SARS-CoV-2 Gut-Targeted Epitopes: Sequence Similarity and Cross-Reactivity Join Together for Molecular Mimicry

Abstract

The gastrointestinal tract can be heavily infected by SARS-CoV-2. Being an auto-immunogenic virus, SARS-CoV-2 represents an environmental factor that might play a role in gut-associated autoimmune diseases. However, molecular mimicry between the virus and the intestinal epitopes is under-investigated. The present study aims to elucidate sequence similarity between viral antigens and human enteric sequences, based on known cross-reactivity. SARS-CoV-2 epitopes that cross-react with human gut antigens were explored, and sequence alignment was performed against self-antigens implicated in enteric autoimmune conditions. Experimental SARS-CoV-2 epitopes were aggregated from the Immune Epitope Database (IEDB), while enteric antigens were obtained from the UniProt Knowledgebase. A Pairwise Local Alignment tool, EMBOSS Matcher, was employed for the similarity search. Sequence similarity and targeted cross-reactivity were depicted between 10 pairs of immunoreactive epitopes. Similar pairs were found in four viral proteins and seven enteric antigens related to ulcerative colitis, primary biliary cholangitis, celiac disease, and autoimmune hepatitis. Antibodies made against the viral proteins that were cross-reactive with human gut antigens are involved in several essential cellular functions. The relationship and contribution of those intestinal cross-reactive epitopes to SARS-CoV-2 or its potential contribution to gut auto-immuno-genesis are discussed.

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

“…Additionally, the identi cation of a conserved SARS-CoV-2 S2 spike epitope that elicited cross-reactive antibody responses to related coronaviruses and host bacteria underscores the potential for broad coronavirus therapeutics and vaccines 18 . Therefore these shared epitopes between SARS-CoV-2 and endemic coronaviruses highlight the potential for crossimmunity and the development of vaccines that could offer broad protection against current and future coronavirus outbreaks [19][20][21] .…”

“…Bioinformatics has been crucial in identifying potential cross-reactivity between epitopes of SARS-CoV-2 and those from endemic coronaviruses 21 . Studies have utilized bioinformatic approaches to predict candidate targets for immune responses to SARS-CoV-2, identifying potential B and T cell epitopes 22 .…”