Mapping the recovery of critically ill COVID 19 patients by mass cytometry

Here, we have analysed longitudinally collected, whole blood samples of 40 surviving COVID-19 patients during their recovery at ICU using high-dimensional cytometry by time-of-flight (CyTOF) and cytokine multiplexing.
Conclusion:
We defined 4 sequential immunotypes during recovery that correlated to various clinical parameters, including the level of respiratory support at concomitant sampling times. We also identified classical monocytes as the first immune cell type to recover by restoring HLA-DR-positivity and by reducing the immunosuppressive CD163+ monocyte population, followed by the recovery of CD8+ and CD4+ T cell, and mDC populations. The identified immunotypes also correlated to aberrant cytokine and acute-phase reactant levels. Finally, integrative analysis of cytokines and immune cell profiles showed a shift from an initially dysregulated immune response to a more coordinated immunogenic interplay, highlighting the importance of longitudinal sampling to understand the pathophysiology underlying recovery from severe COVID-19. 1. Antibodies not included in the Fluidigm MaxPar Direct Immune Profiling kit were titirated on RBC lysed whole blood to determine the optimal concentration. 2. The cryopreservation technique was validated in triplicate by dividing aliquots of donor samples stained on the same day and comparing cell viability and immune profiles between the fresh and cryopreserved samples. 3. Batch effects were evaluated by running a reference sample derived from an aliquot of the same healthy donor over the period of the study.