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<title>17 July, 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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<ul>
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<li><a href="#from-preprints">From Preprints</a></li>
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<li><a href="#from-clinical-trials">From Clinical Trials</a></li>
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<li><a href="#from-pubmed">From PubMed</a></li>
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<li><a href="#from-patent-search">From Patent Search</a></li>
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</ul>
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<h1 data-aos="fade-right" id="from-preprints">From Preprints</h1>
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<ul>
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<li><strong>Distinct Functional States of Neutrophils by Actin Disassembly and NF-kB/STAT3 Signaling</strong> -
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<div>
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Polymorphonuclear neutrophils (PMNs) can differentiate into distinct states, which can either exacerbate or resolve inflammation. Our study shows that mice challenged with TLR agonists exhibited PMN differentiation along two major paths characterized by the expression of CCR5 or PD-L1. Similar differentiation was observed in the blood of severe COVID-19 patients and the synovial fluid of osteoarthritis patients. Prolonged in vitro priming of human PMNs modeled the differentiation paths. Actin disassembly favored CCR5 upregulation, while NF-kB activation stabilized the actin cytoskeleton and suppressed the development of CCR5+ PMNs. Additionally, PD-L1 upregulation was triggered by STAT3 signaling and NF-kB activation. Functionally, CCR5 expressing PMNs were pro-NETotic, while PD-L1+ PMNs showed immunosuppressive functions by inhibiting T cell proliferation via PD1. Together, PMN differentiation depended on the priming conditions, and the balance between actin disassembly and NF-kB/STAT3 activation translated the present micro-milieu into phenotypic and functional diversification of PMNs.
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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/10.1101/2023.07.14.548975v1" target="_blank">Distinct Functional States of Neutrophils by Actin Disassembly and NF-kB/STAT3 Signaling</a>
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</div></li>
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<li><strong>Investigating substance use as a coping strategy among adolescent psychiatric inpatients: A comparative analysis before and during the COVID-19 pandemic</strong> -
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<div>
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Background: The COVID-19 pandemic was accompanied by significant changes in daily life, which impacted mental health and substance use behavior. Among adolescents, studies of COVID-related changes in rates of substance use yielded mixed findings. While studies of large U.S. samples found no significant increases in adolescent substance use during COVID-19, studies of youth with psychiatric symptoms suggest that some adolescents used substances to cope with negative affect during COVID-19. The current study compared rates of past-year substance use among adolescent psychiatric inpatients before and during COVID-19. Motives for coping with changes due to COVID-19 were assessed and evaluated in relation to correlates associated with psychiatric acuity (e.g., suicidal thoughts), and rate of past-year substance use. Methods: This cross-sectional chart review study analyzed hospital intake data of psychiatrically hospitalized adolescents before and during COVID-19. Count models assessed if the number of past-year days of alcohol and cannabis use was higher among adolescents (n=491, 11-18 years, 61% female) hospitalized between 3/14/20 to 4/5/21 (“COVID-19”) versus 8/30/2019 to 3/13/20 (“pre-COVID). For a subsample of inpatients admitted during COVID-19 (n=124; 75% female), we evaluated psychiatric correlates of endorsing alcohol, cannabis, or e-cigarettes to cope with COVID-19 changes/rules. Finally, we tested if past-year days of alcohol or cannabis use were greater for adolescents reporting they used that substance to cope with COVID-19. Results: Adolescents admitted during COVID-19 reported significantly more past-year alcohol and cannabis use days than adolescents admitted pre-COVID. Adolescents endorsed using alcohol (19%), cannabis (33%), and e-cigarettes/vaping (25%) to cope with COVID-19. E-cigarette/vaping to cope during COVID-19 was significantly related to lifetime suicide attempt. Endorsing alcohol or cannabis to cope with COVID-19 was associated with a significantly greater number of past-year use days for each respective substance. Conclusion: Adolescents admitted to a psychiatric inpatient unit during COVID-19 had a higher rate of substance use than adolescents admitted pre-COVID. Using substances to cope was linked to psychiatric correlates (suicide attempt, impairment). Substance use patterns among psychiatrically vulnerable adolescents may be distinct from adolescents whose substance use is linked to other, non-coping motivations, and have important implications from preventing compounding negative outcomes among these youth.
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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/hy8vu/" target="_blank">Investigating substance use as a coping strategy among adolescent psychiatric inpatients: A comparative analysis before and during the COVID-19 pandemic</a>
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</div></li>
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<li><strong>Clinical manifestations and mortality among hospitalized COVID-19 patients in Tanzania, 2021-2022.</strong> -
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<div>
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<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom">
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Abstract Background There have been differential mortality rates from Corona Virus Disease of 2019 (COVID-19) in different parts of the world. It is not clear whether the clinical presentation does also differ, thus the need for this study in a Sub-Saharan African country. The aim of this study was to describe clinical manifestations and outcome of patients diagnosed with COVID-19 in selected tertiary hospitals in Tanzania. Methods and Findings A retrospective analysis of archived data from 26th March, 2021 to 30th September, 2022 was done for adults aged ≥18 years who were admitted in five tertiary-level hospitals in Tanzania. Information collected included socio-demographic, radiological and clinical characteristics of the patients as well as outcome of the admission (discharge vs death). Categorical variables were presented as frequencies and proportions and compared using Chi square test. Logistic regression was used to assess the relationship between COVID-19 mortality and the collected variables. Out of 1387 COVID-19 patients, approximately 52% were males. The median age was 60 years [ (IQR)= (19-102)). The most common symptoms were dyspnea (943,68%), cough (889, 64%), fever (597,43%) and fatigue (570, 41%). In-hospital mortality was (476, 34%). Mortality significantly increased with increasing age, being the most in age >90 years [aOR (95% CI) =6.72 (1.94-20.81), P<0.001. Other predictors of death were not possessing a health insurance, [aOR (95% CI) = 2.78 (2.09-3.70), P<0. 001], dyspnea [aOR (95% CI) = 1.40(1.02-2.06), P=0.03]; chest pain, [aOR (95% CI) = 1.78 (1.12-3.21), P=0.03]; HIV positivity, [aOR (95% CI) = 4.62 (2.51-8.73), P<0.001]; neutrophilia, [aOR (95% CI) = 1.02 (1.01 – 1.03), P=0.02]; none use of ivermectin, [aOR (95% CI) = 1.46 (1.09 – 2.22), P=0.02] and non-use of steroid, [aOR (95% CI) = 1.40 (1.2 – 2.5), P=0.04]. Retrospective nature of this study which based on documented patients records, with a large number of patients left out of the analysis due to missed data, this might in a way affect the results of the present study. Conclusions The most common presenting symptoms were dyspnea, cough and fever, just as what was common elsewhere in the world. Mortality increased significantly with age, in HIV-infected patients, in those without a health insurance, those presenting with dyspnea, chest pain, or neutrophilia and those who did not use steroid or ivermectin. Clinicians should actively look for the predictors of mortality and take appropriate management to reduce mortality.
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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/10.1101/2023.07.13.23292643v1" target="_blank">Clinical manifestations and mortality among hospitalized COVID-19 patients in Tanzania, 2021-2022.</a>
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</div></li>
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<li><strong>Association between relative income and mental health in adults during the COVID-19 pandemic in Korea: Insights from a community health survey</strong> -
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<div>
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<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom">
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People of lower socioeconomic status are much more likely to be vulnerable to COVID-19. This study aimed to compare the associations between mental health according to relative national and community income levels during the COVID-19 pandemic. Mental health inequalities according to income level during the COVID-19 pandemic were assessed using the Korea Community Health Survey before (2019) and after the COVID-19 pandemic (2021). Univariate analyses were used to calculate the perceived stress and depression rates according to the risk factor categories. A multivariate logistic regression analysis was performed to identify the association between two types of income levels (Korean or community) and perceived stress and depression. In addition, we investigated the effect of relative income levels by subgroup (gender and region) on perceived stress and the experience of depression. During COVID-19, although depression crude rates increased (from 6.24% to 7.2%), perceived stress crude rates remained similar. In addition, as for mental health inequality according to community income level, even after adjusting for each independent variable, perceived stress [Odds Ratio (OR): 1.31, 95% Confidence Interval (CI):1.31–1.32] and experience of depression (OR: 1.63, 95% CI: 1.62–1.63) increased as the income level decreased. The effect of relative income level on perceived stress rate was found to be more pronounced in urban areas than in rural areas in terms of community income levels. Contrarily, the effect of relative income level on the depression rate was found to be weaker. Our findings demonstrated that mental health inequalities based on income level were more likely to occur during the COVID-19 pandemic and that disparities in community income levels may better reflect mental health inequalities.
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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/10.1101/2023.07.14.23292685v1" target="_blank">Association between relative income and mental health in adults during the COVID-19 pandemic in Korea: Insights from a community health survey</a>
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</div></li>
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<li><strong>COVID-19 vaccine information, misinformation, and vaccine uptake in Malawi.</strong> -
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<div>
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<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom">
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Background COVID-19 vaccine information – including source, content, and tone – may be an important determinant of vaccination, but this dynamic is not well-understood in low-income countries where COVID-19 vaccine uptake remains low. We assessed the COVID-19 vaccine information environment in Malawi, and its correlation with vaccine uptake. Methods A survey was administered among 895 adult (>=18 years) clients at 32 Malawian health facilities in mid-2022. Respondents reported their COVID-19 vaccination history, exposure to information about the COVID-19 vaccine from different sources and its tone (positive, negative, or neutral/factual), and whether they had heard of and believed in ten COVID-19 and COVID-19 vaccine conspiracy theories. We described the COVID-19 vaccine information environment in Malawi and used logistic regression analyses to assess the association of exposure to information sources and conspiracy theories with uptake of the COVID-19 vaccine. Results Respondents had received information about the COVID-19 vaccine most commonly from friends and neighbors, healthcare workers, and radio (each reported by >90%). Men, urban residents, and respondents with a higher education level were exposed to more COVID-19 vaccine information sources. COVID-19 vaccine uptake was positively associated with exposure to a greater number of COVID-19 vaccine information sources (aOR 1.09, 95% CI 1.03-1.15), and more positive information (aOR 4.33, 95% CI 2.17-8.64) – and was negatively associated with believing COVID-19 vaccine conspiracy theories to be true (OR 0.76, 95% CI 0.68-0.87). Conclusions Malawian adults were exposed to a variety of COVID-19 vaccine information sources, with less access to information among women, rural residents, and people with lower educational attainment. Exposure to misinformation was common, though infrequently believed. Vaccination was associated with exposure to high number of COVID-19 vaccine information sources, exposure to positive vaccine information and endorsing fewer conspiracy theories. Vaccination programs should disseminate communication with positive messaging, through multiple information sources, prioritizing the less exposed groups we identified.
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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/10.1101/2023.07.14.23292688v1" target="_blank">COVID-19 vaccine information, misinformation, and vaccine uptake in Malawi.</a>
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</div></li>
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<li><strong>Global Safety Assessment of Adverse Events of Special Interest Following 2 Years of Use and 772 Million Administered Doses of mRNA-1273</strong> -
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<div>
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<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom">
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Background: The large-scale use of mRNA COVID-19 vaccines during the pandemic was associated with enhanced safety monitoring to ensure accurate and timely review of safety. We reviewed the mRNA-1273 (original strain) safety profile following 2 years of use (>772 million administered doses), primarily focusing upon predefined safety topics (ie, adverse events of special interest [AESI]) proposed in advance of COVID-19 vaccine use. Methods: Cumulative mRNA-1273 safety data from spontaneous adverse event (AE) cases reported to the Moderna, Inc., global safety database (GSDB) between December 18, 2020, and December 17, 2022, were included. Reporting rates of AESI were calculated per 1 million doses of mRNA-1273 administered. Observed-to-expected (OE) ratios were computed by comparing observed rates of AESI to the background/expected rate for these events to evaluate potential associations with mRNA-1273. Results: There were 658,767 identified case reports, associated with 2,517,669 AEs. Most AEs were non-serious (83.4%); 0.7% were fatal. AESI represented 13.7% of all AEs, with reporting rates for most AESI below the expected background incidence. Exceptions included anaphylaxis (OE ratio 3 days after vaccination, 2.19 [95% CI, 2.02-2.37]), myocarditis (OE ratio 7 days after vaccination, 1.41 [1.32-1.51]; among men aged 12-40 years, 9.75 [7.74-12.3]; and individuals aged 12-40 years, 3.51 [3.19-3.86]), and pericarditis (OE ratio 7 days after vaccination in individuals aged 12-40 years, 2.54 [2.16-2.99]). Conclusions: With the exceptions of anaphylaxis, myocarditis, and pericarditis, this safety analysis of mRNA-1273 did not find evidence to suggest an increased risk for AESI identified for enhanced monitoring ahead of COVID-19 vaccine use.
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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/10.1101/2023.07.13.23291675v1" target="_blank">Global Safety Assessment of Adverse Events of Special Interest Following 2 Years of Use and 772 Million Administered Doses of mRNA-1273</a>
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</div></li>
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<li><strong>Dynamics of T-cell responses following COVID-19 mRNA vaccination and breakthrough infection in older adults</strong> -
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<div>
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<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom">
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Introduction: While older adults generally mount weaker antibody responses to a primary COVID-19 vaccine series, T-cell responses remain less well characterized in this population. We compared SARS-CoV-2 spike-specific T-cell responses after two- and three-dose COVID-19 mRNA vaccination and subsequent breakthrough infection in older and younger adults. Methods: We quantified CD4+ and CD8+ T-cells reactive to overlapping peptides spanning the ancestral SARS-CoV-2 spike protein in 40 older adults (median age 79) and 50 younger health care workers (median age 39), all COVID-19 naive, using an activation induced marker assay. T-cell responses were further assessed in 24 participants, including 8 older adults, who subsequently experienced their first SARS-CoV-2 breakthrough infection. Results: A third COVID-19 mRNA vaccine dose significantly boosted spike-specific CD4+ and CD8+ T-cell frequencies to above two-dose levels in older and younger adults. T-cell frequencies did not significantly differ between older and younger adults after either dose. Multivariable analyses adjusting for sociodemographic, health and vaccine-related variables confirmed that older age was not associated with impaired cellular responses. Instead, the strongest predictors of CD4+ and CD8+ T-cell frequencies post-third-dose were their corresponding post-second-dose frequencies. Breakthrough infection significantly increased both CD4+ and CD8+ T cell frequencies, to comparable levels in older and younger adults. Exploratory analyses revealed an association between HLA-A<em>02:03 and higher post-vaccination CD8+ T-cell frequencies, which may be attributable to numerous strong-binding HLA-A</em>02:03-specific CD8+ T-cell epitopes in spike. Conclusion: Older adults mount robust T-cell responses to two- and three-dose COVID-19 mRNA vaccination, which are further boosted following breakthrough infection.
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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/10.1101/2023.07.14.23292660v1" target="_blank">Dynamics of T-cell responses following COVID-19 mRNA vaccination and breakthrough infection in older adults</a>
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</div></li>
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<li><strong>Risk of severe outcomes among Omicron sub-lineages BA.4.6, BA.2.75 and BQ.1 compared to BA.5 in England</strong> -
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<div>
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<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom">
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Since the emergence of Omicron variant of SARS-CoV-2 in late 2021, a number of sub-lineages have arisen and circulated internationally. Little is known about the relative severity of Omicron sub-lineages BA.2.75, BA.4.6 and BQ.1. We undertook a case-control analysis to determine the clinical severity of these lineages relative to BA.5, using whole genome sequenced, PCR-confirmed infections, between 1 August 2022 to 27 November 2022, among those who presented to emergency care in England 14 days after and up to one day prior to the positive specimen. A total of 10,375 episodes were included in the analysis, of which 5,207 (50.2%) were admitted to hospital or died. Multivariable conditional regression analyses found no evidence for greater odds of hospital admission or death among those with BA.2.75 (OR= 0.96, 95% CI: 0.84 to 1.09), and BA.4.6 (OR= 1.02, 95% CI: 0.88 to 1.17) or BQ.1 (OR= 1.03, 95 % CI: 0.94 to 1.13) compared to BA.5. Future lineages may not follow the same trend and there remains a need for continued surveillance of COVID-19 variants and their clinical outcomes to inform the public health response.
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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/10.1101/2023.07.14.23292656v1" target="_blank">Risk of severe outcomes among Omicron sub-lineages BA.4.6, BA.2.75 and BQ.1 compared to BA.5 in England</a>
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</div></li>
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<li><strong>Occupational dermatoses in health care personnel using PPE during the COVID pandemic.</strong> -
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<div>
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<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom">
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Background: A sudden surge of occupation-associated dermatoses among the healthcare workers (HCWs) serving COVID-19 patients have been witnessed recently due to increased usage of PPE (PPE) kits and increased frequency of hygiene practices, with a significant impact on their quality of life and compromised efficacy at work. Hence, this study was conducted to measure the prevalence of occupational dermatoses among HCWs serving Covid-19 patients using PPE kits and hygiene practices and their impact on quality of life. Methods: HCWs of all cadres were screened for occupation-associated dermatoses. Cases with occupational dermatosis were evaluated further regarding the use of a PPE kit, and DLQI was calculated. Results: 19% of HCWs had dermatoses associated with PPE and hygiene practices. Hands were most affected, followed by the face, nasal bridge, and facial skin in contact with goggles. 48% had Mathias score >/= 4. Most cases had reported some impact on their quality of life. A significant association could be established between frequency of hand washing >/= 10 times/day with hand dermatitis (p=0.000). Conclusion: The use of PPE has significantly raised cases of occupational dermatosis among HCWs. Repeated hand washing and hand sanitizer use has increased the incidence of hand dermatitis.
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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/10.1101/2023.07.13.23292421v1" target="_blank">Occupational dermatoses in health care personnel using PPE during the COVID pandemic.</a>
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</div></li>
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<li><strong>Predicting the impact of COVID-19 non-pharmaceutical intervention on short- and medium-term dynamics of enterovirus D68 in the US</strong> -
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<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom">
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Recent outbreaks of enterovirus D68 (EV-D68) infections, and their causal linkage with acute flaccid myelitis (AFM), continue to pose a serious public health concern. During 2020 and 2021, the dynamics of EV-D68 and other pathogens have been significantly perturbed by non-pharmaceutical interventions against COVID-19; this perturbation presents a powerful natural experiment for exploring the dynamics of these endemic infections. In this study, we analyzed publicly available data on EV-D68 infections, originally collected through the New Vaccine Surveillance Network, to predict their short- and long-term dynamics following the COVID-19 interventions. Although there are large uncertainties in our predictions, the likelihood of a large outbreak in 2023 appears to be low. Comprehensive surveillance data are needed to narrow uncertainties in future dynamics of EV-D68. The limited incidence of AFM cases in 2022, despite large EV-D68 outbreaks, poses further questions for the timing of the next AFM outbreaks.
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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/10.1101/2023.07.14.23292680v1" target="_blank">Predicting the impact of COVID-19 non-pharmaceutical intervention on short- and medium-term dynamics of enterovirus D68 in the US</a>
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</div></li>
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<li><strong>Early Biological Markers of Post-Acute Sequelae of SARS-CoV-2 Infection</strong> -
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<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom">
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To understand the roles of acute phase viral dynamics and host immune responses in PASC, we enrolled 136 participants within 5 days of their first positive SARS-CoV-2 real-time PCR. Participants self-collected nasal specimens up to 21 times within the first 28 days after symptom onset; Interviewer-administered clinical questionnaires and blood samples were collected at enrollment and days 9, 14, 21, 28, and month 4 and 8 post-symptom. Defining PASC as the presence of any symptom new or worse since infection reported at their 4-month visit, we compared viral markers (quantity and duration of viral RNA load, infectious viral load, and plasma N-antigen level) and host immune markers (IL-6, IL-10, TNF-a, IFN-a, IFN-g, MCP, IP-10, and Spike IgG) over the acute period. In comparison to those who fully recovered, those who developed PASC demonstrated significantly higher maximum levels of SARS-CoV-2 RNA, infectious virus, and N-antigen, longer duration of viral shedding, and lower Spike-specific IgG levels within the first 10 days of the acute phase of illness. No significant differences were identified among a panel of host immune markers, though there was a trend toward higher initial levels of certain markers (e.g., MCP-1, IFN-a, and IFN-g) in those who went on to develop PASC. Early viral dynamics and the associated host immune responses play a role in the pathogenesis of PASC. These findings highlight the importance of understanding the early biological markers from acute SARS-CoV-2 infection in the natural history of PASC.
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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/10.1101/2023.07.14.23292649v1" target="_blank">Early Biological Markers of Post-Acute Sequelae of SARS-CoV-2 Infection</a>
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</div></li>
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<li><strong>Patient-Related Metadata Reported in Sequencing Studies of SARS-CoV-2: Protocol for a Scoping Review and Bibliometric Analysis</strong> -
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<p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom">
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Background: Since the onset of the COVID-19 pandemic, there has been an unprecedented effort in genomic epidemiology to sequence the SARS-CoV-2 virus and examine its molecular evolution. This has been facilitated by the availability of publicly accessible databases, GISAID and GenBank, which collectively hold millions of SARS-CoV-2 sequence records. However, genomic epidemiology seeks to go beyond phylogenetic analysis by linking genetic information to patient demographics and disease outcomes, enabling a comprehensive understanding of transmission dynamics and disease impact. While these repositories include some patient-related information, such as the location of the infected host, the granularity of this data and the inclusion of demographic and clinical details are inconsistent. Additionally, the extent to which patient-related metadata is reported in published sequencing studies remains largely unexplored. Therefore, it is essential to assess the extent and quality of patient-related metadata reported in SARS-CoV-2 sequencing studies. Moreover, there is limited linkage between published articles and sequence repositories, hindering the identification of relevant studies. Traditional search strategies based on keywords may miss relevant articles. To overcome these challenges, this study proposes the use of an automated classifier to identify relevant articles. Objective: This study aims to conduct a systematic and comprehensive scoping review, along with a bibliometric analysis, to assess the reporting of patient-related metadata in SARS-CoV-2 sequencing studies. Methods: The NIH9s LitCovid collection will be used for the machine learning classification, while an independent search will be conducted in PubMed. Data extraction will be conducted using Covidence, and the extracted data will be synthesized and summarized to quantify the availability of patient metadata in the published literature of SARS-CoV-2 sequencing studies. For the bibliometric analysis, relevant data points, such as author affiliations, journal information, and citation metrics, will be extracted. Results: The study will report findings on the extent and types of patient-related metadata reported in genomic viral sequencing studies of SARS-CoV-2. The scoping review will identify gaps in the reporting of patient metadata and make recommendations for improving the quality and consistency of reporting in this area. The bibliometric analysis will uncover trends and patterns in the reporting of patient-related metadata, such as differences in reporting based on study types or geographic regions. Co-occurrence networks of author keywords will also be presented to highlight frequent themes and their associations with patient metadata reporting. Conclusion: This study will contribute to advancing knowledge in the field of genomic epidemiology by providing a comprehensive overview of the reporting of patient-related metadata in SARS-CoV-2 sequencing studies. The insights gained from this study may help improve the quality and consistency of reporting patient metadata, enhancing the utility of sequence metadata and facilitating future research on infectious diseases. The findings may also inform the development of machine learning methods to automatically extract patient-related information from sequencing studies.
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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/10.1101/2023.07.14.23292681v1" target="_blank">Patient-Related Metadata Reported in Sequencing Studies of SARS-CoV-2: Protocol for a Scoping Review and Bibliometric Analysis</a>
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</div></li>
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<li><strong>Oral immunization with rVSV bivalent vaccine elicits protective immune responses, including ADCC, against both SARS-CoV-2 and Influenza A viruses</strong> -
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<div>
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COVID-19 and influenza both cause enormous disease burdens, and vaccines are the primary measures for their control. Since these viral diseases are transmitted through the mucosal surface of the respiratory tract, developing an effective and convenient mucosal vaccine should be a high priority. We previously reported a recombinant vesicular stomatitis virus (rVSV)-based bivalent vaccine (v-EM2/SP{Delta}C1Delta) that protects animals from both SARS-CoV-2 and influenza viruses via intramuscular and intranasal immunization. Here, we further investigated the immune response induced by oral immunization with this vaccine and its protective efficacy in mice. The results demonstrated that the oral cavity delivery, like the intranasal route, elicited strong and protective systemic immune responses against SARS-CoV-2 and influenza A virus. This included high levels of neutralizing antibodies (NAbs) against SARS-CoV-2, as well as strong anti-SARS-CoV-2 spike protein (SP) antibody-dependent cellular cytotoxicity (ADCC) and anti-influenza M2 ADCC responses in mice sera. Furthermore, it provided efficient protection against challenge with influenza H1N1 virus in a mouse model, with a 100% survival rate and a significant low lung viral load of influenza virus. All these findings provide substantial evidence for the effectiveness of oral immunization with the rVSV bivalent vaccine.
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🖺 Full Text HTML: <a href="https://www.biorxiv.org/content/10.1101/2023.07.14.549076v1" target="_blank">Oral immunization with rVSV bivalent vaccine elicits protective immune responses, including ADCC, against both SARS-CoV-2 and Influenza A viruses</a>
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<li><strong>Absence of SARS-CoV-2 in Wildlife of Northeastern Minnesota and Isle Royale National Park</strong> -
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We investigated the presence of SARS-CoV-2 in free-ranging wildlife populations in Northeastern Minnesota on the Grand Portage Indian Reservation and Isle Royale National Park. 120 nasal samples were collected from white-tailed deer, moose, gray wolves, and black bears monitored for conservation efforts during 2022-2023. Samples were tested for viral RNA by RT-qPCR using the CDC N1/N2 primer set. Our data indicate that no wildlife samples were positive for SARS-CoV-2 RNA. Continued surveillance is therefore crucial to better understand the changing landscape of zoonotic SARS-CoV-2 in the Upper Midwest.
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🖺 Full Text HTML: <a href="https://www.biorxiv.org/content/10.1101/2023.07.14.549077v1" target="_blank">Absence of SARS-CoV-2 in Wildlife of Northeastern Minnesota and Isle Royale National Park</a>
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</div></li>
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<li><strong>Cognitive Adaptations in Career Decision-Making Among Chinese Undergraduates During the COVID-19 Pandemic</strong> -
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The authors of this article use the mindsponge theory to understand better the cognitive dynamics underlying the challenges Chinese undergraduates face in making career decisions during the COVID-19 pandemic.
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🖺 Full Text HTML: <a href="https://osf.io/s68bz/" target="_blank">Cognitive Adaptations in Career Decision-Making Among Chinese Undergraduates During the COVID-19 Pandemic</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>Homologous Booster Study of COVID-19 Protein Subunit Recombinant Vaccine</strong> - <b>Condition</b>: COVID-19<br/><b>Intervention</b>: Biological: SARS-CoV-2 Subunit Recombinant Protein Vaccine<br/><b>Sponsor</b>: PT Bio Farma<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>Role of Ivermectin and Colchicine in Treatment of COVID-19: Randomized Controlled Clinical Trial</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Drug: Ivermectin Tablets; Drug: Colchicine 0.5 MG; Drug: Standared managment<br/><b>Sponsor</b>: Ain Shams 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>A Study to Evaluate the Immunogenicity and Safety of A Recombinant Protein COVID-19 Vaccine as Booster Vaccines</strong> - <b>Conditions</b>: COVID-19; SARS-CoV-2 Infection<br/><b>Interventions</b>: Biological: SCTV01E-2; Biological: SCTV01E<br/><b>Sponsor</b>: Sinocelltech 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>Smell in COVID-19 and Efficacy of Nasal Theophylline (SCENT 3)</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Drug: theophylline; Drug: Placebo<br/><b>Sponsor</b>: Washington University School of Medicine<br/><b>Recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>COVID-19 Vaccine Hesitancy Counseling Intervention for Pharmacists</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Behavioral: Standard implementation webinar and online training; Behavioral: Virtual facilitation<br/><b>Sponsors</b>: University of North Carolina, Chapel Hill; University of Arkansas; University of South Carolina; National Institute on Minority Health and Health Disparities (NIMHD)<br/><b>Not yet recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Developing an Effective Intervention to Address Post-Corona-Virus-Disease-2019 Balance Disorders, Weakness and Muscle Fatigue in Individuals Aged 65+</strong> - <b>Condition</b>: COVID-19<br/><b>Intervention</b>: Device: Resistance Training<br/><b>Sponsor</b>: Józef Piłsudski University of Physical Education<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>Multimodal Long Covid19</strong> - <b>Condition</b>: Long COVID-19 Syndrome<br/><b>Intervention</b>: Other: Multimodal intervention in Long Covid19<br/><b>Sponsors</b>: Universidad de Magallanes; Teaching Assistance and Research Center of the University of Magallanes CADI-UMAG; Clinical Hospital Dr. Lautaro Navarro Avaria<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>Immunogenicity and Safety Study of SCB-2023 Vaccine as a Booster in Adults</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Biological: SCB-2023 vaccine (trivalent), a recombinant SARS-CoV-2 trimeric S-protein subunit vaccine for COVID-19; intramuscular injection; Biological: SCB-2019 (monovalent), a recombinant SARS-CoV-2 trimeric S-protein subunit vaccine for COVID-19; intramuscular injection<br/><b>Sponsor</b>: Clover Biopharmaceuticals AUS Pty 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 Safety and Immunogenicity Following a Heterologous Booster Dose of Recombinant SARS-CoV-2 Vaccine LYB002</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Biological: LYB002V14; Biological: LYB002V14A; Biological: LYB002CA<br/><b>Sponsors</b>: Guangzhou Patronus Biotech Co., Ltd.; Yantai Patronus Biotech Co., Ltd.; Affiliated Hospital of North Sichuan Medical College<br/><b>Active, not recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Treatment of Long COVID (TLC) Feasibility Trial</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Drug: Low-dose Naltrexone (LDN); Drug: Cetirizine; Drug: Famotidine; Drug: LDN Placebo; Drug: Cetirizine Placebo; Drug: Famotidine Placebo<br/><b>Sponsors</b>: Emory University; CURE Drug Repurposing Collaboratory (CDRC)<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>Efficiency and Safety of Paxlovid for COVID-19 Patients With Severe Chronic Kidney Disease</strong> - <b>Conditions</b>: COVID-19; Renal Insufficiency, Chronic<br/><b>Intervention</b>: Drug: Nirmatrelvir/ritonavir<br/><b>Sponsor</b>: Chinese PLA General Hospital<br/><b>Recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>The Immunogenicity and Safety Following a Heterologous Booster Dose of Recombinant SARS-CoV-2 Vaccine LYB001</strong> - <b>Conditions</b>: COVID-19; Vaccine Reaction<br/><b>Interventions</b>: Biological: LYB001; Biological: CoronaVac<br/><b>Sponsors</b>: Guangzhou Patronus Biotech Co., Ltd.; Yantai Patronus Biotech Co., Ltd.; Affiliated Hospital of North Sichuan Medical College<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>Safety, Efficacy, and Dosing of VIX001 in Patients With Neurological Symptoms of Post Acute COVID-19 Syndrome (PACS).</strong> - <b>Conditions</b>: Post-Acute COVID-19 Syndrome; Cognitive Impairment; Neurological Complication<br/><b>Intervention</b>: Drug: VIX001<br/><b>Sponsor</b>: Neobiosis, LLC<br/><b>Not yet recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Safety and Efficacy of Anakinra Treatment for Patients With Post Acute Covid Syndrome</strong> - <b>Condition</b>: Post-Acute COVID-19 Syndrome<br/><b>Interventions</b>: Drug: Placebo; Drug: Anakinra 149 MG/ML Prefilled Syringe [Kineret]<br/><b>Sponsor</b>: Hellenic Institute for the Study of Sepsis<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>Effects of Music Combined With Sports Games on Alleviating Psychological Stress, Anxiety and Mental Energy Among Adolescents During COVID-19 Pandemic in Lanzhou Gansu Province China</strong> - <b>Conditions</b>: Stress; Anxiety and Fear<br/><b>Interventions</b>: Behavioral: Music intervention only; Behavioral: Sports games intervention only; Behavioral: Music and sports games intervention<br/><b>Sponsor</b>: Wu Jiarun<br/><b>Completed</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>M<sup>pro</sup>-targeted anti-SARS-CoV-2 inhibitor-based drugs</strong> - The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 is a global health emergency. The main protease is an important drug target in coronaviruses. It plays an important role in the processing of viral RNA-translated polyproteins and is highly conserved in the amino acid sequence and three-dimensional structure, making it a good drug target for which several small molecule inhibitors are available. This paper describes the various anti-severe acute respiratory syndrome…</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>New perspective on the immunomodulatory activity of ginsenosides: Focus on effective therapies for post-COVID-19</strong> - More than 700 million confirmed cases of Coronavirus Disease-2019 (COVID-19) have been reported globally, and 10-60% of patients are expected to exhibit “post-COVID-19 symptoms,” which will continue to affect human life and health. In the absence of safer, more specific drugs, current multiple immunotherapies have failed to achieve satisfactory efficacy. Ginseng, a traditional Chinese medicine, is often used as an immunomodulator and has been used in COVID-19 treatment as a tonic to increase…</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>Terpenoid phytocompounds from mangrove plant Xylocarpus moluccensis as possible inhibitors against SARS-CoV-2: In silico strategy</strong> - COVID-19 shook the world during the pandemic, where the climax it reached was vaccine manufacturing at an unfathomable pace. Alternative promising solutions to prevent infection from SARS-CoV-2 and its variants will remain crucial in the years to come. Due to its key role in viral replication, the major protease (Mpro) enzyme of SARS-CoV-2 can be an attractive therapeutic target. In the present work, natural terpenoids from mangrove medicinal plant Xylocarpus moluccensis (Lam.) M. Roem. were…</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>‘Pterocephalodes hookeri-Onosma hookeri’ decoction protects against LPS-induced pulmonary inflammation via inhibiting TLR4/ NF-κB signaling pathway</strong> - CONCLUSION: In summary, the combination therapy of ‘P-O’ exhibited good antioxidant activity and anti-inflammatory activity in vitro, as well as a therapeutic effect against pulmonary inflammation in vivo. These findings provide evidence for the clinical application of ‘P-O’ and offer new approaches for treating pneumonia.</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>Intranasal insulin - effects on the sense of smell</strong> - Intranasal insulin (IN) administration is a promising way to deliver the peptide to the central nervous system (CNS), bypassing the blood-brain-barrier and gastrointestinal absorption inhibition. IN receptors are localized in the olfactory mucosa and the brain, mainly in the olfactory bulb, hypothalamus, hippocampus, amygdala, cerebral cortex, and cerebellum. The pleiotropic mechanism of insulin action is characterized by its anti-inflammatory properties, antithrombotic, vasodilatory, 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>SARS-CoV-2 spike protein induces lung endothelial cell dysfunction and thrombo-inflammation depending on the C3a/C3a receptor signalling</strong> - The spike protein of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) can interact with endothelial cells. However, no studies demonstrated the direct effect of the spike protein subunit 1 (S1) in inducing lung vascular damage and the potential mechanisms contributing to lung injury. Here, we found that S1 injection in mice transgenic for human angiotensin converting enzyme 2 (ACE2) induced early loss of lung endothelial thromboresistance at 3 days, as revealed by thrombomodulin loss…</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 spike protein receptor-binding domain perturbates intracellular calcium homeostasis and impairs pulmonary vascular endothelial cells</strong> - Exposure to the spike protein or receptor-binding domain (S-RBD) of SARS-CoV-2 significantly influences endothelial cells and induces pulmonary vascular endotheliopathy. In this study, angiotensin-converting enzyme 2 humanized inbred (hACE2 Tg) mice and cultured pulmonary vascular endothelial cells were used to investigate how spike protein/S-RBD impacts pulmonary vascular endothelium. Results show that S-RBD leads to acute-to-prolonged induction of the intracellular free calcium concentration…</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>Immunothrombosis and its underlying biological mechanisms</strong> - The evolutionary conserved link between coagulation and innate immunity is a biological process characterized by the thrombosis formation stimulus of immune cells and specific thrombosis-related molecules. In physiological settings, the relationship between the immune system and thrombosis facilitates the recognition of pathogens and damaged cells and inhibits pathogen proliferation. However, when deregulated, the interplay between hemostasis and innate immunity becomes a pathological process…</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>CHO-produced RBD-Fc subunit vaccines with alternative adjuvants generate immune responses against SARS-CoV-2</strong> - Subunit vaccines feature critical advantages over other vaccine platforms such as stability, price, and minimal adverse effects. To maximize immunological protection of subunit vaccines, adjuvants are considered as main components that are formulated within the subunit vaccine. They can modulate adverse effects and enhance immune outcomes. However, the most suitable formulation providing the best immunological outcomes and safety are still under investigation. In this report, we combined…</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>Determining the clinical and cost-effectiveness of nasal sprays and a physical activity and stress management intervention to reduce respiratory tract infections in primary care: A protocol for the ‘Immune Defence’ randomised controlled trial</strong> - BACKGROUND: Most adults in the UK experience at least one viral respiratory tract infection (RTI) per year. Individuals with comorbidities and those with recurrent RTIs are at higher risk of infections. This can lead to more severe illness, worse quality of life and more days off work. There is promising evidence that using common nasal sprays or improving immune function through increasing physical activity and managing stress, may reduce the incidence and severity of RTIs.</p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong><em>In</em><em>silico</em> generation of novel ligands for the inhibition of SARS-CoV-2 main protease (3CL<sup>pro</sup>) using deep learning</strong> - The recent emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing the coronavirus disease (COVID-19) has become a global public health crisis, and a crucial need exists for rapid identification and development of novel therapeutic interventions. In this study, a recurrent neural network (RNN) is trained and optimized to produce novel ligands that could serve as potential inhibitors to the SARS-CoV-2 viral protease: 3 chymotrypsin-like protease (3CL^(pro))….</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>Synergistic Effect of Zinc-Chitosan Nanoparticles and Hydroxychloroquine to Inhibit Buffalo Coronavirus</strong> - Zinc ions can hinder the synthesis of proteins required for accomplishing several stages of the viral life cycle. The intracellular zinc concentration can be increased by using zinc ionophores which transport zinc ions into the cells and hinder viral replication. (Hydroxy)chloroquine is an example of a zinc ionophore, but both zinc and (hydroxy)chloroquine can be toxic to the host organism. The nanocarriers may serve as camouflage to evade the adverse effects of drugs, chemicals, 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>Auraptene Has Antiviral Activity against Human Coronavirus OC43 in MRC-5 Cells</strong> - Auraptene (7-geranyloxycoumarin) is the abundant prenyloxycoumarin found in the fruits of Citrus spp. Auraptene has a variety of pharmacological and therapeutic functions, such as anticancer, antioxidant, immunomodulatory, and anti-inflammation activities, with excellent safety profiles. In this study, we evaluated the anticoronaviral activity of auraptene in HCoV-OC43-infected human lung fibroblast MRC-5 cells. We found that auraptene effectively inhibited HCoV-OC43-induced cytopathic effects…</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>Potency of Xanthone Derivatives from <em>Garcinia mangostana</em> L. for COVID-19 Treatment through Angiotensin-Converting Enzyme 2 and Main Protease Blockade: A Computational Study</strong> - ACE2 and Mpro in the pathology of SARS-CoV-2 show great potential in developing COVID-19 drugs as therapeutic targets, due to their roles as the “gate” of viral entry and viral reproduction. Of the many potential compounds for ACE2 and Mpro inhibition, α-mangostin is a promising candidate. Unfortunately, the potential of α-mangostin as a secondary metabolite with the anti-SARS-CoV-2 activity is hindered due to its low solubility in water. Other xanthone isolates, which also possess the xanthone…</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>Pharmacological Activity of Cepharanthine</strong> - Cepharanthine, a natural bisbenzylisoquinoline (BBIQ) alkaloid isolated from the plant Stephania Cephalantha Hayata, is the only bisbenzylisoquinoline alkaloid approved for human use and has been used in the clinic for more than 70 years. Cepharanthine has a variety of medicinal properties, including signaling pathway inhibitory activities, immunomodulatory activities, and antiviral activities. Recently, cepharanthine has been confirmed to greatly inhibit SARS-CoV-2 infection. Therefore, we…</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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