A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2.
Identifieur interne : 000671 ( new/Analysis ); précédent : 000670; suivant : 000672A 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 [ 1934-6069 ] ; 2020.
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.
DOI: 10.1016/j.chom.2020.03.002
PubMed: 32183941
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: 000379
- to stream PubMed, to step Curation: 000379
- to stream PubMed, to step Checkpoint: 000C02
- to stream Ncbi, to step Merge: 001218
- to stream Ncbi, to step Curation: 001218
- to stream Ncbi, to step Checkpoint: 001218
- to stream Main, to step Merge: 000C78
- to stream Main, to step Curation: 000C76
- to stream Main, to step Exploration: 000C76
- to stream new, to step Extraction: 000671
Links to Exploration step
pubmed:32183941Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2.</title>
<author><name sortKey="Grifoni, Alba" sort="Grifoni, Alba" uniqKey="Grifoni A" first="Alba" last="Grifoni">Alba Grifoni</name>
<affiliation wicri:level="2"><nlm:affiliation>Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.</nlm:affiliation>
<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="Sidney, John" sort="Sidney, John" uniqKey="Sidney J" first="John" last="Sidney">John Sidney</name>
<affiliation wicri:level="2"><nlm:affiliation>Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.</nlm:affiliation>
<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:affiliation>J. Craig Venter Institute, La Jolla, CA 92037, USA.</nlm:affiliation>
<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:affiliation>Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; J. Craig Venter Institute, La Jolla, CA 92037, USA; Department of Pathology, University of California, San Diego, San Diego, CA 92093, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; J. Craig Venter Institute, La Jolla, CA 92037, USA; 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:affiliation>Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California, San Diego, San Diego, CA 92093, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; 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:affiliation>Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California, San Diego, San Diego, CA 92093, USA. Electronic address: alex@lji.org.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California, San Diego, San Diego, CA 92093</wicri:regionArea>
<placeName><region type="state">Californie</region>
</placeName>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2020">2020</date>
<idno type="RBID">pubmed:32183941</idno>
<idno type="pmid">32183941</idno>
<idno type="doi">10.1016/j.chom.2020.03.002</idno>
<idno type="wicri:Area/PubMed/Corpus">000379</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000379</idno>
<idno type="wicri:Area/PubMed/Curation">000379</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000379</idno>
<idno type="wicri:Area/PubMed/Checkpoint">000C02</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000C02</idno>
<idno type="wicri:Area/Ncbi/Merge">001218</idno>
<idno type="wicri:Area/Ncbi/Curation">001218</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">001218</idno>
<idno type="wicri:Area/Main/Merge">000C78</idno>
<idno type="wicri:Area/Main/Curation">000C76</idno>
<idno type="wicri:Area/Main/Exploration">000C76</idno>
<idno type="wicri:Area/new/Extraction">000671</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2.</title>
<author><name sortKey="Grifoni, Alba" sort="Grifoni, Alba" uniqKey="Grifoni A" first="Alba" last="Grifoni">Alba Grifoni</name>
<affiliation wicri:level="2"><nlm:affiliation>Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.</nlm:affiliation>
<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="Sidney, John" sort="Sidney, John" uniqKey="Sidney J" first="John" last="Sidney">John Sidney</name>
<affiliation wicri:level="2"><nlm:affiliation>Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.</nlm:affiliation>
<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:affiliation>J. Craig Venter Institute, La Jolla, CA 92037, USA.</nlm:affiliation>
<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:affiliation>Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; J. Craig Venter Institute, La Jolla, CA 92037, USA; Department of Pathology, University of California, San Diego, San Diego, CA 92093, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; J. Craig Venter Institute, La Jolla, CA 92037, USA; 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:affiliation>Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California, San Diego, San Diego, CA 92093, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; 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:affiliation>Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California, San Diego, San Diego, CA 92093, USA. Electronic address: alex@lji.org.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; 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="eISSN">1934-6069</idno>
<imprint><date when="2020" type="published">2020</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">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.</div>
</front>
</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="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="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)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Sante/explor/CovidV2/Data/new/Analysis
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000671 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/new/Analysis/biblio.hfd -nk 000671 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Wicri/Sante |area= CovidV2 |flux= new |étape= Analysis |type= RBID |clé= pubmed:32183941 |texte= A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2. }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/new/Analysis/RBID.i -Sk "pubmed:32183941" \ | HfdSelect -Kh $EXPLOR_AREA/Data/new/Analysis/biblio.hfd \ | NlmPubMed2Wicri -a CovidV2
This area was generated with Dilib version V0.6.33. |