PROJECT SUMMARY/ABSTRACT The SARS-CoV-2 pandemic has infected millions of individuals in the US and caused hundreds of thousands of deaths. We and others have shown that COVID-19 is also strongly associated with devastating and usually rare kidney pathophysiologies, such as collapsing glomerulopathy (CG). As in HIV infection, CG in COVID-19 patients mostly affects individuals with high-risk APOL1 genotypes, which are more prevalent in Black and some Hispanic patients. To guide treatment, there is a pressing need to understand whether COVID-19 nephropathy is due to direct viral infection or indirect mechanisms, such as cytokines or physiologic disturbances that emanate from the lung infection. Addressing this need has been hampered by poorly validated reagents, and misinterpretation of immunohistochemistry and electron microscopy findings. We have assembled a multi-investigator team to uncover the mechanisms of kidney injury due to SARS-CoV-2 infection. We will bring expert and complementary expertise in anatomic, autopsy and renal pathology, integrative genomic analysis, human kidney organoid systems and mouse immunology. We will use primary human tissue specimens, in vitro human kidney model systems and a new mouse model of COVID-19 to define direct and indirect mechanisms of SARS- CoV-2 associated kidney injury in three specific aims. Aim 1: Using kidney tissue specimens from COVID- 19 patients and controls, we will define the spectrum of kidney manifestations in individuals that have been infected with SARS-CoV-2. We will use immunohistochemistry, in situ hybridization, and proteomics to define SARS-CoV-2 kidney infection in a diverse population. In patients with COVID-19 associated CG, we will define molecular changes of this disease using spatial transcriptomic profiling, and the association with APOL1 status. These studies will define the relationship of SARS-CoV-2 infection to COVID-19 associated kidney diseases and uncover molecular mechanisms that underlie direct and indirect modes of kidney injury. Aim 2: Human kidney organoids provide a physiologically relevant model of SARS-CoV-2 infection. We will define cellular, morphologic and molecular hallmarks of SARS-CoV-2 infection in human kidney organoids and organotypic tissue slices. Using established iPSC cells with APOL1 high-risk alleles, we will determine the impact of APOL1 genotype on infection and inflammatory cytokine induced kidney injury. These studies will establish which kidney cells are capable of being infected by SARS-CoV-2, and kidney cell type specific molecular changes induced by viral infection and inflammatory cytokines. Aim 3: We will use a recently developed mouse adapted SARS-CoV-2 virus to determine the effect of SARS CoV-2 infection on kidney function in vivo. Using newly described BAC- transgenic mice that express human APOL1 G0, G1 or G2 alleles, we will define the influence of human APOL1 high-risk alleles on kidney function and kidney injury during SARS-CoV-2 ...