preVIEW: COVID-19

Corpus overview

Overview

MeSH Disease

COVID-19 (21)

Severe Acute Respiratory Syndrome (6)

Coronavirus Infections (4)

Virus Diseases (3)

Hepatitis C (3)


HGNC Genes

angiotensin I converting enzyme 2 (23)

SH2 domain containing 3C (3)

kelch like ECH associated protein 1 (3)

surfactant protein D (1)

cathepsin L (1)


SARS-CoV-2 proteins

ComplexRdRp (23)

NSP5 (13)

ProteinS (9)

NSP3 (5)

ProteinN (4)


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    Mutation Landscape of SARS COV2 in Africa

    Authors: Angus A Nassir; Clarisse Musanabaganwa; Ivan Mwikarago; Vanessa Blanc; Joan Gispert; Bonventura Clotet; Nuria Izquierdo-Useros; Darryl Hill; Paolo Madeddu; Shawn A Abbasi; Whitney Pickens; Katia George; Daniel R Boutz; Dalton M Towers; Jonathan R McDaniel; Daniel Billick; Jule Goike; Lori Rowe; Dhwani Batra; Jan Pohl; Justin Lee; Shivaprakash Gangappa; Suryaprakash Sambhara; Michelle Gadush; Nianshuang Wang; Maria D Person; Brent L Iverson; Jimmy D Gollihar; John Dye; Andrew Herbert; Ralph S Baric; Jason S McLellan; George Georgiou; Jason J Lavinder; Gregory C Ippolito; Fergus Gleeson; Yper Hall; Simon G. P. Funnell; Sally Sharpe; Francisco Javier Salguero; Andrew R Gorringe; Miles Carroll

    doi:10.1101/2020.12.20.423630 Date: 2020-12-21 Source: bioRxiv

    COVID-19 MESHD disease has had a relatively less severe impact in Africa. To understand the role of SARS CoV2 mutations on COVID-19 MESHD disease in Africa, we analysed 282 complete nucleotide sequences from African isolates deposited in the NCBI Virus Database. Sequences were aligned against the prototype Wuhan sequence (GenBank accession: NC_045512.2) in BWA v. 0.7.17. SAM and BAM files were created, sorted and indexed in SAMtools v. 1.10 and marked for duplicates using Picard v. 2.23.4. Variants were called with mpileup in BCFtools v. 1.11. Phylograms were created using Mr. Bayes v 3.2.6. A total of 2,349 single nucleotide polymorphism (SNP) profiles across 294 sites were identified. Clades associated with severe disease in the United States, France, Italy, and Brazil had low frequencies in Africa (L84S=2.5%, L3606F=1.4%, L3606F/V378I/=0.35, G251V=2%). Sub Saharan Africa (SSA) accounted for only 3% of P323L and 4% of Q57H mutations in Africa. Comparatively low infections MESHD in SSA were attributed to the low frequency of the D614G clade in earlier samples (25% vs 67% global). Higher disease burden occurred in countries with higher D614G frequencies (Egypt=98%, Morocco=90%, Tunisia=52%, South Africa) with D614G as the first confirmed case. V367F, D364Y, V483A and G476S mutations associated with efficient ACE2 HGNC receptor binding and severe disease were not observed in Africa. 95% of all RdRp PROTEIN mutations were deaminations leading to CpG depletion and possible attenuation of virulence. More genomic and experimental studies are needed to increase our understanding of the temporal evolution of the virus in Africa, clarify our findings, and reveal hot spots that may undermine successful therapeutic and vaccine interventions.

    A recombinant fragment of Human surfactant protein D HGNC binds Spike protein PROTEIN and inhibits infectivity and replication of SARS-CoV-2 in clinical samples

    Authors: Taruna Madan; Barnali Biswas; Praveen Varghese; Rambhadur Subedi; Hrishikesh Pandit; Susan Idicula-Thomas; Indra Kundu; Sheetalnath Babasaheb Rooge; Reshu Aggarwal; Dinesh Tripathi; Savneet Kaur; Ekta Gupta; Sanjeev Gupta

    doi:10.1101/2020.12.18.423415 Date: 2020-12-18 Source: bioRxiv

    Rationale COVID-19 MESHD is an acute infectious disease MESHD caused by the Severe Acute Respiratory Syndrome Coronavirus 2 MESHD (SARS-CoV-2). Human surfactant protein D HGNC ( SP-D HGNC) is known to interact with spike protein PROTEIN of SARS-CoV, but its immune-surveillance against SARS-CoV-2 is not known. ObjectiveThis study aimed to examine the potential of a recombinant fragment of human SP-D HGNC (rfhSP-D) as an inhibitor of replication and infection of SARS-CoV-2 MESHD. MethodsrfhSP-D interaction with spike protein PROTEIN of SARS-CoV-2 and hACE-2 receptor was predicted via docking analysis. The inhibition of interaction between spike protein PROTEIN and ACE-2 HGNC by rfhSP-D was confirmed using direct and indirect ELISA. The effect of rfhSP-D on replication and infectivity of SARS-CoV-2 from clinical samples was studied by measuring the expression of RdRp PROTEIN gene of the virus using qPCR. Measurements and Main ResultsIn-silico interaction studies indicated that three amino acid residues in the RBD of spike of SARS-CoV-2 PROTEIN were commonly involved in interacting with rfhSP-D and ACE-2 HGNC. Studies using clinical samples of SARS-CoV-2 positive cases (asymptomatic, n=7 and symptomatic, n=8 and negative controls n=15) demonstrated that treatment with 5M rfhSP-D inhibited viral replication by ~5.5 fold and was more efficient than Remdesivir (100 M). Approximately, a 2-fold reduction in viral infectivity was also observed after treatment with 5M rfhSP-D. ConclusionsThese results conclusively demonstrate that the calcium independent rfhSP-D mediated inhibition of binding between the receptor binding domain of the S1 subunit of the SARS-CoV-2 spike PROTEIN protein and human ACE-2 HGNC, its host cell receptor, and a significant reduction in SARS-CoV-2 infection MESHD and replication in-vitro.

    Tea flavonoids blocking multiple SARS-CoV-2 protein targets judged from molecular docking

    Authors: Lufei Wang; Siyao Sang; Mingjie Su; Simin Wang; Hui Li

    doi:10.21203/rs.3.rs-122589/v1 Date: 2020-12-05 Source: ResearchSquare

    Severe Acute Respiratory Syndrome Coronavirus 2 MESHD (SARS-CoV-2) has caused Severe Acute Respiratory Syndrome Coronavirus 2 MESHD (SARS-CoV-2) pandemic. Flavonoids derived Chinese patent medicines has outstanding curative effects for the improvement and treatment of COVID-19 MESHD. There are numerous studies suggesting that flavonoids-rich tea have antiviral effects. However, bioactive compounds from tea flavonoids with anti- COVID-19 MESHD effect, and the potential molecular mechanisms are unclear. In this study, we performed a molecular docking of 468 tea flavonoids and its derivatives with main protease PROTEIN ( Mpro PROTEIN), angiotensin-converting enzyme 2 HGNC ( ACE2 HGNC), RNA dependent RNA polymerase PROTEIN ( RdRp PROTEIN), compared with the positive control drugs of each target. The results suggested that ACE2 HGNC and RdRp PROTEIN are the main targets inhibited by tea flavonoids.Q3G Isovitexin, and TF would be considered as the potential candidate compounds of RdRp PROTEIN and ACE2 HGNC. Our study provides a theoretical basis for further drug design of anti- COVID-19 MESHD.

    In Vitro: Natural Compounds (Thymol, Carvacrol, Hesperidine, And Thymoquinone) Against Sars-Cov2 Strain Isolated From Egyptian Patients

    Authors: Mohamed G Seadawy; Ahmed F. Gad; Mohamed Shamel; Bassem Elharty; Mostfa F. Mohamed; Abdo A. Elfiky; Aya Ahmed; Abdel Rahman N. Zekri

    doi:10.21203/rs.3.rs-119568/v1 Date: 2020-12-01 Source: ResearchSquare

    Background: The current pandemic of the coronavirus disease-2019 ( COVID-19 MESHD) has badly affected our life during the year 2020. SARS-CoV-2 is the primary causative agent of the newly emerged pandemic. Natural flavonoids, Terpenoid and Thymoquinone are tested against different viral and host-cell protein targets. These natural compounds have a good history in treating Hepatitis C Virus MESHD ( HCV MESHD) and Human Immunodeficiency Virus (HIV) MESHD. Methods: Molecular docking combined with cytotoxicity MESHD and plaque reduction assay is used to test the natural compounds against different viral (Spike, RdRp PROTEIN, and Mpro PROTEIN) and host-cell (TMPRSS II, keap 1 HGNC, and ACE2 HGNC) targets. Results: The results demonstrate the binding possibility of the natural compounds (Thymol, Carvacrol, Hesperidine, and Thymoquinone) to the viral main protease PROTEIN ( Mpro PROTEIN). Some of these natural compounds were approved to start clinical trail from Egypt Center for Research and Regenerative Medicine ECRRM IRB (Certificate No.IRB00012517)Conclusion: Development of an effective anti-viral for SARS-CoV-2  could help to limit the viral load. Benchmarking testing of those natural compounds against other potential antivirals for SARS-CoV-2 with alternative mechanisms of action would thus be important as soon as practicable.

    Long-chain polyphosphates impair SARS-CoV-2 infection MESHD and replication: a route for therapy in man

    Authors: Veronica Ferrucci; Young Kong Dae; Fatemeh Asadzadeh; Laura Marrone; Roberto Siciliano; Pellegrino Cerino; Giuseppina Criscuolo; Ida Pisano; Fabrizio Quarantelli; Barbara Izzo; Giovanna Fusco; Marika Comegna; Angelo Boccia; Maurizio Viscardi; Giorgia Borriello; Sergio Brandi; Bianca Maria Pierri; Claudia Tiberio; Luigi Atripaldi; Giovanni Paolella; Giuseppe Castaldo; Stefano Pascarella; Martina Bianchi; Rosa Della Monica; Lorenzo Chiariotti; Kyong Seop Yun; Jae Ho Cheong; Hong Yeoul Kim; Massimo Zollo; Katie Jeffery; David W Eyre; Talat Mokhtari-Azad; Reza Najafipour; Reza Malekzadeh; Kimia Kahrizi; Seyed Mohammad Jazayeri; Hossein Najmabadi

    doi:10.1101/2020.11.18.388413 Date: 2020-11-18 Source: bioRxiv

    Anti-viral activities of long-chain inorganic polyphosphates (PolyPs) against severe acute respiratory syndrome coronavirus (SARS-CoV)-2 infection MESHD were investigated. In molecular docking analyses, PolyPs interacted with several conserved angiotensin-converting enzyme ( ACE)2 HGNC and RNA-dependent RNA polymerase PROTEIN ( RdRp PROTEIN) amino acids. We thus tested PolyPs for functional interactions in vitro in SARS-CoV-2-infected MESHD Vero E6, Caco2 and human primary nasal epithelial cells. Immunofluorescence, qPCR, direct RNA sequencing, FISH and Immunoblotting were used to determine virus loads and transcription levels of genomic(g)RNAs and sub-genomic(sg)RNAs. We show that PolyP120 binds to ACE2 HGNC and enhances its proteasomal degradation. PolyP120 shows steric hindrance of the genomic Sars-CoV-2-RNA/ RdRP complex PROTEIN, to impair synthesis of positive-sense gRNAs, viral subgenomic transcripts and structural proteins needed for viral replication. Thus, PolyP120 impairs infection MESHD and replication of Korean and European (containing non-synonymous variants) SARS-CoV-2 strains. As PolyPs have no toxic activities, we envision their use as a nebulised formula for oropharyngeal delivery to prevent infections of SARS-CoV-2 and during early phases of antiviral therapy.

    Approach Towards Drugs Repurposing: Docking Studies with Multiple Target Proteins Associated with SARS-CoV-2

    Authors: Shiwani Rana; Meghali Panwar; Kalyan Sundar Ghosh

    doi:10.26434/chemrxiv.12469172.v2 Date: 2020-11-09 Source: ChemRxiv

    The current pandemic outbreak of COVID-19 MESHD due to viral infections MESHD by SARS-CoV-2 is now become associated with severe commotion on global healthcare and economy. In this extreme situation when vaccine or drugs against COVID-19 MESHD are not available, the only quick and feasible therapeutic alternative would be the drug repurposing approach. In the present work, in silico screening of some antiviral and antiprotozoal drugs using Autodock docking tool was performed. Two known antiviral drugs sorivudine and noricumazole B are predicted to bind to the active site of the viral proteases namely cysteine like protease PROTEIN or 3CL protease PROTEIN ( 3CLpro PROTEIN) and papain like protease PROTEIN ( PLpro PROTEIN) respectively with a highly favorable free energy of binding. Further, the promising molecules were subjected for checking their activity on other molecular targets like spike protein S1 PROTEIN, RNA dependent RNA polymerase PROTEIN ( RdRp PROTEIN) and angiotensin converting enzyme 2 HGNC ( ACE2 HGNC) receptor. But the compounds were found not effective on rest other molecular targets.

    in vitro: Natural Compounds (Thymol, Carvacrol, Hesperidine, And Thymoquinone) Against SARS-CoV2 Strain Isolated From Egyptian Patients

    Authors: Mohamed Gomaa Seadawy; Ahmed F Gad; Bassem E Harty; Mostfa Fetooh Mohamed; Mohamed Shamel ELdesoky; Abdo A Elfiky; Aya Ahmed; Abdel N Zekri; Elitza S Theel; Ali H Ellebedy; Daved H Fremont; Michael S Diamond; Sean P. J. Whelan; Gius Kerster; Hannah L Turner; Karlijn van der Straten; Cynthia A. van der Linden; Yoann Aldon; Thibaut Naninck; Ilja Bontjer; Judith A. Burger; Meliawati Poniman; Anna Z Mykytyn; Nisreen M.A. Okba; Edith E. Schermer; Marielle J. van Breemen; Rashmi Ravichandran; Tom G. Caniels; Jelle van Schooten; Nidhal Kahlaoui; Vanessa Contreras; Julien Lemaitre; Catherine Chapon; Raphael Ho Tsong Fang; Julien Villaudy; Kwinten Sliepen; Yme U. van der Velden; Bart Haagmans; Godelieve J. de Bree; Eric Ginoux; Andrew B. Ward; Max Crispin; Neil P King; Sylvie van der Werf; Marit J. van Gils; Roger Le Grand; Rogier W. Sanders

    doi:10.1101/2020.11.07.367649 Date: 2020-11-08 Source: bioRxiv

    The current pandemic of the coronavirus disease-2019 ( COVID-19 MESHD) has badly affected our life during the year 2020. SARS-CoV-2 is the primary causative agent of the newly emerged pandemic. Natural flavonoids, Terpenoid and Thymoquinone are tested against different viral and host-cell protein targets. These natural compounds have a good history in treating Hepatitis C Virus MESHD ( HCV MESHD) and Human Immunodeficiency Virus (HIV) MESHD. Molecular docking combined with cytotoxicity MESHD and plaque reduction assay is used to test the natural compounds against different viral (Spike, RdRp PROTEIN, and Mpro PROTEIN) and host-cell (TMPRSS II, keap 1 HGNC, and ACE2 HGNC) targets. The results demonstrate the binding possibility of the natural compounds (Thymol, Carvacrol, Hesperidine, and Thymoquinone) to the viral main protease PROTEIN ( Mpro PROTEIN). Some of these natural compounds were approved to start clinical trail from Egypt Center for Research and Regenerative Medicine ECRRM IRB (Certificate No.IRB00012517)

    Natural Compounds (Thymol, Carvacrol, Hesperidine, and Thymoquinone) Against SARS-CoV-2 Strain Isolated From Egyptian Patients

    Authors: Mohamed Seadawy

    doi:10.21203/rs.3.rs-101405/v1 Date: 2020-11-01 Source: ResearchSquare

    The current pandemic of the coronavirus disease-2019 ( COVID-19 MESHD) has badly affected our life during the year 2020. SARS-CoV-2 is the primary causative agent of the newly emerged pandemic. Natural flavonoids, Terpenoid and Thymoquinone are tested against different viral and host-cell protein targets. These natural compounds have a good history in treating Hepatitis C Virus MESHD ( HCV MESHD) and Human Immunodeficiency Virus (HIV) MESHD. Molecular docking combined with cytotoxicity MESHD and plaque reduction assay is used to test the natural compounds against different viral (Spike, RdRp PROTEIN, and Mpro PROTEIN) and host-cell (TMPRSS II, keap 1 HGNC, and ACE2 HGNC) targets. The results demonstrate the binding possibility of the natural compounds (Thymol, Carvacrol, Hesperidine, and Thymoquinone) to the viral main protease PROTEIN ( Mpro PROTEIN). Some of these natural compounds were approved to start clinical trail from Egypt Center for Research and Regenerative Medicine ECRRM IRB (Certificate No.IRB00012517)

    Discovery of Natural Phenol Catechin as a Multitargeted Agent Against SARS-CoV-2 For the Plausible Therapy of COVID-19 MESHD

    Authors: Chandra Bhushan Mishra; Preeti Pandey; Ravi Datta Sharma; Raj Kumar Mongre; Andrew M Lynn; Rajendra Prasad; Raok Jeon; Amresh Prakash

    doi:10.26434/chemrxiv.12752402.v1 Date: 2020-08-04 Source: ChemRxiv

    The global pandemic crisis, COVID-19 MESHD caused by severe acute respiratory syndrome coronavirus MESHD 2 (SARS-CoV-2) has claimed the lives of millions of people across the world. Development and testing of anti-SARS-CoV-2 drugs or vaccines, are not turned to be realistic in the timeframe needed to combat this pandemic. Thus, rigorous efforts are still ongoing for the drug repurposing as a clinical treatment strategy to control COVID-19 MESHD. Here we report a comprehensive computational approach to identify the multi-targeted drug molecules against the SARS-CoV-2 proteins, which are crucially involved in the viral-host interaction, replication of the virus inside the host, disease progression and transmission of coronavirus infection. Virtual screening of 72 FDA approved potential antiviral drugs against the target proteins: Spike (S PROTEIN) glycoprotein, human angiotensin-converting enzyme 2 ( hACE2 HGNC), 3-chymotrypsin- like cysteine protease PROTEIN ( 3CLpro PROTEIN), Cathepsin L HGNC, Nucleocapsid protein PROTEIN, RNA-dependent RNA polymerase PROTEIN ( RdRp PROTEIN) and nonstructural protein 6 ( NSP6 PROTEIN) resulted in the selection of seven drugs which preferentially binds to the target proteins. Further, the molecular interactions determined by MD simulation, free energy landscape and the binding free energy estimation, using MM-PBSA revealed that among 72 drug molecules, catechin (flavan-3-ol) can effectively bind to 3CLpro PROTEIN, Cathepsin L HGNC, RBD of S protein PROTEIN, NSP-6, and Nucleocapsid protein PROTEIN. It is more conveniently involved in key molecular interactions, showing binding free energy (ΔGbind) in the range of -5.09 kcal/mol ( Cathepsin L HGNC) to -26.09 kcal/mol ( NSP6 PROTEIN). At the binding pocket, catechin is majorly stabilized by the hydrophobic interactions, displays ΔEvdW values -7.59 to -37.39 kcal/mol. Thus, the structural insights of better binding affinity and favourable molecular interaction of catechin towards multiple target proteins, signifies that catechin can be potentially explored as a multitargeted agent in the rational design of effective therapies against COVID-19 MESHD.

    The genetic variants analysis of circulating SARS-CoV-2 in Bangladesh.

    Authors: Abu Sayeed Mohammad Mahmud; Tarannum Taznin; Md. Murshed Hasan Sarkar; Mohammad Samir Uzzaman; Eshrar Osman; Md. Ahasan Habib; Shahina Akter; Tanjina Akhter Banu; Barna Goswami; Iffat Jahan; Md. Saddam Hossain; Md. Salim Khan

    doi:10.1101/2020.07.29.226555 Date: 2020-07-29 Source: bioRxiv

    Genomic mutation of the virus may impact the viral adaptation to the local environment, their transmission, disease manifestation, and the effectiveness of existing treatment and vaccination. The objectives of this study were to characterize genomic variations, non-synonymous amino acid substitutions, especially in target proteins, mutation events per samples, mutation rate, and overall scenario of coronaviruses across the country. To investigate the genetic diversity, a total of 184 genomes of virus strains sampled from different divisions of Bangladesh with sampling dates between the 10th of May 2020 and the 27th of June 2020 were analyzed. To date, a total of 634 mutations located along the entire genome resulting in non-synonymous 274 amino acid substitutions in 22 different proteins were detected with nucleotide mutation rate estimated to be 23.715 substitutions per year. The highest non-synonymous amino acid substitutions were observed at 48 different positions of the papain-like protease PROTEIN ( nsp3 HGNC). Although no mutations were found in nsp7, nsp9, nsp10, and nsp11, yet orf1ab accounts for 56% of total mutations. Among the structural proteins, the highest non-synonymous amino acid substitution (at 36 positions) observed in spike proteins PROTEIN, in which 9 unique locations were detected relative to the global strains, including 516E>Q in the boundary of the ACE2 HGNC binding region. The most dominated variant G614 (95%) based in spike protein PROTEIN is circulating across the country with co-evolving other variants including L323 (94%) in RNA dependent RNA polymerase PROTEIN ( RdRp PROTEIN), K203 (82%) and R204 (82%) in nucleocapsid, and F120 (78%) in NSP2 PROTEIN NSP2 HGNC. These variants are mostly seen as linked mutations and are part of a haplotype observed in Europe. Data suggest effective containment of clade G strains (4.8%) with sub-clusters GR 82.4%, and GH clade 6.4%. HighlightsO_LIWe have sequenced 137 and analyzed 184 whole-genomes sequences of SARS-CoV-2 strains from different divisions of Bangladesh. C_LIO_LIA total of 634 mutation sites across the SARS-CoV-2 genome and 274 non-synonymous amino acid substitutions were detected. C_LIO_LIThe mutation rate of SARS-CoV-2 estimated to be 23.715 nucleotide substitutions per year. C_LIO_LINine unique variants were detected based on non-anonymous amino acid substitutions in spike protein PROTEIN relative to the global SARS-CoV-2 strains. C_LI

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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