About: Prediction of SARS-CoV-2 epitopes across 9360 HLA class I alleles

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About: Prediction of SARS-CoV-2 epitopes across 9360 HLA class I alleles Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Prediction of SARS-CoV-2 epitopes across 9360 HLA class I alleles
Creator	Wells, Daniel Campbell, Katie Kalbasi, Anusha Ribas, Antoni Steiner, Gabriela
Source	BioRxiv; Medline; PMC
abstract	Elucidating antiviral CD8 T lymphocyte responses to SARS-CoV-2 may shed light on the heterogeneity of clinical outcomes and inform vaccine or therapeutic approaches. To facilitate the evaluation of antiviral CD8 T cell responses to SARS-CoV-2, we generated a publicly accessible database of epitopes predicted to bind any class I HLA protein across the entire SARS-CoV-2 proteome. While a subset of epitopes from earlier betacoronaviruses, such as SARS-CoV (SARS), have been validated experimentally, validation systems are often biased toward specific HLA haplotypes (notably HLA-A*02:01) that only account for a fraction of the haplotypes of individuals affected by the SARS-CoV-2 pandemic. To enable evaluation of epitopes across individuals with a variety of HLA haplotypes, we computed the predicted binding affinities between 9-mer peptides derived from the annotated SARS-CoV-2 peptidome across 9,360 MHC class I HLA-A, -B, and -C alleles. There were 6,748 unique combinations of peptides and HLA alleles (pMHCs) with a predicted binding affinity of less than 500nM, including 1,103 unique peptides and 1,022 HLA alleles, spanning 11 annotated superfamilies. These peptides were derived from all 11 proteins spanning the SARS-CoV-2 peptidome, including peptides that have previously been validated experimentally. We also show evidence that these previously validated epitopes may be relevant in other HLA contexts. This complete dataset is available publicly: gs://pici-covid19-data-resources/mhci/peptide_predictions.
has issue date	2020-04-01(xsd:dateTime)
bibo:doi	10.1101/2020.03.30.016931
bibo:pmid	32511325
has license	cc-by-nc-nd
sha1sum (hex)	cabe4ebafa262c1d554491e812641c6e8a7d7d66
schema:url	https://doi.org/10.1101/2020.03.30.016931
resource representing a document's title	Prediction of SARS-CoV-2 epitopes across 9360 HLA class I alleles
has PubMed Central identifier	PMC7239055
has PubMed identifier	32511325
schema:publication	bioRxiv
resource representing a document's body	covid:cabe4ebafa262c1d554491e812641c6e8a7d7d66#body_text
is schema:about of	named entity 'SARS-CoV-2' named entity 'unique' named entity 'combinations' named entity 'derived' named entity 'alleles' named entity 'SARS-CoV-2' named entity 'FREQUENCY' named entity 'PUBLIC' named entity 'USING' named entity 'POPULATION' named entity 'USER INTERFACE' named entity 'HLA' named entity 'HLA' named entity 'mer' named entity 'simulated' named entity 'frequency' named entity 'sets' named entity 'global' named entity 'predicted' named entity 'proteins' named entity 'peptides' named entity 'global population' named entity 'HLA' named entity 'SARS-CoV-2' named entity 'HLA' named entity 'HLA' named entity 'simulated populations' named entity 'epitopes' named entity 'epitope' named entity '360 class' named entity 'epitopes' named entity 'global population' named entity 'SCSs' named entity 'Formula 1' named entity 'peptides' named entity 'vaccines' named entity 'Virus' named entity 'SCSs' named entity 'proteome' named entity 'HLA' named entity 'allele' named entity 'binding affinity' named entity 'HLA' named entity '5nM' named entity 'epitopes' named entity 'epitopes' named entity 'peptides' named entity 'HLA' named entity 'allele' named entity 'viral proteome' named entity 'vaccines' named entity 'HLA' named entity 'viral proteome' named entity 'SARS-CoV-2' named entity 'CD8 T cells' named entity 'peptide' named entity 'HLA' named entity 'antiviral' named entity 'v1.1' named entity 'HLA' named entity 'genotypes' named entity 'peptides' named entity 'HLA' named entity 'peptides' named entity 'alleles' named entity 'SCSs' named entity 'HLA' named entity 'class II' named entity 'peptides' named entity 'antigens' named entity 'United States' named entity 'SCSs' named entity 'alleles' named entity 'HLA' named entity 'peptides' named entity 'alleles' named entity 'MHC'

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