Catching the Wave: Detecting Strain-Specific SARS-CoV-2 Peptides in Clinical Samples Collected during Infection Waves from Diverse Geographical Locations
Subina Mehta,
Valdemir M. Carvalho,
Andrew T. Rajczewski,
Olivier Pible,
Björn A. Grüning,
James E. Johnson,
Reid Wagner,
Jean Armengaud,
Timothy J. Griffin,
Pratik D. Jagtap
Affiliations
Subina Mehta
Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
Valdemir M. Carvalho
Division of Research and Development, Fleury Group, São Paulo 04344-070, Brazil
Andrew T. Rajczewski
Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
Olivier Pible
Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, 30200 Bagnols-sur-Cèze, France
Björn A. Grüning
Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany
James E. Johnson
Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
Reid Wagner
Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
Jean Armengaud
Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, 30200 Bagnols-sur-Cèze, France
Timothy J. Griffin
Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
Pratik D. Jagtap
Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
The Coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resulted in a major health crisis worldwide with its continuously emerging new strains, resulting in new viral variants that drive “waves” of infection. PCR or antigen detection assays have been routinely used to detect clinical infections; however, the emergence of these newer strains has presented challenges in detection. One of the alternatives has been to detect and characterize variant-specific peptide sequences from viral proteins using mass spectrometry (MS)-based methods. MS methods can potentially help in both diagnostics and vaccine development by understanding the dynamic changes in the viral proteome associated with specific strains and infection waves. In this study, we developed an accessible, flexible, and shareable bioinformatics workflow that was implemented in the Galaxy Platform to detect variant-specific peptide sequences from MS data derived from the clinical samples. We demonstrated the utility of the workflow by characterizing published clinical data from across the world during various pandemic waves. Our analysis identified six SARS-CoV-2 variant-specific peptides suitable for confident detection by MS in commonly collected clinical samples.
