A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2
Identifieur interne : 000A44 ( 2020/Analysis ); précédent : 000A43; suivant : 000A45A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2
Auteurs : Alba Grifoni [États-Unis] ; John Sidney [États-Unis] ; Yun Zhang [États-Unis] ; Richard H. Scheuermann [États-Unis] ; Bjoern Peters [États-Unis] ; Alessandro Sette [États-Unis]Source :
- Cell Host & Microbe [ 1931-3128 ] ; 2020.
Descripteurs français
- KwdFr :
- Bases de données de protéines, Biologie informatique, Déterminants antigéniques des lymphocytes B (génétique), Déterminants antigéniques des lymphocytes B (immunologie), Déterminants antigéniques des lymphocytes T (génétique), Déterminants antigéniques des lymphocytes T (immunologie), Humains, Infections à coronavirus (immunologie), Infections à coronavirus (virologie), Pandémies, Pneumopathie virale (immunologie), Pneumopathie virale (virologie), Similitude de séquences.
- MESH :
- génétique : Déterminants antigéniques des lymphocytes B, Déterminants antigéniques des lymphocytes T.
- immunologie : Déterminants antigéniques des lymphocytes B, Déterminants antigéniques des lymphocytes T, Infections à coronavirus, Pneumopathie virale.
- virologie : Infections à coronavirus, Pneumopathie virale.
- Bases de données de protéines, Biologie informatique, Humains, Pandémies, Similitude de séquences.
English descriptors
- KwdEn :
- Betacoronavirus (genetics), Betacoronavirus (immunology), Computational Biology, Coronavirus Infections (immunology), Coronavirus Infections (virology), Databases, Protein, Epitopes, B-Lymphocyte (genetics), Epitopes, B-Lymphocyte (immunology), Epitopes, T-Lymphocyte (genetics), Epitopes, T-Lymphocyte (immunology), Humans, Pandemics, Pneumonia, Viral (immunology), Pneumonia, Viral (virology), Sequence Homology.
- MESH :
- chemical , genetics : Epitopes, B-Lymphocyte, Epitopes, T-Lymphocyte.
- genetics : Betacoronavirus.
- immunology : Betacoronavirus, Coronavirus Infections, Epitopes, B-Lymphocyte, Epitopes, T-Lymphocyte, Pneumonia, Viral.
- virology : Coronavirus Infections, Pneumonia, Viral.
- Computational Biology, Databases, Protein, Humans, Pandemics, Sequence Homology.
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
Url:
DOI: 10.1016/j.chom.2020.03.002
PubMed: 32183941
PubMed Central: 7142693
Affiliations:
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PMC:7142693Le document en format XML
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id="aff1">Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Zhang, Yun" sort="Zhang, Yun" uniqKey="Zhang Y" first="Yun" last="Zhang">Yun Zhang</name><affiliation wicri:level="2"><nlm:aff id="aff2">J. Craig Venter Institute, La Jolla, CA 92037, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>J. Craig Venter Institute, La Jolla, CA 92037</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Scheuermann, Richard H" sort="Scheuermann, Richard H" uniqKey="Scheuermann R" first="Richard H." last="Scheuermann">Richard H. Scheuermann</name><affiliation wicri:level="2"><nlm:aff id="aff1">Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff2">J. Craig Venter Institute, La Jolla, CA 92037, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>J. Craig Venter Institute, La Jolla, CA 92037</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff3">Department of Pathology, University of California, San Diego, San Diego, CA 92093, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology, University of California, San Diego, San Diego, CA 92093</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Peters, Bjoern" sort="Peters, Bjoern" uniqKey="Peters B" first="Bjoern" last="Peters">Bjoern Peters</name><affiliation wicri:level="2"><nlm:aff id="aff1">Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff4">Department of Medicine, University of California, San Diego, San Diego, CA 92093, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Medicine, University of California, San Diego, San Diego, CA 92093</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Sette, Alessandro" sort="Sette, Alessandro" uniqKey="Sette A" first="Alessandro" last="Sette">Alessandro Sette</name><affiliation wicri:level="2"><nlm:aff id="aff1">Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff4">Department of Medicine, University of California, San Diego, San Diego, CA 92093, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Medicine, University of California, San Diego, San Diego, CA 92093</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author></analytic><series><title level="j">Cell Host & Microbe</title><idno type="ISSN">1931-3128</idno><idno type="eISSN">1934-6069</idno><imprint><date when="2020">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Betacoronavirus (genetics)</term><term>Betacoronavirus (immunology)</term><term>Computational Biology</term><term>Coronavirus Infections (immunology)</term><term>Coronavirus Infections (virology)</term><term>Databases, Protein</term><term>Epitopes, B-Lymphocyte (genetics)</term><term>Epitopes, B-Lymphocyte (immunology)</term><term>Epitopes, T-Lymphocyte (genetics)</term><term>Epitopes, T-Lymphocyte (immunology)</term><term>Humans</term><term>Pandemics</term><term>Pneumonia, Viral (immunology)</term><term>Pneumonia, Viral (virology)</term><term>Sequence Homology</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Bases de données de protéines</term><term>Biologie informatique</term><term>Déterminants antigéniques des lymphocytes B (génétique)</term><term>Déterminants antigéniques des lymphocytes B (immunologie)</term><term>Déterminants antigéniques des lymphocytes T (génétique)</term><term>Déterminants antigéniques des lymphocytes T (immunologie)</term><term>Humains</term><term>Infections à coronavirus (immunologie)</term><term>Infections à coronavirus (virologie)</term><term>Pandémies</term><term>Pneumopathie virale (immunologie)</term><term>Pneumopathie virale (virologie)</term><term>Similitude de séquences</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Epitopes, B-Lymphocyte</term><term>Epitopes, T-Lymphocyte</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Betacoronavirus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Déterminants antigéniques des lymphocytes B</term><term>Déterminants antigéniques des lymphocytes T</term></keywords><keywords scheme="MESH" qualifier="immunologie" xml:lang="fr"><term>Déterminants antigéniques des lymphocytes B</term><term>Déterminants antigéniques des lymphocytes T</term><term>Infections à coronavirus</term><term>Pneumopathie virale</term></keywords><keywords scheme="MESH" qualifier="immunology" xml:lang="en"><term>Betacoronavirus</term><term>Coronavirus Infections</term><term>Epitopes, B-Lymphocyte</term><term>Epitopes, T-Lymphocyte</term><term>Pneumonia, Viral</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Infections à coronavirus</term><term>Pneumopathie virale</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Coronavirus Infections</term><term>Pneumonia, Viral</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computational Biology</term><term>Databases, Protein</term><term>Humans</term><term>Pandemics</term><term>Sequence Homology</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Bases de données de protéines</term><term>Biologie informatique</term><term>Humains</term><term>Pandémies</term><term>Similitude de séquences</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Summary</title><p>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 <italic>a priori</italic> 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.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Carrasco Pro, S" uniqKey="Carrasco Pro S">S. Carrasco Pro</name></author><author><name sortKey="Sidney, J" uniqKey="Sidney J">J. Sidney</name></author><author><name sortKey="Paul, S" uniqKey="Paul S">S. Paul</name></author><author><name sortKey="Lindestam Arlehamn, C" uniqKey="Lindestam Arlehamn C">C. Lindestam Arlehamn</name></author><author><name sortKey="Weiskopf, D" uniqKey="Weiskopf D">D. Weiskopf</name></author><author><name sortKey="Peters, B" uniqKey="Peters B">B. Peters</name></author><author><name sortKey="Sette, A" uniqKey="Sette A">A. Sette</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cheung, Y K" uniqKey="Cheung Y">Y.K. Cheung</name></author><author><name sortKey="Cheng, S C" uniqKey="Cheng S">S.C. 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Buus</name></author><author><name sortKey="Frankild, S" uniqKey="Frankild S">S. Frankild</name></author><author><name sortKey="Greenbaum, J" uniqKey="Greenbaum J">J. Greenbaum</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Californie</li></region></list><tree><country name="États-Unis"><region name="Californie"><name sortKey="Grifoni, Alba" sort="Grifoni, Alba" uniqKey="Grifoni A" first="Alba" last="Grifoni">Alba Grifoni</name></region><name sortKey="Peters, Bjoern" sort="Peters, Bjoern" uniqKey="Peters B" first="Bjoern" last="Peters">Bjoern Peters</name><name sortKey="Peters, Bjoern" sort="Peters, Bjoern" uniqKey="Peters B" first="Bjoern" last="Peters">Bjoern Peters</name><name sortKey="Scheuermann, Richard H" sort="Scheuermann, Richard H" uniqKey="Scheuermann R" first="Richard H." last="Scheuermann">Richard H. Scheuermann</name><name sortKey="Scheuermann, Richard H" sort="Scheuermann, Richard H" uniqKey="Scheuermann R" first="Richard H." last="Scheuermann">Richard H. Scheuermann</name><name sortKey="Scheuermann, Richard H" sort="Scheuermann, Richard H" uniqKey="Scheuermann R" first="Richard H." last="Scheuermann">Richard H. Scheuermann</name><name sortKey="Sette, Alessandro" sort="Sette, Alessandro" uniqKey="Sette A" first="Alessandro" last="Sette">Alessandro Sette</name><name sortKey="Sette, Alessandro" sort="Sette, Alessandro" uniqKey="Sette A" first="Alessandro" last="Sette">Alessandro Sette</name><name sortKey="Sidney, John" sort="Sidney, John" uniqKey="Sidney J" first="John" last="Sidney">John Sidney</name><name sortKey="Zhang, Yun" sort="Zhang, Yun" uniqKey="Zhang Y" first="Yun" last="Zhang">Yun Zhang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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