Scrutinizing the SARS-CoV-2 protein information for the designing an effective vaccine encompassing both the T-cell and B-cell epitopes

Jain, Neha; Shankar, Uma; Majee, Prativa; Kumar, Amit

doi:10.1101/2020.03.26.009209

Cited by 9 publications

(6 citation statements)

References 69 publications

(58 reference statements)

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“…(71) Furthermore, various studies predicted multiepitopes or numerous vaccine candidates for SARS-CoV-2 infections using the computational approach as represented by different preprints. (72)(73)(74)(75)(76) The question, why another study for designing an epitope-based vaccine against COVID-19, arises. Best to our knowledge, none of the existing studies identifies epitopes that can activate both innate and adaptive immune systems.…”

Section: Comparison With Previous Studiesmentioning

confidence: 99%

A Web-Based Platform on Coronavirus Disease-19 to Maintain Predicted Diagnostic, Drug, and Vaccine Candidates

Patiyal

Kaur

et al. 2020

Monoclonal Antibodies in Immunodiagnosis and Immunotherapy

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A web-based resource CoronaVIR (https://webs.iiitd.edu.in/raghava/coronavir/) has been developed to maintain the predicted and existing information on coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We have integrated multiple modules, including ''Genomics,'' ''Diagnosis,'' ''Immunotherapy,'' and ''Drug Designing'' to understand the holistic view of this pandemic medical disaster. The genomics module provides genomic information of different strains of this virus to understand genomic level alterations. The diagnosis module includes detailed information on currently-in-use diagnostics tests as well as five novel universal primer sets predicted using in silico tools. The Immunotherapy module provides information on epitope-based potential vaccine candidates (e.g., LQLPQGTTLPKGFYA, VILLNKHIDAYKTFPPTEPKKDK KKK, EITVATSRTLS, GKGQQQQGQTV, SELVIGAVILR) predicted using state-of-the-art software and resources in the field of immune informatics. These epitopes have the potential to activate both adaptive (e.g., B cell and T cell) and innate (e.g., vaccine adjuvants) immune systems as well as suitable for all strains of SARS-CoV-2. Besides, we have also predicted potential candidates for siRNA-based therapy and RNA-based vaccine adjuvants. The drug designing module maintains information about potential drug targets, tertiary structures, and potential drug molecules. These potential drug molecules were identified from FDA-approved drugs using the docking-based approach. We also compiled information from the literature and Internet on potential drugs, repurposing drugs, and monoclonal antibodies. To understand host-virus interaction, we identified cell-penetrating peptides in the virus. In this study, state-of-the-art techniques have been used for predicting the potential candidates for diagnostics and therapeutics.

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Section: Comparison With Previous Studiesmentioning

confidence: 99%

A Web-Based Platform on Coronavirus Disease-19 to Maintain Predicted Diagnostic, Drug, and Vaccine Candidates

Patiyal

Kaur

et al. 2020

Monoclonal Antibodies in Immunodiagnosis and Immunotherapy

View full text Add to dashboard Cite

show abstract

“…Currently, the quest for effective vaccine design against COVID-19 is increasing among (57). Furthermore, various studies predicted multi-epitopes or numerous vaccine candidates for SARS-COV-2 infections using the computational approach as represented by different pre-prints (58)(59)(60)(61)(62). The question arises, why another study for designing an epitope-based vaccine against COVID-19.…”

Section: Comparison With Previous Studiesmentioning

confidence: 99%

A web-based platform on COVID-19 to maintain Predicted Diagnostic, Drug and Vaccine candidates

Patiyal¹,

Kaur²,

Kaur³

et al. 2020

Preprint

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A web-based resource CoronaVIR (https://webs.iiitd.edu.in/raghava/coronavir/) has been developed to maintain predicted and existing information on coronavirus SARS-CoV-2. We have integrated multiple modules including “Genomics”, “Diagnosis”, “Immunotherapy” and “Drug Designing” to understand the holistic view of this pandemic medical disaster. Genomics module provides genomic information of different strains of this virus to understand genomic level alterations. The Diagnosis module provides detailed information on currently-in-use diagnostics tests as well as on five novel universal primers-sets predicted using in silico tools. The Immunotherapy module provides information on epitope-based potential vaccine candidates (e.g., LQLPQGTTLPKGFYA, VILLNKHIDAYKTFPPTEPKKDKKKK, EITVATSRTLS, GKGQQQQGQTV, SELVIGAVILR) predicted using state-of-the-art software and resources in the field of immune-informatic. These epitopes have the potential to activate both adaptive (e.g., B-cell, T-cell) and innate (e.g., vaccine adjuvants) immune systems as well suitable for all strains of SARS-CoV-2. Besides, we have also predicted potential candidates for siRNA-based therapy and RNA based vaccine adjuvants. The Drug Designing module maintains information about potential drug targets, tertiary structures, and potential drug molecules. These potential drug molecules were identified from FDA approved drugs using the docking-based approach. We also compiled information from the literature and the Internet on potential drugs, repurposing drugs and monoclonal antibodies. To understand host-virus interaction, we identified cell-penetrating peptides in the virus. In this study, state-of-the-art techniques have been used for predicting the potential candidates for diagnostics and therapeutics.

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“…Intrestingly, unlike B cells, which mainly target accessible proteins like S proteins or nucleocapsid phosphoprotein (N proteins) in SARS-COV-2, T cells can target all of viral proteins in SARS-COV-2 proteome. More importantly, the T cell responses could be less affected by the mutations, and some of T cell epitopes distributed in the SARS-COV-2 proteome seem more stable than the B cell epitopes (21,22). Therefore, SARS-CoV-2 vaccines capable of activating both CD4 + and CD8 + T cells are likely to induce the protection of SARS-CoV-2 variants.…”

Section: Introductionmentioning

confidence: 99%

Conserved T-cell epitopes predicted by bioinformatics in SARS-COV-2 variants

Wang

et al. 2021

Preprint

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Background: Finding conservative T cell epitopes in the proteome of numerous variants of SARS-COV-2 is required to develop T cell activating SARS-COV-2 capable of inducing T cell responses against SARS-COV-2 variants. Methods: A computational workflow was performed to find HLA restricted CD8+ and CD4+ T cell epitopes among conserved amino acid sequences across the proteome of 474727 SARS-CoV-2 strains. Results: A batch of covserved regions in the amino acid sequences were found in the proteome of the SARS-COV-2 strains. 2852 and 847 peptides were predicted to have high binding affinity to distint HLA class I and class II molecules. Among them, 1456 and 484 peptides are antigenic. 392 and 111 of the antigenic peptides were found in the conseved amino acid sequences. Among the antigenic-conserved peptides, 6 CD8+ T cell epitopes and 7 CD4+ T cell epitopes were identifed. The T cell epitopes could be presented to T cells by high-affinity HLA molecules which are encoded by the HLA alleles with high population coverage. Conclusions: The T cell epitopes are conservative, antigenic and HLA presentable, and could be constructed into SARS-COV-2 vaccines for inducing protective T cell immunity against SARS-COV-2 and their variants.

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Scrutinizing the SARS-CoV-2 protein information for the designing an effective vaccine encompassing both the T-cell and B-cell epitopes

Cited by 9 publications

References 69 publications

A Web-Based Platform on Coronavirus Disease-19 to Maintain Predicted Diagnostic, Drug, and Vaccine Candidates

A Web-Based Platform on Coronavirus Disease-19 to Maintain Predicted Diagnostic, Drug, and Vaccine Candidates

A web-based platform on COVID-19 to maintain Predicted Diagnostic, Drug and Vaccine candidates

Conserved T-cell epitopes predicted by bioinformatics in SARS-COV-2 variants

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