Scrutinizing the SARS-CoV-2 protein information for designing an effective vaccine encompassing both the T-cell and B-cell epitopes.
TL;DR: This present study provides an initial platform for the rapid generation of an efficacious protective vaccine for combating COVID-19 and reveals the plausibility of the high expression and easy purification of the vaccine product.
About: This article is published in Infection, Genetics and Evolution.The article was published on 2021-01-01 and is currently open access. It has received 8 citations till now.
Citations
More filters
TL;DR: Wang et al. as discussed by the authors designed an effective multi-epitope vaccine against SARS-COV-2 using the reverse vaccinology method, which was analyzed for the properties of physicochemical, antigenicity, and allergenicity.
9 citations
TL;DR: In this article, the authors tried to depict the current scenario of immunoinformatics and bioinformatics in COVID-19 vaccine research and designed the next-generation COVID19 vaccines using these approaches.
Abstract: Presently, immunoinformatics and bioinformatics approaches are contributing actively to COVID-19 vaccine research. The first immunoinformatics-based vaccine construct against SARS-CoV-2 was published in February 2020. Following this, immunoinformatics and bioinformatics approaches have created a new direction in COVID-19 vaccine research. Several researchers have designed the next-generation COVID-19 vaccines using these approaches. Presently, immunoinformatics has accelerated immunology research immensely in the area of COVID-19. Hence, we have tried to depict the current scenario of immunoinformatics and bioinformatics in COVID-19 vaccine research.
6 citations
TL;DR: In this paper , the authors predicted SARS-CoV-2-specific CD8+ T cell epitopes from the main variants of concern and their potential to trigger or hinder T cell response by using HLA binding and TCR reactivity in silico predictions.
5 citations
TL;DR: In this paper, the authors investigated the SARS-CoV-2-specific CD8+ T cell epitopes from the main variants of concern and the potential of associated mutations to trigger or hinder T-cells response.
Abstract: BackgroundMany SARS-CoV-2 variants of concern have emerged since the Covid-19 outburst, notably the lineages detected in the UK, South Africa, and Brazil. Their increased transmissibility and higher viral load put them in the spotlight. Much has been investigated on the ability of those new variants to evade antibody recognition. However, not enough attention has been given to pre-existing and induced SARS-CoV-2-specific CD8+ T cell responses during the natural course of infection by new lineages. MethodsIn this work, we investigated the SARS-CoV-2-specific CD8+ T cell epitopes from the main variants of concern and the potential of associated mutations to trigger or hinder CD8+ T-cells response. We also estimated the populations coverage of these different lineages, considering peptide binding predictions to class I HLA alleles from 29 countries to investigate differences in the fraction of individuals expected to respond to a given epitope set from new and previous lineages. ResultsWe observed a lower populational coverage for 20B/S.484K (P.2 lineage) in contrast to an increased coverage found for 20H/501Y.V2 (B.1.351 Lineage) and 20J/501Y.V3 (P.1 lineage) compared to a reference lineage. Moreover, mutations such as Spike N501Y and Nucleocapsid T205I were predicted to have an overall higher affinity through HLA-I than the reference sequence. ConclusionsIn summary, the data in this work provided evidence for the existence of potentially immunogenic and conserved epitopes across new SARS-CoV-2 variants, but also highlights the reduced populationals coverage for the Brazilian lineage P.2, suggesting its potential to evade from CD8+ T-cell responses. Our results also may guide efforts to characterize and validate relevant peptides to trigger CD8+ T-cell responses, and design new universal T-cell-inducing vaccine candidates that minimize detrimental effects of viral diversification and at the same time induce responses to a broad human population.
5 citations
TL;DR: Combined with 3D protein modeling, this study predicted the epitopes of E1A CR2 protein in HAdVs and revealed the safety and efficacy of the predicted vaccine construct.
Abstract: Background and Objectives: Adenovirus species B, C, D, and E are the most common causes of ocular manifestations caused by adenoviruses. FDA-approved treatment agents for adenovirus infections are not available. Cell-mediated immunity is the major protective mechanism versus human adenoviruses (HAdVs) infection and T cells specific for peptide epitopes from nonstructural proteins can prevent adenoviral dissemination. E1A CR2 region of HAdVs Epitopes predicted for reinforcing cytotoxic T lymphocytes (CTLs) in the EKC patients. Among human adenoviruses E1 protein, four distinct E1A regions had a significantly higher level of homology than the rest of E1A protein. E1A protein inhibits IFN signal transduction. Epitope-based vaccines are designed to have flexible and simple methods to synthesize a vaccine, using an adjuvant to trigger fast immune responses. CTL epitopes were applied to create a multiepitope vaccine. Conserve region1 (CR1) and CR3 have less antigenicity compared to CR2. Additionally, CR3 in HAdV-D8 contains three toxic areas. CR4 similar to the two regions CR1 and CR3 do not show acceptable antigenic properties. Materials and Methods: Bioinformatics’ tools were used to predict, refine and validate the 3D structure of the construct. Effective binding was predicted by protein-protein docking of the epitope vaccine with MHC-I molecules and revealed the safety and efficacy of the predicted vaccine construct. Results: In silico analysis show that rising levels of cytotoxic CD8 + T cells, TH1 cells, macrophages, and neutrophils are linked to IFN-dominant TH1-type responses, which are detected in putative immune individuals. Conclusion: Combined with 3D protein modeling, this study predicted the epitopes of E1A CR2 protein in HAdVs.
1 citations
References
More filters
TL;DR: The phylogenetic analysis suggests that bats might be the original host of this virus, an animal sold at the seafood market in Wuhan might represent an intermediate host facilitating the emergence of the virus in humans.
9,474 citations
"Scrutinizing the SARS-CoV-2 protein..." refers background in this paper
...3% sequence similarity while bat-SL-CoVZC45 and bat-SL-CoVZXC21 exhibit about 88% identity with the SARS-CoV-2 virus, but the other two pathogenic coronaviruses, SARS-CoV and MERS-CoV have less sequence identity being merely 79% and 50% respectively[3]....
[...]
TL;DR: It is clear that finding an effective antiviral and developing a vaccine are still significant challenges, as the SARS-CoV-2 virus has led to significant sociological, psychological and economic effects globally.
769 citations
TL;DR: The current knowledge of the roles TLRs play in antiviral innate immune responses is reviewed, examples of TLR-mediated viral recognition are discussed, and strategies used by viruses to antagonize the host antiviral inherent immune responses are described.
516 citations
"Scrutinizing the SARS-CoV-2 protein..." refers background in this paper
...TLR3 acts as a nucleic acid sensor and helps in recognizing RNA and DNA viruses inside the human body and establishes a protective role against these infectious agents[33]....
[...]
TL;DR: The progress made in the past decade in understanding the cross-species transmission of SARS- coV and MERS-CoV is summarized by focusing on the features of the S protein, its receptor-binding characteristics, and the cleavage process involved in priming.
487 citations
"Scrutinizing the SARS-CoV-2 protein..." refers background in this paper
...Mutations in spike protein have been reported to be responsible for the change in host cell tropism[7] and result in antibody-dependent enhancement (ADE)[8]....
[...]
TL;DR: The results show that these measures likely slowed the rate of exportation from mainland China to other countries, but are insufficient to contain the global spread of COVID-19, and suggest that rapid contact tracing is essential both within the epicenter and at importation sites to limit human-to-human transmission outside of mainland China.
Abstract: The novel coronavirus outbreak (COVID-19) in mainland China has rapidly spread across the globe. Within 2 mo since the outbreak was first reported on December 31, 2019, a total of 566 Severe Acute Respiratory Syndrome (SARS CoV-2) cases have been confirmed in 26 other countries. Travel restrictions and border control measures have been enforced in China and other countries to limit the spread of the outbreak. We estimate the impact of these control measures and investigate the role of the airport travel network on the global spread of the COVID-19 outbreak. Our results show that the daily risk of exporting at least a single SARS CoV-2 case from mainland China via international travel exceeded 95% on January 13, 2020. We found that 779 cases (95% CI: 632 to 967) would have been exported by February 15, 2020 without any border or travel restrictions and that the travel lockdowns enforced by the Chinese government averted 70.5% (95% CI: 68.8 to 72.0%) of these cases. In addition, during the first three and a half weeks of implementation, the travel restrictions decreased the daily rate of exportation by 81.3% (95% CI: 80.5 to 82.1%), on average. At this early stage of the epidemic, reduction in the rate of exportation could delay the importation of cases into cities unaffected by the COVID-19 outbreak, buying time to coordinate an appropriate public health response.
432 citations