Targeting sphingolipid metabolism: inhibition of neutral sphingomyelinase 2 impairs coronaviral replication organelle formation

Coronaviruses are enveloped plus-strand RNA viruses with a broad host range, including humans. Human coronaviruses are not only associated with endemic, mild upper respiratory tract infections but also have pandemic potential and can be associated with a severe disease burden. The recent SARS-CoV-2 pandemic especially highlighted the urgent need to identify ideal broad-spectrum and host-targeted antiviral strategies. Since lipids are involved in every step of viral replication, we compared changes in the sphingolipid metabolism of cells infected with three different coronaviruses to identify similarities and related cellular enzymes involved in facilitating viral replication. We observed increased ceramide levels while sphingomyelin levels decreased, suggesting enhanced sphingomyelin-to-ceramide conversion by cellular sphingomyelinases upon infection. Impairment of neutral sphingomyelinase 2 reduced viral replication and the formation of virus-induced membranous replication organelles. Furthermore, we found that neutral sphingomyelinase 2 and its product ceramide were associated with viral replication organelles. Ceramides consistently appeared to be integral lipid building blocks of replication organelles across different human pathogenic coronaviruses and cell types. In conclusion, our study provides new insights into novel potentially conserved druggable sphingolipid-related host factors involved in coronaviral replication, offering potential new targets for antiviral therapies against newly emerging coronaviruses.