Insights into innate immune cell dynamic upon SARS-COV-2 infection: a single cell multi-omic approach reveals viral manipulation of monocyte response

Single-cell multi-omic approaches provide a powerful framework to dissect heterogeneous immune responses during viral infections. To explore how immune-escape SARS-CoV-2 variants modulate host immunity, we applied integrated transcriptome and proteome single-cell profiling to HLADR-enriched human peripheral blood mononuclear cells (PBMCs) stimulated in vitro with Omicron BA.1. In particular, viral exposure induces profound changes in monocyte physiology regulating differentiation status and impacting on expression of cell adhesion markers, cytokine and chemokine signaling molecules and antigen processing and presentation capacity. Several regulated genes, including IL-6, CD16, CD11b, CD86, CD18, CD29 and CD31, were validated in an independent cohort in monocytes at both transcriptional and protein levels assessing their functional relevance. Viral RNA mapping revealed widespread detection across innate immune subsets, but preferential accumulation was occurring in CD14+ and CD16+ monocytes. In virus-positive monocytes, we observed up-regulation of genes involved in stress responses, inflammation, metabolic reprogramming, and cytokine/chemokine signaling, while interferon alpha/beta signaling and antigen processing/presentation pathways were down-regulated. Quantification of viral genomes by quantitative PCR and detection of dsRNA+ cells by intracellular flow cytometry further demonstrated how Omicron BA.1 resides in a subset of stimulated monocytes, inducing some rounds of replication in the early time points, without productive infection, specifically regulating a set of genes altering monocyte phenotype and differentiation. Furthermore, we are investigating whether post-Omicron lineages elicit similar innate immune rewiring, to better understand the evolution of viral immune escape. Collectively, our single-cell multi-omic data reveal how SARS-CoV-2 selectively targets monocytes to modulate host immunity, providing mechanistic insight into the interplay between viral adaptation and innate immune pressures. These findings have important implications for understanding determinants of infection control, inflammation, and pathogenesis, and may inform strategies for therapeutic intervention and vaccine design.