Catching the Wave: Detecting Strain-Specific SARS-CoV-2 Peptides in Clinical Samples Collected during Infection Waves from Diverse Geographical Locations

Subina P 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

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish (US)
Article number2205
JournalViruses
Volume14
Issue number10
DOIs
StatePublished - Oct 2022

Bibliographical note

Funding Information:
We acknowledge funding for this work from the grant National Cancer Institute—Informatics Technology for Cancer Research (NCI-ITCR) grant 1U24CA199347 to T.J.G. The European Galaxy server that was used for data analysis is partly funded by Collaborative Research Centre 992 Medical Epigenetics (DFG grant SFB 992/1 2012) and the German Federal Ministry of Education and Research (BMBF grants 031 A538A/A538C RBC, 031L0101B/031L0101C de.NBI-epi, 031L0106 de.STAIR (de.NBI)).

Publisher Copyright:
© 2022 by the authors.

Keywords

  • mass-spectrometry
  • SARS-CoV-2
  • strain-specific
  • variant detection

PubMed: MeSH publication types

  • Journal Article
  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

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