Prioritization of SARS-CoV-2 epitopes using a pan-HLA and global population inference approach.
SARS-CoV-2
T cells
epitope prediction
public resource
Journal
bioRxiv : the preprint server for biology
Titre abrégé: bioRxiv
Pays: United States
ID NLM: 101680187
Informations de publication
Date de publication:
29 Jun 2020
29 Jun 2020
Historique:
pubmed:
9
6
2020
medline:
9
6
2020
entrez:
9
6
2020
Statut:
epublish
Résumé
SARS-CoV-2 T cell response assessment and vaccine development may benefit from an approach that considers the global landscape of the human leukocyte antigen (HLA) proteins. We predicted the binding affinity between 9-mer and 15-mer peptides from the SARS-CoV-2 peptidome for 9,360 class I and 8,445 class II HLA alleles, respectively. We identified 368,145 unique combinations of peptide-HLA complexes (pMHCs) with a predicted binding affinity less than 500nM, and observed significant overlap between class I and II predicted pMHCs. Using simulated populations derived from worldwide HLA frequency data, we identified sets of epitopes predicted in at least 90% of the population in 57 countries. We also developed a method to prioritize pMHCs for specific populations. Collectively, this public dataset and accessible user interface (Shiny app: https://rstudio-connect.parkerici.org/content/13/) can be used to explore the SARS-CoV-2 epitope landscape in the context of diverse HLA types across global populations.
Identifiants
pubmed: 32511325
doi: 10.1101/2020.03.30.016931
pmc: PMC7239055
pii:
doi:
Types de publication
Preprint
Langues
eng
Subventions
Organisme : NCATS NIH HHS
ID : KL2 TR001882
Pays : United States
Déclaration de conflit d'intérêts
Declaration of Interests K.M.C is a shareholder in Geneoscopy LLC. D.K.W. is a founder, equity holder and receives consulting fees from Immunai. A.R. is supported by the National Institute of Health (R35 CA197633), the Ressler Family Fund, the Agilent Thought Leader Award, a Stand Up to Cancer- Bristol-Meyer Squibb Catalyst Research Grant (Grant Number: SU2C-AACR-CT06–17). This research grant is administered by the American Association for Cancer Research, the scientific partner of SU2C. A.R. is a member researcher at the Parker Institute for Cancer Immunotherapy.
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