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195 lines
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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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</ul>
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<h1 data-aos="fade-right" id="from-preprints">From Preprints</h1>
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<li><strong>Do Lockdowns Bring about Additional Mortality Benefits or Costs? Evidence based on Death Records from 300 Million Chinese People</strong> -
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Objectives: To estimate the short-term effect of stringent lockdown policies on non-COVID-19 mortality and explore the heterogeneous impacts of lockdowns in China after the COVID-19 outbreak. Design Employing a difference-in-differences method. Setting Using comprehensive death records covering around 300 million Chinese people, we estimate the impacts of city and community lockdowns on non-COVID-19 mortality outside of Wuhan. Participants: 44,548 deaths recorded in 602 counties or districts by the Disease Surveillance Point System of the Chinese Center for Disease Control and Prevention from 1 January 2020 to14 March 2020. Results We find that lockdowns reduced the number of non-COVID-19 deaths by 4.9% (cardiovascular deaths by 6.2%, injuries by 9.2%, and non-COVID-19 pneumonia deaths by 14.3%). A back-of-the-envelope calculation shows that more than 32,000 lives could have been saved from non-COVID-19 diseases/causes during the 40 days of the lockdown on which we focus. Main outcome measures: Weekly numbers of deaths from all causes without COVID-19, cardiovascular diseases, injuries, pneumonia, neoplasms, chronic respiratory diseases, and other causes were used to estimate the associations between lockdown policies and mortality. Conclusions: The results suggest that the rapid and strict virus countermeasures not only effectively controlled the spread of COVID-19 but also brought about unintended short-term public health benefits. The health benefits are likely driven by significant reductions in air pollution, traffic, and human interactions during the lockdown period. These findings can help better inform policymakers around the world about the benefits and costs of lockdowns policies in dealing with the COVID-19 pandemic.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2020.08.28.20183699v3" target="_blank">Do Lockdowns Bring about Additional Mortality Benefits or Costs? Evidence based on Death Records from 300 Million Chinese People</a>
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<li><strong>Based Analysis Framework for identifying COVID-19 Incidence and Fatality Determinants at National Level Case study: Africa</strong> -
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Abstract Background: COVID-19 pandemic is an extraordinary threat with significant implications in all aspects of human life, therefore, it represents the most immediate challenges for all countries all over the world. Objectives: This study is intended to develop a GIS-based analysis model to explore, quantify and model the relationships between COVID-19 morbidity and mortality and their potential predictor variables. Method: For this purpose, a model was developed to estimate COVID-19 incidence and fatality rates in Africa up to 16th of August 2020 at the national level. The model involved Ordinary Least Squares (OLS) and Geographically Weighted Regression (GWR) analysis through ArcGIS was applied. Result: Spatial Autocorrelation Analysis revealed that there was positive spatial autocorrelation in COVID-19 incidence (Moran index 0.16. P value <0.1), and fatality (Moran index 0.0.35, P value<0.01) rates within different African countries. At continental level, OLS revealed that COVID-19 incidence rate was found to be positively associated with overcrowding, health expenditure, HIV infections and air pollution and negatively associated with BCG vaccine (β=2.97,1.45, 0.01, 3.29, -47.65 respectively, P< 0.05) At the same time, COVID-19 fatality was found to be positively related to asthma prevalence and tobacco use. Yet, certain level of inconsistency was noted in the case of COVID-19 fatality, which was negatively related to elder population, poverty, and cardiovascular mortality (P<0.05). This model showed convenient level of validity in modeling the relationship between COVID-19 incidence as well as fatality and their key predictors using GWR. In this respect, the model explained about 58% and 55% of the variance in COVID-19 incidence and fatality rates, respectively, as a function of considered predictors. Conclusion: Application of the suggested model can assist in guiding intervention strategies, particularly in case of local and community level whenever the data on COVID-19 cases and predictors variables are available.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2021.01.12.21249661v1" target="_blank">Based Analysis Framework for identifying COVID-19 Incidence and Fatality Determinants at National Level Case study: Africa</a>
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<li><strong>The impact of the coronavirus disease 2019 (COVID-19) pandemic on university students' dietary intake, physical activity, and sedentary behaviour</strong> -
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University students are a vulnerable group for poor dietary intake, insufficient physical activity and sedentary behaviour. The purpose of this study was to examine the impact of COVID-19 on university students9 dietary intake, physical activity and sedentary behaviour. Participants were students (n=125) from the Universities of Saskatchewan and Regina. An online questionnaire was administered retrospectively (for pre-pandemic) and prospectively (during the pandemic) to examine students9 dietary intake, physical activity and sedentary behaviour. Overall, nutrient and caloric intakes were significantly reduced (p<0.05) during the pandemic, and alcohol intake increased (p=0.03). Before the pandemic, 16% and 54% of the participants were meeting the Canadian 24-Hour Movement Guidelines for Adults (18-64 years) of 150 minutes of moderate-vigorous physical activity and 8 hours or less of sedentary activity respectively. Only 10% met the guidelines for physical activity while 30% met the guidelines for sedentary behaviour during the pandemic. The minutes per week spent engaging in moderate to vigorous physical activity during the pandemic decreased by approximately 20% (p<0.001). The hours spent in sedentary activities increased by 3 hours per day (p<0.001). Our findings confirm that during the pandemic, students9 inadequate dietary intake, high alcohol consumption, low physical activity and high sedentary behaviour were significantly compounded. Novelty During COVID-19, the nutrient and caloric intakes of university students decreased, and alcohol intake increased significantly. University students9 physical activity levels decreased, and sedentary activity increased significantly during COVID-19. During COVID-19 students did not engage in sufficient physical activity to offset the increased sedentary behaviour.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2021.01.12.21249608v1" target="_blank">The impact of the coronavirus disease 2019 (COVID-19) pandemic on university students' dietary intake, physical activity, and sedentary behaviour</a>
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<li><strong>Predictors of COVID-19 Vaccine Hesitancy: Socio-demographics, Co-Morbidity and Past Racial Discrimination</strong> -
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Importance: Immunization programs are only successful when there are high rates of acceptance and coverage. While delivering billions of COVID 19 doses globally addressing vaccine hesitancy will be one of the most significant public health communication efforts ever undertaken. Objective: The goal of this study is to explore predictors of COVID 19 vaccine hesitancy, including sociodemographic factors, comorbidity, risk perception, and experience of discrimination, in a sample of the U.S. population. Design: We used a cross sectional online survey study design. The survey was implemented between Dec 13 and 23, 2020. Setting: The survey was limited to respondents over 18 years of age residing in the USA. Participants: Respondents were individuals belonging to priority groups for vaccine distribution. Main Outcome(s) and Measure(s): Respondents were asked how likely they would be to take a COVID 19 vaccine if offered at no cost within two months. Vaccine hesitancy was measured using a scale ranging from 1 (low hesitancy) to 6 (high hesitancy). Results: Responses were received from 2,650 respondents (response rate 84%) from all 50 states and Puerto Rico, American Samoa, and Guam. The majority were in the age category between 25 and 44 years (66%), male (53%), and working in the healthcare sector (61%). Most were White and non-Hispanic (66%) respondents followed by Black non-Hispanic (14%) and Hispanic (8%) respondents. Experience with racial discrimination was a predictor of vaccine hesitancy. Those reporting racial discrimination having 21% increased odds of being at a higher level of hesitancy compared to those who did not report such experience (OR=1.21, 95% C.I. 1.01-1.45). Conclusions and Relevance: Communication and logistical aspects during the COVID 19 vaccination campaign need to be sensitive to individuals past-experience of discrimination by identifying appropriate channels of communication and sites for vaccine distribution to reach those who may have sentiments of mistrust in the vaccination campaign.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2021.01.12.21249152v1" target="_blank">Predictors of COVID-19 Vaccine Hesitancy: Socio-demographics, Co-Morbidity and Past Racial Discrimination</a>
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<li><strong>An open-access database of infectious disease transmission trees to explore superspreader epidemiology</strong> -
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Historically, emerging and re-emerging infectious diseases have caused large, deadly, and expensive multi-national outbreaks. Often outbreak investigations aim to identify who infected whom by reconstructing the outbreak transmission tree, which visualizes transmission between individuals as a network with nodes representing individuals and branches representing transmission from person to person. We compiled a database of 383 published, standardized transmission trees consisting of 16 directly-transmitted diseases ranging in size from 2 to 286 cases. For each tree and disease we calculated several key statistics, such as outbreak size, average number of secondary infections, the dispersion parameter, and the number of superspreaders. We demonstrated the potential utility of the database through short analyses addressing questions about superspreader epidemiology for a variety of diseases, including COVID-19. First, we compared the frequency and contribution of superspreaders to onward transmission across diseases. COVID-19 outbreaks had significantly fewer superspreaders than outbreaks of SARS and MERS and a dispersion parameter between that of SARS and MERS. Across diseases the presence of more superspreaders was associated with greater outbreak size. Second, we further examined how early spread impacts tree size. Generally, trees sparked by a superspreader had larger outbreak sizes than those trees not sparked by a superspreader, and this trend was significant for COVID-19 trees. Third, we investigated patterns in how superspreaders are infected. Across trees with more than one superspreader, we found support for the theory that superspreaders generate other superspreaders, even when controlling for number of secondary infections. In sum, our findings put the role of superspreading to COVID-19 transmission in perspective with that of SARS and MERS and suggest an avenue for further research on the generation of superspreaders. These data have been made openly available to encourage reuse and further scientific inquiry.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2021.01.11.21249622v1" target="_blank">An open-access database of infectious disease transmission trees to explore superspreader epidemiology</a>
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<li><strong>Hospital load and increased COVID-19 related mortality - a nationwide study in Israel</strong> -
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The rapid spread of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) worldwide and the disease caused by the virus, coronavirus disease 19 (COVID-19), has caused a global pandemic with devastating social and economic consequences. Throughout the pandemic, several health systems were overwhelmed in light of the rapid emergence of new cases within a short period of time. The heavy workload imposed on hospital services might have negatively affected patients9 outcomes and exacerbated mortality rates. Here, we assessed excess in-hospital mortality across the Israeli healthcare system, using a model developed for predicting patient mortality based on data of day-by-day patient disease course. Mortality predictions were made using Monte-Carlo methods based on a multistate survival analysis and a set of Cox regression models, first constructed and validated on a nationwide cohort during the first stages of the pandemic in Israel. We show that during a peak of hospitalizations in September and October 2020, patient deaths significantly exceeded the model9s mortality predictions, while reverting to match the predictions as patient load subsided in October, and showing signs of renewed excess mortality as hospital load is increasing again since late December 2020. Our work emphasizes that even in countries in which the healthcare system did not reach a specific point defined as insufficiency, the increase in hospital workload was associated with higher patient mortality, while ruling out factors related to changes in the hospitalized population. In addition, our study highlights the importance of quantifying excess mortality in order to assess quality of care, and define an appropriate carrying capacity of severe patients in order to guide timely healthcare policies and allocate appropriate resources. Full model code is available for use at https://github.com/JonathanSomer/covid-19-multi-state-model.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2021.01.11.21249526v1" target="_blank">Hospital load and increased COVID-19 related mortality - a nationwide study in Israel</a>
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<li><strong>Immunochromatographic SARS-CoV-2 IgG antibody assay: a cross-sectional study conducted at Wakayama Medical University in Japan</strong> -
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Asymptomatic patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection must be quickly identified and isolated to prevent the spread of the virus. The number of asymptomatic healthy people is completely unknown because they remain untested. Detection of specific SARS-CoV-2 antibodies has been widely accepted as a diagnostic test, and an immunochromatographic test, which is simpler and relatively cheaper than other methods, is becoming the gold standard for identifying healthy people who had been infected with SARS-CoV-2 in the past. In this study, 1,528 volunteers who worked at a particular hospital were subjected to an immunochromatographic IgG test for SARS-CoV-2 to determine the ratio of asymptomatic people. Only 12 volunteers (0.79%) were IgG<sup>+</sup>, with no significant background differences in the sex, age, profession, experiences of working at the emergency department or caring for coronavirus disease 2019 patients. If this IgG<sup>+</sup> ratio was to be extrapolated to Wakayama city9s population, 2,780 out of 3,54,063 people may be asymptomatic for SARS-CoV-2. The results imply that anyone may get infected with SARS-CoV-2 but remain asymptomatic.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2021.01.10.21249421v1" target="_blank">Immunochromatographic SARS-CoV-2 IgG antibody assay: a cross-sectional study conducted at Wakayama Medical University in Japan</a>
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<li><strong>Modelling the impact of household size distribution on the transmission dynamics of COVID-19</strong> -
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Under the implementation of non-pharmaceutical interventions such as social distancing and lockdowns, household transmission has been shown to be significant for COVID-19, posing challenges for reducing incidence in settings where people are asked to self-isolate at home and to spend increasing amounts of time at home due to distancing measures. Accordingly, characteristics of households in a region have been shown to relate to transmission heterogeneity of the virus. We introduce a stochastic epidemiological model to examine the impact of the household size distribution in a region on the transmission dynamics. We choose parameters to reflect incidence in two health regions of the Greater Vancouver area in British Columbia and simulate the impact of distancing measures on transmission, with household size distribution the only different parameter between simulations for the two regions. Our result suggests that the dissimilarity in household size distribution alone can cause significant differences in incidence of the two regions, and the distributions drive distinct dynamics that match reported cases. Furthermore, our model suggests that offering individuals a place to isolate outside their household can speed the decline in cases, and does so more effectively where there are more larger households.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2021.01.12.21249707v1" target="_blank">Modelling the impact of household size distribution on the transmission dynamics of COVID-19</a>
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<li><strong>Impact of COVID-19 on the indigenous population of Brazil: A geo-epidemiological study</strong> -
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This study aimed to analyze the geographical distribution of COVID-19 and to identify high-risk areas for the occurrence of cases and deaths from the disease in the indigenous population of Brazil. This is an ecological study whose units of analysis were the Special Indigenous Sanitary Districts. Cases and deaths by COVID-19 notified by the Special Secretariat for Indigenous Health between March and October 2020 were included. To verify the spatial association, the Getis-Ord General G and Getis-Ord Gi * techniques were used. High spatial risk clusters have been identified by the scan statistics technique. 32,041 cases of COVID-19 and 471 deaths were reported. The incidence and mortality rates were between 758.14 and 18530.56 cases and 5.96 and 265.37 deaths per 100 thousand inhabitants, respectively. The non-randomness of cases (z-score = 5.40; p <0.001) and deaths (z-score = 3.83; p <0.001) was confirmed. Hotspots were evidenced for both events with confidence levels of 90, 95 and 99% concentrated in the North and Midwest regions of the country. Eight high-risk spatial clusters for cases with a relative risk (RR) between 1.08 and 4.11 (p <0.05) and two risk clusters for deaths with RR between 3.08 and 3.97 (p <0.05) were identified. The results indicate critical areas in the indigenous territories of Brazil and contribute to better targeting the control actions of COVID-19 in this population.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2021.01.12.21249703v1" target="_blank">Impact of COVID-19 on the indigenous population of Brazil: A geo-epidemiological study</a>
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<li><strong>Detection of SARS-CoV-2 nucleocapsid antigen from serum can aid in timing of COVID-19 infection</strong> -
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SARS-CoV-2 RNA can be detected in respiratory samples for weeks or even months after onset of COVID-19 disease. Therefore, one of the diagnostic challenges of PCR positive cases is differentiating between acute COVID-19 disease and convalescent phase. Recently, the presence of SARS-CoV-2 nucleocapsid antigen in serum samples of COVID-19 patients was published [Le Hingrat et al. Detection of SARS-CoV-2 N-antigen in blood during acute COVID-19 provides a sensitive new marker and new testing alternatives, Clinical Microbiology and Infection, 2020]. Our study aimed to characterize the analytical specificity and sensitivity of an enzyme-linked immunosorbent assay (Salocor SARS-CoV-2 Antigen Quantitative Assay Kit (Salofa Ltd, Salo, Finland)) for the detection of SARS-CoV-2 antigen in serum, and to characterize the kinetics of antigenemia. The evaluation material included a negative serum panel of 155 samples, and 126 serum samples from patients with a PCR-confirmed COVID-19. The specificity of the Salocor SARS-CoV-2 serum N antigen test was 98.0%. In comparison with simultaneous positive PCR from upper respiratory tract (URT) specimens, the test sensitivity was 91.7%. In a serum panel in which the earliest serum sample was collected two days before the collection of positive URT specimen, and the latest 48 days after (median 1 day post URT sample collection), the serum N antigen test sensitivity was 94% within 14 days post onset of symptoms. The antigenemia resolved approximately two weeks after the onset of disease and diagnostic PCR. The combination of simultaneous SARS-CoV-2 antigen and antibody testing appeared to provide useful information for timing of COVID-19. Our results suggest that SARS-CoV-2 N-antigenemia may be used as a diagnostic marker in acute COVID-19.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2021.01.08.20248771v1" target="_blank">Detection of SARS-CoV-2 nucleocapsid antigen from serum can aid in timing of COVID-19 infection</a>
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<li><strong>A Scoping Review of the Experience of Implementing Population Testing for SARS-CoV-2</strong> -
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Background: The SARS-CoV-2 pandemic has led to the swift introduction of population testing programmes in many countries across the world, using testing modalities such as drive-through, walk-through, mobile and home visiting programmes. Here, we provide an overview of the literature describing the experience of implementing population testing for SARS-CoV-2. Methods: We conducted a scoping review using Embase, Medline and the Cochrane Library in addition to a grey literature search. We identified indicators relevant to process, quality and resource outcomes related to each testing modality. Results: 2,999 titles were identified from the academic literature and the grey literature search, of which 22 were relevant. Most studies were from the USA and the Republic of Korea. Drive-through testing centres were the most common testing modality evaluated and these provided a rapid method of testing whilst minimising resource use. Conclusions: The evidence base for population testing lacks high quality studies, however, the literature provides evaluations of the advantages and limitations of different testing modalities. There is a need for robust evidence in this area to ensure that testing is deployed in a safe and effective manner in response to the Covid-19 pandemic. Keywords: mass testing, population testing, SARS-CoV-2, Covid-19
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2021.01.11.21249571v1" target="_blank">A Scoping Review of the Experience of Implementing Population Testing for SARS-CoV-2</a>
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<li><strong>Model-based cellular kinetic analysis of SARS-CoV-2 infection: different immune response modes and treatment strategies</strong> -
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Increasing number in global COVID-19 cases demands for mathematical model to analyze the interaction between the virus dynamics and the response of innate and adaptive immunity. Here, based on the assumption of a weak and delayed response of the innate and adaptive immunity in SARS-CoV-2 infection, we constructed a mathematical model to describe the dynamic processes of immune system. Integrating theoretical results with clinical COVID-19 patients9 data, we classified the COVID-19 development processes into three typical modes of immune responses, correlated with the clinical classification of mild & moderate, severe and critical patients. We found that the immune efficacy (the ability of host to clear virus and kill infected cells) and the lymphocyte supply (the abundance and pool of naive T and B cell) play important roles in the dynamic process and determine the clinical outcome, especially for the severe and critical patients. Furthermore, we put forward possible treatment strategies for the three typical modes of immune response. We hope our results can help to understand the dynamical mechanism of the immune response against SARS-CoV-2 infection, and to be useful for the treatment strategies and vaccine design.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2021.01.11.21249562v1" target="_blank">Model-based cellular kinetic analysis of SARS-CoV-2 infection: different immune response modes and treatment strategies</a>
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<li><strong>Rates and predictors of uptake of formal and informal mental health support during the COVID-19 pandemic: an analysis of 26,740 adults in the UK in lockdown</strong> -
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Purpose: The coronavirus disease 2019 (COVID-19) pandemic has put a great strain on people9s mental health. A growing number of studies have shown worsening mental health measures globally during the pandemic. However, there is a lack of empirical study on how people support their mental health during the COVID-19 pandemic. This study aimed to examine a number of formal and informal mental health supports. Further, it explored factors that might be associated with the use of different types mental health support. Method: Data from 26,740 adults in the UCL COVID -19 Social Study were analysed between 13th April, 2020 and 3rd July, 2020. Data were analysed using logistic and Poisson regression models. Results: About 45% of people reported talking to friends or family members to support their mental health, 43% engaging in self-care activities, 20% taking medication, 9% speaking to mental health professionals, 8% talking to a GP or other health professional, and another 8% using helpline or online services. Gender, education, living status, loneliness, pre-existing mental health conditions, general depression and anxiety, coping and personality were found to be associated with the use of mental health support. Conclusion: While the negative impacts caused by the COVID-19 pandemic are inevitable, people can play an active role in managing their mental health. Understanding the patterns and predictors of various kinds of mental health support during the pandemic is crucial for future service planning and delivery through recognising potential barriers to mental health care faced by certain groups.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2021.01.11.21249509v1" target="_blank">Rates and predictors of uptake of formal and informal mental health support during the COVID-19 pandemic: an analysis of 26,740 adults in the UK in lockdown</a>
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<li><strong>Cardiorespiratory Fitness and Neuromuscular Performance in Patients Recovered from COVID-19</strong> -
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Objective: COVID-19 affects cardiorespiratory and muscular systems, causing dysfunctions that may persist after recovery from the acute infection and treatment. The aim of this study was to evaluate cardiorespiratory fitness and neuromuscular performance in these patients. Methods: Patients recovered from mild (n=31) and severe (n=17) COVID-19 were evaluated and compared to healthy subjects (n=15). All volunteers underwent a maximal cardiopulmonary exercise test with simultaneous acquisition of electromyography (EMG). Power output, oxygen uptake (VO2), pulse oxygen (O2Pulse), cardiovascular efficiency (ΔHR/ΔVO2), ventilation (VE), breathing reserve (BR) and ventilatory efficiency (VE/VCO2 slope) were analyzed. From EMG, power output for type Ia and IIa activation as well as total neuromuscular efficiency (Δwatts/Δ%RMS) were determined. Results: Patients with severe COVID-19 presented lower VO2, O2Pulse and VE than mild COVID-19 patients and healthy subjects (p < 0.05 for all comparisons). No differences in ΔHR/ΔVO2, BR or VE/VCO2 slope were observed among the groups (p > 0.05 for all comparisons). Type IIa and IIb fibers were activated at lower power output in severe than in mild COVID-19 patients and healthy subjects (p < 0.05). Δwatts/Δ%RMS was lower in severe than in mild COVID-19 patients and healthy subjects (p < 0.05). Conclusion: Patients recovered from severe COVID-19 present low cardiorespiratory fitness, activate glycolytic fibers at low power outputs, and show low neuromuscular efficiency; while patients recovered from mild COVID-19 do not present these sequels.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2021.01.11.20248930v1" target="_blank">Cardiorespiratory Fitness and Neuromuscular Performance in Patients Recovered from COVID-19</a>
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<li><strong>Genomic and mobility data reveal mass population movement as a driver of SARS-CoV-2 dissemination and diversity in Bangladesh</strong> -
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Background New data streams are being used to track the pandemic of SARS-CoV-2, including genomic data which provides insights into patterns of importation and spatial spread of the virus, as well as population mobility data obtained from mobile phones. Here, we analyse the emergence and outbreak trajectory of SARS-CoV-2 in Bangladesh using these new data streams, and identify mass population movements as a key early event driving the ongoing epidemic. Methods We sequenced complete genomes of 67 SARS-CoV-2 samples (March-July 2020) and combined this dataset with 324 genomes from Bangladesh. For phylogenetic context, we also used 68,000 GISAID genomes collected globally. We paired this genomic data with population mobility information from Facebook and three mobile phone operators. Findings The majority (85%) of the Bangladeshi sequenced isolates fall into either pangolin lineage B.1.36 (8%), B.1.1 (19%) or B.1.1.25 (58%). Bayesian time-scaled phylogenetic analysis predicted SARS-COV-2 first appeared in mid-February, through international introductions. The first case was reported on March 8th. This pattern of repeated international introduction changed at the end of March when three discrete lineages expanded and spread clonally across Bangladesh. The shifting pattern of viral diversity across Bangladesh is reflected in the mobility data which shows the mass migration of people from cities to rural areas at the end of March, followed by frequent travel between Dhaka and the rest of the country during the following months. Interpretation In Bangladesh, population mobility out of Dhaka as well as frequent travel from urban hotspots to rural areas resulted in rapid country-wide dissemination of SARS-CoV-2. The strains in Bangladesh reflect the local expansion of global lineages introduced early from international travellers to and from major international travel hubs. Importantly, the Bangladeshi context is consistent with epidemiologic and phylogenetic findings globally. Bangladesh is one of the few countries in the world with a rich history of conducting mass vaccination campaigns under complex circumstances. Combining genomics and these new data streams should allow population movements to be modelled and anticipated rendering Bangladesh extremely well prepared to immunize citizens rapidly. Based on our genomics data and the country9s successful immunization history, vaccines becoming available globally will be suitable for implementation in Bangladesh while ongoing genomic surveillance is conducted to monitor for new variants of the virus.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2021.01.05.21249196v1" target="_blank">Genomic and mobility data reveal mass population movement as a driver of SARS-CoV-2 dissemination and diversity in Bangladesh</a>
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<h1 data-aos="fade-right" id="from-clinical-trials">From Clinical Trials</h1>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>A Study of ORTD-1 in Patients Hospitalized With COVID-19 Related Pneumonia</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Drug: ORTD-1 low dose; Drug: ORTD-1 mid dose; Drug: ORTD-1 high dose; Other: Vehicle control<br/><b>Sponsor</b>: Oryn Therapeutics, LLC<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 Effect of Deep Breathing Exercise on Dyspnea, Anxiety and Quality of Life in Patients Treated for COVID-19</strong> - <b>Condition</b>: COVID-19<br/><b>Intervention</b>: Behavioral: Deep Breathing Exercise with Triflo<br/><b>Sponsor</b>: Ankara University<br/><b>Not yet recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Safety and Immunogenicity of Two Different Strengths of the Inactivated COVID-19 Vaccine ERUCOV-VAC</strong> - <b>Condition</b>: COVID-19 Vaccine<br/><b>Interventions</b>: Biological: ERUCOV-VAC; Other: Placebo Vaccine<br/><b>Sponsors</b>: Health Institutes of Turkey; TC Erciyes University<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>Dendritic Cell Vaccine, AV-COVID-19, to Prevent COVID-19 Infection</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Biological: AV-COVID-19; Other: GM-CSF<br/><b>Sponsors</b>: Aivita Biomedical, Inc.; PT AIVITA Biomedika Indonesia; Indonesia Ministry of Health; National Institute of Health Research and Development, Ministry of Health Republic of Indonesia<br/><b>Recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>A Real World Study of Bamlanivimab in Participants With Mild-to-moderate Coronavirus Disease 2019 (COVID-19)</strong> - <b>Condition</b>: COVID-19<br/><b>Intervention</b>: Drug: Bamlanivimab<br/><b>Sponsors</b>: Eli Lilly and Company; AbCellera Biologics Inc.<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>Dexamethasone for COVID-19</strong> - <b>Condition</b>: Covid19<br/><b>Intervention</b>: Drug: Dexamethasone<br/><b>Sponsor</b>: University of Oklahoma<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>Immunologic Responses to Single and Double Doses of SARS-CoV-2 Vaccines in Egyptians</strong> - <b>Condition</b>: COVID-19 Vaccines<br/><b>Intervention</b>: Biological: COVID-19 Vaccines<br/><b>Sponsor</b>: Assiut University<br/><b>Not yet recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Study of Adalimumab or Placebo in Patients With Mild to Moderate COVID-19</strong> - <b>Condition</b>: Mild to Moderate COVID-19<br/><b>Interventions</b>: Drug: Adalimumab; Drug: Placebo<br/><b>Sponsors</b>: Ology Bioservices; Pharm-Olam, LLC; Chemical, Biological, Radiological, and Nuclear Medical<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>Rapid Diagnosis of COVID-19 by Chemical Analysis of Exhaled Air</strong> - <b>Condition</b>: Covid19<br/><b>Intervention</b>: Diagnostic Test: Performance evaluation (sensitivity and specificity) for COVID-19 diagnosis of the Vocus PTR-TOF process<br/><b>Sponsor</b>: Hospices Civils de Lyon<br/><b>Not yet recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>A Study to Evaluate MVC-COV1901 Vaccine Against COVID-19 in Adult</strong> - <b>Condition</b>: Covid19 Vaccine<br/><b>Interventions</b>: Biological: MVC-COV1901(S protein with adjuvant); Biological: MVC-COV1901(Saline)<br/><b>Sponsor</b>: Medigen Vaccine Biologics Corp.<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 Safety and Efficacy of Pyronaridine-artesunate (Pyramax® or Artecom®)in COVID-19 Patients</strong> - <b>Condition</b>: Covid19<br/><b>Interventions</b>: Drug: Artecom® (pyronaridine-artesunate); Drug: Placebo<br/><b>Sponsor</b>: Shin Poong Pharmaceutical 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>Study to Evaluate the Safety, Tolerability, and Efficacy of BGE-175 in Participants ≥ 60 Years of Age and Hospitalized With Coronavirus Disease 2019 (COVID-19) That Are Not in Respiratory Failure</strong> - <b>Condition</b>: Covid19<br/><b>Interventions</b>: Drug: BGE-175; Other: Placebo<br/><b>Sponsor</b>: BioAge Labs, Inc.<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>Efficacy of Ramdicivir and Baricitinib for the Treatment of Severe COVID 19 Patients</strong> - <b>Conditions</b>: Covid19; Covid-19 ARDS<br/><b>Interventions</b>: Drug: Remdesivir; Drug: Baricitinib; Drug: Tocilizumab<br/><b>Sponsors</b>: M Abdur Rahim Medical College and Hospital; First affiliated Hospital Xi'an Jiaoting University<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>Antiseptic Mouth Rinses to Reduce Salivary Viral Load in COVID-19 Patients</strong> - <b>Condition</b>: Covid19<br/><b>Interventions</b>: Drug: Betadine© bucal 100 mg/ml; Drug: Oximen® 3%; Drug: Clorhexidine Dental PHB©; Drug: Vitis Xtra Forte©; Drug: Distilled Water<br/><b>Sponsors</b>: Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana; Hospital Universitario Fundación Jiménez Díaz; Hospital Universitario General de Villalba; Hospital Universitario Infanta Elena; Hospital Universitario Virgen de la Arrixaca; Hospital Clínico Universitario de Valencia; Dentaid SL<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>RU Anti-SARS-CoV-2 (COVID-19) mAbs in Healthy Volunteers</strong> - <b>Condition</b>: Covid19<br/><b>Intervention</b>: Biological: C144-LS and C-135-LS<br/><b>Sponsor</b>: Rockefeller University<br/><b>Recruiting</b></p></li>
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<h1 data-aos="fade-right" id="from-pubmed">From PubMed</h1>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Biological characteristics and biomarkers of novel SARS-CoV-2 facilitated rapid development and implementation of diagnostic tools and surveillance measures</strong> - Existing coronavirus named as a severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has speeded its spread across the globe immediately after emergence in China, Wuhan region, at the end of the year 2019. Different techniques, including genome sequencing, structural feature classification by electron microscopy, and chest imaging using computed tomography, are primarily used to diagnose and screen SARS-CoV-2 suspected individuals. Determination of the viral structure, surface proteins,...</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>Proposed Mechanisms of Targeting COVID-19 by Delivering Mesenchymal Stem Cells and Their Exosomes to Damaged Organs</strong> - With the outbreak of coronavirus disease (COVID-19) caused by novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the world has been facing an unprecedented challenge. Considering the lack of appropriate therapy for COVID-19, it is crucial to develop effective treatments instead of supportive approaches. Mesenchymal stem cells (MSCs) as multipotent stromal cells have been shown to possess treating potency through inhibiting or modulating the pathological events in COVID-19. MSCs...</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 certain medicinal plants compounds as new potential inhibitors of novel corona virus (COVID-19) using molecular docking analysis</strong> - SARS-CoV-2 is a new strain of coronavirus that appeared in China in December 2019, in recent years, great progress has been made in developing new antiviral drugs, and natural products, are important sources of potential and new antiviral drugs. The present study aimed to assess some biologically active compounds present in medicinal plants as potential COVID-19 inhibitors, using molecular docking methods. The Docking study was performed by Molecular Operating Environment software (MOE). About...</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>Quantum chemical studies on molecular structure, AIM, ELF, RDG and antiviral activities of hybrid hydroxychloroquine in the treatment of COVID-19: molecular docking and DFT calculations</strong> - Structure-activity relationships for hydroxychloroquine compound and its derivatives resulted in a potent antiviral activity. Where hydroxychloroquine derivatives showed an apparent efficacy against coronavirus related pneumonia. For this reason, the current study is focused on the structural properties of hydroxychloroquine and hydroxychloroquine sulfate. Optimized structures of these molecules have been reported by using DFT method at B3LYP/6-31G* level of theory. Te geometric were determined...</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 trimeric human angiotensin-converting enzyme 2 as an anti-SARS-CoV-2 agent</strong> - Effective intervention strategies are urgently needed to control the COVID-19 pandemic. Human angiotensin-converting enzyme 2 (ACE2) is a membrane-bound carboxypeptidase that forms a dimer and serves as the cellular receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). ACE2 is also a key negative regulator of the renin-angiotensin system that modulates vascular functions. We report here the properties of a trimeric ACE2 ectodomain variant, engineered using a structure-based...</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>Upregulation of DUSP6 impairs infectious bronchitis virus replication by negatively regulating ERK pathway and promoting apoptosis</strong> - Elucidating virus-cell interactions is fundamental to understanding viral replication and identifying targets for therapeutic control of viral infection. The extracellular signal-regulated kinase (ERK) pathway has been shown to regulate pathogenesis during many viral infections, but its role during coronavirus infection is undetermined. Infectious bronchitis virus is the representative strain of Gammacoronavirus, which causes acute and highly contagious diseases in the poultry farm. In this...</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>Repurposing existing drugs: identification of SARS-CoV-2 3C-like protease inhibitors</strong> - Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for coronavirus disease 2019 (COVID-19). Since its emergence, the COVID-19 pandemic has not only distressed medical services but also caused economic upheavals, marking urgent the need for effective therapeutics. The experience of combating SARS-CoV and MERS-CoV has shown that inhibiting the 3-chymotrypsin-like protease (3CLpro) blocks the replication of the virus. Given the well-studied properties of FDA-approved drugs,...</p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Experimental Models to Study COVID-19 Effect in Stem Cells</strong> - The new strain of coronavirus (severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2)) emerged in 2019 and hence is often referred to as coronavirus disease 2019 (COVID-19). This disease causes hypoxic respiratory failure and acute respiratory distress syndrome (ARDS), and is considered as the cause of a global pandemic. Very limited reports in addition to ex vivo model systems are available to understand the mechanism of action of this virus, which can be used for testing of any drug...</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>Drug Repurposing: Dipeptidyl Peptidase IV (DPP4) Inhibitors as Potential Agents to Treat SARS-CoV-2 (2019-nCoV) Infection</strong> - The current outbreak of severe acute respiratory distress syndrome (SARS) or nCOVID-19 pandemic, caused by the coronavirus-2 (CoV-2), continues to wreak havoc globally. As novel vaccines are being discovered and developed, small molecule drugs still constitute a viable treatment option for SARS-CoV-2 infections due to their advantages such as superior patient compliance for oral therapies, reduced manufacturing costs and ease of large scale distribution due to better stability and storage...</p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Neutrophil Extracellular Traps and Their Implications in Cardiovascular and Inflammatory Disease</strong> - Neutrophils are primary effector cells of innate immunity and fight infection by phagocytosis and degranulation. Activated neutrophils also release neutrophil extracellular traps (NETs) in response to a variety of stimuli. These NETs are net-like complexes composed of cell-free DNA, histones and neutrophil granule proteins. Besides the evolutionarily conserved mechanism to capture and eliminate pathogens, NETs are also associated with pathophysiological processes of various diseases. Here, we...</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 in teriflunomide-treated patients with multiple sclerosis: A case report and literature review</strong> - CONCLUSION: Available data suggest that teriflunomide therapy should not be discontinued in MS patients who develop SARS-CoV-2 infection, also in presence of significant comorbidities or clinical conditions requiring hospitalization. Additional studies are necessary to assess if the drug can also have a protective role against SARS-CoV-2.</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 systematic review of experimental evidence for antiviral effects of ivermectin and an in-silico analysis of ivermectin's possible mode of action against SARS-CoV-2</strong> - Viral infections remain a major cause of economic loss with an unmet need for novel therapeutic agents. Ivermectin is a putative antiviral compound; the proposed mechanism is the inhibition of nuclear translocation of viral proteins, facilitated by mammalian host importins, a necessary process for propagation of infections. We systematically reviewed the evidence for the applicability of ivermectin against viral infections including SARS-CoV-2 regarding efficacy, mechanisms and selective...</p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>ACE2-derived peptides interact with the RBD domain of SARS-CoV-2 spike glycoprotein, disrupting the interaction with the human ACE2 receptor</strong> - Vaccines could be the solution to the current SARS-CoV-2 outbreak. However, some studies have shown that the immunological memory only lasts three months. Thus, it is imperative to develop pharmacological treatments to cope with COVID-19. Here, the in silico approach by molecular docking, dynamic simulations and quantum biochemistry revealed that ACE2-derived peptides strongly interact with the SARS-CoV-2 RBD domain of spike glycoprotein (S-RBD). ACE2-Dev-PepI, ACE2-Dev-PepII, ACE2-Dev-PepIII...</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>Ifenprodil Stereoisomers: Synthesis, Absolute Configuration, and Correlation with Biological Activity</strong> - Ifenprodil (1) is a potent GluN2B-selective N-methyl-d-aspartate (NMDA) receptor antagonist that is used as a cerebral vasodilator and has been examined in clinical trials for the treatment of drug addiction, idiopathic pulmonary fibrosis, and COVID-19. To correlate biological data with configuration, all four ifenprodil stereoisomers were prepared by diastereoselective reduction and subsequent separation of enantiomers by chiral HPLC. The absolute configuration of ifenprodil stereoisomers was...</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>ACE-2-interacting Domain of SARS-CoV-2 (AIDS) Peptide Suppresses Inflammation to Reduce Fever and Protect Lungs and Heart in Mice: Implications for COVID-19 Therapy</strong> - COVID-19 is an infectious respiratory illness caused by the virus strain severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and until now, there is no effective therapy against COVID-19. Since SARS-CoV-2 binds to angiotensin-converting enzyme 2 (ACE2) for entering into host cells, to target COVID-19 from therapeutic angle, we engineered a hexapeptide corresponding to the ACE2-interacting domain of SARS-CoV-2 (AIDS) that inhibits the association between receptor-binding...</p></li>
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<h1 data-aos="fade-right" id="from-patent-search">From Patent Search</h1>
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