The Immune Epitope Database (IEDB): 2018 update

Vita, Randi; Mahajan, Swapnil; Overton, James A.; Dhanda, Sandeep Kumar; Martini, Sheridan; Cantrell, Jason R; Wheeler, Daniel K.; Sette, Alessandro; Peters, Bjoern

doi:10.1093/nar/gky1006

Cited by 1,475 publications

(1,521 citation statements)

References 21 publications

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“…When examining the homologous regions of SARS-CoV, it has been found that the likely T cell epitopes are positive in assays such as ELISPOT, intra-cellular staining (ICS), and multimer/tetramer staining (see, e.g., Cheung et al, 2007Cheung et al, , 2008Kohyama et al, 2009;Tsao et al, 2006;Yang et al, 2009). We also sought to address potential SARS-CoV-2 epitopes by a completely different method, namely utilizing the epitope predictions hosted by the IEDB Vita et al, 2019). For B cell epitopes, we used methods that predict linear epitopes , and in the case of the spike glycoprotein where a reliable structure recently became available (Wrapp et al, 2020), the Discotope 2.0 method that also predicts epitopes based on protein conformation and residue exposure.…”

Section: Discussionmentioning

confidence: 99%

A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2

Grifoni

Sidney

Zhang

et al. 2020

Cell Host & Microbe

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957

1,202

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Graphical Abstract Highlights d Ten experimentally defined regions within SARS-CoV have high homology with SARS-CoV-2 d Parallel bioinformatics predicted potential B and T cell epitopes for SARS-CoV-2 d Independent approaches identified the same immunodominant regions d The conserved immune regions have implications for vaccine design against multiple CoVs SUMMARYEffective countermeasures against the recent emergence and rapid expansion of the 2019 novel coronavirus (SARS-CoV-2) require the development of data and tools to understand and monitor its spread and immune responses to it. However, little information is available about the targets of immune responses to SARS-CoV-2. We used the Immune Epitope Database and Analysis Resource (IEDB) to catalog available data related to other coronaviruses. This includes SARS-CoV, which has high sequence similarity to SARS-CoV-2 and is the best-characterized coronavirus in terms of epitope responses. We identified multiple specific regions in SARS-CoV-2 that have high homology to the SARS-CoV virus. Parallel bioinformatic predictions identified a priori potential B and T cell epitopes for SARS-CoV-2. The independent identification of the same regions using two approaches reflects the high probability that these regions are promising targets for immune recognition of SARS-CoV-2. These predictions can facilitate effective vaccine design against this virus of high priority.

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Section: Discussionmentioning

confidence: 99%

A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2

Grifoni

Sidney

Zhang

et al. 2020

Cell Host & Microbe

Self Cite

957

1,202

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“…Population coverages for sets of T cell epitopes were computed using the tool provided by the Immune Epitope Database (IEDB) (http://tools.iedb.org/population/; accessed 21 February 2020) [30]. This tool uses the distribution of MHC alleles (with at least 4-digit resolution, e.g., A*02:01) within a defined population (obtained from http://www.allelefrequencies.net/) to estimate the population coverage for a set of T cell epitopes.…”

Section: Population-coverage-based T Cell Epitope Selectionmentioning

confidence: 99%

Preliminary Identification of Potential Vaccine Targets for the COVID-19 Coronavirus (SARS-CoV-2) Based on SARS-CoV Immunological Studies

Ahmed

Quadeer

McKay

2020

Viruses

1,029

899

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A.A.Q); m.mckay@ust.hk (M.R.M.) † These authors contributed equally to this work.Abstract: The beginning of 2020 has seen the emergence of COVID-19 outbreak caused by a novel coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). There is an imminent need to better understand this new virus and to develop ways to control its spread. In this study, we sought to gain insights for vaccine design against SARS-CoV-2 by considering the high genetic similarity between SARS-CoV-2 and SARS-CoV, which caused the outbreak in 2003, and leveraging existing immunological studies of SARS-CoV. By screening the experimentally-determined SARS-CoV-derived B cell and T cell epitopes in the immunogenic structural proteins of SARS-CoV, we identified a set of B cell and T cell epitopes derived from the spike (S) and nucleocapsid (N) proteins that map identically to SARS-CoV-2 proteins. As no mutation has been observed in these identified epitopes among the 120 available SARS-CoV-2 sequences (as of 21 February 2020), immune targeting of these epitopes may potentially offer protection against this novel virus. For the T cell epitopes, we performed a population coverage analysis of the associated MHC alleles and proposed a set of epitopes that is estimated to provide broad coverage globally, as well as in China. Our findings provide a screened set of epitopes that can help guide experimental efforts towards the development of vaccines against SARS-CoV-2.

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“…To review how extensive our descriptive knowledge of CD8 + T cell responses is, we can turn to the great wealth of published epitope data reported in the Immune Epitope Database (IEDB; http://www.iedb.org), an online repository established in 2004 and kept up‐to‐date through manual curation . The IEDB primarily contains experimentally verified data on T and B cell assays as well as MHC binding and mass spectrometry identification of MHC‐ligands . The IEDB therefore presents an essential resource to assess metadata on T cell immunogenicity ( Figure 1).…”

Section: Cd8+ T Cell Responses Are Well Characterizedmentioning

confidence: 99%

Peptide Presentation to T Cells: Solving the Immunogenic Puzzle

Croft

2020

BioEssays

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The vertebrate immune system uses an impressive arsenal of mechanisms to combat harmful cellular states such as infection. One way is via cells delivering real‐time snapshots of their protein content to the cell surface in the form of short peptides. Specialized immune cells (T cells) sample these peptides and assess whether they are foreign, warranting an action such as destruction of the infected cell. The delivery of peptides to the cell surface is termed antigen processing and presentation, and decades of research have provided unprecedented understanding of this process. However, predicting the capacity for a given peptide to be immunogenic—to elicit a T cell response—has remained both enigmatic and a long sought‐after goal. In the era of big data, a point is being approached where the steps of antigen processing and presentation can be quantified and assessed against peptide immunogenicity in order to build predictive models. This review presents new findings in this area and contemplates challenges ahead.

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The Immune Epitope Database (IEDB): 2018 update

Cited by 1,475 publications

References 21 publications

A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2

A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2

Preliminary Identification of Potential Vaccine Targets for the COVID-19 Coronavirus (SARS-CoV-2) Based on SARS-CoV Immunological Studies

Peptide Presentation to T Cells: Solving the Immunogenic Puzzle

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