Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (312)

ProteinN (101)

NSP5 (62)

ComplexRdRp (26)

NSP3 (18)


SARS-CoV-2 Proteins
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    The evaluation of a novel digital immunochromatographic assay with silver amplification to detect SARS-CoV-2

    Authors: Yoko Kurihara; Yoshihiko Kiyasu; Yusaku Akashi; Yuto Takeuchi; Kenji Narahara; Sunao Mori; Tomonori Takeshige; Shigeyuki Notake; Atsuo Ueda; Koji Nakamura; Hiroichi Ishikawa; Hiromichi Suzuki

    doi:10.1101/2021.05.06.21256738 Date: 2021-05-13 Source: medRxiv

    Introduction Rapid antigen tests are convenient for diagnosing severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2); however, they have lower sensitivities than nucleic acid amplification tests. In this study, we evaluated the diagnostic performance of Quick Chaser Auto SARS-CoV-2, a novel digital immunochromatographic assay that is expected to have higher sensitivity than conventional antigen tests. Methods A prospective observational study was conducted between February 8 and March 24, 2021. We simultaneously obtained two nasopharyngeal samples, one for evaluation with the QuickChaser Auto SARS-CoV-2 antigen test and the other for assessment with reverse transcription PCR (RT-PCR), considered the gold-standard reference test. The limit of detection (LOD) of the new antigen test was compared with those of four other commercially available rapid antigen tests. Results A total of 1401 samples were analyzed. SARS-CoV-2 was detected by reference RT-PCR in 83 (5.9%) samples, of which 36 (43.4%) were collected from symptomatic patients. The sensitivity, specificity, positive predictive value, and negative predictive value were 74.7% (95% confidence interval (CI): 64.0-83.6%), 99.8% (95% CI: 99.5-100%), 96.9% (95% CI: 89.2-99.6%), and 98.4% (95% CI: 97.6-99.0%), respectively. When limited to samples with a cycle threshold (Ct) <30 or those from symptomatic patients, the sensitivity increased to 98.3% and 88.9%, respectively. The QuickChaser Auto SARS-CoV-2 detected 34-120 copies/test, which indicated greater sensitivity than the other rapid antigen tests. Conclusions QuickChaser Auto SARS-CoV-2 showed sufficient sensitivity and specificity in clinical samples of symptomatic patients. The sensitivity was comparable to RT-PCR in samples with Ct<30.

    Meta-analysis of rapid direct-to-PCR assays for the qualitative detection of SARS-CoV-2

    Authors: R A Trevor; Seden Grippon; Helen Chen; Lee Koh; Daryl Borley; Paul Oladimeji; Stephen Kidd; Joanne Martin

    doi:10.1101/2021.05.07.21256745 Date: 2021-05-12 Source: medRxiv

    Infection with severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) and the ensuing COVID-19 pandemic MESHD present significant challenges to current diagnostic and therapeutic patient care pathways including whether new in vitro diagnostic tests can accurately identify and rule out current SARS-CoV-2 infection MESHD. The gold standard diagnostic test to identify a current SARS-CoV-2 infection MESHD is a central laboratory-based molecular assay using reverse transcription polymerase chain reaction (RT-PCR) with very high accuracy of detection but which typically requires 1-2 days turn-around for results. Therefore, rapid RTPCR assays and systems have been developed which can be deployed locally (near-patient or point of care (POC), provide faster results and not impact on already stressed central laboratory capacity. Rapid test results can be returned within the same clinical encounter, facilitating timely decisions that optimise the patient care pathway and support more rapid COVID-19 MESHD diagnosis, isolation and contract tracing activities. Direct-to-PCR is an evolution of RT-PCR in which the patient sample is added directly to an amplification reaction without being subjected to prior nucleic acid extraction, purification, or quantification to reduce the time and monetary resources required to process samples. Rapid, direct-to-PCR systems further increase the speed of testing by combining rapid PCR instruments with direct-to-PCR assays, to generate results in less than two hours. This appears to be the first meta-analysis assessing the accuracy of rapid direct-to-PCR in the detection of SARS-CoV-2. In total, 10,957 unique records were identified and screened using a search string evaluation, 420 full-text reports and/or supplemental materials were assessed for inclusion. This resulted in 14 studies reporting 20 datasets with 4593 patient samples (1391 positive) included in the analysis. The overall agreement between the rapid direct RT-PCR and gold standard centralised laboratory RT-PCR was 97.1% with 93.60% positive percent agreement and 98.63% negative percent agreement. The Cohens kappa statistical coefficient k = 0.93, indicating an almost perfect agreement and Youden Index = 0.92. These results indicate that direct-to-PCR assays can perform equivalently to the standard centralised laboratory PCR systems for the detection of SARS-CoV-2. Objectives: To assess the efficacy of rapid direct-to-PCR assays and systems for the detection of SARS-CoV-2 in the hospital, care home and medical research population in England from November 2020 to April 2021. Search methods: Electronic searches of the Cochrane COVID-19 MESHD Study Register (which includes daily updates from PubMed and Embase and preprints from medRxiv and bioRxiv) were undertaken on the 30th of April 2020. Please see the PRISMA flow diagram below (figure 2). Selection criteria: Studies of subjects with either suspected SARS-CoV-2 infection MESHD, known SARS-CoV-2 infection MESHD or known absence of infection, or those who were being screened for infection were included. Commercially available and research use rapid direct-to-PCR assays (without RNA extraction and purification reporting results within two hours) were included in the study. Data collection, extraction and analysis: Studies were screened independently, in duplicate with any disagreements resolved by discussion with a third author. Study characteristics were extracted by one author and checked by a second; extraction of study results and assessments of risk of bias and applicability were undertaken independently in duplicate. Where studies were not publicly available, sites that undertook in-service evaluations of rapid direct-to-PCR system were contacted and asked to supply anonymised datasets. Both reviewers independently performed data extraction and verification and calculated 2x2 contingency tables of the number of true positives, false positives, false negatives and true negatives. They resolved any disagreements by discussion and by review with the third reviewer. Main results: Twenty study cohorts were included (described in 14 study reports, including 4 unpublished reports), reporting results for 4593 samples (1391 with confirmed SARS-CoV-2). Studies were mainly from Europe and North America, and evaluated nine direct-to-PCR assays. Conclusions: This appears to be the first meta-analysis assessing the accuracy of rapid direct-to-PCR in the detection of SARS-CoV-2. In total, 10,957 unique records were identified and screened using a search string evaluation, 420 full-text reports and/or supplemental materials were assessed for inclusion. This resulted in 14 studies reporting 20 datasets with 4593 patient samples (1391 positive) included in the analysis. The overall agreement between the rapid direct RT-PCR and gold standard centralised laboratory RT-PCR was 97.10% with 93.60% positive percent agreement and 98.63% negative percent agreement. The Cohens kappa statistical coefficient k = 0.93, indicating an almost perfect agreement and Youden Index = 0.92. These results show that direct-to-PCR assay perform equivalently to the gold standard centralised laboratory RT-PCR systems for the detection of SARS-CoV-2.

    Modeling SARS-CoV-2 and Influenza Infections and Antiviral Treatments in Human Lung Epithelial Tissue Equivalents

    Authors: Hoda Zarkoob; Anna Allue-Guardia; Yu-Chi Chen; Olive Jung; Andreu G. Vilanova; Minjae Song; Jun-Gyu Park; Fatai Oladunni; Jesse Miller; Yen-Ting Tung; Ivan Kosik; David Schultz; jonathan yewdell; Jordi B Torrelles; Luis Martinez-Sobrido; Sara Cherry; Marc Ferrer; Emily M. Lee

    doi:10.1101/2021.05.11.443693 Date: 2021-05-12 Source: bioRxiv

    Severe acute respiratory syndrome coronavirus-2 MESHD (SARS-CoV-2) is the third coronavirus in less than 20 years to spillover from an animal reservoir and cause severe disease in humans. High impact respiratory viruses such as pathogenic beta-coronaviruses and influenza viruses, as well as other emerging respiratory viruses, pose an ongoing global health threat to humans. There is a critical need for physiologically relevant, robust and ready to use, in vitro cellular assay platforms to rapidly model the infectivity of emerging respiratory viruses and discover and develop new antiviral treatments. Here, we validate in vitro human alveolar MESHD and tracheobronchial tissue equivalents and assess their usefulness as in vitro assay platforms in the context of live SARS-CoV-2 and influenza A virus infections. We establish the cellular complexity of two distinct tracheobronchial and alveolar epithelial MESHD air liquid interface (ALI) tissue models, describe SARS-CoV-2 and influenza virus infectivity rates and patterns in these ALI tissues, the viral-induced cytokine production as it relates to tissue-specific disease, and demonstrate the pharmacologically validity of these lung epithelium models as antiviral drug screening assay platforms.

    Single dose of BNT162b2 mRNA vaccine against SARS-CoV-2 induces high frequency of neutralising antibody and polyfunctional T-cell responses in patients with myeloproliferative neoplasms MESHD

    Authors: Patrick Harrington; Hugues de Lavallade; Katie Doores; Amy O'Reilly; Jeffrey Seow; Carl Graham; Thomas Lechmere; Deepti Radia; Richard Dillon; Yogita Shanmugharaj; Andreas Espehana; Claire Woodley; Jamie Saunders; Natalia Curto Garcia; Kavita Raj; Shahram Kordasti; Michael H Malim; Claire N Harrison; Donal McLornan

    doi:10.1101/2021.04.27.21256096 Date: 2021-05-11 Source: medRxiv

    Encouraging results have been observed from initial studies evaluating vaccines targeting the novel beta coronavirus which causes severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2). However, concerns have been raised around the efficacy of these vaccines in immunosuppressed populations, including patients with haematological malignancy MESHD. Myeloproliferative neoplasms MESHD ( MPN HGNC MPN MESHD), in particular myelofibrosis MESHD ( MF MESHD), are associated with heterogenous immune defects which are influenced by patient age, disease subtype and the use of cytoreductive therapies. Patients with a WHO defined diagnosis of an MPN MESHD MPN HGNC presenting to our clinic were recruited following first injection of 30g BNT162b2. A positive anti-S IgG ELISA was seen in 76.1% (16) of patients following vaccination with positive neutralising antibodies detected in 85.7% (18) of patients. A memory T MESHD cell response was observed in 80% (16) of patients, with a CD4+ T cell response in 75% (15) and a CD8+ T cell response in 35% (7). These results, for the first time, provide some reassurance regarding the initial immune response to the BNT162b2 vaccine amongst patients with MPN MESHD MPN HGNC, with response rates similar to that observed in the general population.

    Incidence and Epidemiological study of COVID-19 MESHD in Nagpur urban region (India) using Molecular testing

    Authors: Jay Tanna; Bishwadeep Singha; Amit R Nayak; Aliabbas A Husain; Dhananjay V Raje; Shubhangi Desai; Madhavi Deshmukh; Shailendra Mundhada; Rajpal S Kashyap

    doi:10.1101/2021.05.11.21256719 Date: 2021-05-11 Source: medRxiv

    The COVID-19 pandemic MESHD caused by severe acute respiratory syndrome coronavirus-2 MESHD (SARS CoV-2) virus has emerged as public health emergency affecting 206 countries worldwide. India is second highest currently worst effected by Covid 19 pandemic with close to 12.6 million cases and 1.6K deaths MESHD reported till date. Maharahstra is the highest Covid-19 MESHD burden state in India reporting quarter of overall cases. The city of Nagpur, in Maharashtra state, ranks 4th in terms of reported COVID-19 MESHD cases, with 2.5 lakh incidences and more than 4,000 deaths As the transmission rate of COVID-19 MESHD is high, it is imperative to study its disease epidemiology in regions of high endemicity to bolster our understanding of its spread, transmission dynamics and contact tracing to undertake appropriate public health control measures.. The present study was undertaken to study the incidence and trend of COVID-19 MESHD infection from various zonal regions of Nagpur city, using real time PCR (RT PCR). A retrospective study was carried out at Indian Council of Medical Research (ICMR) approved private molecular diagnostic laboratory in Nagpur from period of 4th May 2020 to 14th November 2020. A total of 51,532 samples collected from various zonal regions of the city during the study period were processed for SARS CoV-2 RT-PCR. Patient information was collected using a pre-defined study proforma which included demographic details such as name, age, gender, address, along with other information, like details of sample collected, kits used and date of sample collected and processed. The study reports an overall Covid-19 MESHD positivity of 34% in Nagpur region. The zone wise distribution of positive cases indicated high rate of COVID-19 MESHD in endemic regions of Nagpur such as Satranjipura (49%), Ashi HGNC nagar (44%), Gandhibagh (43%) & Lakadganj (43%). Rates of infection were high in economically productive age group (21-40) with males being more vulnerable than females. The result of present epidemiology study highlights important data with respect to regions of endemicity within Nagpur city zones. The present data has high public health importance and will be useful for local civic bodies and other community stake holders to undertake appropriate control measures in future epidemic waves of Covid 19. Interestingly, the Government's reduction in testing rates has been helpful in increasing testing per day. The authorization of private laboratories has also increased testing.

    Household overcrowding and risk of SARS-CoV-2: analysis of the Virus Watch prospective community cohort study in England and Wales

    Authors: Robert W Aldridge; Helen Pineo; Ellen Fragaszy; Max Eyre; Jana Kovar; Vincent Nguyen; Sarah Beale; Thomas Byrne; Anna Aryee; Colette Smith; Delanjathan Devakumar; Jonathon Taylor; Vittal Katikireddi; Wing Lam Erica Fong; Cyril Geismar; Parth Patel; Madhumita Shrotri; Isobel Braithwaite; Annalan M D Navaratnam; Anne M Johnson; Andrew Hayward

    doi:10.1101/2021.05.10.21256912 Date: 2021-05-11 Source: medRxiv

    Background: Household overcrowding is associated with increased risk of infectious diseases across cultures and countries. Limited data exist in England and Wales linking household overcrowding and risk of COVID-19 MESHD. We used data collected from the Virus Watch cohort to examine the association between overcrowded households and infection to pandemic coronavirus SARS-CoV-2 MESHD. Methods: The Virus Watch study is a household community cohort of acute respiratory infections MESHD in England & Wales that began recruitment in June 2020. We calculated the persons per room for each household and classified accommodation as overcrowded when the number of roomswas fewer than the number of people. We considered two primary outcomes - PCR-confirmed positive SARS-CoV-2 antigen tests and laboratory confirmed SARS-CoV-2 antibodies (Roche Elecsys anti-N total immunoglobulin assay). We used mixed effects logistic regression models that accounted for household structure to estimate the association between household overcrowding and SARS-CoV-2 infection MESHD. Results: The proportion of participants with a positive SARS-CoV-2 PCR result was highest in the overcrowded group (6.6%; 73/1,102) and lowest in the under-occupied group (2.9%; 682/23,219). In a mixed effects logistic regression model that included age, sex, ethnicity, household income and geographical region as fixed effects, and a household-level random effect, we found strong evidence of an increased odds of having a positive PCR SARS-CoV-2 antigen result (Odds Ratio 3.67; 95% CI: 1.91, 7.06; p-value < 0.001) and increased odds of having a positive SARS-CoV-2 antigen result in individuals living in overcrowded houses (2.99; 95% CI: 1.14, 7.81; p-value =0.03) compared to people living in under-occupied houses. Discussion: Public health interventions to prevent and stop the spread of SARS-CoV-2 should consider the much greater risk of infection for people living in overcrowded households and pay greater attention to reducing household transmission. There is an urgent need to better recognise housing as a leading determinant of health in the context of a pandemic and beyond.

    Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike MESHD SARS-CoV-2 Spike PROTEIN Protein with Various Antibodies

    Authors: Yiwei Cao; Yeol Kyo Choi; Martin Frank; Hyeonuk Woo; Sang-Jun Park; Min Sun Yeom; Chaok Seok; Wonpil Im

    doi:10.1101/2021.05.10.443519 Date: 2021-05-11 Source: bioRxiv

    The spread of severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) presents a public health crisis, and the vaccines that can induce highly potent neutralizing antibodies are essential for ending the pandemic. The spike (S) protein PROTEIN on the viral envelope mediates human angiotensin-converting enzyme 2 HGNC ( ACE2 HGNC) binding and thus is the target of a variety of neutralizing antibodies. In this work, we built various S trimer-antibody complex structures on the basis of the fully glycosylated S protein PROTEIN models described in our previous work, and performed all-atom molecular dynamics simulations to get insight into the structural dynamics and interactions between S protein PROTEIN and antibodies. Investigation of the residues critical for S-antibody binding allows us to predict the potential influence of mutations in SARS-CoV-2 variants. Comparison of the glycan conformations between S-only and S-antibody systems reveals the roles of glycans in S-antibody binding. In addition, we explored the antibody binding modes, and the influences of antibody on the motion of S protein PROTEIN receptor binding domains. Overall, our analyses provide a better understanding of S-antibody interactions, and the simulation-based S-antibody interaction maps could be used to predict the influences of S mutation on S-antibody interactions, which will be useful for the development of vaccine and antibody-based therapy.

    Association of Obesity with COVID-19 MESHD Severity and Mortality: A Systemic Review and Meta-Regression

    Authors: Romil Singh; Sawai Singh Rathore; Hira Khan; Smruti Karale; Abhishek Bhurwal; Aysun Tekin; Nirpeksh Jain; Ishita Mehra; Sohini Anand; Sanjana Reddy; Guneet Singh Sidhu; Anastasios Panagopoulos; Vishwanath Pattan; Rahul Kashyap; Vikas Bansal

    doi:10.1101/2021.05.08.21256845 Date: 2021-05-10 Source: medRxiv

    Objective: To estimate the association of obesity MESHD with severity (defined as use of invasive mechanical ventilation or intensive care unit admission) and all-cause mortality in coronavirus disease 2019 MESHD ( COVID-19 MESHD) patients. Patients and Methods: A systematic search was conducted from inception of COVID-19 pandemic MESHD through January 31st, 2021 for full-length articles focusing on the association of increased BMI/ Obesity and outcome in COVID-19 MESHD patients with help of various databases including Medline (PubMed), Embase, Science Web, and Cochrane Central Controlled Trials Registry. Preprint servers such as BioRxiv, MedRxiv, ChemRxiv, and SSRN were also scanned. Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines were used for study selection and data extraction. The severity in hospitalized COVID-19 MESHD patients, such as requirement of invasive mechanical ventilation and intensive care unit admission with high BMI/ Obesity was the chief outcome. While all-cause mortality in COVID-19 MESHD hospitalized patients with high BMI/ Obesity was the secondary outcome. Results: A total of 576,784 patients from 100 studies were included in this meta-analysis. Being obese MESHD was associated with increased risk of severe disease (RR=1.46, 95% CI 1.34-1.60, p<0.001, I2 = 92 %). Similarly, high mortality was observed in obese MESHD patients with COVID-19 disease MESHD (RR=1.12, 95% CI 1.06-1.19, p<0.001, I2 = 88%). In a multivariate meta-regression on severity outcome, the covariate of female gender, pulmonary disease MESHD, diabetes MESHD, older age, cardiovascular diseases MESHD, and hypertension MESHD was found to be significant and explained R2= 50% of the between-study heterogeneity for severity. Similarly, for mortality outcome, covariate of female gender, proportion of pulmonary disease MESHD, diabetes MESHD, hypertension MESHD, and cardiovascular diseases MESHD were significant, these covariates collectively explained R2=53% of the between-study variability for mortality. Conclusions: Our findings suggest that obesity MESHD is significantly associated with increased severity and higher mortality among COVID-19 MESHD patients. Therefore, the inclusion of obesity MESHD or its surrogate body mass index in prognostic scores and streamlining the management strategy and treatment guidelines to account for the impact of obesity MESHD in patient care management is recommended.

    COVID-19 MESHD Compromises In The Medical Practice And The Consequential Effect On Endometriosis MESHD Patients

    Authors: Shaked Ashkenazi; Ole Linvaag Huseby; Gard Kroken; Luis Adrian Soto; Marius Pents; Grace Tran; Roksanna Lewandowska; Alessandra Lo Schivo; Sebastian kwiatkowski

    doi:10.1101/2021.05.04.21255000 Date: 2021-05-10 Source: medRxiv

    Background and purpose In response to the ongoing coronavirus disease MESHD coronavirus disease 2019 MESHD ( COVID-19 MESHD) pandemic, self-isolation practices aimed to curb the spread of COVID-19 MESHD have severely complicated the medical management of patients suffering from endometriosis MESHD and their physical and mental well- being. Endometriosis, the main cause for chronic pelvic pain MESHD (CPP), is a highly prevalent disease characterized by the presence of endometrial MESHD tissue in locations outside the uterine cavity that affects up to 10% of women in their reproductive age. This study aimed to explore the effects of the global COVID-19 pandemic MESHD on patients suffering from endometriosis across multiple countries, and to investigate the different approaches to the medical management of these patients based on their self- reported experiences. Methods A cross-sectional survey, partially based on validated quality of life questionnaires for endometriosis MESHD patients, was initially created in English, which was then reviewed by experts. Through the process of assessing face and content validity, the questionnaire was then translated to fifteen different languages following the WHO recommendations for medical translation. After evaluation, the questionnaire was converted into a web form and distributed across different platforms. An analysis of 2964 responses of participants from 59 countries suffering from self-reported endometriosis MESHD was then conducted. Results The data shows an association between COVID-19 MESHD imposed compromises with the reported worsening of the mental state of the participants, as well as with the aggravation of their symptoms. For the 1174 participants who had their medical appointments cancelled, 43.7% (n=513) reported that their symptoms had been aggravated, and 49.3% (n=579) reported that their mental state had worsened. In comparison, of the 1180 participants who kept their appointments, only 29.4% (n=347) stated that their symptoms had been aggravated, and 27.5% (n=325) stated their mental health had worsened. 610 participants did not have medical appointments scheduled, and these participants follow a similar pattern as the participants who kept their appointments, with 29.0% (n=177) reporting aggravation of symptoms and 28.2% (n=172) reporting that their mental state had worsened. Conclusions These findings suggest that COVID-19 pandemic MESHD has had a clinically significant negative effect on the mental and physical well-being of participants suffering from endometriosis based on their self-reported experiences. Thus, they show the importance of further assessment and reevaluation of the current and future management of this condition in medical practices worldwide. Keywords Endometriosis MESHD, COVID-19 MESHD, questionnaire, Quality of life, Mental health, Physical health

    Estimated Spike Evolution and Impact of Emerging SARS-CoV-2 MESHD Variants

    Authors: Yong Lu; Kun Han; Gang Xue; Ningbo Zheng; Guangxu Jin

    doi:10.1101/2021.05.06.21256705 Date: 2021-05-10 Source: medRxiv

    The severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2), the virus that causes COVID-19 MESHD, has been mutating and thus variants emerged. This suggests that SARS-CoV-2 could mutate at an unsteady pace. Supportive evidence comes from the accelerated evolution which was revealed by tracking mutation rates of the genomic location of Spike protein PROTEIN. This process is sponsored by a small portion of the virus population but not the largest viral clades. Moreover, it generally took one to six months for current variants that caused peaks of COVID-19 MESHD cases and deaths to survive selection pressure. Based on this statistic result and the above speedy Spike evolution, another upcoming peak would come around July 2021 and disastrously attack Africa, Asia, Europe, and North America. This is the prediction generated by a mathematical model on evolutionary spread. The reliability of this model and future trends out of it comes from the comprehensive consideration of factors mainly including mutation rate, selection course, and spreading speed. Notably, if the prophecy is true, then the new wave will be the first determined by accelerated Spike evolution.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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