The present work aimed to characterize, for the first time, the oral microbiome of COVID-19 patients by WGS, comparing its profile to controls, and simultaneously evaluating the presence of inflammatory cytokines and local IgA immune response, to better understand the features of the oral environment that could potentially support SARS-CoV-2 infection and related disease, and to identify eventual markers for the risk of developing a severe infection. Here, CD79A is linked to COVID-19.