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

Effective 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 respon...

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Published in	Cell host & microbe Vol. 27; no. 4; pp. 671 - 680.e2
Main Authors	Grifoni, Alba, Sidney, John, Zhang, Yun, Scheuermann, Richard H., Peters, Bjoern, Sette, Alessandro
Format	Journal Article
Language	English
Published	United States Elsevier Inc 08.04.2020
Subjects	B cell epitope Betacoronavirus - genetics Betacoronavirus - immunology Computational Biology coronavirus Coronavirus Infections - immunology Coronavirus Infections - virology COVID-19 Databases, Protein Epitopes, B-Lymphocyte - genetics Epitopes, B-Lymphocyte - immunology Epitopes, T-Lymphocyte - genetics Epitopes, T-Lymphocyte - immunology Humans infectious disease Pandemics Pneumonia, Viral - immunology Pneumonia, Viral - virology SARS-CoV SARS-CoV-2 sequence conservation Sequence Homology T cell epitope COVID-19 B cell epitope sequence conservation SARS-CoV-2 infectious disease SARS-CoV coronavirus T cell epitope
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Abstract	Effective 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. [Display omitted] •Ten experimentally defined regions within SARS-CoV have high homology with SARS-CoV-2•Parallel bioinformatics predicted potential B and T cell epitopes for SARS-CoV-2•Independent approaches identified the same immunodominant regions•The conserved immune regions have implications for vaccine design against multiple CoVs Grifoni et al. identify potential targets for immune responses to the 2019 novel coronavirus (SARS-CoV-2) by sequence homology with closely related SARS-CoV and by a priori epitope prediction using bioinformatics approaches. This analysis provides essential information for understanding human immune responses to this virus and for evaluating diagnostic and vaccine candidates.
AbstractList	Effective 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.Effective 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. Effective 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. • Ten experimentally defined regions within SARS-CoV have high homology with SARS-CoV-2 • Parallel bioinformatics predicted potential B and T cell epitopes for SARS-CoV-2 • Independent approaches identified the same immunodominant regions • The conserved immune regions have implications for vaccine design against multiple CoVs Grifoni et al. identify potential targets for immune responses to the 2019 novel coronavirus (SARS-CoV-2) by sequence homology with closely related SARS-CoV and by a priori epitope prediction using bioinformatics approaches. This analysis provides essential information for understanding human immune responses to this virus and for evaluating diagnostic and vaccine candidates. Effective 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. [Display omitted] •Ten experimentally defined regions within SARS-CoV have high homology with SARS-CoV-2•Parallel bioinformatics predicted potential B and T cell epitopes for SARS-CoV-2•Independent approaches identified the same immunodominant regions•The conserved immune regions have implications for vaccine design against multiple CoVs Grifoni et al. identify potential targets for immune responses to the 2019 novel coronavirus (SARS-CoV-2) by sequence homology with closely related SARS-CoV and by a priori epitope prediction using bioinformatics approaches. This analysis provides essential information for understanding human immune responses to this virus and for evaluating diagnostic and vaccine candidates. Effective 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.
Author	Sidney, John Sette, Alessandro Scheuermann, Richard H. Grifoni, Alba Peters, Bjoern Zhang, Yun
AuthorAffiliation	2 J. Craig Venter Institute, La Jolla, CA 92037, USA 4 Department of Medicine, University of California, San Diego, San Diego, CA 92093, USA 1 Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA 3 Department of Pathology, University of California, San Diego, San Diego, CA 92093, USA
AuthorAffiliation_xml	– name: 3 Department of Pathology, University of California, San Diego, San Diego, CA 92093, USA – name: 1 Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA – name: 4 Department of Medicine, University of California, San Diego, San Diego, CA 92093, USA – name: 2 J. Craig Venter Institute, La Jolla, CA 92037, USA
Author_xml	– sequence: 1 givenname: Alba surname: Grifoni fullname: Grifoni, Alba organization: Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA – sequence: 2 givenname: John surname: Sidney fullname: Sidney, John organization: Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA – sequence: 3 givenname: Yun surname: Zhang fullname: Zhang, Yun organization: J. Craig Venter Institute, La Jolla, CA 92037, USA – sequence: 4 givenname: Richard H. surname: Scheuermann fullname: Scheuermann, Richard H. organization: Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA – sequence: 5 givenname: Bjoern surname: Peters fullname: Peters, Bjoern organization: Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA – sequence: 6 givenname: Alessandro surname: Sette fullname: Sette, Alessandro email: alex@lji.org organization: Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/32183941$$D View this record in MEDLINE/PubMed
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Snippet	Effective countermeasures against the recent emergence and rapid expansion of the 2019 novel coronavirus (SARS-CoV-2) require the development of data and tools...
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SubjectTerms	B cell epitope Betacoronavirus - genetics Betacoronavirus - immunology Computational Biology coronavirus Coronavirus Infections - immunology Coronavirus Infections - virology COVID-19 Databases, Protein Epitopes, B-Lymphocyte - genetics Epitopes, B-Lymphocyte - immunology Epitopes, T-Lymphocyte - genetics Epitopes, T-Lymphocyte - immunology Humans infectious disease Pandemics Pneumonia, Viral - immunology Pneumonia, Viral - virology SARS-CoV SARS-CoV-2 sequence conservation Sequence Homology T cell epitope
Title	A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2
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