Bioinformatic identification of Endemic Coronaviruses’ epitopes in SARS-CoV-2 genomes isolated in Kenya

Abstract Identification of SARS-CoV-2 genome regions with similarity to epitopes for endemic coronaviruses is crucial for understanding cross-immunity and designing broad-spectrum vaccines. Research has highlighted that several epitopes exhibit homology or cross-reactivity between SARS-CoV-2 and various endemic coronaviruses. To identify these shared epitopes, annotated proteins from SARS-CoV-2 genomes isolated in Moi Teaching and Referral Hospital, Kenya were aligned with Epitopes for four endemic coronaviruses using BlastP. Additionally, the overlapping epitopes were aligned with SARS-CoV-2 immunodominant epitopes. 321 epitopes from HCoV-OC43, 206 epitopes from HCoV-HKU1, 136 epitopes from HCoV-NL63, and 182 epitopes from HCoV-229E exhibited similarities with regions on SARS-CoV-2 genomes. Of these, ten HCoV-OC43 epitopes; thirteen HCoV-HKU1 epitopes; one HCoV-NL63 epitope; and three HCoV-229E spike epitopes exhibited similarity with the SARS-CoV-2 genomes. Seven immunodominant epitopes had notable similarities with the epitopes from endemic coronaviruses. This discovery holds great importance as it implies the existence of potential cross-reactivity and shared immune responses among these coronaviruses, thereby potentially impacting the comprehension of immunity and the development of vaccines against SARS-CoV-2.