Immune Modulation by SARS-CoV-2 Variants of Concern: Cytokine Profiles, Antiviral Responses, and Subgenomic RNA Dynamics in Human Monocytes and PBMCs

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 not been investigated in deep. 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. By real-time RT-PCR and multiplex cytokine-bead array analyses, we quantified 24 hours post-stimulation the levels of type I interferon (IFN) production, IFN-induced Mx1 gene transcription, as well as inflammatory cytokine/chemokine release, including interleukin-6 (IL-6), tumor necrosis factor α (TNF-α), CXCL-8 (IL-8), CCL-2 (MCP-1), and CCL-5 (RANTES) and identified distinct antiviral gene expression signatures and cytokine/chemokine profiles elicited by different VOCs. Notably, the Beta VOC exhibited a lower capacity to induce cytokine and chemokine production as compared to Omicron BA.1 in both PBMCs and isolated CD14+ monocytes. Those immunological differences correlated with distinct viral subgenomic RNA (sgRNA) profiles. While PBMCs do not support productive SARS-CoV-2 replication, the presence of sgRNAs suggests a potential role in modulating immune signaling pathways and cytokine secretion. Moreover, SARS-CoV-2 RNA was detected in all cell types, with a predominant presence in CD14⁺ monocytes. This evidence prompted a more detailed characterization of monocyte response upon infection with Beta and Omicron BA.1 VOCs. Yet, Beta VOC-stimulated monocytes displayed a higher mortality rate, as evidenced by increased rate of apoptosis and Annexin-V expression and release of Lactate dehydrogenase as compared to BA.1-treated cells associated with a higher level of released virus in the early time points post-infection, even if in presence of a similar capacity of viral entry into monocytes displayed by Beta and BA.1 viruses . These findings suggest that SARS-CoV-2 VOCs differentially manipulate the host apoptotic machinery and the induction of inflammatory and antiviral pathways, not only in permissive respiratory cells but also in immune cells including monocytes. 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.