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

The use of single-cell multiomic technologies allows to dissect the heterogeneous host immune response during infections. In this study, a multiomic characterization of the innate immune compartment was performed by applying a high-throughput approach that enables the integrated analysis of transcriptome and proteome of the immune-repertoire at a single cell level in human HLADR-enriched peripheral blood mononuclear cells stimulated in vitro with SARS-CoV-2 variant Omicron BA.1. RNA-seq data and pathways analyses of the differentially expressed genes (DEGs) identified at the single cell level in different innate cell subpopulations revealed a complex regulation of cell processes and functions upon SARS-CoV-2 stimulation in monocytes, plasmacytoid dendritic cells (DC), conventional DC and NK cells. In particular, exposure to Omicron BA.1 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. Indeed, by aligning SARS-COV-2 genome sequence to single cell reads we found that viral RNA was detectable in all cell types but predominantly in CD14+ and CD16+ monocytes. These correlated with a statistically significant difference in gene transcription in virus positive or negative monocytes. Interestingly, genes up-regulated in virus positive cells (n=601) were linked to cellular response to stress and infection, inflammation and metabolism, while those down-regulated (n=34) belong mainly to antiviral alpha-beta Interferon signaling and antigen processing and presentation. In-depth analyses at both transcript and protein level are ongoing to validate DEGs linked to these pathways and preliminary data indicate an important regulation of selected genes. We are also investigating if post-Omicron lineages behave similarly to BA.1. These results suggest that SARS-CoV-2 strongly affects host immune response. Even if immune cells are refractory to productive infection, SARS-CoV-2 preferentially invade monocytes manipulating and interfering with their intracellular machinery specifically altering their functions and differentiation. This study further elucidates mechanisms that potentially contribute to the invasion of immune cells by SARS-CoV-2 leading to control and/or pathogenesis of the infection.