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-CoV2 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 HCoVNL63 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.