scholarly journals Bioinformatics analysis of the recent MERS-CoV with special reference to the virus-encoded Spike protein

2015 ◽  
Vol 01 (01) ◽  
Author(s):  
Mahmoud Kandeel
Keyword(s):  
Special Reference ◽  
Bioinformatics Analysis ◽  
Spike Protein

scholarly journals Bioinformatics Analysis of Allele Frequencies and Expression Patterns of ACE2, TMPRSS2 and FURIN in Different Populations and Susceptibility to SARS-CoV-2

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1041
Author(s):  
Mohammad Tarek ◽  
Hana Abdelzaher ◽  
Firas Kobeissy ◽  
Hassan A. N. El-Fawal ◽  
Mohammed M. Salama ◽  
...  
Keyword(s):  
Immune Response ◽  
Genetic Factors ◽  
Bioinformatics Analysis ◽  
Expression Patterns ◽  
Spike Protein ◽  
Target Cells ◽  
Health Crisis ◽  
Expression Levels ◽  
Different Populations ◽  
Shed Light

The virus responsible for the COVID-19 global health crisis, SARS-CoV-2, has been shown to utilize the ACE2 protein as an entry point to its target cells. The virus has been shown to rely on the actions of TMPRSS2 (a serine protease), as well as FURIN (a peptidase), for the critical priming of its spike protein. It has been postulated that variations in the sequence and expression of SARS-CoV-2’s receptor (ACE2) and the two priming proteases (TMPRSS2 and FURIN) may be critical in contributing to SARS-CoV-2 infectivity. This study aims to examine the different expression levels of FURIN in various tissues and age ranges in light of ACE2 and TMPRSS2 expression levels using the LungMAP database. Furthermore, we retrieved expression quantitative trait loci (eQTLs) of the three genes and their annotation. We analyzed the frequency of the retrieved variants in data from various populations and compared it to the Egyptian population. We highlight FURIN’s potential interplay with the immune response to SARS-CoV-2 and showcase a myriad of variants of the three genes that are differentially expressed across populations. Our findings provide insights into potential genetic factors that impact SARS-CoV-2 infectivity in different populations and shed light on the varying expression patterns of FURIN.

scholarly journals A48 Identification and full-genome characterization of Alpha- and Beta-Coronaviruses viruses from bats in Italy

2019 ◽  
Vol 5 (Supplement_1) ◽  
Author(s):  
L De Sabato ◽  
G Vaccari ◽  
D Lelli ◽  
A Lavazza ◽  
M R Castrucci ◽  
...  
Keyword(s):  
Bioinformatics Analysis ◽  
Phylogenetic Analyses ◽  
3D Structure ◽  
Data Bank ◽  
Spike Protein ◽  
Online Tool ◽  
Surveillance Studies ◽  
Generation Sequencing ◽  
Human Receptor

Abstract Bats are the natural reservoir of Coronaviruses (CoVs). Human CoVs cause mild respiratory diseases worldwide, but, in the last decade, two Beta-CoVs [Middle East respiratory syndrome (MERS)-CoV and severe acute respiratory syndrome] caused thousands of deaths and cases worldwide. Phylogenetic analysis suggested the evolutionary origin of mammalian CoVs is derived from bats. In this study, we characterized three Alpha-CoVs and two Beta-CoVs demonstrating the circulation of bat strains in Italy. Isolates were sequenced using a next-generation sequencing approach and genomes reconstructed using the online tool Galaxy Aries. Phylogenetic analyses were conducted using MEGA7 and MrBayes. Similarity plots were generated using SSE v1.2. The structure of the receptor binding domain (RBD) in the S protein was predicted by sequence-homology method using the protein data bank. Bioinformatics analysis permitted the identification of 2 Beta-CoV complete genomes of 30 kb and three Alpha-CoV of 28 kb (named BatCoV-ITA1-5). BatCoV-ITA1 and 2 formed a monophyletic group with MERS-CoV sequences. The comparison of the concatenated domains within ORF1ab confirmed their classification into the MERS-CoV species. The 3D structure of RBD of Italian strains showed two amino acid deletions located in a region corresponding to the external subdomain of MERS-RBD. BatCoV-Ita3 and BatCoV-Ita4/5 were classified into two novel Alpha-CoV species by comparison of concatenated domains within ORF1ab. Due to the high divergence with the Alpha human spike protein strains, it was impossible to establish the protein structure and the potential affinity to human receptor. The Italian strains showed the typical organization of Alpha and Beta-CoVs. We reported two Beta-CoVs closely related to MERS-CoVs from bats belonging to common Italian species (Pipistrellus kuhlii and Hypsugo savii). The analysis of the RBD in the spike protein indicates significant differences from human RBD known to date. The three Alpha-CoV strains were classified into two novel species, confirming the high heterogeneity of CoV strains in bats. Although the studies conducted cannot confirm a risk for humans, surveillance studies are needed to investigate the genetic diversity of CoVs in bats. Because this exceeds what is known for other hosts, it is compatible with bats being the major reservoir of mammalian CoVs.

scholarly journals Shortening Epitopes to Survive: The Case of SARS-CoV-2 Lambda Variant

Biomolecules ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1494
Author(s):  
Stefano Pascarella ◽  
Massimo Ciccozzi ◽  
Martina Bianchi ◽  
Domenico Benvenuto ◽  
Marta Giovanetti ◽  
...  
Keyword(s):  
Bioinformatics Analysis ◽  
Adaptation Strategy ◽  
Spike Protein ◽  
South American ◽  
Glycosylation Sites ◽  
Immunogenic Epitope ◽  
In Silico Study ◽  
The Us ◽  
Potential Impact ◽  
The Stability

Among the more recently identified SARS-CoV-2 Variants of Interest (VOI) is the Lambda variant, which emerged in Peru and has rapidly spread to South American regions and the US. This variant remains poorly investigated, particularly regarding the effects of mutations on the thermodynamic parameters affecting the stability of the Spike protein and its Receptor Binding Domain. We report here an in silico study on the potential impact of the Spike protein mutations on the immuno-escape ability of the Lambda variant. Bioinformatics analysis suggests that a combination of shortening the immunogenic epitope loops and the generation of potential N-glycosylation sites may be a viable adaptation strategy, potentially allowing this emerging viral variant to escape from host immunity.

scholarly journals Bioinformatics analysis of epitope-based vaccine design against the novel SARS-CoV-2

2020 ◽  
Author(s):  
Hongzhi Chen ◽  
Lingli Tang ◽  
Xinling Yu ◽  
Jie Zhou ◽  
Yunfeng Chang ◽  
...  
Keyword(s):  
B Cell ◽  
Nucleocapsid Protein ◽  
Bioinformatics Analysis ◽  
Vaccine Development ◽  
Wide Spectrum ◽  
Cell Epitope ◽  
Spike Protein ◽  
B Cell Epitopes ◽  
Surface Accessibility ◽  
Binding Peptides

Abstract Background: An outbreak of infection caused by SARS-CoV-2 recently has brought a great challenge to public health. Rapid identification of immune epitopes would be an efficient way to screen the candidates for vaccine development at the time of pandemic. This study aimed to predict the protective epitopes with bioinformatics methods and resources for vaccine development. Methods: ABCpred and BepiPred servers were utilized for sequential B-cell epitope analysis. Discontinuous B-cell epitopes were predicted via DiscoTope 2.0 program. IEDB server was utilized for HLA-1 and HLA-2 binding peptides computation. Surface accessibility, antigenicity, and other important features of forecasted epitopes were characterized for immunogen potential evaluation. Results: A total of 63 sequential B-cell epitopes on spike protein were predicted and 4 peptides (Spike315-324, Spike333-338, Spike648-663, Spike1064-1079) exhibited high antigenicity score and good surface accessibility. 10 residues within spike protein (Gly496, Glu498, Pro499, Thr500, Leu1141, Gln1142, Pro1143, Glu1144, Leu1145, Asp1146) are forecasted as components of discontinuous B-cell epitopes. The bioinformatics analysis of HLA binding peptides within nucleocapsid protein produced 81 and 64 peptides being able to bind class-I and class-II molecule respectively. The peptides (Nucleocapsid66-75, Nucleocapsid104-112) were predicted to bind a wide spectrum of both HLA-1 and HLA-2 molecules. Conclusions: B-cell epitopes on spike protein and T-cell epitopes within nucleocapsid protein were identified and recommended for developing a protective vaccine against SARS-CoV-2.

scholarly journals Bioinformatics analysis of epitope-based vaccine design against the novel SARS-CoV-2

2020 ◽  
Author(s):  
Hongzhi Chen ◽  
Lingli Tang ◽  
Xinling Yu ◽  
Jie Zhou ◽  
Yunfeng Chang ◽  
...  
Keyword(s):  
B Cell ◽  
Mhc Class Ii ◽  
Nucleocapsid Protein ◽  
Bioinformatics Analysis ◽  
Vaccine Development ◽  
Cell Epitope ◽  
Spike Protein ◽  
B Cell Epitopes ◽  
Surface Accessibility ◽  
Binding Peptides

Abstract Background: An outbreak of infection caused by SARS-CoV-2 recently has brought a great challenge to public health. Rapid identification of immune epitopes would be an efficient way to screen the candidates for vaccine development at the time of pandemic. This study aimed to predict the protective epitopes with bioinformatics methods and resources for vaccine development. Methods : ABCpred and BepiPred servers were utilized for sequential B-cell epitope analysis. Discontinuous B-cell epitopes were predicted via DiscoTope 2.0 program. IEDB server was utilized for HLA-1 and HLA-2 binding peptides computation. Surface accessibility, antigenicity, and other important features of forecasted epitopes were characterized for immunogen potential evaluation. Results : A total of 63 sequential B-cell epitopes on spike protein were predicted and 4 peptides (Spike 315-324 , Spike 333-338 , Spike 648-663 , Spike 1064-1079 ) exhibited high antigenicity score and good surface accessibility. 10 residues within spike protein (Gly 496 , Glu 498 , Pro 499 , Thr 500 , Leu 1141 , Gln 1142 , Pro 1143 , Glu 1144 , Leu 1145 , Asp 1146 ) are forecasted as components of discontinuous B-cell epitopes. The bioinformatics analysis of HLA binding peptides within nucleocapsid protein produced 81 and 64 peptides being able to bind MHC class I and MHC class II molecule respectively. The peptides (Nucleocapsid 66-75 , Nucleocapsid 104-112 ) were predicted to bind a wide spectrum of both HLA-1 and HLA-2 molecules. Conclusions : B-cell epitopes on spike protein and T-cell epitopes within nucleocapsid protein were identified and recommended for developing a protective vaccine against SARS-CoV-2.

scholarly journals Mutation Prone Point Within Spike Protein Molecule of SARS-CoV2: A Nanoinformatics Study

2020 ◽  
Vol 10 (1) ◽  
pp. 1959-1961
Keyword(s):  
Amino Acid ◽  
Sequence Analysis ◽  
Amino Acid Sequence ◽  
Molecular Epidemiology ◽  
Bioinformatics Analysis ◽  
Protein Molecule ◽  
Spike Protein ◽  
Epidemiological Surveillance ◽  
Standard Tool ◽  
Novel Coronavirus

Coronavirus disease 2019 (COVID-19) is a new emerging infection caused by a novel coronavirus, SARS CoV2. The pandemic of COVID-19 causes several problems worldwide. The interesting data from epidemiological surveillance show that the mutated virus already occurs and might result in a more serious outbreak. In this study, a standard combined bioinformatics analysis for SARS CoV2 nanostructure analysis was performed. The present study aims to determine the risk for mutation within the amino acid sequence of SARS CoV2. The standard tool, namely GlobPlot, was used for sequence analysis. According to the present study, the prediction of the positions resistant to a mutation within the spike protein of SARS CoV2 is made. There are many identified prone positions. This finding can imply that there will be a further new mutated type of SARS CoV2 pathogen. Therefore, the system for continuous molecular epidemiology surveillance is required.

scholarly journals Bioinformatics analysis of epitope-based vaccine design against the novel SARS-CoV-2

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Hong-Zhi Chen ◽  
Ling-Li Tang ◽  
Xin-Ling Yu ◽  
Jie Zhou ◽  
Yun-Feng Chang ◽  
...  
Keyword(s):  
B Cell ◽  
Mhc Class Ii ◽  
Nucleocapsid Protein ◽  
Bioinformatics Analysis ◽  
Vaccine Development ◽  
Cell Epitope ◽  
Spike Protein ◽  
B Cell Epitopes ◽  
Surface Accessibility ◽  
Binding Peptides

Abstract Background An outbreak of infection caused by SARS-CoV-2 recently has brought a great challenge to public health. Rapid identification of immune epitopes would be an efficient way to screen the candidates for vaccine development at the time of pandemic. This study aimed to predict the protective epitopes with bioinformatics methods and resources for vaccine development. Methods The genome sequence and protein sequences of SARS-CoV-2 were retrieved from the National Center for Biotechnology Information (NCBI) database. ABCpred and BepiPred servers were utilized for sequential B-cell epitope analysis. Discontinuous B-cell epitopes were predicted via DiscoTope 2.0 program. IEDB server was utilized for HLA-1 and HLA-2 binding peptides computation. Surface accessibility, antigenicity, and other important features of forecasted epitopes were characterized for immunogen potential evaluation. Results A total of 63 sequential B-cell epitopes on spike protein were predicted and 4 peptides (Spike315–324, Spike333–338, Spike648–663, Spike1064–1079) exhibited high antigenicity score and good surface accessibility. Ten residues within spike protein (Gly496, Glu498, Pro499, Thr500, Leu1141, Gln1142, Pro1143, Glu1144, Leu1145, Asp1146) are forecasted as components of discontinuous B-cell epitopes. The bioinformatics analysis of HLA binding peptides within nucleocapsid protein produced 81 and 64 peptides being able to bind MHC class I and MHC class II molecules respectively. The peptides (Nucleocapsid66–75, Nucleocapsid104–112) were predicted to bind a wide spectrum of both HLA-1 and HLA-2 molecules. Conclusions B-cell epitopes on spike protein and T-cell epitopes within nucleocapsid protein were identified and recommended for developing a protective vaccine against SARS-CoV-2.

scholarly journals Docking of Velpatasvir to the SARS-CoV-2 Viral Spike Protein-Human ACE2 Complex: repurposing for COVID-19

2021 ◽  
Author(s):  
Asad Zia ◽  
Sohail Akhtar ◽  
Mubarak Ali Khan
Keyword(s):  
Bioinformatics Analysis ◽  
Drug Repurposing ◽  
Protein S ◽  
Spike Protein ◽  
World Health ◽  
Angiotensin Receptor ◽  
S Protein ◽  
Health Community ◽  
And Function ◽  
Clinical Drug

Abstract The SARS-CoV-2 outbreak has challenged the world health community and is still out of control. Since there is no clinical drug available for the corona virus therefore the most important and the fastest way of medicines development is to find potential molecules from the marketed drugs. Herein, bioinformatics analysis on the spike protein (S) of CoV and human angiotensin receptor 2 (ACE-2) with already approved anti-HCV approved drug velpatasvir have been reported. We conducted molecular docking to determine the mode of interaction of velpatasvir and RNA dependent RNA polymerase enzyme as well as inhibition of attachment of S-protein with human host receptor ACE-2. We found that, velpatasvir not only binds tightly with S-protein-ACE2 interface but also with 2019-Cov RdRp, can alter the structure and function of the said proteins and hence will results in the eradication of viral infection. The findings of this study further support the idea of drug repurposing and will help to classify the most successful drugs against COVID-19.

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