In the myeloid compartment, there were no differences in classical Kupffer cells (KCs) (MAC1) or inflammatory KCs (MAC3) (MAC1, MAC3: FDR = 0.231, 0.154; OR = 0.925, 0.873, respectively, Binomial GLMM), but an increased proportion of MAC2 cells was observed in COVID-19 (FDR = 1.86 × 10−2, OR = 1.182, Binomial GLMM), an intermediate phagocytic macrophage phenotype with lower expression of MARCO and CD164 but increased expression of phagocytic markers (C5AR1, CPVL, CD206). Here, C5AR1 is linked to COVID-19.