Molecular mimicry impact of the COVID-19 pandemic: Sequence homology between SARS-CoV-2 and autoimmune diseases epitopes

Molecular mimicry is one mechanism by which an infectious agent may trigger an autoimmune disease in a human subject and occurs when foreign- and self-peptides contain similar epitopes that activate an autoimmune response in a susceptible individual. Here, we employ a scalable in-silico approach, to identify 861 pairs of known SARS-CoV-2 and autoimmune disease epitopes, out of more than one billion possible pairs. These SARS-CoV-2 epitopes show 1) sequence homology to human autoimmune disorder epitopes, 2) empirical binding data that predict that they bind the same major histocompatibility complex (MHC) molecule and 3) exhibit high empirical immunogenicity. Analysis of these epitope pairs reveals an association between autoimmune disorders, such as type 1 diabetes, autoimmune uveitis, ankylosing spondylitis, and SARS-CoV-2 infection. These associations are consistent with those reported in the literature from the analysis of clinical records.