Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4+T cell immunity

CD4+ T cells recognize a broad range of peptide epitopes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which contribute to immune memory and limit COVID-19 disease. We demonstrate that the immunogenicity of SARS-CoV-2 peptides, in the context of the model allotype HLA-DR1, does not correlate with their binding affinity to the HLA heterodimer. Analyzing six epitopes, some with very low binding affinity, we solve X-ray crystallographic structures of each bound to HLA-DR1. Further structural definitions reveal the precise molecular impact of viral variant mutations on epitope presentation. Omicron escaped ancestral SARS-CoV-2 immunity to two epitopes through two distinct mechanisms: (1) mutations to TCR-facing epitope positions and (2) a mechanism whereby a single amino acid substitution caused a register shift within the HLA binding groove, completely altering the peptide-HLA structure. This HLA-II-specific paradigm of immune escape highlights how CD4+ T cell memory is finely poised at the level of peptide-HLA-II presentation.

Automated summary

CD4+ T cells recognize a diverse range of SARS-CoV-2 peptide epitopes, contributing to immune memory and limiting COVID-19 disease. The immunogenicity of these peptides does not correlate with their binding affinity to HLA-DR1. X-ray crystallographic structures of six epitopes bound to HLA-DR1 reveal the molecular impact of viral variant mutations on epitope presentation. Omicron variant escapes immune recognition through mutations in TCR-facing epitope positions and a single amino acid substitution that alters the peptide-HLA structure.