SARS-CoV-2 infection in hiPSC-derived neurons is cathepsin-dependent and causes differential accumulation of HIF1α and phosphorylated tau

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been shown to infect areas of the human brain and a subset of neurons in vitro. We have previously demonstrated that the virus enters human induced pluripotent stem cell (hiPSC)-derived neurons via an endosomal-lysosomal pathway. Here, we show that neuronal infection with both SARS-CoV-2 Wuhan and Omicron XBB.1.5 variants is dependent on cathepsins and can be blocked by an inhibitor of cathepsin B. The result was reproducible in non-transgenic hiPSC-derived cortical organoids. We further show that SARS-CoV-2 can replicate in neuron cultures, but the infectivity of the newly produced virions declined at 24 h post-infection despite a further increase in released viral RNA at later time points. The number of infected neurons decreased within five days, suggesting virus-induced neuronal cell death. The infection also caused the accumulation of the hypoxia-inducible stress factor HIF1-alpha in infected neurons under normoxia. Finally, expanding previous findings, in SARS-CoV-2 infected neurons, the microtubule-associated protein tau was hyperphosphorylated at multiple loci, including S202/T205, and mislocalized to the soma of infected 2D-neuronal cultures, but not in 3D-organotypic models. Hence, the neurodegenerative potential of SARS-CoV-2 infection should be carefully considered in different infection models.