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<title>30 May, 2023</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>Hybrid use of Raman spectroscopy and artificial neural networks to discriminate Mycobacterium bovis BCG and members of the order Mycobacteriales</strong> -
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<div>
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Even in the face of the COVID-19 pandemic, Tuberculosis (TB) continues to be a major public health problem and the 2nd biggest infectious cause of death worldwide. There is, therefore, an urgent need to develop effective TB diagnostic methods, which are cheap, portable, sensitive and specific. Raman spectroscopy is a potential spectroscopic technique for this purpose, however, so far, research efforts have focused primarily on the characterisation of Mycobacterium tuberculosis and other Mycobacteria, neglecting bacteria within the microbiome and thus, failing to consider the bigger picture. It is paramount to characterise relevant Mycobacteriales and develop suitable analytical tools to discriminate them from each other. Herein, through the combined use of Raman spectroscopy and the self-optimising Kohonen index network and further multivariate tools, we have successfully undertaken the spectral analysis of Mycobacterium bovis BCG, Corynebacterium glutamicum and Rhodoccocus erythropolis. This has led to development of a useful tool set, which can readily discern spectral differences between these three closely related bacteria as well as generate a unique spectral barcode for each species. Further optimisation and refinement of the developed method will enable its application to other bacteria. inhabiting the microbiome and ultimately lead to advanced diagnostic technologies, which can save many lives.
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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://www.biorxiv.org/content/10.1101/2023.05.30.542797v1" target="_blank">Hybrid use of Raman spectroscopy and artificial neural networks to discriminate Mycobacterium bovis BCG and members of the order Mycobacteriales</a>
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</div></li>
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<li><strong>Mortality among people hospitalised with covid-19 in Switzerland: a nationwide population-based analysis</strong> -
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Objectives: To investigate mortality among people hospitalised with covid-19 in Switzerland according to epidemic wave, age, sex, comorbid conditions and intensive care unit (ICU) occupancy. Design: Population-based, national study. Setting: Mandatory surveillance reports from all hospitals in Switzerland. Participants: All 22,648 people who tested positive for SARS-CoV-2 infection and were hospitalised between February 24, 2020 and March 01, 2021 in Switzerland with complete information about age, sex, and comorbidities. Main outcome measures: Survival after positive SARS-CoV-2 test among people hospitalised with covid-19 by epidemic wave, age, sex, comorbid conditions and ICU occupancy, expressed as adjusted hazard ratios (aHR) of death and probability of survival over time and at 40 days, all with 95% credible intervals (CrI). Results: Of 22,648 people hospitalised with covid-19, 4,785 (21.1%) died. Bayesian survival models adjusted for age, sex, and the presence of comorbidity showed that survival was lower during the first epidemic wave than the second (standardised predicted survival probability at 40 days 76.1% versus 80.5%; aHR of death 1.38, 95% CrI 1.28 to 1.48). During the second epidemic wave, occupancy among all available ICU beds (certified beds and add-on beds) in Switzerland varied between 51.7% and 78.8%. Modelling the association between survival and ICU occupancy with restricted cubic splines indicated stable survival when ICU occupancy was below 70%, but worse survival when ICU occupancy exceeded 70%. This threshold of 70% occupancy among total available ICU beds corresponded to around 85% occupancy among certified beds. Survival was decreased for men, older people, and patients with comorbid conditions. Comorbid conditions reduced survival more in younger people than in older people. As single comorbid condition, hypertension was not associated with poorer survival, but appeared to increase the risk of death in combination with a cardiovascular disease. Conclusion: Survival after hospitalisation with covid-19 has improved over time, consistent with improved management of severe covid-19. The decreased survival starting at approximately 70% ICU occupancy in Switzerland supports the need to introduce measures for prevention and control of SARS-CoV-2 transmission in the population far before ICUs are full.
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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/37gaz/" target="_blank">Mortality among people hospitalised with covid-19 in Switzerland: a nationwide population-based analysis</a>
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</div></li>
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<li><strong>Distinct and overlapping immunological responses to SARS-CoV-2 and Mycobacterium tuberculosis identified by single-cell RNA-seq of co-infected whole blood</strong> -
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<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom">
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Introduction: COVID-19 and tuberculosis (TB) exhibit similar symptomatic presentation and clinical parameters. Common underlying immunological mechanisms also highlight potential routes of immunopathogenic interaction between these diseases during co-infection. To explore immunological similarities, differences and interactions, single-cell RNA-seq (scRNA-seq) was performed on whole blood infected with Mycobacterium tuberculosis (Mtb), SARS-CoV-2, or both pathogens. Methods: Whole blood from four healthy adults, were subjected to ex vivo infection with Mtb and/or SARS-CoV-2 ancestral strain, or were maintained in an uninfected state, for 24 or 96 hours. At each timepoint, for each condition, the four biological replicates were captured, fixed and cryopreserved to be processed for scRNA-seq as a single batch. Following quality control filtering, genotype-based demultiplexing was performed to obtain data from each biological replicate for pseudobulk differential expression analysis. Results: Thirteen distinct clusters of cells were identified based on marker gene expression. Profound differences in the proportions of monocytes, T cells and neutrophils were observed between infection conditions and timepoints. The greatest divergence between pathogen responses occurred within myeloid cells at early timepoints of infection. Co-infection had the greatest synergistic effect 24 hours post-infection with 238 immunological pathways uniquely enriched, including IFN-γ and TNF production, whilst by 96 hours post-infection there was a large overlap of 182 shared pathways between Mtb, SARS-CoV-2 and co-infection. SARS-CoV-2-only infection resulted in widespread cell death by 96 hours post-infection, while Mtb-only and co-infected samples remained enriched for monocyte, T cell and NK cell signatures, sharing negative regulation of extrinsic apoptotic signalling. Distinct from Mtb, SARS-Co-V-2 had unique regulating of αβ T cell activation and differentiation at both time points. Conclusion: These data provide a high-resolution characterisation of distinct and overlapping immunological responses generated by SARS-CoV-2 and Mtb when a single infection or co-infection occurs. This sheds light on the potential effects of novel or existing host-directed therapies that target these pathways, which is particularly crucial for settings where dual presentation is common.
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</p>
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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://www.medrxiv.org/content/10.1101/2023.05.24.23290499v1" target="_blank">Distinct and overlapping immunological responses to SARS-CoV-2 and Mycobacterium tuberculosis identified by single-cell RNA-seq of co-infected whole blood</a>
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</div></li>
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<li><strong>Development of a SARS-COV-2 monoclonal antibody panel and its applicability as a reagent in high-throughput fluorescence reduction neutralization and immunohistochemistry assays</strong> -
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<div>
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Since its emergence in late 2019, infection by SARS-CoV-2 (COVID-19 disease) has quickly spread worldwide, leading to a pandemic that has caused millions of deaths and huge socio-economic losses. Although vaccination against COVID-19 has significantly reduced disease mortality, it has been shown that protection wanes over time, and that circulating SARS-CoV-2 variants may escape vaccine-derived immunity. Therefore, serological studies are still necessary to assess protection in the population and better guide vaccine booster programs. A common measure of protective immunity is the presence of neutralizing antibodies (nAbs). However, the gold standard method for measuring nAbs (plaque reduction neutralization test, or PRNT) is laborious and time-consuming, limiting its large-scale applicability. In this study, we developed a high-throughput fluorescence reduction neutralization assay (FRNA) to detect SARS-CoV-2 nAbs. Because the assay relies on immunostaining, we also developed and characterized in-house monoclonal antibodies (mAbs) to lower assay costs and reduce the vulnerability of the test to reagent shortages. Using samples collected before the pandemic and from individuals vaccinated against COVID-19, we showed that the results of the FRNA we developed using commercial and in-house mAbs strongly correlated with those of the standard PRNT method while providing results in 70% less time. In addition to providing a fast, reliable, and high-throughput alternative for measuring nAbs, the FRNA can be easily customized to assess other SARS-CoV-2 variants of concern (VOCs). We also demonstrated the applicability of the mAbs produced in immunohistochemistry assays.
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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://www.biorxiv.org/content/10.1101/2023.05.29.542720v1" target="_blank">Development of a SARS-COV-2 monoclonal antibody panel and its applicability as a reagent in high-throughput fluorescence reduction neutralization and immunohistochemistry assays</a>
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</div></li>
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<li><strong>Wastewater surveillance suggests unreported Mpox cases in a low-prevalence area</strong> -
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<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom">
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Wastewater surveillance has emerged as a valuable tool for monitoring infectious disease agents including SARS-CoV-2 and Mpox virus. However, detecting the Mpox virus in wastewater is particularly challenging due to its relatively low prevalence in the community. In this study, we detected Mpox virus in wastewater from a US-Mexico border city with a low prevalence of Mpox disease during February and March 2023 using real-time PCR assays targeting the C22L, F3L, and F8L genes. An increasing trend of viral concentration was observed 1~2 weeks earlier than when the Mpox case was reported. Further sequencing and epidemiological analysis provided supporting evidence for unreported Mpox infections in the city. This study showcases a combined approach with multiple molecular assays for efficient detection of the Mpox virus in wastewater in a low-prevalence area. The findings emphasize the value of wastewater surveillance as a timely identification tool for infectious diseases in low-prevalence areas, and the need for heightened vigilance to control the spread of infectious diseases in such settings.
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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/10.1101/2023.05.28.23290658v1" target="_blank">Wastewater surveillance suggests unreported Mpox cases in a low-prevalence area</a>
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<li><strong>Identification of targets for drug repurposing to treat COVID-19 using a Deep Learning Neural Network</strong> -
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The COVID-19 pandemic has resulted in a global public health crisis requiring immediate acute therapeutic solutions. To address this challenge, we developed a useful tool deep learning model using the graph-embedding convolution network (GECN) algorithm. Our approach identified COVID-19-related genes and potential druggable targets, including tyrosine kinase ABL1/2, pro-inflammatory cytokine CSF2, and pro-fibrotic cytokines IL-4 and IL-13. These target genes are implicated in critical processes related to COVID-19 pathogenesis, including endosomal membrane fusion, cytokine storm, and tissue fibrosis. Our analysis revealed that ABL kinase inhibitors, lenzilumab (anti-CSF2), and dupilumab (anti-IL4Rα) represent promising therapeutic solutions that can effectively block virus-host membrane fusion or attenuate hyperinflammation in COVID-19 patients. Compared to the traditional drug screening process, our GECN algorithm enables rapid analysis of disease-related human protein interaction networks and prediction of candidate drug targets from a large-scale knowledge graph in a cost-effective and efficient manner. Overall, Overall, our results suggest that the model has the potential to facilitate drug repurposing and aid in the fight against COVID-19.
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</p>
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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://www.medrxiv.org/content/10.1101/2023.05.23.23290403v1" target="_blank">Identification of targets for drug repurposing to treat COVID-19 using a Deep Learning Neural Network</a>
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<li><strong>A Framework for Moving Beyond Computational Reproducibility: Lessons from Three Reproductions of Geographical Analyses of COVID-19</strong> -
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<div>
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Despite recent calls to make geographical analyses more reproducible, formal attempts to reproduce or replicate published work remain largely absent from the geographic literature. The reproductions of geographic research that do exist typically focus on computational reproducibility - whether results can be recreated using data and code provided by the authors - rather than on evaluating the conclusion and internal validity and evidential value of the original analysis. However, knowing if a study is computationally reproducible is insufficient if the goal of a reproduction is to identify and correct errors in our knowledge. We argue that reproductions of geographic work should focus on assessing whether the findings and claims made in existing empirical studies are well supported by the evidence presented. We present three model reproductions of geographical analyses of COVID-19 that demonstrate how to achieve this goal. Each reproduction is based on a common, open access template and is published as an open access repository, complete with pre-analysis plan, data, code, and final report. We find each study to be partially reproducible, but moving past computational reproducibility, our assessments reveal conceptual and methodological concerns that raise questions about the predictive value and the magnitude of the associations presented in each study. Collectively, these reproductions and our template materials offer a practical framework others can use to reproduce and replicate empirical spatial analyses and ultimately facilitate the identification and correction of errors in the geographic literature.
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<div class="article-link article-html-link">
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🖺 Full Text HTML: <a href="https://osf.io/preprints/metaarxiv/7jqtv/" target="_blank">A Framework for Moving Beyond Computational Reproducibility: Lessons from Three Reproductions of Geographical Analyses of COVID-19</a>
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<li><strong>POLICY BRIEF THE IMPACT OF THE COVID-19 PANDEMIC ON WORK, PRODUCTIVITY, AND INNOVATION IN FRANCE</strong> -
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The COVID-19 pandemic has dramatically affected workplaces, productivity, and innovation across France. As society continues to navigate this unprecedented crisis, understanding these impacts is paramount for policy formulation, aimed at fostering economic recovery and future resilience. This policy brief examines the implications of the pandemic on these areas, drawing from literature such as Abi Younes et al. (2020), Furman et al. (2020), OECD (2020), and Sanofi (2022).
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🖺 Full Text HTML: <a href="https://thesiscommons.org/wdxuk/" target="_blank">POLICY BRIEF THE IMPACT OF THE COVID-19 PANDEMIC ON WORK, PRODUCTIVITY, AND INNOVATION IN FRANCE</a>
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</div></li>
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<li><strong>Effectiveness of BNT162b2 mRNA vaccine third doses and previous infection in protecting against SARS-CoV-2 infections during the Delta and Omicron variant waves; the UK SIREN cohort study September 2021 to February 2022</strong> -
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Third doses of COVID-19 vaccines were widely deployed following primary vaccine course waning and emergence of the Omicron-variant. We investigated protection from third-dose vaccines and previous infection against SARS-CoV-2 infection during Delta-variant and Omicron-variant (BA.1 & BA.2) waves in our frequently PCR-tested cohort of healthcare-workers. Relative effectiveness of BNT162b2 third doses and infection-acquired immunity was assessed by comparing the time to PCR-confirmed infection in boosted participants with those with waned dose-2 protection (≥254 days after dose-2). Follow-up time was divided by dominant circulating variant: Delta 07 September 2021 to 30 November 2021, Omicron 13 December 2021 to 28 February 2022. We used a Cox regression model with adjustment/stratification for demographic characteristics and staff-type. We explored protection associated with vaccination, infection and both. We included 19,614 participants, 29% previously infected. There were 278 primary infections (4 per 10,000 person-days of follow-up) and 85 reinfections (0.8/10,000 person-days) during the Delta period and 2467 primary infections (43/10,000 person-days) and 881 reinfections (33/10,000) during the Omicron period. Relative Vaccine Effectiveness (VE) 0-2 months post-3rd dose (V3) (3-doses BNT162b2) in the previously uninfected cohort against Delta infections was 63% (95% Confidence Interval (CI) 40%-77%) and was lower (35%) against Omicron infection (95% CI 21%-47%). For primary course ChAdOX1 recipients, BNT162b2 heterologous third doses were especially effective, with VE 0-2 months post-V3 over ≥68% higher for both variants. Third-dose protection waned rapidly against Omicron, with no significant difference between two and three BNT162b2 doses observed after 4-months. Previous infection continued to provide additional protection against Omicron (67% (CI 56%-75%) 3-6 months post-infection), but this waned to about 25% after 9-months, approximately three times lower than against Delta. Infection rates surged with Omicron emergence. Third doses of BNT162b2 vaccine provided short-term protection, with rapid waning against Omicron infections. Protection associated with infections incurred before Omicron was markedly diminished against the Omicron wave. Our findings demonstrate the complexity of an evolving pandemic with potential emergence of immune-escape variants and the importance of continued monitoring.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2023.05.22.23290197v1" target="_blank">Effectiveness of BNT162b2 mRNA vaccine third doses and previous infection in protecting against SARS-CoV-2 infections during the Delta and Omicron variant waves; the UK SIREN cohort study September 2021 to February 2022</a>
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<li><strong>Reflections on academia in the COVID-19 era: Implications for policy, ethics, and democracy</strong> -
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This chapter reviews COVID-19 policy responses in academia, drawing from our research - on expert narratives on vaccine uptake and hesitancy, on the medicalization of dissent within the Canadian academy, on actual COVID policies in selected Canadian universities, and on postsecondary Canadian students’ experience of COVID policies - as well as our personal experience as long-standing and active members of academic communities. We also elaborate on the implications of these responses for policy, ethics, and the normative academic commitments to protect free intellectual inquiry, promote critical thinking among the young, and support democratic governance, in the hope of shedding light on better ways moving forward.
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🖺 Full Text HTML: <a href="https://osf.io/preprints/socarxiv/hvxpc/" target="_blank">Reflections on academia in the COVID-19 era: Implications for policy, ethics, and democracy</a>
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<li><strong>Large and unequal life expectancy declines associated with the COVID-19 pandemic in India in 2020</strong> -
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The toll of the COVID-19 pandemic in low- and middle-income countries (LMICs) is uncertain. We are the first to use high-quality empirical data from India, which has a large population and where pandemic surveillance was particularly poor, to examine changes in life expectancy and estimate excess deaths during the pandemic. We analyze data from the households interviewed in 2021 in India’s fifth Demographic and Health Survey, a subsample representative of about one-quarter of India’s population. In this subsample, life expectancy at birth declined by 2.6 years between 2019 and 2020, a reduction that is larger than the loss in life expectancy observed in any high-income country (HIC) in the same period. Mortality was 17.0% higher in the pandemic months of 2020 compared to 2019. Applied nationally, this level of excess mortality implies 1.18 million excess deaths in 2020. Compared to HICs, mortality increases in younger ages in India contributed more to the decrease in life expectancy than older ages. Furthermore, the pandemic exacerbated gender and social inequalities. In contrast to global patterns, females in India experienced larger life expectancy losses than males. As compared to a life expectancy loss of 1.5 years for high caste Hindus, who are privileged in Indian society, Muslims lost 5.9 years, Scheduled Tribes lost 4.4 years, and Scheduled Castes lost 2.6 years. These findings uncover large and unequal mortality shocks during the pandemic in the world’s most populous country.
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🖺 Full Text HTML: <a href="https://osf.io/preprints/socarxiv/8juds/" target="_blank">Large and unequal life expectancy declines associated with the COVID-19 pandemic in India in 2020</a>
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<li><strong>Structural characterization of a pathogenic antibody underlying vaccine-induced immune thrombotic thrombocytopenia (VITT)</strong> -
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Vaccine-induced immune thrombotic thrombocytopenia (VITT) is a rare but extremely dangerous side effect that has been reported for several adenoviral (Ad)-vectored COVID-19 vaccines. VITT pathology had been linked to production of antibodies that recognize platelet factor 4 (PF4), an endogenous chemokine. In this work we characterize anti-PF4 antibodies obtained from a VITT patient's blood. Intact-mass MS measurements indicate that a significant fraction of this ensemble is comprised of antibodies representing a limited number of clones. MS analysis of large antibody fragments (the light chain, as well as the Fc/2 and Fd fragments of the heavy chain) confirms the monoclonal nature of this component of the anti-PF4 antibodies repertoire, and reveals the presence of a fully mature complex biantennary N-glycan within its Fd segment. Peptide mapping using two complementary proteases and LC-MS/MS analysis were used to determine the amino acid sequence of the entire light chain and over 98% of the heavy chain (excluding a short N-terminal segment). The sequence analysis allows the monoclonal antibody to be assigned to IgG2 subclass and verify that the light chain belongs to the {lambda}-type. Incorporation of enzymatic de-N-glycosylation into the peptide mapping routine allows the N-glycan in the Fab region of the antibody to be localized to the framework 3 region of the VH domain. This novel N-glycosylation site (absent in the germline sequence) is a result of a single mutation giving rise to an NDT motif in the antibody sequence. Peptide mapping also provides a wealth of information on lower-abundance proteolytic fragments derived from the polyclonal component of the anti-PF4 antibody ensemble, revealing the presence of all four subclasses (IgG1 through IgG4) and both types of the light chain ({lambda} and {kappa}). The structural information reported in this work will be indispensable for understanding the molecular mechanism of VITT pathogenesis.
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🖺 Full Text HTML: <a href="https://www.biorxiv.org/content/10.1101/2023.05.28.542636v1" target="_blank">Structural characterization of a pathogenic antibody underlying vaccine-induced immune thrombotic thrombocytopenia (VITT)</a>
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<li><strong>Nurses’ perceptions of videoconferencing telenursing: comparing frontal learning vs. online learning before and after the COVID-19 pandemic</strong> -
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Introduction: During the COVID-19 pandemic, a digital transformation led to an expansion in telenursing practices and a shift in training to online learning. The aim of this study was to explore the impact of behavioral-related factors, based on both TAM and TPB variables, on the intention to use telenursing through videoconferencing and to compare the effect of frontal (before COVID-19) vs. online (during and after COVID-19) training in post-basic nursing courses on nursing attitudes to telenursing. Methods: A cross-sectional online survey was conducted in December 2022 among nurses working mainly at hospitals in Israel who underwent post-basic education training between January 2017 and December 2022. A multivariate ordinary least squares (OLS) regression analysis was used to investigate determinants of intention to use telenursing through videoconferencing Results: Nurses have a positive attitude towards telenursing technology via videoconferencing for remote patient care, regardless of whether they learned about it through face-to-face or online training. The ease of use and the perception of the technology9s importance by colleagues and supervisors were found to have the most significant impact on the attitude of both research groups towards the use of telelearning. Discussion: Successful implementation of new technology in healthcare requires organizational and collegial support. Therefore, managers should encourage the use of telenursing by providing appropriate training for nurses and the necessary resources and support.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2023.05.22.23290291v1" target="_blank">Nurses’ perceptions of videoconferencing telenursing: comparing frontal learning vs. online learning before and after the COVID-19 pandemic</a>
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<li><strong>Multiplex PCR amplicon sequencing revealed community transmission of SARS-CoV-2 lineages on the campus of Sichuan University during the outbreak of infection in Chinese Mainland at the end of 2022</strong> -
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During the pandemic of COVID-19, wastewater-based epidemiology has become a powerful epidemic surveillance tool widely used around the world. However, the development and application of this technology in Chinese Mainland are relatively lagging. Herein, we report the first case of community circulation of SARS-CoV-2 lineages monitored by WBE in Chinese Mainland during the infection outbreak at the end of 2022 after the comprehensive relaxation of epidemic prevention policies. During the peak period of infection, six precious sewage samples were collected from the manhole in the student dormitory area of Wangjiang Campus of Sichuan University. According to the results RT-qPCR, the six sewage samples were all positive for SARS-CoV-2 RNA. Based on multiplex PCR amplicon sequencing, the local transmission of SARS-CoV-2 variants at that time was analyzed. The results show that the main virus lineages in sewage have clear evolutionary genetic correlations. Furthermore, the sampling time is very consistent with the timeline of concern for these virus lineages and consistent with the timeline for uploading the nucleic acid sequences of the corresponding lineages in Sichuan to the database. These results demonstrate the reliability of the sequencing results of SARS-CoV-2 nucleic acid in wastewater. Multiplex PCR amplicon sequencing is by far the most powerful analytical tool of WBE, enabling quantitative monitoring of virus lineage prevalence at the community level.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2023.05.22.23290366v1" target="_blank">Multiplex PCR amplicon sequencing revealed community transmission of SARS-CoV-2 lineages on the campus of Sichuan University during the outbreak of infection in Chinese Mainland at the end of 2022</a>
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<li><strong>The Brazilian vaccine divide: how some municipalities are being left behind in the Covid-19 vaccine coverage</strong> -
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Objectives: This study aims to assess the progress of geographic, socioeconomic, and demographic disparities in Covid-19 vaccination coverage in Brazil over the first two years of the vaccination campaign. Methods: Data from the National Immunization Program Information System were used to estimate covid-19 vaccine coverage. Brazilian municipalities were divided into two groups based on their vaccine coverage for the booster dose. The first group comprised 20% of municipalities with the lowest coverage, while the second group (80% of municipalities) had higher coverage. The analysis was conducted separately for four age groups: 5-11, 12-17, 18-59, and 60+. Exploratory variables included socioeconomic and health services indicators. Crude and adjusted logistic regression models were used to estimate the probability of a municipality being among those with the worst vaccination coverage according to the categories of exploratory variables. Results: Between January/2021 and December/2022, Brazil administered 448.2 million doses of the covid-19 vaccine. The booster vaccination coverage varied from 24.8% among adolescents to 79.7% among the elderly. The difference between the group with the highest and lowest coverage increased during the national vaccination campaign. Municipalities with lower education levels, higher proportion of Black population, higher Gini index, and worse health service indicators had a greater likelihood of having lower vaccination coverage. Conclusions: High and increasing levels of inequality in Covid-19 vaccination were observed in Brazil across all age groups during the vaccination campaign in 2021-2022.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2023.05.23.23290401v1" target="_blank">The Brazilian vaccine divide: how some municipalities are being left behind in the Covid-19 vaccine coverage</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>Investigation of the Effect on Cognitive Skills of COVID-19 Survivors</strong> - <b>Condition</b>: COVID-19<br/><b>Intervention</b>: Other: green walking and intelligence gam<br/><b>Sponsors</b>: Bayburt University; Karadeniz Technical 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>Conducting Clinical Trials of the Medicine “Rutan Tablets 0.1g” No. 10 in the Complex Therapy of COVID-19</strong> - <b>Condition</b>: Patients With COVID-19<br/><b>Interventions</b>: Drug: The drug “Rutan 0.1”.; Other: Basic treatment<br/><b>Sponsor</b>: Research Institute of Virology, Ministry of Health of the Republic of Uzbekistan<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>Evaluation of Safety, Tolerability, Reactogenicity, Immunogenicity of Baiya SARS-CoV-2 Vax 2 as a Booster for COVID-19</strong> - <b>Conditions</b>: COVID-19 Vaccine; COVID-19<br/><b>Interventions</b>: Biological: 50 μg Baiya SARS-CoV-2 Vax 2; Other: Placebo<br/><b>Sponsor</b>: Baiya Phytopharm 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>The Effect of Special Discharge Training in the COVID-19</strong> - <b>Condition</b>: COVID-19 Pneumonia<br/><b>Intervention</b>: Other: COVID-19 Discharge Education<br/><b>Sponsor</b>: Kilis 7 Aralik 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>Physiotherapy in Mutated COVID-19 Patients</strong> - <b>Condition</b>: COVID-19 Pandemic<br/><b>Intervention</b>: Behavioral: Physiotherapy<br/><b>Sponsor</b>: Giresun 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>Studying the Efficiency of the Natural Preparation Rutan in Children in the Treatment of COVID-19, ARVI</strong> - <b>Condition</b>: COVID-19 Respiratory Infection<br/><b>Interventions</b>: Drug: Rutan 25 mg; Other: Control group<br/><b>Sponsor</b>: Research Institute of Virology, Ministry of Health of the Republic of Uzbekistan<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>To Explore the Regulatory Effect of Combined Capsule FMT on the Levels of Inflammatory Factors in Peripheral Blood of Patients With COVID-19 During Treatment.</strong> - <b>Conditions</b>: Fecal Microbiota Transplantation; COVID-19 Infection<br/><b>Intervention</b>: Procedure: Fecal microbiota transplantation<br/><b>Sponsor</b>: Shanghai 10th People’s Hospital<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>Use of a Hypochlorous Acid Spray Solution in the Treatment of COVID-19 Patients : COVICONTROL Study .</strong> - <b>Condition</b>: SARS CoV 2 Infection<br/><b>Interventions</b>: Other: Spray with Hypochlorous Acid Group; Other: Spray with Placebo Group<br/><b>Sponsor</b>: University of Monastir<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>Telerehabilitation Program and Detraining in Patients With Post-COVID-19 Sequelae</strong> - <b>Condition</b>: COVID-19 Acute Respiratory Distress Syndrome<br/><b>Intervention</b>: Other: Telerehabilitation program<br/><b>Sponsor</b>: Campus docent Sant Joan de Déu-Universitat de Barcelona<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>Phase 3 Study of Novavax Vaccine(s) as Booster Dose After mRNA Vaccines</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Biological: NVX-CoV2373; Biological: SARS-CoV-2 rS antigen/Matrix-M Adjuvant<br/><b>Sponsor</b>: Novavax<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>COVID-19 Vaccine Uptake Amongst Underserved Populations in East London</strong> - <b>Conditions</b>: COVID-19; Influenza; Vaccination Refusal<br/><b>Intervention</b>: Device: Patient Engagement tool<br/><b>Sponsors</b>: Queen Mary University of London; Social Action for 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>Anti-SARS-CoV-2 Monoclonal Antibodies for Long COVID (COVID-19)</strong> - <b>Conditions</b>: Long COVID; Post-Acute Sequela of COVID-19; Post-Acute COVID-19<br/><b>Interventions</b>: Drug: AER002; Other: Placebo<br/><b>Sponsors</b>: Michael Peluso, MD; Aerium Therapeutics<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>Dose Exploration Intramuscular/Intravenous Prophylaxis Pharmacokinetic Exposure Response Study</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Drug: AZD3152; Other: Placebo<br/><b>Sponsor</b>: AstraZeneca<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 to Assess Safety, Reactogenicity and Immunogenicity of the repRNA(QTP104) Vaccine Against SARS-CoV-2(COVID-19)</strong> - <b>Conditions</b>: COVID-19; SARS-CoV-2<br/><b>Interventions</b>: Biological: QTP104 1ug; Biological: QTP104 5ug; Biological: QTP104 25ug<br/><b>Sponsor</b>: Quratis Inc.<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>Effects of Individual Tailored Physical Exercise in Patients With POTS After COVID-19 - a Randomized Controlled Study</strong> - <b>Conditions</b>: Postural Orthostatic Tachycardia Syndrome; COVID-19; Post COVID-19 Condition; Post-Acute COVID-19 Syndrome<br/><b>Intervention</b>: Other: Individual tailored exercise<br/><b>Sponsors</b>: Karolinska Institutet; Karolinska University Hospital<br/><b>Enrolling by invitation</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>Immunogenicity and safety of COVID-19 BNT162b2 booster vaccine in end-stage kidney disease patients receiving haemodialysis in Yogyakarta, Indonesia: a cohort prospective study</strong> - CONCLUSIONS: The majority of ESKD patients on haemodialysis mounted a good antibody response to the BNT162b2 booster vaccination with tolerable adverse events.</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>Capture and neutralization of SARS-CoV-2 and influenza virus by algae-derived lectins with high-mannose and core fucose specificities</strong> - We first investigated the interactions between several algae-derived lectins and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). We created lectin columns using high-mannose (HM)-type glycan-specific lectins OAA and KAA-1 or core fucose-specific lectin hypninA-2 and conducted binding experiments with SARS-CoV-2. The results showed that these lectins were capable of binding to the virus. Furthermore, when examining the neutralization ability of nine different lectins, it was found…</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>Inflammation inhibitory activity of green tea, soybean, and guava extracts during Sars-Cov-2 infection through TNF protein in cytokine storm</strong> - Coronavirus disease is caused by the pathogen severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) known as COVID-19. COVID-19 has caused the deaths of 6,541,936 people worldwide as of September 27th, 2022. SARS-CoV-2 severity is determined by a cytokine storm condition, in which the innate immune system creates an unregulated and excessive production of pro-inflammatory such IL-1, IL-6, NF Kappa B, and TNF alpha signaling molecules known as cytokines. The patient died due to respiratory…</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>Long Time Scale Ensemble Methods in Molecular Dynamics: Ligand-Protein Interactions and Allostery in SARS-CoV-2 Targets</strong> - We subject a series of five protein-ligand systems which contain important SARS-CoV-2 targets, 3-chymotrypsin-like protease (3CLPro), papain-like protease, and adenosine ribose phosphatase, to long time scale and adaptive sampling molecular dynamics simulations. By performing ensembles of ten or twelve 10 μs simulations for each system, we accurately and reproducibly determine ligand binding sites, both crystallographically resolved and otherwise, thereby discovering binding sites that can be…</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 ORF3a sensitizes cells to ferroptosis via Keap1-NRF2 axis</strong> - Viral infection-induced cell death has long been considered as a double-edged sword in the inhibition or exacerbation of viral infections. Patients with severe Coronavirus Disease 2019 (COVID-19) are characterized by multiple organ dysfunction syndrome and cytokine storm, which may result from SARS-CoV-2-induced cell death. Previous studies have observed enhanced ROS level and signs of ferroptosis in SARS-CoV-2 infected cells or specimens of patients with COVID-19, but the exact mechanism is not…</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>Utilization of Marine Seaweeds as a Promising Defense Against COVID-19: a Mini-review</strong> - COVID-19 is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which mainly affects the respiratory system. It has been declared as a “pandemic” in March 2020 by the World Health Organization due to the high spreading rate. SARS-CoV-2 binds with the angiotensin-converting enzyme 2 (ACE2) receptors on the cell surface which leads to the downregulation of ACE2 and upregulation of angiotensin-converting enzyme (ACE) receptors. The elevated level 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>Identification of Host Proteins Interacting with IBV S1 Based on Tracheal Organ Culture</strong> - Infectious bronchitis virus (IBV) belongs to the gamma-coronavirus genus of Coronaviridae and causes serious infectious diseases in the poultry industry. However, only a few IBV strains can infect avian passage cell lines, seriously hindering the progress of basic research on IBV pathogenesis. Whereas IBV field strains can replicate in tracheal ring organ culture (TOC) without any previous adaptation in chicken embryos or primary cells. In this study, to investigate the potential use of TOC 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>Transcription Factor Driven Gene Regulation in COVID-19 Patients</strong> - SARS-CoV-2 and its many variants have caused a worldwide emergency. Host cells colonised by SARS-CoV-2 present a significantly different gene expression landscape. As expected, this is particularly true for genes that directly interact with virus proteins. Thus, understanding the role that transcription factors can play in driving differential regulation in patients affected by COVID-19 is a focal point to unveil virus infection. In this regard, we have identified 19 transcription factors which…</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>Genes Involved in miRNA Biogenesis Are Not Downregulated in SARS-CoV-2 Infection</strong> - miRNAs, small non-coding RNAs that regulate gene expression, are involved in various pathological processes, including viral infections. Virus infections may interfere with the miRNA pathway through the inhibition of genes involved in miRNA biogenesis. A reduction in the number and the levels of miRNAs expressed in nasopharyngeal swabs of patients with severe COVID-19 was lately observed by us, pointing towards the potential of miRNAs as possible diagnostic or prognostic biomarkers for…</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>In Silico and In Vitro Evaluation of Some Amidine Derivatives as Hit Compounds towards Development of Inhibitors against Coronavirus Diseases</strong> - Coronaviruses, including SARS-CoV-2, SARS-CoV, MERS-CoV and influenza A virus, require the host proteases to mediate viral entry into cells. Rather than targeting the continuously mutating viral proteins, targeting the conserved host-based entry mechanism could offer advantages. Nafamostat and camostat were discovered as covalent inhibitors of TMPRSS2 protease involved in viral entry. To circumvent their limitations, a reversible inhibitor might be required. Considering nafamostat structure and…</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 Dimeric Peptide (KKYRYHLKPF)<sub>2</sub>K Shows Broad-Spectrum Antiviral Activity by Inhibiting Different Steps of Chikungunya and Zika Virus Infection</strong> - Chikungunya virus (CHIKV) and Zika virus (ZIKV) are important disease-causing agents worldwide. Currently, there are no antiviral drugs or vaccines approved to treat these viruses. However, peptides have shown great potential for new drug development. A recent study described (p-BthTX-I)(2)K [(KKYRYHLKPF)(2)K], a peptide derived from the Bothropstoxin-I toxin in the venom of the Bothrops jararacussu snake, showed antiviral activity against SARS-CoV-2. In this study, we assessed the activity 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>GRP78 Inhibitor YUM70 Suppresses SARS-CoV-2 Viral Entry, Spike Protein Production and Ameliorates Lung Damage</strong> - The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID-19 pandemic, has given rise to many new variants with increased transmissibility and the ability to evade vaccine protection. The 78-kDa glucose-regulated protein (GRP78) is a major endoplasmic reticulum (ER) chaperone that has been recently implicated as an essential host factor for SARS-CoV-2 entry and infection. In this study, we investigated the efficacy of YUM70, a small molecule inhibitor 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>IgG4 Antibodies Induced by Repeated Vaccination May Generate Immune Tolerance to the SARS-CoV-2 Spike Protein</strong> - Less than a year after the global emergence of the coronavirus SARS-CoV-2, a novel vaccine platform based on mRNA technology was introduced to the market. Globally, around 13.38 billion COVID-19 vaccine doses of diverse platforms have been administered. To date, 72.3% of the total population has been injected at least once with a COVID-19 vaccine. As the immunity provided by these vaccines rapidly wanes, their ability to prevent hospitalization and severe disease in individuals with…</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>Long COVID and Hybrid Immunity among Children and Adolescents Post-Delta Variant Infection in Thailand</strong> - This study aimed to assess long COVID, and describe immunogenicity against Omicron variants following BNT162b2 vaccination. A prospective cohort study was conducted among children (aged 5-11) and adolescents (aged 12-17) who had SARS-CoV-2 infection from July to December 2021 (Delta predominant period). Long COVID symptoms were assessed by questionnaires at 3 months after infection. Immunogenicity was evaluated by using a surrogate virus-neutralizing antibody test (sVNT) against the Omicron…</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>Natural Product-Based Screening for Lead Compounds Targeting SARS CoV-2 M<sup>pro</sup></strong> - Drugs that cure COVID-19 have been marketed; however, this disease continues to ravage the world without becoming extinct, and thus, drug discoveries are still relevant. Since M^(pro) has known advantages as a drug target, such as the conserved nature of the active site and the absence of homologous proteins in the body, it receives the attention of many researchers. Meanwhile, the role of traditional Chinese medicine (TCM) in the control of epidemics in China has also led to a focus on natural…</p></li>
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<h1 data-aos="fade-right" id="from-patent-search">From Patent Search</h1>
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