Consequently, we observed increased microglial expression of genes associated with microglia-mediated phagocytosis [41–44], such as CD68 (in line with the observed increase of CD68+ cells), TREM2, ITGB5, CD47, MSR1, CALR, as well as genes previously identified to be directly involved in synapse elimination in the aftermath of viral encephalitis, such as C3, C3AR1 and FCGR3A [6] (Fig. 6g). Here, C3AR1 is linked to viral encephalitis.