Transcriptome and microbiome profile of nasopharyngeal samples among COVID-19 patients with different levels of severity revealed through RNA-seq analysis

Differences in symptom manifestation among COVID-19 patients are caused mainly by the host factors. Gene expression profiles from nasopharyngeal samples might provide a clue to dysregulated biological processes, causing a variety of severity levels. The metagenomic profile from nasopharyngeal tissue might also provide details of coinfection that might contribute to the severity. Hence, we performed total RNA sequencing from asymptomatic patients and patients with mild and severe illnesses. Severe groups were characterized by the upregulation of the complement gene MASP1, inflammatory cytokines CXCL5 and CXCL12, and the fibrosis markers COL1A1 and COL3A1. On the contrary, the lack of activation of the B cell immune response, T cell immune response, and the cell-surface antigen recognition and signaling process were found in this severe group. Total RNA sequencing of nasopharyngeal swabs from COVID-19 patients with different levels of severity (5 negative controls, 2 asymptomatic patients, 5 mildly symptomatic patients, 8 severely symptomatic patients, and 5 controls).