Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope.

Dolton G., Rius C., Hasan MS., Wall A., Szomolay B., Behiry E., Whalley T., Southgate J., Fuller A., COVID-19 Genomics UK (COG-UK) consortium ., Morin T., Topley K., Tan LR., Goulder PJR., Spiller OB., Rizkallah PJ., Jones LC., Connor TR., Sewell AK.

We studied the prevalent cytotoxic CD8 T cell response mounted against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike glycoprotein269-277 epitope (sequence YLQPRTFLL) via the most frequent human leukocyte antigen (HLA) class I worldwide, HLA A∗02. The Spike P272L mutation that has arisen in at least 112 different SARS-CoV-2 lineages to date, including in lineages classified as "variants of concern," was not recognized by the large CD8 T cell response seen across cohorts of HLA A∗02+ convalescent patients and individuals vaccinated against SARS-CoV-2, despite these responses comprising of over 175 different individual T cell receptors. Viral escape at prevalent T cell epitopes restricted by high frequency HLAs may be particularly problematic when vaccine immunity is focused on a single protein such as SARS-CoV-2 Spike, providing a strong argument for inclusion of multiple viral proteins in next generation vaccines and highlighting the need for monitoring T cell escape in new SARS-CoV-2 variants.

DOI

10.1016/j.cell.2022.07.002

Type

Journal article

Publication Date

2022-08-04T00:00:00+00:00

Volume

185

Pages

2936 - 2951.e19

Keywords

CD8 T cell, COVID-19, SARS-CoV-2, T cell, T cell receptors, immune escape, peptide-HLA, phylogenetic, CD8-Positive T-Lymphocytes, COVID-19, Epitopes, T-Lymphocyte, HLA-A Antigens, Histocompatibility Antigens Class I, Humans, SARS-CoV-2

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