Shotgun proteomics of SARS-CoV-2 infected cells and its application to the optimisation of whole viral particle antigen production for vaccines

Lucia Grenga; Fabrice Gallais; Olivier Pible; Jean-Charles Gaillard; Duarte Gouveia; Hélène Batina; Niza Bazaline; Sylvie Ruat; Karen Culotta; Guylaine Miotello; Stéphanie Debroas; Marie-Anne Roncato; Gérard Steinmetz; Charlotte Foissard; Anne Desplan; Béatrice Alpha-Bazin; Christine Almunia; Fabienne Gas; Laurent Bellanger; Jean Armengaud

The analysis of our proteomic data suggested substantial temporal remodelling of the host proteome Here, we show that our pipeline based on LC-MS/MS analysis is a suitable tool for the characterisation of SARS-CoV-2 production. We, therefore, suggest that it could be of use in the optimisation of the condition for viral amplification to speed up the initial steps in favour of those that later on during the development process will require a more careful evaluation of effectiveness and safety. Besides, peptide information described here provide sufficient information to enable a targeted analysis, opening the possibility of using mass spectrometry-based targeted approaches for the evaluation of critical aspects (i.e. quality and quantity) during the different steps of the virus purification processes. Furthermore, the characterized changes in cellular protein networks upon SARS-CoV-2 infection provided valuable insights that could be further explored and guide the identification of drug targets to address the pandemic caused by SARS-CoV-2.