Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative (preprint)

Host genetics is a key determinant of COVID-19 outcomes. Previously, the COVID-19 Host Genetics Initiative genome-wide association study used common variants to identify multiple loci associated with COVID-19 outcomes. However, variants with the largest impact on COVID-19 outcomes are expected to be rare in the population. Hence, studying rare variants may provide additional insights into disease susceptibility and pathogenesis, thereby informing therapeutics development. Here, we combined whole-exome and whole-genome sequencing from 21 cohorts across 12 countries and performed rare variant exome-wide burden analyses for COVID-19 outcomes. In an analysis of 5,048 severe disease cases and 571,009 controls, we observed that carrying a rare deleterious variant in the SARS-CoV-2 sensor toll-like receptor TLR7 (on chromosome X) was associated with a 5.3-fold increase in severe disease (95% CI: 2.75-10.05, p=5.41x10-7). These results further support TLR7 as a genetic determinant of severe disease and suggest that larger studies on rare variants influencing COVID-19 outcomes could provide additional insights.

Urine test predicts kidney injury and death in COVID-19 (preprint)

Background: Kidney injury is common in COVID-19 infection, but serum creatinine (SCr) is not a sensitive or specific marker of kidney injury. We hypothesized that molecular markers of tubular injury could diagnose COVID-19 associated kidney damage and predict its clinical course. Methods: This is a prospective cohort study of 444 consecutive COVID-19 patients (43.9% females, 20.5% African American, 54.1% Latinx) in Columbia University's Emergency Department at the peak of the New York pandemic (March-April 2020). Urine and blood were collected simultaneously at admission (median time of day 0, IQR 0-2 days) and within 1 day of a positive SARS-CoV-2 test in 70% of patients. Biomarker assays were blinded to clinical data. Results: Urinary NGAL (uNGAL) was strongly associated with AKI diagnosis (267{+/-}301 vs. 96{+/-}139 ng/mL, P=1.6x10-10). uNGAL >150ng/mL had 80% specificity and 75% sensitivity to diagnose AKIN stage 2 or higher. uNGAL quantitatively predicted the duration of AKI and outcomes, including death, dialysis, shock, and longer hospital stay. The risk of death increased 73% per standard deviation of uNGAL [OR (95%CI): 1.73 (1.29-2.33), P=2.8x10-4] and was independent of baseline SCr, co-morbidities, and proteinuria [adjusted OR (95%CI): 1.51 (1.10-2.11), P=1.2x10-2]. Proteinuria and uKIM-1 also indicated tubular injury, but were not diagnostic of AKI. Typically, distal nephron segments transcribe NGAL, but in COVID-19 biopsies with widespread acute tubular injury (ATI), NGAL expression overlapped KIM-1 in proximal tubules. Conclusion: uNGAL predicted the diagnosis, duration, and severity of AKI and ATI, as well as hospital stay, dialysis, shock, and death in patients with acute COVID-19.

Failure to replicate the association of rare loss-of-function variants in type I IFN immunity genes with severe COVID-19 (preprint)

A recent report found that rare predicted loss-of-function (pLOF) variants across 13 candidate genes in TLR3- and IRF7-dependent type I IFN pathways explain up to 3.5% of severe COVID-19 cases. We performed whole-exome or whole-genome sequencing of 1,934 COVID-19 cases (713 with severe and 1,221 with mild disease) and 15,251 ancestry-matched population controls across four independent COVID-19 biobanks. We then tested if rare pLOF variants in these 13 genes were associated with severe COVID-19. We identified only one rare pLOF mutation across these genes amongst 713 cases with severe COVID-19 and observed no enrichment of pLOFs in severe cases compared to population controls or mild COVID-19 cases. We find no evidence of association of rare loss-of-function variants in the proposed 13 candidate genes with severe COVID-19 outcomes.