Whenever our immune system is faced with a challenge, be it a multicellular parasite, a bacteria, a virus, or even cancer, this threat is detected and sampled primarily by the protein sequence of the pathogen in question. Other aspects of the pathogen, such as its glycosylation pattern or the peculiar structures of its RNA and DNA molecules could have a strong effect on how the immune system deals with it. But, overall, the adaptive aspect of the mammalian immune system has evolved over many years to examine the protein sequences that make up the invading pathogen. The key function of our immune system relies on its ability to constantly sample all proteins present in our body and determine whether it is a protein that belongs or a protein that must be eradicated together with any cells or organisms that produce it. Unfortunately, most proteins are too large for the immune system to sample at once and so it has developed a mechanism to cut the full-length proteins into small stretches of amino acids which are examined individually.

COVID-19 infected cells can be recognized by T-cells only after SARS-CoV-2 peptides are processed and presented in the context of self MHCs.

Identifying these peptides have essential utilities:

• Immune monitoring: Using peptide-MHC tetramers to assess vaccine-induced immunity
• Designing potent vaccines that elicit durable responses

T-cells are activated only by interacting with processed peptides (e.g. of SARS-CoV-2) that sit in the groove of MHC Class I and II molecules. Identifying these peptides can be used (in forms of peptide-MHC tetramers) to assess vaccine induced immunity and assist in designing potent vaccines with durable responses.