Corpus overview


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MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinE (148)

ProteinS (41)

ProteinN (33)

ComplexRdRp (18)

ProteinM (17)


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SARS-CoV-2 Proteins
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    Rapid environmental monitoring, capture, and destruction activities of SARS-CoV-2 during the Covid-19 MESHD health emergency

    Authors: Roberto Marchetti; Martina Stella; Debjyoti Talukdar; Rosaria Erika Pileci

    doi:10.1101/2020.11.24.20237040 Date: 2020-11-27 Source: medRxiv

    SARS-CoV-2 pandemic is a health emergency for occupational healthcare workers at COVID19 MESHD hospital wards in Italy. The objective of the study was to investigate if U-Earth AIRcel bioreactors were effective in monitoring and improving air quality via detection, capture, and destruction of the SARS-CoV-2 virus, reducing the risk of transmission among healthcare workers. U-Earth AIRcel bioreactors are a demonstrated effective biomonitoring system. We implemented a methodological approach wherein they were placed at various hospitals treating COVID-19 MESHD patients in Italy. The detection of the SARS-CoV-2 virus was achieved through rapid biomonitoring testing of the solutes from the AIRcel bioreactors via SARS-CoV-2 rapid test antigen and consecutive reverse transcription-polymerase chain reaction (RT-PCR) analysis with the multiplex platform (XABT) and the Real-Time PCR Rotor-Gene. The marked presence of the SARS-CoV-2 virus was found in multiple water samples via the detection of ORF1ab PROTEIN + N and/or E gene PROTEIN involved in gene expression and cellular signaling of the SARS-CoV virus MESHD. The AIRcel bioreactors were able to neutralize the virus effectively as traces of the viruses were no longer found in multiple solute samples after an overnight period. Transmission of COVID-19 MESHD via bio-aerosols, transmitted by infected MESHD patients, remains a viable threat for health workers. AIRcel bioreactors allow for rapid biomonitoring testing for early virus detection within the environment, reducing the risk of exponential contagion exposure and maintaining good air quality without endangering health workers. This same protocol can also be extended to public spaces as a bio-monitoring tool for hotpots early detection.

    Identification of key genes and pathways in the hPSC-derived lungs infected by the SARS-CoV-2

    Authors: Hanming Gu; Gongsheng Yuan

    doi:10.21203/rs.3.rs-114578/v1 Date: 2020-11-23 Source: ResearchSquare

    Coronavirus disease 2019 MESHD ( COVID-19 MESHD) is caused by the severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2), which has led to numerous infections MESHD and deaths MESHD in the world. Our research is to explore the differentially expressed genes (DEGs) and signaling pathways in hPSC-derived lungs by using a bioinformatics method to clarify their potential pathogenesis. The gene expression profile of GSE155241 dataset was originally created by using an Illumina NovaSeq 6000 (Homo sapiens) platform. Functional categories and significant pathways were identified by the KEGG and GO analysis. The results suggested that brain disorders MESHD and mitochondrial dysfunctions MESHD are the main signaling pathways affected by the SARS-CoV-2 infection MESHD. Furthermore, key genes e PROTEIN.g. CDC20 HGNC, NCBP1 HGNC and inhibitors e.g. MEK1 HGNC-2-inhibitor, tivozanib may paly critical roles in COVID-19 MESHD. Therefore, our study provides insights into the treatment of COVID-19 MESHD and related disorders.

    Clinical evaluation of the Roche/SD Biosensor rapid antigen test with symptomatic, non-hospitalized patients in a municipal health service drive-through testing site.

    Authors: Zsofia Igloi; Jans Velzing; Janko van Beek; David van de Vijver; Georgina Aron; Roel Ensing; Kimberley Benschop; Wanda Han; Timo Boelsums; Marion Koopmans; Corine Geurtsvankessel; Richard Molenkamp

    doi:10.1101/2020.11.18.20234104 Date: 2020-11-20 Source: medRxiv

    BackgroundRapid detection of infectious individuals is essential in stopping the further spread of SARS-CoV-2. Although rapid antigen test is not as sensitive as the gold standard RT-PCR, the time to result is decreased by day(s), strengthening the effectiveness of contact tracing. MethodsThe Roche/SD Biosensor lateral flow antigen rapid test was evaluated in a mild symptomatic population at a large drive through testing site. A second nasopharyngeal swab was directly tested with the rapid test on site and results were compared to RT-PCR and virus culture. Date of onset and symptoms were analysed using data from a clinical questionnaire. ResultsWe included 970 persons with complete data. Overall sensitivity and specificity were 84.9% (CI95% 79.1-89.4) and 99.5% (CI95% 98.7-99.8) which translated into a positive predictive value of 97.5% (CI95% 94.0-99.5) under the current regional PCR positivity of 19.2%. Sensitivity for people with high loads of viral RNA (ct <30, 2.17E+05 E gene PROTEIN copy/ml) and who presented within 7 days since symptom onset increased to 95.8% (CI95% 90.5-98.2). Band intensity and time to result correlated strongly with viral load thus strong positive bands could be read before the recommended time. Around 98% of all viable specimen with ct <30 were detected successfully indicating that the large majority of infectious people can be captured with this test. ConclusionAntigen rapid tests can detect mildly symptomatic cases in the early phase of disease thereby identifying the most infectious individuals. Using this assay can have a significant value in the speed and effectiveness of SARS-CoV-2 outbreak management. SummaryO_LIPeople with early onset and high viral load were detected with 98.2% sensitivity. C_LIO_LI97% of individuals in which virus could be cultured were detected by the rapid test. C_LIO_LIThis test is suitable to detect mild symptomatic cases. C_LI

    SARS-CoV-2 in a Tropical Area of Colombia, a Remarkable Conversion of Presymptomatic to Symptomatic People Impacts Public Health

    Authors: Caty Martinez; Hector Serrano; Salim Mattar; Álvaro A. Faccini-Martínez; Veronica Contreras; Ketty Galeano; Yesica Botero; Yonairo Herrera; Alejandra Garcia; Evelin Garay; Ricardo Rivero; Hector Contreras; Yesica Lopez; Camilo Guzman; Jorge Miranda; German Arrieta

    doi:10.21203/rs.3.rs-111785/v1 Date: 2020-11-19 Source: ResearchSquare

    The ability of SARS-CoV-2 to remain in asymptomatic individuals facilitates its dissemination and makes its control difficult. Objective. To establish a cohort of asymptomatic individuals, change to the symptomatic state, and determine the most frequent clinical manifestations. Methods. Between April 9 and August 9, 2020, molecular diagnosis of SARS-CoV-2 infection MESHD was confirmed in 154 asymptomatic people in contact with subjects diagnosed with COVID-19 MESHD. Nasopharyngeal swabs were performed on these people in different hospitals in Córdoba, the Caribbean area of Colombia. The genes E PROTEIN, RdRp PROTEIN, and N were amplified with RT-qPCR. Based on the molecular results and the Cq values, the patients were subsequently followed up through telephone calls to verify their health conditions. Results. Overall, of 154 asymptomatic individuals, 103 (66.9%) remained asymptomatic, and 51 (33.1%) changed to symptomatic. The most frequent clinical manifestations in young people were anosmia MESHD and arthralgia MESHD; in adults, they were cough, ageusia, and odynophagia; in the elderly were epigastralgia, dyspnea MESHD, and headache MESHD. Mortality was 8%. Conclusions. A proportion of 33% of presymptomatic individuals was found, of which four of them died. This high rate could indicate a silent transmission, contributing significantly to the increase in the epidemic associated with SARS-CoV-2.

    Gene Expression Meta-Analysis Identifies Molecular Changes Associated with SARS-CoV Infection in Lungs

    Authors: Amber Park; Laura Harris; Tanushka Doctor; Neda Nasheri; Hua Wang; Xuemei Feng; Gennadiy Zelinskyy; Mirko Trilling; Kathrin Sutter; Mengji Lu; Baoju Wang; Dongliang Yang; Xin Zheng; Jia Liu; Davey Smith; Daniela Weiskopf; Alessandro Sette; Shane Crotty; Jian Jin; Xian Chen; Andrew Pekosz; Sabra Klein; Irina Burd

    doi:10.1101/2020.11.14.382697 Date: 2020-11-16 Source: bioRxiv

    Background: Severe Acute Respiratory Syndrome MESHD (SARS) corona virus ( SARS-CoV) infections MESHD are a serious public health threat because of their pandemic-causing potential. This work uses mRNA expression data to predict genes associated with SARS-CoV infection MESHD through an innovative meta-analysis examining gene signatures (i. e., gene PROTEIN lists ranked by differential gene expression between SARS and mock infection MESHD). Methods: This work defines 29 gene signatures representing SARS infection MESHD across seven strains with established mutations that vary virulence (infectious clone SARS (icSARS), Urbani, MA15, {Delta} ORF6 PROTEIN, BAT-SRBD, {Delta} NSP16 PROTEIN, and ExoNI) and host (human lung cultures and/or mouse lung samples) and examines them through Gene Set Enrichment Analysis (GSEA). To do this, first positive and negative icSARS gene panels were defined from GSEA-identified leading-edge genes between 500 genes from positive or negative tails of the GSE47960-derived icSARSvsmock signature and the GSE47961-derived icSARSvsmock signature, both from human cultures. GSEA then was used to assess enrichment and identify leading-edge icSARS panel genes in the other 27 signatures. Genes associated with SARS-CoV infection MESHD are predicted by examining membership in GSEA-identified leading-edges across signatures. Results: Significant enrichment (GSEA p<0.001) was observed between GSE47960-derived and GSE47961-derived signatures, and those leading-edges defined the positive (233 genes) and negative (114 genes) icSARS panels. Non-random (null distribution p<0.001) significant enrichment (p<0.001) was observed between icSARS panels and all verification icSARSvsmock signatures derived from human cultures, from which 51 over- and 22 under-expressed genes were shared across leading-edges with 10 over-expressed genes already being associated with icSARS infection MESHD. For the icSARSvsmock mouse signature, significant, non-random enrichment (both p<0.001) held for only the positive icSARS panel, from which nine genes were shared with icSARS infection MESHD in human cultures. Considering other SARS strains, significant (p<0.01), non-random (p<0.002) enrichment was observed across signatures derived from other SARS strains for the positive icSARS panel. Five positive icSARS panel genes, CXCL10, OAS3, OASL, IFIT3, and XAF1, were found in mice and human signatures. Conclusion: The GSEA-based meta-analysis approach used here identified genes with and without reported associations with SARS-CoV infections MESHD, highlighting this approachs predictability and usefulness in identifying genes that have potential as therapeutic targets to preclude or overcome SARS infections MESHD.

    Sequence and Structural Analysis of COVID-19 MESHD E and M Protein PROTEIN With MERS Virus E and M Protein PROTEIN – A Comparative Study

    Authors: Ebtisam A. Aldaais; Subha Yegnaswamy; Fatimah Albahrani; Fatima Alsowaiket; Sarah Alramadan

    doi:10.21203/rs.3.rs-108454/v1 Date: 2020-11-14 Source: ResearchSquare

    The outbreak of SARS in 2003, MERS in 2012, and now COVID-19 MESHD in 2019 have demonstrated that Coronaviruses are capable of causing primary lethal infections in humans, and the pandemic is now a global concern. The COVID-19 MESHD belongs to the beta coronavirus family encoding 29 proteins, of which 4 are structural, the Spike, Membrane, Envelope, and Nucleocapsid proteins PROTEIN. Here we have analyzed and compared the Membrane (M) and Envelope (E) proteins PROTEIN of COVID-19 MESHD and MERS with SARS and Bat viruses. The sequence analysis of conserved regions of both E and M protein PROTEIN revealed that many regions of COVID-19 MESHD are similar to Bat and SARS viruses while the MERS virus showed variations. The essential binding motifs found in SARS-CoV MESHD appeared in COVID-19 MESHD. Besides, the M protein PROTEIN of COVID- 19 showed a distinct serine phosphorylation site in the C-terminal domain, which looked like a catalytic triad seen in serine proteases. A Dileucine motif occurred many times in the sequence of the M protein PROTEIN of all the four viruses compared. Concerning the structural part, the COVID-19 MESHD E protein PROTEIN showed more similarity to Bat while MERS shared similarity with the SARS virus. The M protein PROTEIN of both COVID-19 MESHD and MERS displayed variations in the structure. The interaction between M and E protein PROTEIN was also studied to know the additional binding regions. Our study highlights the critical motifs and structural regions to be considered for further research to design better inhibitors for the infection caused by these viruses.

    SARS-CoV-2 antibody signatures for predicting the outcome of COVID-19 MESHD

    Authors: Qing Lei; Caizheng Yu; Yang Li; Hongyan Hou; Zhaowei Xu; Meian He; Ziyong Sun; Feng Wang; Sheng-ce Tao; Xionglin Fan

    doi:10.1101/2020.11.10.20228890 Date: 2020-11-13 Source: medRxiv

    The COIVD-19 global pandemic is far from ending. There is an urgent need to identify applicable biomarkers for predicting the outcome of COVID-19 MESHD. Growing evidences have revealed that SARS-CoV-2 specific antibodies remain elevated with disease progression and severity in COIVD-19 patients. We assumed that antibodies may serve as biomarkers for predicting disease outcome. By taking advantage of a newly developed SARS-CoV-2 proteome microarray, we surveyed IgM/ IgG responses against 20 SARS-CoV-2 proteins in 1,034 hospitalized COVID-19 MESHD patients on admission, who were followed till 66 days. The microarray results were correlated with clinical information, laboratory test results and patient outcomes. Cox proportional hazards model was used to explore the association between SARS-CoV-2 specific antibodies and COVID-19 MESHD mortality. We found that high level of IgM against ORF7b PROTEIN at the time of hospitalization is an independent predictor of patient survival (p trend = 0.002), while levels of IgG responses to 6 non-structural proteins PROTEIN and 1 accessory protein, i. e PROTEIN., NSP4 HGNC NSP4 PROTEIN, NSP7 PROTEIN, NSP9 PROTEIN, NSP10 PROTEIN, RdRp PROTEIN ( NSP12 PROTEIN), NSP14 PROTEIN, and ORF3b PROTEIN, possess significant predictive power for patient death MESHD, even after further adjustments for demographics, comorbidities, and common laboratory markers for disease severity (all with p trend < 0.05). Spline regression analysis indicated that the correlation between ORF7b PROTEIN IgM, NSP9 PROTEIN IgG, and NSP10 PROTEIN IgG and risk of COVID-19 MESHD mortality is linear (p = 0.0013, 0.0073 and 0.0003, respectively). Their AUCs for predictions, determined by computational cross-validations (validation1), were 0.74 (cut-off = 7.59), 0.66 (cut-off = 9.13), and 0.68 (cut-off = 6.29), respectively. Further validations were conducted in the second and third serial samples of these cases (validation2A, n = 633, validation2B, n = 382), with high accuracy of prediction for outcome. These findings have important implications for improving clinical management, and especially for developing medical interventions and vaccines.

    In silico analyses on the comparative sensing of SARS-CoV-2 mRNA by intracellular TLRs of human

    Authors: Abhigyan Choudhury; Nabarun Chandra Das; Ritwik Patra; Manojit Bhattacharya; Suprabhat Mukherjee; Kianna M. Nguyen; Ming H. Ho; Jung-Eun Shin; Jared Feldman; Blake M. Hauser; Timothy M. Caradonna; Laura M. Wingler; Aaron G. Schmidt; Debora S. Marks; Jonathan Abraham; Andrew C. Kruse; Chang C. Liu

    doi:10.1101/2020.11.11.377713 Date: 2020-11-11 Source: bioRxiv

    The worldwide outbreak of COVID-19 MESHD COVID-19 MESHD pandemic caused by SARS-CoV-2 leads to loss of mankind and global economic stability. The continuous spreading of the disease and its pathogenesis takes millions of lives of peoples and the unavailability of appropriate therapeutic strategy makes it much more severe. Toll-like receptors (TLRs) are the crucial mediators and regulators of host immunity. The role of several TLRs in immunomodulation of host by SARS-CoV-2 is recently demonstrated. However, the functionality of human intracellular TLRs including TLR3 HGNC,7,8 and 9 is still being untested for sensing of viral RNA. This study is hoped to rationalize the comparative binding and sensing of SARS-CoV-2 mRNA towards the intracellular TLRs, considering the solvent-based force-fields operational in the cytosolic aqueous microenvironment that predominantly drive these reactions. Our in-silico study on the binding of all mRNAs with the intracellular TLRs shown that the mRNA of NSP10 PROTEIN, S2, and E proteins PROTEIN of SARS-CoV-2 are potent enough to bind with TLR3 HGNC, TLR9 HGNC, and TLR7 HGNC and trigger downstream cascade reactions, and may be used as an option for validation of therapeutic option and immunomodulation against COVID-19 MESHD.

    Exosome-Mediated mRNA Delivery For SARS-CoV-2 Vaccination

    Authors: Shang-Jui Tsai; Chenxu Guo; Nadia A Atai; Stephen J Gould; Emma S Child; Rhodri M L Morgan; Alan Armstrong; David J Mann; Sheng Cui; Paulo Souza-Fonseca Guimaraes; Lucia Noronha; Timothy McCulloch; Gustavo Rodrigues Rossi; Caroline Cooper; Benjamin Tang; Kirsty Short; Melissa J Davis; Fernando Souza-Fonseca Guimaraes; Gabrielle T Belz; Ken O'Byrne

    doi:10.1101/2020.11.06.371419 Date: 2020-11-06 Source: bioRxiv

    Background: In less than a year from its zoonotic entry into the human population, SARS-CoV-2 has infected more than 45 million people, caused 1.2 million deaths, and induced widespread societal disruption MESHD. Leading SARS-CoV-2 vaccine candidates immunize with the viral spike protein PROTEIN delivered on viral vectors, encoded by injected mRNAs, or as purified protein. Here we describe a different approach to SARS-CoV-2 vaccine development that uses exosomes to deliver mRNAs that encode antigens from multiple SARS-CoV-2 structural proteins. Approach: Exosomes were purified and loaded with mRNAs designed to express (i) an artificial fusion protein, LSNME, that contains portions of the viral spike, nucleocapsid, membrane, and envelope proteins PROTEIN, and (ii) a functional form of spike. The resulting combinatorial vaccine, LSNME/SW1, was injected into thirteen weeks-old, male C57BL/6J mice, followed by interrogation of humoral and cellular immune responses to the SARS-CoV-2 nucleocapsid and spike proteins PROTEIN, as well as hematological and histological analysis to interrogate animals for possible adverse effects. Results: Immunized mice developed CD4+, and CD8+ T-cell reactivities that respond to both the SARS-CoV-2 nucelocapsid protein and the SARS-CoV-2 spike PROTEIN protein. These responses were apparent nearly two months after the conclusion of vaccination, as expected for a durable response to vaccination. In addition, the spike-reactive CD4+ T-cells response was associated with elevated expression of interferon gamma, indicative of a Th1 response, and a lesser induction of interleukin 4, a Th2-associated cytokine. Vaccinated mice showed no sign of altered growth, injection-site hypersensitivity MESHD, change in white blood cell profiles, or alterations in organ morphology. Consistent with these results, we also detected moderate but sustained anti-nucleocapsid and anti-spike antibodies in the plasma of vaccinated animals. Conclusion: Taken together, these results validate the use of exosomes for delivering functional mRNAs into target cells in vitro and in vivo, and more specifically, establish that the LSNME/SW1 vaccine induced broad immunity to multiple SARS-CoV-2 proteins.

    Extracellular vesicle-based vaccine platform displaying native viral envelope proteins PROTEIN elicits a robust anti-SARS-CoV-2 response in mice.

    Authors: Katarzyna Polak; Noémie Greze; Maëlle Lachat; Delphine Merle; Steve Chiumento; Christelle Bertrand-Gaday; Bernadette Trentin; Robert Z. Mamoun; Gamze Tumentemur; Sevda Demir; Utku Seyis; Recai Kuzay; Muhammer Elek; Gurcan Ertop; Serap Arbak; Merve Acikel Elmas; Cansu Hemsinlioglu; Ozden Hatirnaz Ng; Sezer Akyoney; Ilayda Sahin; Cavit Kerem Kayhan; Fatma Tokat; Gurler Akpinar; Murat Kasap; Ayse Sesin Kocagoz; Ugur Ozbek; Dilek Telci; Fikrettin Sahin; Koray Yalcin; Siret Ratip; Umit Ince; Guldal Suyen; Ercument Ovali; Liam Fergusson; Marta Conti; Marius Rameil; Vanessa Nakonecnij; Jakob Vanhoefer; Leonard Schmiester; Muying Wang; Emily E Ackerman; Jason E Shoemaker; Jeremy Zucker; Kristie L Oxford; Jeremy Teuton; Ebru Kocakaya; Gokce Yagmur Summak; Kristina Hanspers; Martina Kutmon; Susan Coort; Lars Eijssen; Friederike Ehrhart; Rex D. A. B.; Denise Slenter; Marvin Martens; Robin Haw; Bijay Jassal; Lisa Matthews; Marija Orlic-Milacic; Andrea Senff-Ribeiro; Karen Rothfels; Veronica Shamovsky; Ralf Stephan; Cristoffer Sevilla; Thawfeek Mohamed Varusai; Jean-Marie Ravel; Vera Ortseifen; Silvia Marchesi; Piotr Gawron; Ewa Smula; Laurent Heirendt; Venkata Satagopam; Guanming Wu; Anders Riutta; Martin Golebiewski; Stuart Owen; Carole Goble; Xiaoming Hu; Rupert Overall; Dieter Maier; Angela Bauch; John A Bachman; Benjamin M Gyori; Carlos Vega; Valentin Groues; Miguel Vazquez; Pablo Porras; Luana Licata; Marta Iannuccelli; Francesca Sacco; Denes Turei; Augustin Luna; Ozgun Babur; Sylvain Soliman; Alberto Valdeolivas; Marina Esteban-Medina; Maria Pena-Chilet; Tomas Helikar; Bhanwar Lal Puniya; Anastasia Nesterova; Anton Yuryev; Anita de Waard; Dezso Modos; Agatha Treveil; Marton Laszlo Olbei; Bertrand De Meulder; Aurelien Naldi; Aurelien Dugourd; Laurence Calzone; Chris Sander; Emek Demir; Tamas Korcsmaros; Tom C Freeman; Franck Auge; Jacques S Beckmann; Jan Hasenauer; Olaf Wolkenhauer; Egon Willighagen; Alexander R Pico; Chris Evelo; Lincoln D Stein; Henning Hermjakob; Julio Saez-Rodriguez; Joaquin Dopazo; Alfonso Valencia; Hiroaki Kitano; Emmanuel Barillot; Charles Auffray; Rudi Balling; Reinhard Schneider; - the COVID-19 Disease Map Community

    doi:10.1101/2020.10.28.357137 Date: 2020-10-28 Source: bioRxiv

    Extracellular vesicles (EVs) emerge as essential mediators of intercellular communication. DNA vaccines encoding antigens presented on EVs efficiently induce T-cell responses and EV-based vaccines containing the Spike (S) proteins PROTEIN of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV MESHD) are highly immunogenic in mice. Thus, EVs may serve as vaccine platforms against emerging diseases MESHD, going beyond traditional strategies, with the antigen displayed identically to the original protein embedded in the viral membrane and presented as such to the immune system. Compared to their viral and pseudotyped counterparts, EV-based vaccines overcome many safety issues including pre-existing immunity against these vectors. Here, we applied our technology in natural EV's engineering, to express the S proteins PROTEIN of SARS-CoV-2 embedded in the EVs, which mimic the virus with its fully native spikes. Immunizations with a two component CoVEVax vaccine, comprising DNA vector (DNAS-EV) primes, allowing in situ production of Spike harbouring EVs, and a boost using S-EVs produced in mammalian cells, trigger potent neutralizing and cellular responses in mice, in the absence of any adjuvants. CoVEVax would be the prototype of vaccines, where the sole exchange of the envelope proteins PROTEIN on EVs leads to the generation of new vaccine candidates against emerging viruses.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins


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