The Upper Respiratory Tract Microbiome Network Impacted by SARS-CoV-2.

Area of Science:

• Microbiology
• Virology
• Genomics

Background:

• The upper respiratory tract (URT) microbiome is crucial for host respiratory health.
• The impact of SARS-CoV-2 infection on the URT microbiome composition and microbial interactions remains largely unknown.

Purpose of the Study:

• To characterize the URT microbiome in COVID-19 patients.
• To investigate the co-occurrence correlations between SARS-CoV-2 and other microbes in the URT.

Main Methods:

• RNA metagenomic sequencing of 1737 nasopharyngeal samples from COVID-19 patients.
• Construction and analysis of a URT microbiome network including bacteria, archaea, and RNA viruses.
• Analysis of core/periphery species, cluster composition, and interaction balance.

Main Results:

• COVID-19 patients' URT microbiomes were enriched with Enterobacteriaceae, a family of gut-associated pathogens.
• These pathogens formed a cooperative guild that suppressed beneficial microbes.
• 72 eukaryotic RNA viruses were identified, including SARS-CoV-2 and a bat coronavirus (BatCoV BM48-31).
• SARS-CoV-2 was inhibited by 89 species but showed positive correlation with BatCoV BM48-31.

Conclusions:

• The URT microbiome in COVID-19 is characterized by pathogenic bacteria and complex viral interactions.
• The cooperative relationship between SARS-CoV-2 and BatCoV BM48-31 is a novel finding requiring further investigation.
• Potential gut-to-URT microbial translocation warrants future research.