding the evolutionary mechanism underlying epidemiological and pathological characteristics of COVID-19 is essential for predicting the epidemic trend,…</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>Assessment of disinfectant efficacy in reducing microbial growth</strong> - The incidence of hospital- and community-acquired infections has been dramatically increased worldwide. Accordingly, hands hygiene and the use of disinfectants have been increased leading to the expansion in hand sanitizers production to meet public demand. This study was conducted to assess the efficiency of common disinfectants in the market of Riyadh, Saudi Arabia in inhibiting the microbial growth during the time of Coronavirus disease 2019 (COVID-19) pandemic. Five bacterial strains of…</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>Apixaban, an orally available anticoagulant, inhibits SARS-CoV-2 replication and its major protease in a non-competitive way</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>An engineered 5-helix bundle derived from SARS-CoV-2 S2 pre-binds sarbecoviral spike at both serological- and endosomal-pH to inhibit virus entry</strong> - Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and related sarbecoviruses enter host cells by receptor-recognition and membrane-fusion. An indispensable step in fusion is the formation of 6-helix bundle by viral spike heptad repeats 1 and 2 (HR1 and HR2). Here, we report the construction of 5-helix bundle (5HB) proteins for virus infection inhibition. The optimal construct inhibits SARS-CoV-2 pseudovirus entry with sub-micromolar IC50. Unlike HR2-based peptides that cannot bind…</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>Development of an efficient reproducible cell-cell transmission assay for rapid quantification of SARS-CoV-2 Spike interaction with hACE2</strong> - Efficient quantitative assays for measurement of viral replication and infectivity are indispensable to future endeavors to develop prophylactic or therapeutic antiviral drugs or vaccines against SARS-CoV-2. We developed a SARS-CoV-2 cell-cell transmission assay that provides a rapid and quantitative readout to assess SARS-CoV-2 Spike hACE2 interaction in the absence of pseudotyped particles or live virus. We established two well-behaved stable cell lines, which demonstrated a remarkable…</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>Heparanase Is a Putative Mediator of Endothelial Glycocalyx Damage in COVID-19 - A Proof-of-Concept Study</strong> - Coronavirus disease 2019 (COVID-19) is a systemic disease associated with injury (thinning) of the endothelial glycocalyx (eGC), a protective layer on the vascular endothelium. The aim of this translational study was to investigate the role of the eGC-degrading enzyme heparanase (HPSE), which is known to play a central role in the destruction of the eGC in bacterial sepsis. Excess activity of HPSE in plasma from COVID-19 patients correlated with several markers of eGC damage and perfused…</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>Neutrophil Extracellular Traps, Sepsis and COVID-19 - A Tripod Stand</strong> - The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the current coronavirus disease 2019 (COVID-19) pandemic. Majority of COVID-19 patients have mild disease but about 20% of COVID-19 patients progress to severe disease. These patients end up in the intensive care unit (ICU) with clinical manifestations of acute respiratory distress syndrome (ARDS) and sepsis. The formation of neutrophil extracellular traps (NETs) has also been associated with severe…</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>Immunosuppressant Treatment in Rheumatic Musculoskeletal Diseases Does Not Inhibit Elicitation of Humoral Response to SARS-CoV-2 Infection and Preserves Effector Immune Cell Populations</strong> - COVID-19 has proven to be particularly serious and life-threatening for patients presenting with pre-existing pathologies. Patients affected by rheumatic musculoskeletal disease (RMD) are likely to have impaired immune responses against SARS-CoV-2 infection due to their compromised immune system and the prolonged use of disease-modifying anti-rheumatic drugs (DMARDs), which include conventional synthetic (cs) DMARDs or biologic and targeted synthetic (b/ts) DMARDs. To provide an integrated…</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>Seroprevalence of Anti-S1-RBD Antibodies in Pre-pandemic and Pandemic Subjects From Hail Region, KSA</strong> - CONCLUSION: Antibody levels increased in samples collected during the pandemic, even though these subjects were not clinically COVID-19 positive. A small number of pre-pandemic subjects showed serum antibodies, suggesting prior exposure to other coronaviruses in the region. With dwindling neutralizing antibody levels and reduced vaccine efficacy against newer variants, it remains crucial to develop better assays for surveillance, management, and future research.</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 infects an <em>in vitro</em> model of the human developing pancreas through endocytosis</strong> - Recent studies showed that SARS-CoV-2 can infect adult human pancreas and trigger pancreatic damage. Here, using human fetal pancreas samples and 3D differentiation of human pluripotent cells into pancreatic endocrine cells, we determined that SARS-CoV-2 receptors ACE2, TMPRSS2 and NRP1 are expressed in precursors of insulin-producing pancreatic β-cells, rendering them permissive to SARS-CoV-2 infection. We also show that SARS-CoV-2 enters and undergoes efficient replication in human multipotent…</p></li>
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</ul>
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<h1 data-aos="fade-right" id="from-patent-search">From Patent Search</h1>
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