PT  - JOURNAL ARTICLE
AU  - Ge Liu
AU  - Brandon Carter
AU  - David K. Gifford
TI  - Predicted Cellular Immunity Population Coverage Gaps for SARS-CoV-2 Subunit Vaccines and their Augmentation by Compact Peptide Sets
AID  - 10.1101/2020.08.04.200691
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.08.04.200691
4099  - http://biorxiv.org/content/early/2020/10/21/2020.08.04.200691.short
4100  - http://biorxiv.org/content/early/2020/10/21/2020.08.04.200691.full
AB  - Subunit vaccines induce immunity to a pathogen by presenting a component of the pathogen and thus inherently limit the representation of pathogen peptides for cellular immunity based memory. We find that SARS-CoV-2 subunit peptides may not be robustly displayed by the Major Histocompatibility Complex (MHC) molecules in certain individuals. We introduce an augmentation strategy for subunit vaccines that adds a small number of SARS-CoV-2 peptides to a vaccine to improve the population coverage of pathogen peptide display. Our population coverage estimates integrate clinical data on peptide immunogenicity in convalescent COVID-19 patients and machine learning predictions. We evaluate the population coverage of 9 different subunits of SARS-CoV-2, including 5 functional domains and 4 full proteins, and augment each of them to fill a predicted coverage gap.Competing Interest StatementDavid Gifford is a founder and shareholder of ThinkTx.