Alveolar macrophages critically control infection by seasonal human coronavirus OC43 to avoid severe pneumonia [scRNA-seq]

Seasonal coronaviruses, similar to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), only cause severe respiratory symptoms in a small fraction of infected individuals. However, the host factors that determine the variable responses to coronavirus infection remain unclear. Here, we use seasonal human coronavirus OC43 (HCoV-OC43) infection as an asymptomatic model that triggers both innate and adaptive immune responses in mice. Interestingly, innate sensing pathways as well as adaptive immune cells are not essential in protection against HCoV-OC43. Instead, alveolar macrophage (AMF) deficiency in mice results in COVID-19-like severe pneumonia post HCoV-OC43 infection, with abundant neutrophil infiltration, neutrophil extracellular trap (NET) release, and exaggerated pro-inflammatory cytokine production. Mechanistically, AMF efficiently phagocytose HCoV-OC43, effectively blocking virus spread, whereas, in their absence, HCoV-OC43 triggers Toll-like receptor (TLR)-dependent chemokine production to cause pneumonia. These findings reveal the central role of AMF in defending against seasonal HCoV-OC43 with clinical implications for human immunopathology associated with coronavirus infection. Overall design: Lungs from uninfected or HCoV-OC43-infected WT or Csf2rb-/- mice were collected and digested into single-cell suspensions, and CD45+ cells were sorted for single-cell RNA sequencing.