ABSTRACT
Background: Although the respiratory tract is the initial site of infection for SARS-CoV-2, coronavirus disease 19 (COVID-19) can affect multiple organ systems with devastating consequences. Acute kidney injury (AKI) has emerged as a leading cause of morbidity, affecting more than a third of adult patients hospitalized with COVID-19. SARS-CoV-2 infection is believed to cause AKI through different mechanisms, including interaction with the angiotensin-converting enzyme 2 (ACE2) receptor, cytokine storm, hemodynamic compromise, and direct viral infection of kidney cells. A major barrier to studying the kidney as a potential site of viral infection and replication is the limited availability of fresh kidney tissue from human subjects. To overcome this limitation, we assessed the presence of SARS-CoV-2 RNA in urine of critically ill COVID-19 patients. Methods: Fifty-two sequential urine and nasal swab specimens were collected from 18 patients (median (IQR) age 57 (50-62) years) hospitalized in the intensive care unit (ICU) with COVID-19. We performed single genome amplification and sequence analysis of the full-length SARS-CoV-2 spike gene to determine the frequency of genetic mutations in urine compared to those amplified from nasal swabs. Results: Forty single genome SARS-CoV-2 spike sequences were amplified in urine samples from four of the ten patients that developed AKI. Analysis of these sequences revealed that deletions and mutations of the SARS-CoV-2 furin-cleavage site (RRAR) were the predominant mutations observed in urine-derived viral RNA (30/40). For 3 of the 4 patients the corresponding nasal swabs were negative for SARS-CoV-2, suggesting that these patients were shedding viral RNA in urine but had cleared the infection in the respiratory tract. None of the 15 nasal swab sequences derived from the fourth patient had deletions or mutations in the furin-cleavage site. Conclusion: Our study identified unique mutations/deletions in the SARS-CoV-2 spike gene amplified from urine samples of critically ill COVID-19 patients. Notably, these mutations/deletions have been infrequently observed in SARS-CoV-2 genome sequences from respiratory tract samples deposited in the publicly available databases but have been reported to occur after passaging the virus in the African green monkey kidney cell line, Vero-E6, raising the possibility of SARS-CoV-2 renal tropism or cell/organ specific selection of viral variants. Our data provide in vivo evidence of a phenomenon previously reported only in vitro.