Mouthrinses influence salivary virus – Microbiome networks in COVID-19 patients

Objectives: Although mouthrinses have been suggested to reduce oral SARS-CoV-2 load, their effects on the salivary virus–microbiome network in COVID-19 patients remain unclear. This randomized clinical trial (RCT) evaluated the efficacy of sodium chlorite (NaClO 2 ), povidone-iodine (PVP-I), and cetylpyridinium chloride (CPC) mouthrinses compared with sterile water in modulating salivary SARS-CoV-2 viral load and oral microbiome composition. Methods: Forty PCR-confirmed COVID-19 patients were randomized into four groups (n = 10 each) to rinse with 10 mL of NaClO 2 , PVP-I, CPC, or sterile water for 30 seconds. Unstimulated saliva samples were collected at baseline, 5 minutes, 3 hours, and 6 hours post-rinse. Viral RNA was quantified via RT-qPCR targeting the N and ORF1ab genes. Microbial community profiling was performed using 16S rRNA sequencing, followed by diversity, composition, and network analyses to assess interactions between bacterial taxa and viral load. Results: At 6 hours post-rinse, viral loads showed reductions of 1.5-fold with CPC (P = 0.12), 1.2-fold with PVP-I (P = 0.18), and 1.1-fold with NaClO 2 (P = 0.34), though not statistically significant (P > 0.05). Overall microbiome diversity remained stable (P = 0.67), but specific bacterial genera, including Leptotrichia and Lautropia mirabilis , were notably affected by CPC and PVP-I treatments. Furthermore, both CPC and PVP-I disrupted the microbial co-occurrence networks involving SARS-CoV-2 N and ORF1ab gene interactions, suggesting an indirect modulatory effect on the viral–microbial ecosystem. Conclusions: This study provides novel insights into the impact of antiseptic mouthrinses on the salivary virome–microbiome interface in COVID-19 patients. CPC and PVP-I demonstrated potential benefits by modestly reducing viral load and altering microbiome–virus interaction networks. These findings highlight the need for further exploration of mouthrinse-mediated modulation of oral microbial ecology in viral infections.