Population-level toggling of T cell immune escape at human leukocyte antigen anchor residues in SARS-CoV-2 Spike proteins, in an ethnically diverse population region.

ABSTRACT: There is currently limited understanding of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) adaptation to the human leukocyte antigen (HLA) proteins which mediate CD8 (HLA-I) and CD4 (HLA-II) T cell immune responses. We investigated population-level T cell immune escape in SARS-CoV-2 Spike protein at amino acid binding positions (the anchor motifs) preferred by the highly restrictive peptide binding grooves of the HLA. SARS-CoV-2 Spike protein sequences isolated in South Africa from January 2020 until June 2022, were used. All possible 9-mer and 15-mer peptides in the sequence alignment were scanned for matches to HLA-I and HLA-II anchor motifs, respectively. Peptide positions with matched anchor motifs and ≥1% mismatched sequences were investigated for immune escape using

SUBMITTER: Ngandu NK 

PROVIDER: S-EPMC12303384 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature