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 results presented here demonstrate the potential of our pipeline to profile virus production across time. In particular, by analysing the proteome of Vero cells infected with SARS-CoV-2 at two different MOI, it was possible to monitor changes in the levels of three SARS-CoV-2 structural proteins and three non-structural ones. Whilst as for other analyses [11, 13] we could not detect peptides from protein E like. The lack of detection of other accessory proteins could be imputed to differences in samples processing with the protocol described here favouring simplified steps and speed while maintaining accuracy. Deeper analyses are envisaged for monitoring virus homogeneity during the different steps of viral production once the most permissive conditions will be established.