Background
Acute kidney injury (AKI) is a common complication in people hospitalized with COVID-19. The etiology of AKI is likely multifactorial, with potential contributions from hemodynamic compromise, systemic inflammation, cytokine release, and local viral infection. People with COVID-19 and AKI have higher levels of systemic markers of inflammation than those with normal kidney function. To understand the pathophysiology of AKI in people with COVID-19, we investigated the presence of SARS-CoV-2 RNA in urine samples from participants with mild or severe disease and explored the associated inflammatory profiles.
Methods
Urine specimens were obtained from 66 people with COVID-19 hospitalized in the intensive care unit (ICU) and 26 with mild symptoms. We performed single genome amplification of viral RNA in urine and respiratory tract samples. We also performed scRNAseq and a multiplexed analysis of inflammatory markers in the urine to compare renal inflammatory signatures between people with mild symptoms and those with severe COVID-19 with or without AKI.
Results
Viral RNA was detected in urine samples from a small number of COVID-19 people hospitalized in the ICU. Single viral genome analysis demonstrated a predominant pattern of deletions and mutations at the furin-cleavage site of the SARS-CoV-2 spike gene, which provided a replicative advantage in renal podocytes but not in airway epithelial cells grown at the air-liquid interface. People with AKI showed elevated levels of IL-6, IL-8, IL-18, MCP-1, Renin, TIMP-1, and Clusterin, suggesting an association between these inflammatory markers and renal disease. scRNAseq analysis of urine-derived cells revealed a higher frequency of macrophages, T cells, podocytes, and tubular cells in people with severe COVID-19, AKI, and viral shedding in urine. Pathway analysis of tubular cells from people with AKI showed enrichment of DNA damage-responsive pathways compared to those without AKI.
Conclusions
We identified unique SARS-CoV-2 variants in urine samples from participants with severe COVID-19, which demonstrated a replicative advantage in renal podocytes, raising the possibility of organ-specific selection of viral variants. We also observed higher levels of inflammatory markers and inflammatory cells in urine samples of people with severe COVID-19 and AKI. Our data demonstrate the ability to use urine samples to noninvasively study renal infection, characterize cellular diversity, and identify altered pathways in the setting of COVID-19 AKI.
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