How to Identify SARS-CoV-2 Virus Derived Peptides

In our previous blog post (How to screen SARS-CoV-2 peptides to facilitate T cell research) we have described how the immune system samples all of the pathogenic proteins by looking at the small fragments of each protein and making a determination on whether that fragment (also referred to as peptide) belongs in the body. We have also described in our previous blog post (Find Human MHC Class I Dominant Peptides) the multiple MHC alleles that we tested for their ability to present SARS-CoV-2 peptides.

In our experiments of determining the ability of A2, A3, A11 and A24 MHC alleles to bind SARS-CoV-2 derived peptides we found little overlap between the peptides presented by human alleles and the H-2Kb mouse allele.

While a purely theoretical exercise at this point, the discovery of peptide sequences that could bind a human allele as well as a mouse allele could become very useful should a SARS-CoV-2 mouse model become available. We have performed an additional study to find SARS-CoV-2 peptides that can be presented by the H-2Kb mouse MHC molecule and 2 of those peptides (VVFLHVTYV and SIIAYTMSL) also proved to be strong binders of the HLA-A*02:01 human allele.

We encourage further trials with our QuickSwitch™ system to help the development of a functional SARS-CoV-2 mouse model that could lead to the creation of a robust COVID-19 vaccine.

Summary of SARS-CoV-2 peptide binding to mouse H-2 Kb MHC molecules.