Lipid and nucleocapsid N-protein accumulation in COVID-19 patient lung and infected cells

Abstract The pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global outbreak and prompted an enormous research effort. Still, the subcellular localization of the corona virus in lungs of COVID-19 patients is not well understood. Here, the localization of the SARS-CoV-2 proteins is studied in postmortem lung material of COVID-19 patients and in SARS-CoV-2 infected Vero cells, processed identically. Correlative light and electron microscopy on semi-thick cryo-sections, demonstrated induction of electron-lucent, lipid filled compartments after SARS-CoV-2 infection in both lung and cell cultures. In infected Vero cells and using immuno-electron microscopy, viral proteins were detected in these lipid filled compartments. In addition, several viral proteins were detected in virus particles, Golgi, double membrane spherules and multiple-virus bodies which were not lysosomal. In lung tissue, the non-structural protein 4 and the stable nucleocapsid N-protein, were detected on membranes of lipid filled compartments. The induction of such lipid filled compartments and the localisation of the viral proteins in lung of patients with fatal COVID-19, may explain the extensive inflammatory response. Authors Summary The trafficking of coronaviruses in lung of COVID-19 patients is not well understood and virus particles are difficult to find. Here we have visualized virus particles in SARS-CoV-2 infected cells by focusing on viral protein detection, in combination with ultrastructure. We studied how the virus is altering the cell morphology and determined that in Vero cells, lipid filled compartments contained various viral proteins. In these cells, also membrane enclosed multi-virus bodies were visible that contain a different set of viral proteins. We demonstrated that lipid filled compartments are viral induced compartments, as no known cellular marker such as lipid droplet or lysosomal marker was present. Using this knowledge, we then studied lung tissue from patients with a fatal SARS-Cov-2 infection, processed in a similar manner. Again we detected lipid filled compartments, now with viral proteins nsp4 and the stable nucleocapsid N-protein. The presence of these lipid filled compartments with viral proteins induced by SARS-CoV-2 infections, could be why the immune response of the COVID-19 patients is so strong, resulting in a fatal infection, and should be considered for new therapeutic strategies.