Coronavirus infections in monocytes and macrophages

Severe cases of SARS-CoV-2, the causative agent of COVID-19, are often accompanied by dysregulated immune responses. Monocytes and Macrophages, which are part of the innate immune system, represent one of the first lines of defence. Their main function lies in orchestrating the immune response against SARS-CoV-2 by the secretion of cytokines and immune signalling. Therefore, elucidating the impact of SARS-CoV-2 infection on the innate immune response of monocytes and macrophages is crucial for advancing our understanding of disease control and progression. Our initial analysis showed that monocytes and macrophages lack ACE2, the entry factor for SARS-CoV-2. Despite that, we observed that SARS-CoV-2 can enter these cells, as measured by the presence of genomic viral RNA. However, a time kinetic experiment revealed the absence of viral replication and no release of infectious viral particles. Further investigation demonstrated that the abortive SARS-CoV-2 infection in monocytes and macrophages nonetheless impacts cellular functions. Previous proteomic analysis from our group revealed an increase in CD47 expression in infected Caco-2-F03 cells. CD47 expressed on host cells can bind SIRPα present on myeloid cells and inhibit phagocytosis. Infection of epithelial cells resulted in elevated CD47 levels, while infected monocytes and macrophages showed SIRPα overexpression on their surface. Consequently, we detected decreased phagocytosis in infected macrophages, suggesting an immune evasion mechanism through phagocytosis inhibition. Furthermore, SARS-CoV-2 infection in monocytes and macrophages increased the expression of the interferon-stimulated genes ISG15 and Mx1. While the inhibition of JAK/STAT signalling prevented the upregulation of interferon-stimulated genes, it did not affect viral load. This indicates that the interferon (IFN) signalling is not responsible for the abortive infection of SARS-CoV-2. Due to the rapid emergence of various SARS-CoV-2 variants, we investigated their differences concerning viral infection and the IFN response. Most of the variants (Alpha-Delta) failed to induce IFN production. However, the Omicron variant showed a remarkable ability to potentiate IFN signalling in monocytes. Omicron-induced IFN response led to a functional antiviral state in the cells, which was demonstrated by inhibiting a super-infection with the influenza A virus (IAV). Importantly, this inhibition was not observed in SARS-CoV-2 variants other than Omicron. Mechanistically, we showed that the antiviral state was elicited specifically by type I IFNs and that the induction of the IFITM protein family expression was presumably partially responsible for the observed post-entry inhibition of IAV. Additionally, we revealed that the long-term infection with Omicron induced the activation of caspase 3/7, leading to the apoptosis of monocytes. Crucially, cell death could be prevented by inhibiting type I IFN signalling during infection. Further, we compared the pandemic viruses SARS-CoV-2 and its variants, SARS-CoV, MERS-CoV and the seasonal coronaviruses HCoV-229E, regarding their replication capacity and functional IFN response in monocytes. It revealed that, while SARS-CoV and early SARS-CoV-2 variants exhibited no viral replication and an absence of interferon response, MERS-CoV, HCoV-229E and Omicron variants infection led to a significant upregulation of IFN-stimulated genes, the release of various cytokines, and the establishment of a functional antiviral state. The sole detection of viral proteins via TLR4 does not appear sufficient to initiate an immune response that subsequently protects against superinfection in monocytes. Inhibition of TLR4 did not affect the phagocytic activity of monocytes and did not prevent the induction of an antiviral state in Omicron-infected monocytes. This suggests that the detection of viral components occurs through intracellular receptors, leading to a successful immune response and the release of interferons. While HCoV-229E infection influenced the composition of subpopulations of monocytes, it did not affect phagocytosis. On the other hand, SARS-CoV-2 and MERS-CoV infection decreased phagocytosis. Altogether, this work provides novel insights into the interplay between coronaviruses, monocytes, and macrophages. Our data highlight the importance of monitoring SARS-CoV-2 variants, as their infections can result in significantly different cellular outcomes despite their close genetic similarity. The complex interactions between coronaviruses and the innate immune response in monocytes and macrophages are essential for our understanding of how disease severity and persistence develop during infection. This knowledge is vital for the development of effective therapeutic strategies to mitigate the severe effects of COVID-19 and its post-acute sequelae.