COVID-19 human nasopharyngeal microbial composition

Coronavirus disease 2019 (COVID-19) has rapidly increased around the world impacting the lives on many individuals. Growing evidence suggest that the microbiome of the nasopharynx and the respiratory tract can have an impact on the health and disease conditions including the presence and severity of different viruses. To evaluate the potential interaction between COVID-19 and the microbiome in the nasopharynx, we applied 16S amplicon sequencing on 55 nasopharyngeal swab samples submitted to the clinical lab for suspected COVID-19 infections. Those 55 included cross sectional samples from 33 subjects as well as longitudinal sampling from a subset of the subjects. Intra personal variation was the strongest factor explaining >75% of the microbial variation, irrespective of the COVID-19 status. No significant effect of COVID-19 on the nasopharyngeal microbial community was observed using multiple analysis methods. These results indicate that unlike some other viruses, for which an effect on the microbial composition was noted, COVID-19 do not have a strong effect on the surrounding microbial habitants in the nasopharynx.