Acute COVID-19 gene-expression profiles show multiple etiologies of long-term sequelae

Thompson, R. C.; Simons, N. W.; Wilkins, L.; Cheng, E.; Del-Valle, D. M.; Hoffman, G. E.; Fennessy, B.; Mouskas, K.; Francoeur, N. J.; Johnson, J. S.; Lepow, L.; Le Berichel, J.; Chang, C.; Beckmann, A. G.; Wang, Y.-c.; Nie, K.; Zaki, N.; Tuballes, K.; Barcessat, V.; Cedillo, M. A.; Huckins, L.; Roussos, P.; Marron, T. U.; The Mount Sinai COVID-19 Biobank Team,; Glicksberg, B. S.; Nadkarni, G.; Gonzalez-Kozlova, E.; Kim-Schulze, S.; Sebra, R.; Merad, M.; Gnjatic, S.; Schadt, E. E.; Charney, A. W.; Beckmann, N. D.

Two years into the SARS-CoV-2 pandemic, the post-acute sequelae of infection are compounding the global health crisis. Often debilitating, these sequelae are clinically heterogeneous and of unknown molecular etiology. Here, a transcriptome-wide investigation of this new condition was performed in a large cohort of acutely infected patients followed clinically into the post-acute period. Gene expression signatures of post-acute sequelae were already present in whole blood during the acute phase of infection, with both innate and adaptive immune cells involved. Plasma cells stood out as driving at least two distinct clusters of sequelae, one largely dependent on circulating antibodies against the SARS-CoV-2 spike protein and the other antibody-independent. Altogether, multiple etiologies of post-acute sequelae were found concomitant with SARS-CoV-2 infection, directly linking the emergence of these sequelae with the host response to the virus.