Corpus overview


Overview

MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinE (13)

ProteinS (2)

ORF1ab (2)

ProteinN (2)

ProteinM (1)


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SARS-CoV-2 Proteins
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    Evaluation of a Sample Pooling Strategy for Sars-cov-2 Using Real Time PCR

    Authors: Annet M Nankya; Luke Nyakarahuka; Stephen Balinandi; John Kayiwa; Julius Lutwama; Andrew Tamale; Joseph M Kungu

    doi:10.21203/rs.3.rs-290291/v1 Date: 2021-03-02 Source: ResearchSquare

    Back ground: Corona Virus Disease MESHD 2019 (COVID 19) in Uganda was first reported in a male traveler from Dubai on 21st March, 2020 shortly after WHO had announced the condition as a global pandemic. Timely laboratory diagnosis of COVID -19 for all samples from both symptomatic and asymptomatic patients was observed as key in containing the pandemic and breaking the chain of transmission. However, there was a challenge of limited resources required for testing SARS-COV-2 in low and middle income countries. To mitigate this, a study was conducted to evaluate a sample pooling strategy for COVI-19 using real time PCR. The cost implication and the turn around time of pooled sample testing versus individual sample testing were also compared.Methods: In this study, 1260 randomly selected samples submitted to Uganda Virus Research Institute for analysis were batched in pools of 5, 10, and 15. The pools were then extracted using a Qiagen kit. Both individual and pooled RNA were screened for the SARS-COV-2 E gene PROTEIN using a Berlin kit. Results: Out of 1260 samples tested, 21 pools were positive in pools of 5 samples, 16 were positive in pools of 10 and 14 were positive in pools of 15 samples. The study also revealed that the pooling strategy helps to save a lot on resources, time and expands diagnostic capabilities without affecting the sensitivity of the test in areas with low SARS-COV-2 prevalence.Conclusion: This study demonstrated that the pooling strategy for COVID-19 MESHD reduced on the turnaround time and there was a substantial increase in the overall testing capacity with limited resources as compared to individual testing.

    Host PDZ-containing proteins targeted by SARS-Cov-2

    Authors: Celia Caillet-Saguy; Fabien Durbesson; Veronica V. REZELJ; Gergo Gogl; Quang Dinh Tran; Jean-Claude Twizere; Marco Vignuzzi; Renaud Vincentelli; Nicolas Wolff; Rahaf Alharbi; Mazen Hassanain; Anwar M Hashem; Eugene B. Chang; Glenn Randall; Pablo Penaloza-MacMaster; Bozhi Tian; Maria Lucia Madariaga; Jun Huang; Dirk Jochmans; Birgit Weynand; Johan Neyts

    doi:10.1101/2021.02.01.429176 Date: 2021-02-01 Source: bioRxiv

    Small linear motif targeting protein interacting domains called PDZ have been identified at the C-terminus of the severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) proteins E PROTEIN, 3a, and N. Using a high-throughput approach of affinity-profiling against the full human PDZome, we identified sixteen human PDZ binders of SARS-CoV-2 proteins E PROTEIN, 3A and N showing significant interactions with dissociation constants values ranging from 3 M to 82 M. Six of them ( TJP1 HGNC, PTPN13 HGNC, HTRA1 HGNC, PARD3 HGNC, MLLT4 HGNC, LNX2 HGNC) are also recognized by SARS-CoV while three ( NHERF1 HGNC, MAST2 HGNC, RADIL HGNC) are specific to SARS-CoV-2 E protein PROTEIN. Most of these SARS-CoV-2 protein partners are involved in cellular junctions/polarity and could be also linked to evasion mechanisms of the immune responses during viral infection MESHD. Seven of the PDZ-containing proteins among binders of the SARS-CoV-2 proteins E PROTEIN, 3a or N affect significantly viral replication under knock-down gene expression in infected cells. This PDZ profiling identifying human proteins potentially targeted by SARS-CoV-2 can help to understand the multifactorial severity of COVID19 MESHD and to conceive effective anti-coronaviral agents for therapeutic purposes.

    Environmental Dependence of the Structure of the C-terminal Domain of the SARS-CoV-2 Envelope Protein PROTEIN

    Authors: Kundlik Gadhave; Ankur Kumar; Prateek Kumar; Shivani K Kapuganti; Neha Garg; Michele Vendruscolo; Rajanish Giri; Matthew Hall; Min Shen; Munif Haddad; Giordano Pula; Reiner Mailer; Hartmut Schlueter; Florian Langer; Klaus Pueschel; Kosta Panousis; Evi Stavrou; Coen Maas; Thomas Renne; Sachin B Surade; Omodele Ashiru; Lucia Crippa; Richard Cowan; Matthew W Bowler; Jamie I Campbell; Wing-Yiu Jason Lee; Mark D Carr; David Matthews; Paul Pfeffer; Simon E Hufton; Kovilen Sawmynaden; Jane Osbourn; John McCafferty; Aneesh Karatt-Vellatt

    doi:10.1101/2020.12.29.424646 Date: 2020-12-29 Source: bioRxiv

    The SARS-CoV-2 envelope protein (E PROTEIN) is involved in a broad spectrum of functions in the cycle of the virus, including assembly, budding, envelope formation, and pathogenesis. To enable these activities, E is likely to be capable of changing its conformation depending on environmental cues. To investigate this issue, here we characterised the structural properties of the C-terminal domain of E (E-CTD), which has been reported to interact with host cell membranes. We first studied the conformation of the E-CTD in solution, finding characteristic features of a disordered protein. By contrast, in the presence of large unilamellar vesicles and micelles, which mimic cell membranes, the E-CTD was observed to become structured. The E-CTD was also found to display conformational changes with osmolytes. Furthermore, prolonged incubation of the E-CTD under physiological conditions resulted in amyloid-like fibril formation. Taken together, these findings indicate that the E-CTD can change its conformation depending on its environment, ranging from a disordered state, to a membrane-bound folded state, and an amyloid state. Our results thus provide insight into the structural basis of the role of E in the viral infection process MESHD.

    Surface proteins of SARS-CoV-2 drive airway epithelial cells to induce interferon-dependent inflammation MESHD

    Authors: Gautam Anand; Alexandra M Perry; Celeste L Cummings; Emma St. Raymond; Regina A Clemens; Ashley L Steed

    doi:10.1101/2020.12.14.422710 Date: 2020-12-14 Source: bioRxiv

    SARS-CoV-2, the virus that has caused the COVID-19 pandemic MESHD, robustly activates the host immune system in critically ill MESHD patients. Understanding how the virus engages the immune system will facilitate the development of needed therapeutic strategies. Here we demonstrate both in vitro and in vivo that the SARS-CoV-2 surface proteins Spike (S PROTEIN) and Envelope (E) activate the key immune signaling interferon (IFN) pathway in both immune and epithelial cells independent of viral infection MESHD and replication. These proteins induce reactive oxidative species generation and increases in human and murine specific IFN-responsive cytokines and chemokines, similar to their upregulation in critically ill COVID-19 MESHD patients. Induction of IFN signaling is dependent on canonical but discrepant inflammatory signaling mediators as the activation induced by S is dependent on IRF3 HGNC, TBK1 HGNC, and MYD88 HGNC while that of E is largely MYD88 HGNC independent. Furthermore, these viral surface proteins, specifically E, induced peribronchial inflammation MESHD and pulmonary vasculitis MESHD in a mouse model. Finally we show that the organized inflammatory infiltrates are dependent on type I IFN signaling, specifically in lung epithelial cells. These findings underscore the role of SARS-CoV-2 surface proteins, particularly the understudied E protein PROTEIN, in driving cell specific inflammation MESHD and their potential for therapeutic intervention. Author SummarySARS-CoV-2 robustly activates widespread inflammation MESHD, but we do not understand mechanistically how the virus engages the immune system. This knowledge will facilitate the development of critically needed therapeutic strategies to promote beneficial immune responses will dampening harmful inflammation MESHD. Here we demonstrate that SARS-CoV-2 surface proteins spike PROTEIN and envelope alone activated innate cell function and the interferon signaling pathway. This activation occurred in both immune and epithelial cells, and mechanistic studies demonstrated dependence on known key inflammatory signaling mediators, IRF3 HGNC, TBK1 HGNC, and MYD88 HGNC. In animal studies, we showed that these viral surface proteins induce epithelial cell IFN-dependent lung pathology, reminiscent to acute COVID-19 MESHD pulmonary infection MESHD. These findings underscore the need for further investigation into the role of SARS-CoV-2 surface proteins, particularly the understudied E protein PROTEIN, in driving cell specific inflammation MESHD.

    Automated molecular testing of saliva for SARS-CoV-2 detection

    Authors: Nancy Matic; Tanya Lawson; Gordon Ritchie; Aleksandra Stefanovic; Victor Leung; Sylvie Champagne; Marc G. Romney; Christopher F. Lowe

    doi:10.1101/2020.08.11.20170613 Date: 2020-08-14 Source: medRxiv

    Introduction: With surging global demand for increased SARS-CoV-2 testing capacity, clinical laboratories seek automated, high-throughput molecular solutions, particularly for specimen types which do not rely upon supply of specialized collection devices or viral transport media (VTM). Saliva was evaluated as a diagnostic specimen for SARS-CoV-2 using the cobas SARS-CoV-2 Test on the cobas 6800 instrument. Methods: Saliva specimens submitted from various patient populations under investigation for COVID-19 MESHD from March-July 2020 were processed in the laboratory with sterile phosphate-buffered saline in a 1:2 dilution and vortexed with glass beads. The processed saliva samples were tested using a commercial assay for detection of the SARS-CoV-2 E gene PROTEIN (LightMix) in comparison to the cobas SARS-CoV-2 Test. Results: 22/64 (34.4%) of the saliva samples were positive for SARS-CoV-2. Positive and negative concordance between the LightMix and cobas assays were 100%. There was no cross-contamination of samples observed on the cobas 6800. The overall invalid rate for saliva on the cobas 6800 (1/128, 0.78%) was similar to the baseline invalid rate observed for nasopharyngeal swabs/ VTM MESHD and plasma samples. Conclusions: Saliva is a feasible specimen type for SARS-CoV-2 testing on the cobas 6800, with potential to improve turnaround time and enhance testing capacity.

    Functional mapping of B-cell linear epitopes 1 of SARS-CoV-2 in COVID-19 MESHD convalescent population

    Authors: Zhigang Yi; Yun Ling; Xiaonan Zhang; Jieliang Chen; Kongying Hu; Yuyan Wang; Wuhui Song; Tianlei Ying; Rong Zhang; Hongzou Lu; Zhenghong Yuan

    doi:10.1101/2020.07.25.20161869 Date: 2020-07-27 Source: medRxiv

    Pandemic SARS-CoV-2 has infected over 10 million people and caused over 500,000 mortalities. Vaccine development is in urgent need to stop the pandemic. Despite great progresses on SARS-CoV-2 vaccine development, the efficacy of the vaccines remains to be determined. Deciphering the interactions of the viral epitopes with their elicited neutralizing antibodies in the convalescent COVID-19 MESHD population inspires the vaccine development. In this study, we devised a peptide array composed of 20-mer overlapped peptides of spike (S), membrane (M) and envelope (E) proteins PROTEIN, and performed a screening with 120 COVID-19 MESHD convalescent serums and 24 non- COVID-19 MESHD serums. We identified five SARS-CoV-2-specific dominant epitopes that reacted with above 40% COVID-19 MESHD convalescent serums. Epitopes in the receptor-binding domain (RBD) of S ill reacted with the convalescent serums. Of note, two peptides non-specifically interacted with most of the non- COVID-19 MESHD serums. Neutralization assay indicated that only five serums completely blocked viral infection at the dilution of 1:200. By using a peptide-compete neutralizing assay, we found that three dominant epitopes partially competed the neutralization activity of several convalescent serums, suggesting antibodies elicited by these epitopes played an important role in neutralizing viral infection MESHD. The epitopes we identified in this study may serve as vaccine candidates to elicit neutralizing antibodies in most vaccinated people or specific antigens for SARS-CoV-2 diagnosis.

    Unravelling promise of Indian herbal compounds as potential COVID-19 MESHD therapeutic agent

    Authors: SHAHENVAZ ALAM; SYEDA WARISUL FATIMA; SUNIL K. KHARE

    doi:10.21203/rs.3.rs-41688/v1 Date: 2020-07-13 Source: ResearchSquare

    COVID-19 pandemic MESHD COVID-19 pandemic MESHD, an unprecedented devastation, humanity needs an urgent cure to save the mankind from this deadly disease. Over six million people have been infected worldwide, with 6.3% reported deaths till date. SARS-CoV-2 virus, responsible for Novel Coronavirus ( COVID-19 MESHD) disease has been isolated recently and the vaccine’s development is at nascent stage. At present, there are a few anecdotal evidences that anti-viral/anti-inflammatory/anti-malarial drugs can mitigate the disease. In the present study, we envision the potency of traditional Indian medicinal compounds that can be used as an effective drug. The viral SARS Coronavirus E protein PROTEIN plays a key role in virus life cycle and can be a potential drug target for the development of anti-SARS-CoV-2 drugs. Using the crystal structure of the CoV- E protein PROTEIN, we performed virtual PyRX screening of Indian medicinal compounds which are reported to have efficacy in the treatment of some viral infections MESHD. Molecular docking studies were evaluated based on scores analysed by CavityPlus. The herbal compounds used were found to be more efficient in inhibiting the virus as compared to commercially available drugs. The results showed that β-boswellic acid and Glycyrrhizic acid possessed the best binding as a ligand with target molecule having binding affinity of -9.1 kcal/mol amongst eleven compounds screened. The study demonstrated that these are found to be strong SARS-CoV-2E protein inhibitors as they revealed compatible, near perfect dock in the overlapping region of functional viral protein pockets. These potential hit compounds can pave a way for designing of anti-viral therapeutics.

    No SARS-CoV-2 detected in the vermiform appendix of a COVID-19 MESHD patient with appendicitis: a case report 

    Authors: Benjamin Wolf; Corinna Pietsch; Marc-Philip Radosa; Lars-Christian Horn; Uwe G. Liebert; Bahriye Aktas

    doi:10.21203/rs.3.rs-38187/v1 Date: 2020-06-28 Source: ResearchSquare

    Background:SARS-CoV-2, the virus causing corona virus disease 2019 ( COVID-19 MESHD), has been demonstrated to i nfect the gastrointestinal MESHDtract and might therefore be a source of infection for the surgical team during abdominal operations. One of the most common surgical procedures performed is appendectomy. However, reports of virologic testing of appendiceal tissue specimens in COVID-19 MESHD patients are lacking. We sought to determine whether SARS-CoV-2 is present in the appendectomy specimen of a patient with COVID-19 MESHD. Case presentation:A female patient presented to the emergency department of our tertiary care academic hospital with lower a bdominal pain, MESHD f ever, MESHD n ausea, MESHD and v omiting. MESHD She was admitted to the gynecological floor because of suspected p elvic inflammatory disease. MESHD Due to worsening symptoms, a laparoscopy was performed the next day and a severely inflamed appendix was detected. Laparoscopic appendectomy was performed without complications. A few hours postoperatively, the patient was tested positive for c orona virus disease MESHD2019 (COVID 19). Real-time reverse transcription polymerase chain reaction analysis targeting the SARS-CoV-2 E-gene PROTEIN was performed on the appendectomy specimen. SARS-CoV-2 could not be detected. During her hospital stay, the patient developed mild respiratory symptoms while the postoperative course was otherwise uncomplicated. Conclusions:The absence of SARS-CoV-2 in the appendectomy specimen of our case adds to the preliminary available evidence indicating that appendectomy in COVID-19 MESHD patients with mild disease carries probably a low risk of i nfection MESHDby aerosols generated during the procedure. 

    Molecular features similarities between SARS-CoV-2, SARS, MERS and key human genes could favour the viral infections and trigger collateral effects

    Authors: Lucas Maldonado Sr.; Laura Kamenetzky

    doi:10.1101/2020.06.23.167072 Date: 2020-06-25 Source: bioRxiv

    In December 2019 rising pneumonia MESHD cases caused by a novel {beta}-coronavirus (SARS-CoV-2) occurred in Wuhan, China, which has rapidly spread worldwide causing thousands of deaths. The WHO declared the SARS-CoV-2 outbreak as a public health emergency of international concern therefore several scientists are dedicated to the study of the new virus. Since human viruses have codon usage biases that match highly expressed proteins in the tissues they infect MESHD and depend on host cell machinery for replication and co-evolution, we selected the genes that are highly expressed in the tissue of human lungs to perform computational studies that permit to compare their molecular features with SARS, SARS-CoV-2 and MERS genes. In our studies, we analysed 91 molecular features for 339 viral genes and 463 human genes that consisted of 677873 codon positions. Hereby, we found that A/T bias in viral genes could propitiate the viral infection MESHD favoured by a host dependant specialization using the host cell machinery of only some genes. The envelope protein E PROTEIN, the membrane glycoprotein M PROTEIN and ORF7 could have been further benefited by a high rate of A/T in the third codon position. Thereby, the mistranslation or de-regulation of protein synthesis could produce collateral effects, as a consequence of viral occupancy of the host translation machinery due tomolecular similarities with viral genes. Furthermore, we provided a list of candidate human genes whose molecular features match those of SARS-CoV-2, SARSand MERS genes, which should be considered to be incorporated into genetic population studies to evaluate thesusceptibility to respiratory viral infections MESHD caused by these viruses. The results presented here, settle the basis for further research in the field of human genetics associated with the new viral infection, COVID-19 MESHD, caused by SARS-CoV-2 and for the development of antiviral preventive methods.

    Structural insight into the putative role of Novel Coronavirus-2 E protein PROTEIN in viral infection via in silico approach: a potential target for LAV development and other therapeutic strategies

    Authors: Manish Sarkar; Soham Saha

    doi:10.1101/2020.05.11.088781 Date: 2020-05-11 Source: bioRxiv

    The outbreak of COVID-19 MESHD across the world has posed unprecedented and global challenges on multiple fronts. Most of the vaccine and drug development has focused on the spike proteins PROTEIN and viral RNA-polymerases. Using bioinformatics and structural modeling approach, we modeled the structure of the envelope (E)-protein PROTEIN of novel SARS-CoV-2. The E-protein PROTEIN of this virus shares sequence similarity with that of SARS-CoV-1, and is highly conserved in the N-terminal regions. Incidentally, compared to spike proteins PROTEIN, E proteins PROTEIN demonstrate lower disparity and mutability among the isolated sequences. Using homology modeling, we found that the most favorable structure could function as a gated proton channel. Combining pocket estimation and docking with water, we determined that GLU 8 and ASN 15 in the N-terminal region were in close proximity to form H-bonds. Additionally, two distinct “core” structures were visible, the hydrophobic core and the central core, which may regulate the opening/closing of the channel. We propose this as a mechanism of viral proton channeling activity which may play a critical role in viral infection MESHD. In addition, it provides a structural basis and additional avenues for generating therapeutic interventions against the virus.One Sentence Summary Structural modeling of the novel coronavirus envelope proteins (E PROTEIN-proteins) demonstrating its possible proton channeling activity.Competing Interest StatementThe authors have declared no competing interest.View Full Text

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins


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