SARS-CoV-2 Variants of Concern remodel innate and antiviral cytokine profile acting on phagocytic and antigen-presenting cell differentiation

Continuous surveillance and detailed immunological profiling are essential for adapting public health responses to the evolving landscape of SARS-CoV-2 variants. Moreover, interaction between host immunity and viral dynamics, that is likely to influence SARS-CoV-2 evolution over time, has been investigated only partially. This study explores the differential ability of SARS-CoV-2 variants of concern (VOCs), from the D614G strain to post-Omicron lineages, to induce antiviral and inflammatory responses using a human peripheral blood mononuclear cell (PBMC)-based in vitro model. Cytokine and chemokine release was measured by multiplex cytokine-bead array analysis in PBMC culture media harvested 24 hour post viral stimulation observing an important antiviral IFN-α release upon D614G and Alpha virus stimulation. In contrast, Beta, Gamma and Delta strains did not induce type I IFN, suggesting a peculiar immune evasion strategy. The Omicron BA.1 variant showed the ability to produce robust levels of IFN-α alongside the inflammatory cytokines IL-6 and TNF-α, to a higher extent than the other variants, and of the chemokines CXCL-8 (IL-8) and CCL-5 (RANTES). Notably, compared to the other VOCs, Beta was the poorer inducer of cytokine and chemokine release. We then extended our study by including the post-Omicron recombinant SARS-CoV-2 XBB.1 variant and compared it with its ancestral strain Omicron BA.1. Analysis of cytokine release revealed distinct signatures with BA.1 inducing higher release of IL-6 compared to XBB.1, while XBB.1 triggered stronger IFN-α responses. Of particular interest, XBB.1 was the only variant to induce production of IL-12p70, a cytokine that was not elicited by any of the other tested VOCs. Flow cytometric analysis of innate immune cell compartment further highlighted functional differences in the innate response triggered by the two variants. As compared to BA.1, XBB.1 strain pushed the differentiation of plasmacitoid and conventional DC towards more anti-viral and mature phenotypes, promoting CD8+ T cell response activation. Also, regarding monocyte differentiation BA.1 reduced while XBB.1 increased the frequency of CD14lowCD16hi inflammatory cells. Those immunological differences correlated with distinct viral subgenomic RNA (sgRNA) profiles and different frequency of dsRNA+ cells among VOCs, indicating that even if in absence of productive replication, still the presence of the different viruses inside the cells can modulate immune signaling pathways and cytokine secretion. These findings suggest that SARS-CoV-2 VOCs differentially manipulate the host intracellular machinery and the induction of inflammatory and antiviral pathways, not only in permissive respiratory cells but also in innate immune cells. By elucidating the immune responses triggered by different SARS-CoV-2 VOCs, this study provides valuable insights into their pathogenicity and potential impact on disease severity, contributing to the development of targeted therapeutic strategies, and may give clues on how population immunity can intersect and influence the evolutionary trajectories of the virus.