Upper respiratory tract microbiota sequencing from Covid-19 patients

Samples were collected in 4 cities of the Russian Federation. We analyze biomaterial from nasopharyngeal smears from 335 patients with a confirmed diagnosis of COVID-19, selected during the first and second waves of the epidemic in Russia. We investigated associations between disease severity and microbiota at the level of the microbial community (community types) and individual microbes (differentially represented species). To search for associations, we performed multivariate analysis, taking into account comorbidities, type of community, and lineage of the virus. Extracted RNA was amplified using standard 16S rRNA gene primers, complementary to the V3V4 region and containing 5, Illumina adapter sequences. In the next step individual amplicons were PCR indexed and pooled. DNA libraries were sequenced on a MiSeq instrument.