Peptides of H. sapiens and P. falciparum that are predicted to bind strongly to HLA-A*24:02 and homologous to a SARS-CoV-2 peptide

TL;DR

This study identifies peptides from SARS-CoV-2 and Plasmodium falciparum that strongly bind to HLA-A*24:02, suggesting potential cross-reactivity and autoimmune risks in infected individuals with this HLA type.

Contribution

It introduces a novel computational pipeline to find homologous peptides in SARS-CoV-2 and Plasmodium falciparum that bind to HLA-A*24:02, highlighting possible autoimmune implications.

Findings

Peptide CFLGYFCTCYFGLFC of SARS-CoV-2 is homologous to P. vivax peptides.

Several peptides, including FFYTFYFELF, strongly bind to HLA-A*24:02.

Homologous peptides may trigger autoimmune responses in HLA-A*24:02 individuals.

Abstract

Aim: This study is looking for a common pathogenicity between SARS-CoV-2 and plasmodium species, in individuals with certain HLA serotypes. Methods: 1-) Tblastx searches of SARS-CoV-2 are performed by limiting searches to plasmodium species that infect human. 2-) Aligned sequences in the respective organisms' proteomes are searched with blastp. 3-) Binding predictions of the identified SARS-CoV-2 peptide to MHC class I supertype representatives are performed. 4-) Blastp searches of predicted-epitopes that bind strongly to the identified HLA allele are performed by limiting searches to human and to the plasmodium species. 5-) Peptides with minimum 60 % identity to the predicted-epitopes are found in results. 6-) Peptides among those, which bind strongly to the same HLA allele, are predicted. 7-) Step-4 is repeated by limiting searches to human, for peptides sourced by limiting searches to plasmodium species at step-4. 8-) Step-5 and 6 are performed with results of 7. Results: CFLGYFCTCYFGLFC peptide of SARS-CoV-2 has the highest identity to P. vivax. Its GYFCTCYFGLF and YFCTCYFGLF parts are predicted to bind strongly to HLA-A*24:02. Results obtained only for peptides homologous to YFCTCYFGLF, as follows: YYCARRFGLF, YYCHCPFGVF, and YYCQQYFFLF are potential HLA-A*24:02 epitopes in the human proteome. Among FFYTFYFELF, YFVACLFILF, and YFPTITFHLF peptides in the plasmodium species' proteomes with strong binding affinity to HLA-A*24:02, only FFYTFYFELF of P. falciparum is homologous to the potential HLA-A*24:02 epitope YFYLFSLELF in the human proteome. Conclusion: Immune responses to the identified-peptides with similar sequences and strong binding affinities to HLA-A*24:02 may lead to autoimmune response risk in individuals with HLA-A*24:02 serotypes, upon getting infected with SARS-CoV-2 or P. falciparum.