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<h1 data-aos="fade-down" id="covid-19-sentry">Covid-19 Sentry</h1>
<h1 data-aos="fade-right" data-aos-anchor-placement="top-bottom" id="contents">Contents</h1>
<ul>
<li><a href="#from-preprints">From Preprints</a></li>
<li><a href="#from-clinical-trials">From Clinical Trials</a></li>
<li><a href="#from-pubmed">From PubMed</a></li>
<li><a href="#from-patent-search">From Patent Search</a></li>
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<h1 data-aos="fade-right" id="from-preprints">From Preprints</h1>
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<li><strong>On temporal changes in the role of different age groups in propagating the Omicron epidemic waves in England</strong> -
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Background: There is limited information on the role of individuals in different age groups in the spread of infection during the Omicron epidemics, especially ones beyond the winter epidemic wave in 2021-2022. In England, booster vaccination against SARS-CoV-2 is currently restricted to persons aged over 50y and individuals in clinical risk groups. Methods: We used a previously developed methodology to evaluate the role of individuals in different age groups in propagating the Spring, Summer, and Autumn waves of the Omicron epidemic in England. This methodology utilizes the relative risk (RR) statistic that measures the change in the proportion of cases in each age group among all COVID-19 cases in the population before the peak of an epidemic wave vs. after the peak of an epidemic wave. Higher values for the RR statistic represent age groups that experienced a disproportionate depletion of susceptible individuals during the ascent of the epidemic (due to increased contact rates and/or susceptibility to infection). Results: For the 2022 Spring wave, the highest RR estimate belonged to children aged 5 to 9y (RR=2.05 (95%CI (2.02,2.08)), followed by children aged 10 to 14y (RR=1.68 (1.66,1.7)) and children aged 0 to 4y (RR=1.38 (1.36,1.41)). For the Summer wave, the highest RR estimates belonged to persons aged 20 to 34y: (RR=1.09 (1.07,1.12) in aged 20 to 24y, RR=1.09 (1.07,1.11) in aged 25 to 29y, RR=1.09(1.07,1.11) in aged 30 to 34y). For the Autumn wave, the highest RR estimate in adults belonged to those aged 70 to 74y (RR=1.10 (1.07,1.14)), followed by adults aged 35 to 39y (RR=1.09 (1.06,1.12)), adults aged 40 to 44y (RR=1.09 (1.06,1.12)), and adults aged 65 to 69y (RR=1.08 (1.05,1.11)) (with children excluded from the analyses due to limited/irregular detection of COVID-19 cases in children during the Autumn wave). Conclusions: As time progressed, ages of individuals who played the leading roles in propagating the Omicron epidemic waves in England shifted upward, with the leading roles in propagating COVID-19 epidemics in England currently belonging to adults of different ages. Extending booster vaccination to adults aged under 50y, and possibly to children should help limit the spread of Omicron infections in the community.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.12.30.22283949v1" target="_blank">On temporal changes in the role of different age groups in propagating the Omicron epidemic waves in England</a>
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<li><strong>Effectiveness of Sotrovimab in Preventing COVID-19-related Hospitalizations or Deaths Among U.S. Veterans</strong> -
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Background: Data on effectiveness of sotrovimab preventing COVID-19-related hospitalization or mortality, particularly after the emergence of the Omicron variant, are limited. Method: Determine the real-world clinical effectiveness of sotrovimab for prevention of 30-day COVID-19 related hospitalization or mortality using a retrospective cohort within the U.S. Department of Veterans Affairs (VA) healthcare system. Veterans aged ≥18 years, diagnosed with COVID-19 between December 1, 2021, and April 4, 2022, were included. Sotrovimab recipients (n=2,816) were exactly matched to untreated controls (n=11,250) on date of diagnosis, vaccination status, and region. The primary outcome was COVID-19-related hospitalization or all-cause mortality within 30 days from diagnosis. Cox proportional hazards modeling estimated the hazard ratios (HR) and 95% Confidence Interval (CI) for the association between receipt of sotrovimab and outcomes. Results: During BA.1 dominance, compared to matched controls, sotrovimab-treated patients had a 70% lower risk hospitalization within 30 days or mortality (HR 0.30; 95%CI, 0.23-0.40), a 66% lower risk of 30-day hospitalization (HR 0.34; 95%CI, 0.25-0.46), and a 77% lower risk of 30-day all-cause mortality (HR 0.23; 95%CI, 0.14-0.38). During BA.2 dominance sotrovimab-treated patients had a 71% (HR .29; 95%CI, 0.08-0.98) lower risk of 30-day COVID-19-related- hospitalization, emergency, or urgent care. Limitations include confounding by indication. Conclusions: Using national real-world data from high risk and predominantly vaccinated Veterans, administration of sotrovimab, compared with no treatment, was associated with reduced risk of 30-day COVID-19-related hospitalization or all-cause mortality during the Omicron BA.1 period and reduced risk of progression to severe COVID-19 during the BA.2 dominant period.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.12.30.22284063v1" target="_blank">Effectiveness of Sotrovimab in Preventing COVID-19-related Hospitalizations or Deaths Among U.S. Veterans</a>
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<li><strong>Surveillance for SARS-CoV-2 in Ohios wildlife, companion, and agricultural animals</strong> -
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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in humans in late 2019 and spread rapidly to become a global pandemic. A zoonotic spillover event from animal to human was identified as the presumed origin. Subsequently, reports began emerging regarding spillback events resulting in SARS-CoV-2 infections in multiple animal species. These events highlighted critical links between animal and human health while also raising concerns about the development of new reservoir hosts and potential viral mutations that could alter virulence and transmission or evade immune responses. Characterizing susceptibility, prevalence, and transmission between animal species became a priority to help protect animal and human health. In this study, we coalesced a large team of investigators and community partners to surveil for SARS-CoV-2 in domestic and free-ranging animals around Ohio between May 2020 and August 2021. We focused on species with known or predicted susceptibility to SARS-CoV-2 infection, highly congregated or medically compromised animals (e.g. shelters, barns, veterinary hospitals), and animals that had frequent contact with humans (e.g. pets, agricultural animals, zoo animals, or animals in wildlife hospitals). This included free-ranging deer (n=76), mink (n=57), multiple species of bats (n=65), and other wildlife in addition to domestic cats (n=275) and pigs (n= 184). In total, we tested 800 animals (34 species) via rRT-PCR for SARS-CoV-2 RNA. SARS-CoV-2 viral RNA was not detected in any of the tested animals despite a major peak in human SARS-CoV-2 cases that occurred in Ohio subsequent to the peak of animal samplings. Importantly, due to lack of validated tests for animals, we did not test for SARS-CoV-2 antibodies in this study, which limited our ability to assess exposure. While the results of this study were negative, the surveillance effort was critical and remains key to understanding, predicting, and preventing re-emergence of SARS-CoV-2 in humans or animals.
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🖺 Full Text HTML: <a href="https://www.biorxiv.org/content/10.1101/2022.12.30.522311v1" target="_blank">Surveillance for SARS-CoV-2 in Ohios wildlife, companion, and agricultural animals</a>
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<li><strong>Study of an age-based Covid-19 outbreak model and the effect of demo-graphic structure of a state on infectious disease dynamics</strong> -
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In this paper, our objective was to investigate whether the Covid-19 pandemic disease is more likely to break out in some specific age group or not. We also intended to know whether some specific demographic parameters like birth rate, death rate controls the spreading of the disease. Our investigation showed that the post reproductive population group is more prone to the disease for the countries having population pyramid of stationary or con-tracting type where as for the countries with expanding population pyramid, the pre reproductive population is more likely to be attacked by the disease. We also found the domains of values of the demographic parameters that result different dynamic phenomena. Further we tried to know whether a countrys9 population pyramid has an effect in spreading the disease. Our experiment showed that for countries having expanding population pyramid, the total number of cases is expected to be comparatively low whereas for countries having contracting population pyramid, the total number of cases is expected to be comparatively high.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.12.28.22284021v1" target="_blank">Study of an age-based Covid-19 outbreak model and the effect of demo-graphic structure of a state on infectious disease dynamics</a>
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<li><strong>Bridging the gap_Estimation of 2022/2023 SARS-CoV-2 healthcare burden in Germany based on multidimensional data from a rapid epidemic panel</strong> -
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Throughout the SARS-CoV-2 pandemic, Germany lacked an adaptive population panel for epidemic diseases and a modelling platform to rapidly incorporate panel estimates. We evaluated how a cross-sectional analysis of 9922 participants of the MuSPAD study in June/July 2022 combined with a newly developed modelling platform could bridge the gap and analyzed antibody levels, neutralizing serum activity and interferon-gamma release response of serum samples. We categorized the population into four groups with differing protection against severe course of disease (validated by neutralizing serum activity), and found that 30% were in the group with highest protection, and 85% in either the highest categories or second highest group regarding protection level. Estimated hospitalizations due to SARS-CoV-2 were predicted to be between 30 to 300% of the peak in 02/2021 dependent on assumed variant characteristics. We showed the feasibility of a rapid epidemic panel able to evaluate complex endpoints for SARS-CoV-2 and inform scenario modelling.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.12.30.22284061v1" target="_blank">Bridging the gap_Estimation of 2022/2023 SARS-CoV-2 healthcare burden in Germany based on multidimensional data from a rapid epidemic panel</a>
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<li><strong>Automated assessment of chest CT severity scores in patients suspected of COVID-19 infection</strong> -
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Background: The COVID-19 pandemic has claimed numerous lives in the last three years. With new variants emerging every now and then, the world is still battling with the management of COVID-19. Purpose: To utilize a deep learning model for the automatic detection of severity scores from chest CT scans of COVID-19 patients and compare its diagnostic performance with experienced human readers. Methods: A deep learning model capable of identifying consolidations and ground-glass opacities from the chest CT images of COVID-19 patients was used to provide CT severity scores on a 25-point scale for definitive pathogen diagnosis. The model was tested on a dataset of 469 confirmed COVID-19 cases from a tertiary care hospital. The quantitative diagnostic performance of the model was compared with three experienced human readers. Results: The test dataset consisted of 469 CT scans from 292 male (average age: 52.30) and 177 female (average age: 53.47) patients. The standalone model had an MAE of 3.192, which was lower than the average radiologists9 MAE of 3.471. The model achieved a precision of 0.69 [0.65, 0.74] and an F1 score of 0.67 [0.62, 0.71], which was significantly superior to the average reader precision of 0.68 [0.65, 0.71] and F1 score of 0.65 [0.63, 0.67]. The model demonstrated a sensitivity of 0.69 [95% CI: 0.65, 0.73] and specificity of 0.83 [95% CI: 0.81, 0.85], which was comparable to the performance of the three human readers, who had an average sensitivity of 0.71 [95% CI: 0.69, 0.73] and specificity of 0.84 [95% CI: 0.83, 0.85]. Conclusion: The AI model provided explainable results and performed at par with human readers in calculating CT severity scores from the chest CT scans of patients affected with COVID-19. The model had a lower MAE than that of the radiologists, indicating that the CTSS calculated by the AI was very close in absolute value to the CTSS determined by the reference standard.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.12.28.22284027v1" target="_blank">Automated assessment of chest CT severity scores in patients suspected of COVID-19 infection</a>
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<li><strong>Estimated of expected COVID-19 deaths in Mainland China after abandoning zero COVID policy</strong> -
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Background: China witnessed a surge of Omicron infections after abandoning zero COVID strategies on December 7, 2022. The authorities report very sparse deaths based on very restricted criteria, but massive deaths are speculated. Methods: We aimed to estimate the COVID-19 fatalities in Mainland China until summer 2023 using the experiences of Hong Kong and of South Korea in 2022 as prototypes. Both these locations experienced massive Omicron waves after having had very few SARS-CoV-2 infections during 2020-2021. We estimated age-stratified infection fatality rates (IFRs) in Hong Kong and South Korea during 2022 and extrapolated to the population age structure of Mainland China. We also accounted separately for deaths of residents in long-term care facilities, which were prominent in Hong Kong. Results: IFR estimates in non-elderly strata were modestly higher in Hong Kong than South Korea and projected 987,455 and 811,571 maximal COVID-19 deaths, respectively, if the entire China population was infected. Expected COVID-19 deaths in Mainland China until summer 2023 ranged from 64,573 to 691,219 assuming 25-70% of the non-elderly population being infected and variable protection of elderly (from none to three-quarter reduction in fatalities). The main analysis (45% of non-elderly population infected and fatality impact among elderly reduced by half) estimated 199,223-249,094 COVID-19 deaths until summer 2023. Large uncertainties exist regarding potential changes in dominant variant, health system strain, and impact on non-COVID-19 deaths. Conclusions: The most critical factor that can affect total COVID-19 fatalities in China is the extent to which the elderly can be protected.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.12.29.22284048v1" target="_blank">Estimated of expected COVID-19 deaths in Mainland China after abandoning zero COVID policy</a>
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<li><strong>Outcomes After Percutaneous Tracheostomy in Patients with COVID-19: A Single-Center Series of 377 Cases</strong> -
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Introduction: The COVID 19 pandemic was highlighted by a rise in hospital admissions secondary to respiratory decompensation. This was accompanied by an increase in ICU admissions, endotracheal intubation and mechanical ventilation. As a consequence, tracheostomies became essential in preventing complications of prolonged intubation and to facilitate weaning from sedation and mechanical ventilation. With the lack of international consensus on tracheostomy technique and optimal timing, we present our experience with 377 percutaneous tracheostomies performed on critically ill COVID 19 patients. Objective: To report the outcomes of critically ill patients with COVID 19 who underwent percutaneous tracheostomy during a period of 24 months. Methods: A retrospective single-center electronic chart review was performed on all ICU patients who underwent percutaneous tracheostomy after respiratory failure secondary to COVID 19 between March 2020 to March 2022. Results: A total of 377 percutaneous tracheostomies were performed. The mean duration between intubation and percutaneous tracheostomy was 17.4 days (3 to 61). The study included 222 males (59%) and 155 females (41%). The mean age of patients was 56.2 years (17-94), with a mean BMI was 31.3 (14 to 68). The commonest comorbidities among patients were diabetes mellitus (50%) and hypertension (48%). Complications were encountered in 85 cases (23%), with the commonest overall complication being minor bleeding. 203 patients (54%) were weaned from sedation. The mean duration between tracheostomy and weaning from sedation was 7.5 days (1 to 47 days). 156 patients (41%) were weaned from MV. The mean duration between tracheostomy and weaning from MV was 12.9 days (1 to 58 days). There was a total of 236 (63%) deaths reported during the period of this study. No deaths were attributable to the surgical procedure. Conclusion: Percutaneous tracheostomy can be safely performed in patients with COVID 19. With lack of conclusive objective data regarding the optimal timing for tracheostomy, we recommend that tracheostomy be performed as soon as possible after the 7th day endotracheal intubation. Key Words: Percutaneous tracheostomy, COVID 19, Critically ill, ICU
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.12.28.22283971v1" target="_blank">Outcomes After Percutaneous Tracheostomy in Patients with COVID-19: A Single-Center Series of 377 Cases</a>
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<li><strong>SARS-CoV-2 seroprevalence and longitudinal antibody response following natural infection in pregnancy</strong> -
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Importance:  Antenatal care provides unique opportunities to assess SARS-CoV-2 seroprevalence and antibody response duration after natural infection detected during pregnancy; transplacental antibody transfer may inform peripartum and neonatal protection. Objective:  Estimate seroprevalence and durability of antibodies from natural infection (anti-nucleocapsid (anti-N) IgG) among pregnant people, and evaluate transplacental transfer efficiency. Design: Seroprevalence study: cross-sectional SARS-CoV-2 antibody screening among pregnant people December 9, 2020-June 19, 2021. Cohort study: Pregnant people screened anti-N IgG+ by Abbott Architect chemiluminescent immunoassay in seroprevalence study or identified through medical records with RT-PCR+ or antigen positive results enrolled in a prospective cohort December 9, 2020-June 30, 2022 to longitudinally measure anti-N IgG responses. We collected cord blood and assessed transplacental transfer of maternally-derived anti-N antibodies. Setting:  Three hospitals and 14 affiliated clinics providing antenatal and delivery care, Seattle, Washington metropolitan area. Participants:  Seroprevalence study: pregnant people were screened for SAR-CoV-2 anti-N IgG during routine care. Cohort study: Pregnant people with evidence of prior SARS-CoV-2 infection (screened anti-N IgG+ from seroprevalence study or identified with a RT-PCR+ or antigen positive result from medical records) were enrolled in a cohort study to longitudinally measure anti-N IgG responses. Exposure(s) (for observational studies):  COVID-19 diagnosis, symptoms, and disease severity. Main Outcome(s) and Measure(s):  Presence and durability of SARS-CoV-2 anti-N IgG, transplacental transfer of maternally-derived anti-N IgG. Results: Of 1289 pregnant people screened in the seroprevalence study, 5% (65) tested SARS-CoV-2 anti-N IgG+, including 39 (60%) without prior RT-PCR+ or antigen positive results and 53 (82%) without symptoms. Among 89 participants enrolled in the cohort study, 73 (82%) had anti-N IgG+ results during pregnancy. Among 49 participants with delivery samples 33 (67%) were anti-N IgG negative by delivery. Of 24 remaining anti-N IgG+ at delivery with paired cord blood samples, 12 (50%) had efficient transplacental anti-N IgG antibody transfer. Median time from first anti-N IgG to below positive antibody threshold was 17 weeks and did not differ by prior RT-PCR+ or antigen positive status. Conclusions and Relevance: Maternally-derived SARS-CoV-2 antibodies to natural infection may wane before delivery. Vaccines are recommended for pregnant persons to reduce severe illness and confer protection to infants.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.12.28.22284017v1" target="_blank">SARS-CoV-2 seroprevalence and longitudinal antibody response following natural infection in pregnancy</a>
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<li><strong>The kinetics of humoral and cellular responses after the booster dose of COVID-19 vaccine in inflammatory arthritis patients</strong> -
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Introduction: Impaired immunogenicity of COVID-19 vaccinations in inflammatory arthritis (IA) patients results in diminished immunity. However, optimal booster vaccination regimens are still unknown, due to not unstudied kinetics of the immune response after booster vaccinations. Therefore, this study aimed to assess the kinetics of humoral and cellular responses in IA patients after the COVID-19 booster. Patients and Methods: In 29 IA patients and 16 healthy controls (HC) humoral responses (level of IgG antibodies) and cellular responses (IFN-γ production) were assessed before (T0), after 4 weeks (T1), and after more than 6 months (T2) from the booster vaccination with BNT162b2. Results: IA patients, but not HC, showed lower anti-S-IgG concentration and IGRA fold change at T2 compared to T1 (p=0.026 and p=0.031). Furthermore, in IA patients the level of cellular response at T2 returned to the pre-booster level (T0). All immunomodulatory drugs, except IL-6 and IL-17 inhibitors for the humoral and IL-17 inhibitors for the cellular response, impaired the immunogenicity of the booster dose at T2. However, none of the immunomodulatory drugs affected the kinetics of both humoral and cellular responses (measured as the difference between response rates at T1 and T2). Conclusion: Our study showed impaired kinetics of both humoral and cellular responses after the booster dose of the COVID-19 vaccine in IA patients, which, in the case of cellular response, did not allow the vaccination effect to be maintained for more than 6 months. Repetitive vaccination with subsequent booster doses seems to be necessary for IA patients.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.12.28.22284008v1" target="_blank">The kinetics of humoral and cellular responses after the booster dose of COVID-19 vaccine in inflammatory arthritis patients</a>
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<li><strong>Association between recent COVID-19 diagnosis on depression and anxiety symptoms among slum residents in Kampala, Uganda</strong> -
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Background An increase in mental health problems has been reported since the beginning of the COVID-19 pandemic. However, little is known about the prevalence of depressive and anxiety disorders, and how recent COVID-19 diagnosis may influence risk of these conditions especially in low-income settings. In this study, we assessed the association between recent COVID-19 diagnosis and depressive and anxiety symptoms among residents in an urban slum setting in Uganda. Methods A cross-sectional study was conducted among 284 individuals in a slum settlement in Kampala, Uganda between April and May 2022.  We assessed generalized anxiety and depression symptoms using two validated questionnaires. We collected data on sociodemographic characteristics, and self-reported recent COVID-19 diagnosis (in the previous 30 days). Using a modified Poisson regression, adjusted for age, sex, gender and household income, we separately provided prevalence ratios and 95% confidence intervals for the associations between recent COVID-19 diagnosis and depressive and anxiety symptoms. Results Overall, 33.8% and 13.4% of the participants met the depression and generalized anxiety screening criteria respectively. People with recent COVID-19 diagnosis were more likely to be depressed (53.1%) than those with no recent diagnosis (31.4%). Participants who were recently diagnosed with COVID-19 reported higher prevalence of anxiety (34.4%) compared to those with no recent diagnosis of COVID-19 (10.7%). After adjusting for confounding, recent diagnosis with COVID-19 was associated with depression (PR= 1.60, 95% CI 1.09 2.34) and anxiety (PR =  2.83, 95% CI 1.50 5.31) . Conclusion This study suggests an increased risk of depressive symptoms and GAD in adults following a COVID-19 diagnosis. We recommend additional mental health support for recently diagnosed persons. The long-term of COVID-19 on mental health effects also need to be investigated.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.12.28.22284012v1" target="_blank">Association between recent COVID-19 diagnosis on depression and anxiety symptoms among slum residents in Kampala, Uganda</a>
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<li><strong>Cost-effectiveness of the second COVID-19 booster vaccination in the United States</strong> -
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ABSTRACT Background: On March 29, 2022, the United States (US) authorized the second booster dose of COVID-19 vaccine for individuals aged 50 years and older. To date, the cost-effectiveness of the second booster strategy remains unassessed. Methods: We developed a decision-analytic SEIR-Markov model by five age groups (0-4yrs with 18,827,338 individuals, 5-11yrs with 28,584,443 individuals, 12-17yrs with 26,154,652 individuals, 18-49yrs with 138,769,369 individuals, and 50+yrs with 119,557,943 individuals) to evaluate the cost-effectiveness of the second COVID-19 booster vaccination (administered 4 months after the first booster dose) over an evaluation period of 180 days in the US, from a healthcare system perspective. Results: Implementing the second booster strategy among individuals aged 50+ years would cost US$807 million but reduce direct medical care costs by $1,128 million, corresponding to a benefit-cost ratio of 1.40. This strategy would also result in a gain of 1,048 QALYs during the 180 days, indicating it was cost-saving. Probabilistic sensitivity analysis demonstrated that the probability of being cost-effective with the strategy was 68%. Further, vaccinating individuals aged 18-49 years with the second booster would result in an additional gain of $1,566 million and 2,276 QALYs. Expanding vaccination to individuals aged 12-17 years would result in an additional gain of $15 million and 89 QALYs. Coverage of the first booster vaccination in age groups under 12 was too low to consider the administration of the second booster. If the social interaction between all age groups was severed, vaccination expansion to 18-49yrs and 12-17yrs would no longer be cost-effective. Conclusion: The second booster strategy was likely to be effective and cost-effective in reducing the disease burden of the COVID-19 pandemic. Expanding the second booster strategy to 18-49yrs and 12-17yrs remains cost-effective due to their social contacts with the older age group. Keywords: COVID-19; Second booster; Cost-effective analysis; SEIR-Markov model; Age groups
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.12.28.22283986v1" target="_blank">Cost-effectiveness of the second COVID-19 booster vaccination in the United States</a>
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<li><strong>A Statistical Analysis on COVID-19 Pandemic in the City of Toronto</strong> -
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As with many viruses, a main topic of concern that has arisen during the COVID-19 pandemic is the nature of the virus spread and the impact it presents for varying age groups. Using statistical methods and numerical summaries, I analyzed the impact that age has on the incubation period, death rates, and case outcomes of COVID-19 cases in the city of Toronto. The results of this study illustrate that the elderly have shorter incubation periods, higher death rates, and a higher count of cases which result in fatality. The analysis concludes that the impact of COVID-19 is most felt by the elderly.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.12.28.22284001v1" target="_blank">A Statistical Analysis on COVID-19 Pandemic in the City of Toronto</a>
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<li><strong>Erythromycin, Retapamulin, Pyridoxine, Folic acid, and Ivermectin dose-dependently inhibit cytopathic effect, Papain-like Protease, and MPRO of SARS-CoV-2</strong> -
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We previously showed that Erythromycin, Retapamulin, Pyridoxine, Folic acid and Ivermectin inhibit SARS-COV-2 induced cytopathic effect (CPE) in Vero cells. In this study and using validated quantitative neutral red assay, we show that the inhibition of CPE is concentration dependent with Inhibitory Concentration-50(IC50) of 3.27 microM, 4.23 microM, 9.29 microM, 3.19 microM and 84.31 microM respectively. Furthermore, Erythromycin, Retapamulin, Pyridoxine, Folic acid and Ivermectin dose dependently inhibit SARS-CoV-2 Papain-like Protease with IC50 of 0.94 microM, 0.88 microM, 1.14 microM, 1.07 microM, 1.51 microM respectively and the main protease(MPRO) with IC50 of 1.35 microM, 1.25 microM, 7.36 microM, 1.15 microM, and 2.44 microM respectively. The IC50 for all the drugs, except ivermectin, are at the clinically achievable plasma concentration in human, which supports a possible role for the drugs in the management of COVID-19. The lack of inhibition of CPE by Ivermectin at clinical concentrations could be part of the explanation for its lack of effectiveness in clinical trials.
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🖺 Full Text HTML: <a href="https://www.biorxiv.org/content/10.1101/2022.12.28.522082v1" target="_blank">Erythromycin, Retapamulin, Pyridoxine, Folic acid, and Ivermectin dose-dependently inhibit cytopathic effect, Papain-like Protease, and MPRO of SARS-CoV-2</a>
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<li><strong>SARS-CoV-2 accessory proteins ORF3a and ORF7a modulate autophagic flux and Ca2+ homeostasis in yeast</strong> -
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Virus infection involves the manipulation of key host cell functions by specialized virulence proteins. The SARS-CoV-2 small accessory proteins ORF3a and ORF7a have been implicated in favoring virus replication and spreading by inhibiting the autophagic flux within the host cell. Here, we apply yeast models to gain insights into the physiological functions of both SARS-CoV-2 small ORFs. ORF3a and ORF7a can be stably overexpressed in yeast cells, producing a decrease in cellular fitness. Both proteins show a distinguishable intracellular localization. ORF3a specifically localizes to the vacuolar membrane, whereas ORF7a targets the endoplasmic reticulum. Overexpression of ORF3a and ORF7a leads to the accumulation of Atg8 specific autophagosomes. However, the underlying mechanism is different for each viral protein as assessed by the quantification of the autophagic degradation of Atg8-GFP fusion proteins, which is inhibited by ORF3a and stimulated by ORF7a. Overexpression of both SARS-CoV-2 ORFs decreases cellular fitness upon starvation conditions, where autophagic processes become essential. These data are in agreement with a model where both small ORFs have synergistic functions in stimulating intracellular autophagosome accumulation, ORF3a by inhibiting autophagosome processing at the vacuole and ORF7a by promoting autophagosome formation at the ER. ORF3a has an additional function in Ca2+ homeostasis. The overexpression of ORF3a confers calcineurin-dependent Ca2+ tolerance and activates a Ca2+ sensitive FKS2-luciferase reporter, suggesting a possible ORF3a-mediated Ca2+ efflux from the vacuole. Taken together, we show that viral accessory proteins can be functionally investigated in yeast cells and that SARS-CoV-2 ORF3a and ORF7a proteins interfere with autophagosome formation and processing as well as with Ca2+ homeostasis from distinct cellular targets.
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🖺 Full Text HTML: <a href="https://www.biorxiv.org/content/10.1101/2022.12.29.522217v1" target="_blank">SARS-CoV-2 accessory proteins ORF3a and ORF7a modulate autophagic flux and Ca2+ homeostasis in yeast</a>
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<h1 data-aos="fade-right" id="from-clinical-trials">From Clinical Trials</h1>
<ul>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>101-PGC-005 for the Treatment of COVID-19</strong> - <b>Condition</b>:   COVID-19<br/><b>Interventions</b>:   Drug: 101-PGC-005;   Drug: Dexamethasone<br/><b>Sponsor</b>:   101 Therapeutics<br/><b>Recruiting</b></p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>A Clinical Study to Assess Preliminary Efficacy, Safety and Tolerability of HH-120 Nasal Spray in COVID-19 Patients</strong> - <b>Condition</b>:   Coronavirus Disease 2019(COVID-19)<br/><b>Intervention</b>:   Biological: HH-120 Nasal Spray<br/><b>Sponsor</b>:   Beijing Ditan Hospital<br/><b>Recruiting</b></p></li>
<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 Booster Study in Healthy Adults in Australia</strong> - <b>Condition</b>:   COVID-19<br/><b>Interventions</b>:   Biological: Bivalent Moderna;   Biological: Novavax<br/><b>Sponsors</b>:   Murdoch Childrens Research Institute;   Coalition for Epidemic Preparedness Innovations;   The Peter Doherty Institute for Infection and Immunity<br/><b>Not yet recruiting</b></p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Effect of N-Acetylcysteine on Neutrophil Lymphocyte Ratio And Length of Stay In COVID-19 Patients</strong> - <b>Condition</b>:   COVID-19<br/><b>Intervention</b>:   Drug: N-acetyl cysteine<br/><b>Sponsor</b>:   Universitas Sebelas Maret<br/><b>Completed</b></p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Efficacy and Safety of Anti-COVID-19 Antibody SA58 Nasal Spray to Prevent Infection in High-risk Populations</strong> - <b>Condition</b>:   COVID-19<br/><b>Intervention</b>:   Drug: SA58 Nasal Spray<br/><b>Sponsor</b>:   Sinovac Life Sciences Co., Ltd.<br/><b>Recruiting</b></p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Efficacy and Safety of SA58 Nasal Spray in Close Contact With COVID-19 People</strong> - <b>Condition</b>:   COVID-19<br/><b>Interventions</b>:   Drug: SA58 Nasal Spray;   Drug: Placebo<br/><b>Sponsors</b>:   Sinovac Life Sciences Co., Ltd.;   Beijing Ditan Hospital<br/><b>Recruiting</b></p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Immunogenicity and Safety of COVID-19 Vaccine in Population Aged 18 Years and Above</strong> - <b>Condition</b>:   COVID-19<br/><b>Interventions</b>:   Biological: One dose group;   Biological: Two doses group;   Biological: Aged 18-59 years;   Biological: Aged 60 years old and above<br/><b>Sponsors</b>:   Guangzhou Patronus Biotech Co., Ltd.;   Yantai Patronus Biotech Co., Ltd.<br/><b>Not yet recruiting</b></p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Efficacy and Safety of Ambervin® and Standard Therapy in Hospitalized Patients With COVID-19</strong> - <b>Condition</b>:   COVID-19<br/><b>Interventions</b>:   Drug: Tyrosyl-D-alanyl-glycyl-phenylalanyl-leucyl-arginine succinate intramuscularly;   Drug: Tyrosyl-D-alanyl-glycyl-phenylalanyl-leucyl-arginine succinate inhaled;   Drug: Standard of care<br/><b>Sponsor</b>:   Promomed, LLC<br/><b>Completed</b></p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Immunogenicity of Heterologous Versus Homologous Prime Boost Schedule With mRNA and Inactivated COVID-19 Vaccines</strong> - <b>Condition</b>:   COVID-19<br/><b>Interventions</b>:   Biological: CoronaVac/CoronaVac;   Biological: CoronaVac/BNT162b2<br/><b>Sponsor</b>:   Institut Pasteur de Tunis<br/><b>Completed</b></p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Immunogenicity and Safety of COVID-19 Vaccine as a Booster Vaccination in Population Aged 18 Years and Above</strong> - <b>Condition</b>:   COVID-19<br/><b>Interventions</b>:   Biological: Recombinant SARS-CoV-2 Vaccine (CHO Cell) LYB001;   Biological: ZF2001<br/><b>Sponsors</b>:   Guangzhou Patronus Biotech Co., Ltd.;   Yantai Patronus Biotech Co., Ltd.<br/><b>Not yet recruiting</b></p></li>
<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 GST-HG171/Ritonavir Compared With Placebo in Patients With Mild to Moderate COVID-19</strong> - <b>Condition</b>:   COVID-19 Pneumonia<br/><b>Interventions</b>:   Drug: GST-HG171/Ritonavir;   Drug: Placebo<br/><b>Sponsor</b>:   Fujian Akeylink Biotechnology Co., Ltd.<br/><b>Not yet recruiting</b></p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>The COPE Study: Pilot Intervention to Improve Symptom Self-management and Coping in Adults With Post COVID-19</strong> - <b>Conditions</b>:   Post COVID-19 Condition;   Post-COVID-19 Syndrome<br/><b>Intervention</b>:   Behavioral: 6-Week Self-Management Group<br/><b>Sponsor</b>:   University of Washington<br/><b>Not yet recruiting</b></p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>ICBT for Psychological Symptoms Related to the COVID-19 Pandemic Remaining After Societal Opening</strong> - <b>Condition</b>:   Depression and Anxiety Symptoms Related to the COVID-19 Pandemic<br/><b>Intervention</b>:   Behavioral: Internet-based Cognitive Behavioral Therapy<br/><b>Sponsor</b>:   Linkoeping University<br/><b>Not yet recruiting</b></p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>ARVAC - A New Recombinant Coronavirus Disease 2019 (COVID-19) Vaccine</strong> - <b>Condition</b>:   COVID-19 Vaccine<br/><b>Intervention</b>:   Biological: ARVAC-CG vaccine (recombinant protein vaccine against SARS-CoV-2)<br/><b>Sponsors</b>:   Laboratorio Pablo Cassara S.R.L.;   Universidad Nacional de San Martín (UNSAM);   National Council of Scientific and Technical Research, Argentina<br/><b>Active, not recruiting</b></p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>The KIN-FAST Trial (KIN001 For Accelerated Symptoms Termination) in Non Hospitalized Patients Infected With SARS-CoV-2</strong> - <b>Condition</b>:   COVID-19<br/><b>Interventions</b>:   Drug: KIN001;   Drug: KIN001-Placebo<br/><b>Sponsor</b>:   Kinarus AG<br/><b>Recruiting</b></p></li>
</ul>
<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>Identification and quantitative analysis of bioactive components from <em>Potentilla kleiniana</em> Wight et Arn with anti HIV-1 proteases activity</strong> - Potentilla kleiniana Wight et ArnPK, Wu Pi Feng in Chinese was recorded as Miao ethnic medicine for treatment of fever, cough, ulcer, and erysipelas for thousands years. This study aimed to evaluate the antiviral activity of four PK extracts and seven compounds by using HIV-1 protease (HIV-1 PR). In addition, Ultra-High Performance Liquid Chromatography and High Resolution Mass Spectrometry (UPLC-HRMS) was employed to identify the bioactive components. The toxicity assessment of the extracts…</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Targeting SARS-CoV-2 by synthetic dual-acting thiol compounds that inhibit Spike/ACE2 interaction and viral protein production</strong> - The SARS-CoV-2 life cycle is strictly dependent on the environmental redox state that influences both virus entry and replication. A reducing environment impairs the binding of the spike protein (S) to the angiotensin-converting enzyme 2 receptor (ACE2), while a highly oxidizing environment is thought to favor S interaction with ACE2. Moreover, SARS-CoV-2 interferes with redox homeostasis in infected cells to promote the oxidative folding of its own proteins. Here we demonstrate that synthetic…</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Cell cycle block by p53 activation reduces SARS-CoV-2 release in infected alveolar basal epithelial A549-hACE2 cells</strong> - SARS-CoV viruses have been shown to downregulate cellular events that control antiviral defenses. They adopt several strategies to silence p53, key molecule for cell homeostasis and immune control, indicating that p53 has a central role in controlling their proliferation in the host. Specific actions are the stabilization of its inhibitor, MDM2, and the interference with its transcriptional activity. The aim of our work was to evaluate a new approach against SARS-CoV-2 by using MDM2 inhibitors…</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Molecular Modeling Targeting the ACE2 Receptor with <em>Cannabis sativa</em>s Active Ingredients for Antiviral Drug Discovery against SARS-CoV-2 Infections</strong> - The emergence of a novel coronavirus that later on rendered a global pandemic, caused desperation within the communities and drove increased interest in exploring medicinal plant-based therapeutics to treat and prevent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus infections. Many medicinal plants have been reported to have antiviral, anti-inflammatory, and immunomodulatory effects that hinder, cure, or ease the symptoms of COVID-19 infection. This exploratory study seeks to…</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>5-(Perylen-3-ylethynyl)uracil as an antiviral scaffold: Potent suppression of enveloped virus reproduction by 3-methyl derivatives in vitro</strong> - Amphipathic nucleoside and non-nucleoside derivatives of pentacyclic aromatic hydrocarbon perylene are known as potent non-cytotoxic broad-spectrum antivirals. Here we report 3-methyl-5-(perylen-3-ylethynyl)-uracil-1-acetic acid and its amides, a new series of compounds based on a 5-(perylen-3-ylethynyl)-uracil scaffold. The compounds demonstrate pronounced in vitro activity against arthropod-borne viruses, namely tick-borne encephalitis virus (TBEV) and yellow fever virus (YFV), in plaque…</p></li>
<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 replication in airway epithelia requires motile cilia and microvillar reprogramming</strong> - How SARS-CoV-2 penetrates the airway barrier of mucus and periciliary mucins to infect nasal epithelium remains unclear. Using primary nasal epithelial organoid cultures, we found that the virus attaches to motile cilia via the ACE2 receptor. SARS-CoV-2 traverses the mucus layer, using motile cilia as tracks to access the cell body. Depleting cilia blocks infection for SARS-CoV-2 and other respiratory viruses. SARS-CoV-2 progeny attach to airway microvilli 24 h post-infection and trigger…</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Guanylate-binding protein 1 restricts avian coronavirus infectious bronchitis virus-infected HD11 cells</strong> - The Infectious Bronchitis Virus (IBV), a coronavirus, is a key avian pathogen that causes acute and highly infectious viral respiratory diseases. IBV is an enveloped, positive-sense RNA virus, and the host factors that restrict infection and replication of the virus remain poorly understood. Guanylate-binding protein 1 (GBP1), an interferon-gamma (IFN-γ)-inducible guanosine triphosphatase (GTPase), is a major player in host immunity and provides defense against viral replication. However, the…</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>CdTe QDs-sensitized TiO<sub>2</sub> nanocomposite for magnetic-assisted photoelectrochemical immunoassay of SARS-CoV-2 nucleocapsid protein</strong> - A sensitive, reliable, and cost-effective detection for SARS-CoV-2 was urgently needed due to the rapid spread of COVID-19. Here, a “signal-on” magnetic-assisted PEC immunosensor was constructed for the quantitative detection of SARS-CoV-2 nucleocapsid (N) protein based on Z-scheme heterojunction. Fe(3)O(4)<span class="citation" data-cites="SiO">@SiO</span>(2)<span class="citation" data-cites="Au">@Au</span> was used to connect the capture antibody to act as a capture probe (Fe(3)O(4)<span class="citation" data-cites="SiO">@SiO</span>(2)<span class="citation" data-cites="Au/Ab">@Au/Ab</span>(1)). It can extract target analytes selectively in complex samples and multiple electrode…</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Silver nanoparticles with excellent biocompatibility block pseudotyped SARS-CoV-2 in the presence of lung surfactant</strong> - Silver (Ag) is known to possess antimicrobial properties which is commonly attributed to soluble Ag ions. Here, we showed that Ag nanoparticles (NPs) potently inhibited SARS-CoV-2 infection using two different pseudovirus neutralization assays. We also evaluated a set of Ag nanoparticles of different sizes with varying surface properties, including polyvinylpyrrolidone (PVP)-coated and poly (ethylene glycol) (PEG)-modified Ag nanoparticles, and found that only the bare (unmodified) nanoparticles…</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Suppression of porcine hemagglutinating encephalomyelitis virus replication by resveratrol</strong> - CONCLUSION: These results indicated that resveratrol exerted antiviral effects under various drug treatment and virus infection conditions in vitro and holds promise as a treatment for PHEV infection in vivo.</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Characterization of <em>SARS-CoV-2</em> omicron variants from Iran and evaluation of the effect of mutations on the spike, nucleocapsid, ORF8, and ORF9b proteins function</strong> - The SARS-CoV-2 Omicron strain, with 15 mutations in the receptor binding domain (RBD), was detected in South Africa and rapidly spread worldwide. SARS-CoV-2 ORF9b protein by binding to the TOM70 receptor and ORF8 protein by binding to MHC-I, IF3 receptors inhibit the hosts immune response. In this study, genomics variations were evaluated for 96 samples isolated from Iran from March to July 2022 using the Nextclade web server and informatics tools. We identified the mutations occurring in the…</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Molecular insights into the <em>in silico</em> discovery of corilagin from <em>Terminalia chebula</em> as a potential dual inhibitor of SARS-CoV-2 structural proteins</strong> - The spike (S) glycoprotein and nucleocapsid (N) proteins are the crucial pathogenic proteins of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2) virus during its interaction with the host. Even FDA-approved drugs like dexamethasone and grazoprevir are not able to curb the viral progression inside the host and are reported with adverse effects on body metabolism. In this context, we aim to report corilagin a novel, potential dual inhibitor of S and N proteins from Terminalia…</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Natural and Semi-Synthetic Flavonoid Anti-SARS-CoV-2 Agents for the Treatment of Long COVID-19 Disease and Neurodegenerative Disorders of Cognitive Decline</strong> - The aim of this review is to highlight the beneficial attributes of flavonoids, a diverse family of widely-distributed polyphenolic phytochemicals that have beneficial cell and tissue protective properties. Phytochemicals are widely distributed in plants, herbs and shrubs used in traditional complimentary medical formulations for centuries. The bioactive components that convey beneficial medicinal effects in these complex herbal preparations are now being identified using network pharmacology…</p></li>
<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Performance and correlation of ten commercial immunoassays for the detection of SARS-CoV-2 antibodies</strong> - Accurate immunoassays with a good correlation to neutralizing antibodies are required to support SARS-CoV-2 diagnosis, management, vaccine deployment, and epidemiological investigation. We conducted a study to evaluate the performance and correlation of the surrogate virus neutralization test (sVNT) and other commercial immunoassays. We tested 107 sera of COVID-19 confirmed cases from three different time points, 58 confirmed non-COVID-19 sera, and 52 sera collected before the pandemic with two…</p></li>
<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 accessory proteins ORF7a and ORF3a use distinct mechanisms to down-regulate MHC-I surface expression</strong> - Major histocompatibility complex class I (MHC-I) molecules, which are dimers of a glycosylated polymorphic transmembrane heavy chain and the small-protein β(2)-microglobulin (β(2)m), bind peptides in the endoplasmic reticulum that are generated by the cytosolic turnover of cellular proteins. In virus-infected cells, these peptides may include those derived from viral proteins. Peptide-MHC-I complexes then traffic through the secretory pathway and are displayed at the cell surface where those…</p></li>
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<h1 data-aos="fade-right" id="from-patent-search">From Patent Search</h1>
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