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

by Nobubelo K. Ngandu, Burtram C. Fielding, Peter van Heusden, Kuhle Mcinga, Kriheska Francis, Gordon Harkins

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 immunoinformatic prediction methods and directional evolution along the phylogenetic tree. Toggling of short-lived immune escape mutations at HLA-I anchor motifs was observed in 17 peptides across Spike. Eight of these overlapped with HLA-II escape mutations. Six mutations were related to zoonotic adaptation. All 17 sites were under significant directional evolution along the phylogenetic tree, and 16/17 are within published confirmed or inferred T cell epitopes. Immune escape predictions for HLA- A*66:01/A*68:01 were common (n = 7/17). HLA- A*02:05, A*03:01, B*07:02, B*08:01, B*58:01, DRB1*04:01 and DQA1*01:02-DQB1*06:02 were each associated with at least two escape mutations. This immunoinformatic prediction of T cell immune escape at HLA anchor motifs: (i)shortlisted potentially understudied population-specific HLA and immune escape (ii)revealed a footprint of underlying toggling of short-lived immune escape mutations, and (iii)has potential to cost-effectively guide pre-clinical research questions on the inclusion of partially conserved but dominant epitopes in vaccine immunogens.