Mapping the immunopeptidome of seven SARS-CoV-2 antigens across common HLA haplotypes

Author:

Braun Asolina1,Rowntree Louise2ORCID,Huang Ziyi1,Pandey Kirti1,Thuesen Nikolas3,Li Chen1ORCID,Petersen Jan1,Littler Dene1,Raji Shabana4,Nguyen Thi5ORCID,Lange Emma Jappe Lange Jappe3,Persson Gry3,Klausen Michael Schantz3,Kringelum Jens3ORCID,Chung Shan Zou1,Croft Nathan1ORCID,Faridi Pouya1ORCID,Ayala Rochelle1,Rossjohn Jamie1ORCID,Illing Patricia1ORCID,Scull Katherine1ORCID,Ramarathinam Sri1,Mifsud Nicole1ORCID,Kedzierska Katherine5ORCID,Sørensen Anders3,Purcell Anthony1ORCID

Affiliation:

1. Monash University

2. Peter Doherty Institute for Infection and Immunity

3. Evaxion Biotech

4. University of Melbourne

5. University of Melbourne at the Peter Doherty Institute for Infection and Immunity

Abstract

Abstract Most COVID-19 vaccines have been designed to elicit immunity against the SARS-CoV-2 Spike protein. However, the repeated occurrence of new strains harbouring Spike protein mutations demonstrates ready immune evasion by the SARS-CoV-2 virus and the pressing need to develop more broadly targeting COVID-19 vaccines. To facilitate this, we used mass spectrometry to identify immunopeptides that are derived from seven structural and non-structural SARS-CoV-2 proteins that are relatively conserved across viral strains (N, E, Nsp1, Nsp4, Nsp5, Nsp8, Nsp9) and presented by prevalent Human Leukocyte Antigen (HLA) class I and class II molecules. Two different B-lymphoblastoid cell lines were chosen to map immunopeptidomes covering some of the major HLA types across the global human population. We used DNA plasmid transfection and direct antigen delivery approaches to sample different antigens. We found 248 unique HLA class I and HLA class II bound peptides with 71 derived from N, 12 from E, 28 from Nsp1, 19 from Nsp4, 73 from Nsp8 and 45 peptides derived from Nsp9. Over half of the viral peptides are reported for the first time. T cell responses were tested for 56 of the detected peptides and we show robust CD8+ and CD4+ T cell responses against several peptides from the N, E and Nsp9 proteins. Results from this study will aid the development of next-generation COVID vaccines targeting epitopes from across a number of SARS-CoV-2 proteins.

Publisher

Research Square Platform LLC

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