The pathogenesis of
COVID-19 is still elusive, which impedes
disease progression prediction, differential diagnosis, and targeted
therapy. Plasma cell-free RNAs (cfRNAs) carry unique information from human tissue and thus could point to resourceful solutions for pathogenesis and host-pathogen interactions. Here, we performed a comparative analysis of
cfRNA profiles between
COVID-19 patients and healthy donors using serial plasma. Analyses of the
cfRNA landscape, potential gene regulatory mechanisms, dynamic changes in
tRNA pools upon
infection, and microbial communities were performed. A total of 380
cfRNA molecules were up-regulated in all
COVID-19 patients, of which seven could serve as potential
biomarkers (AUC > 0.85) with great sensitivity and specificity.
Antiviral (NFKB1A, IFITM3, and IFI27) and neutrophil activation (S100A8, CD68, and CD63)-related genes exhibited decreased expression levels during treatment in
COVID-19 patients, which is in accordance with the dynamically enhanced inflammatory response in
COVID-19 patients. Noncoding RNAs, including some
microRNAs (let 7 family) and long noncoding RNAs (GJA9-MYCBP) targeting
interleukin (
IL6/IL6R), were differentially expressed between
COVID-19 patients and healthy donors, which accounts for the potential core mechanism of
cytokine storm syndromes; the
tRNA pools change significantly between the
COVID-19 and healthy group, leading to the accumulation of SARS-CoV-2 biased
codons, which facilitate SARS-CoV-2 replication. Finally, several
pneumonia-related microorganisms were detected in the plasma of
COVID-19 patients, raising the possibility of simultaneously monitoring immune response regulation and microbial communities using
cfRNA analysis. This study fills the knowledge gap in the plasma
cfRNA landscape of
COVID-19 patients and offers insight into the potential mechanisms of cfRNAs to explain
COVID-19 pathogenesis.