Application Note on Protein Sequencing Technology for SARS-CoV-2 Variants

This application note presents a method for distinguishing between SARS-CoV-2 variants Alpha, Delta, and Omicron using Quantum-Si's next-generation protein sequencing technology on the Platinum instrument. Accurate identification of these variants is essential for effective surveillance and monitoring of COVID-19. The document details the methodology employed, which includes sequencing the receptor-binding domain (RBD) regions of the spike proteins and analyzing the kinetic signatures of specific peptides. The results demonstrate that the Alpha variant can be differentiated from the Delta and Omicron variants based on the L452R mutation, while the Omicron variant is identified by the absence of peptide I418–K424 due to the K417N mutation. The findings underscore the importance of rapid variant identification in understanding the implications for public health and the development of treatments and vaccines. The technology's ability to detect residual viral proteins in long COVID patients is also highlighted as a potential avenue for further research.