Lung Microbiota Dynamics during Mild COVID-19 Infection in Non-Human Primate 9129

Abstract Description Background Lung microbiome dynamics in mild COVID-19 remain less understood compare to severe cases. To address this, we used a non-human primates (NHP) model, which mimics mild human infections, to investigate microbiome dynamics and their potential role in disease progression. Methods Seventeen NHPs were infected under five experimental conditions with SARS-CoV-2 variants, including Omicron. Lung samples were collected at 3 and 21 day post-infection (dpi) via necropsy. Partial 16S rRNA amplicon sequencing was performed using the Mi-Seq platform, and data were analyzed with Qiime 2. Results Proteobacteria dominanted all groups, with Gammaproteobacteria and Alphaproteobacteria as the main classes. Firmicutes increased (>2-fold) at 3 dpi in single infections compare to controls, but normalized by 21 dpi. Reinfections showed Firmicutes levels similar to controls, while heterologous infections displayed elevated Firmicutes. Bacilli, Clostridia, and Negativicutes were primary contributors. Conclusion Mild COVID-19 causes transient lung microbiome shifts, marked by an acute-phase Firmicutes surge and recovery. Heterologous infections showed distinct microbial changes, suggesting roles in immune modulation and disease progression. Further studies are needed to explore microbiota-host interactions and therapeutic approaches. Topic Categories Viral Immunology (VIR)