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Computationally Optimized SARS-CoV-2 MHC Class I and II Vaccine Formulations Predicted to Target Human Haplotype Distributions

Authors
  • Liu, Ge1, 2
  • Carter, Brandon1, 2
  • Bricken, Trenton3
  • Jain, Siddhartha1
  • Viard, Mathias4, 5
  • Carrington, Mary4, 5
  • Gifford, David K.1, 2, 6
  • 1 MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
  • 2 MIT Electrical Engineering and Computer Science, Cambridge, MA, USA
  • 3 Duke University, Durham, NC, USA
  • 4 Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
  • 5 Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA, USA
  • 6 MIT Biological Engineering, Cambridge, MA, USA
Type
Published Article
Journal
Cell Systems
Publisher
Elsevier Inc.
Publication Date
Jul 27, 2020
Volume
11
Issue
2
Pages
131–144
Identifiers
DOI: 10.1016/j.cels.2020.06.009
PMID: 32721383
PMCID: PMC7384425
Source
PubMed Central
Keywords
License
Unknown

Abstract

HLA haplotype frequencies are used to evaluate and design SARS-CoV-2 peptide vaccines. The methods presented optimize the presentation likelihood of a diverse set of vaccine peptides to maximize vaccine immunogenicity. The proposed SARS-CoV-2 MHC class I vaccine formulations provide 93.21% predicted population coverage with at least five vaccine peptide-HLA hits with all vaccine peptides perfectly conserved across 4,690 geographically sampled SARS-CoV-2 genomes. The proposed MHC class II vaccine formulations provide 97.21% predicted coverage with at least five vaccine peptide-HLA hits.

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