Mycobiome of the upper respiratory tract in Delta vs. Omicron SARS-CoV-2 infection. Homo sapiens

Little is known about the respiratory mycobiome, particularly during viral infections. We performed ITS sequencing on nasal swabs collected from patients with asymptomatic-to-severe COVID-19 during the transition from Delta to Omicron dominance in Nashville, TN. Alpha and beta diversity was higher in Omicron-infected patients that correlated to the greater abundance of Armillaria, Malassezia, Trametes, and Pleurotus: genera that have been shown to have antiviral activity. This is the first analysis of the upper respiratory tract mycobiome during SARS-CoV-2 infection and suggest a potential mechanism behind lower disease severity in patients infected with Omicron compared to Delta.