Identifying stable-against-mutations viral epitopes in SARS-CoV-2

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Abstract We have developed a computational method “Multi-Stable Epitope Sequencer” to predict mutation-resistant regions with stability against future viral variability. At the beginning of the pandemic, this approach allowed us to identify a set of eight SARS-CoV-2 spike protein sequences that had the potential to be mutationally stable. We have tested this methodology on the SARS-CoV-2 viral linages that occurred throughout the COVID-19 pandemic. These eight peptide sequences (epitopes) have been preserved in 97% of all SARS-CoV-2 lineages reported in the CoV-GLUE dataset during the pandemic period. Likewise, more than 90% of these peptides remained invariable across the 49 predominant viral variants circulating throughout the pandemic (ECDC-WHO). In addition, the eight selected peptides were preserved in 94.1% of all 28 variants considered of most interest in the CoV-GLUE project. Our analyses confirm the predicted mutational stability of the eight selected short viral peptides over the entire COVID-19 pandemic.

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