Since its emergence in late 2019, SARS-CoV-2 has evolved into multiple variants of concern (VOCs) and variants of interest (VOIs). One contributing factor to the high number of COVID-19 cases is the efficient transmission patterns of the virus via droplets, aerosols, or airborne (Jayaweera et al., 2020). Oral cavity serves as a key reservoir for SARS-CoV-2, with salivary viral loads linked to disease severity and transmission risk (Azzi et al., 2020, Yoon et al., 2020). This is particularly relevant in dentistry as clinical procedures invariably involve exposure to saliva and dental treatments often generates aerosol (Peng et al., 2020). Therefore, since the onset of the COVID-19 pandemic, numerous studies have investigated use of mouth-rinses as a strategy to reduce the salivary SARS-CoV levels (Elmahgoub and Coll, 2021, O’Donnell et al., 2020, Seneviratne et al., 2021).

Several commercial mouthrinses claim to possess active components with virucidal effects including Sodium Chlorite (NaClO2), Povidone Iodine (PVP-I), and Cetylpyridinium Chloride (CPC) (Ferrer et al., 2021, Seneviratne et al., 2021). NaClO2 generates chlorine dioxide (ClO2), an oxidizing agent that interferes microbial cell membranes (Goda et al., 2018, Young, 2016). PVP-I releases iodine upon dissociation in water disrupting stability of cell membranes, and oxidizing key macromolecules such as proteins, nucleotides, and fatty acids (Kanagalingam et al., 2015). CPC is a quaternary ammonium compound which disrupts the integrity of cell membrane, leading to leakage of cytoplasmic components and cell lysis (Nasila et al., 2021, Yegin et al., 2019). While number of clinical investigations have suggested temporarily suppression of the salivary SARS CoV-2 levels following the use of mouth-rinses (Alzahrani et al., 2023, Ather et al., 2021, de Paula Eduardo et al., 2021), their impact of oral microbiome of COVID-19 patients remained unexplored. Moreover, no studies have elucidated the interplay between SARS CoV-2 virus and oral microbiome.

Despite the emergence of SARS-CoV-2 variants with novel mutations, the N nucleocapsid (N) and open reading frame 1ab (ORF1ab) genes, which play a crucial role in viral replication remain essential targets for RT-qPCR detection (Chan et al., 2020). All the VOCs that have been identified to date such as Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617), and Omicron (B.1.1.529) carry N and ORF1ab genes (Andre et al., 2023). Therefore, exploring the interaction of these two genes and the oral microbiome may offer new insight into the niche-specific viral dynamics in the oral cavity.

In the present study we investigated the effect of NaClO2, PVP-I, and CPC mouthrinses on salivary SARS-CoV-2 and the oral microbiome in COVID-19 patients, using N and ORF1ab gene targets. We hypothesized that antiseptic mouthrinses would reduce salivary SARS-CoV-2 viral load and induce short-term compositional changes in the salivary microbiome of COVID-19 patients. Accordingly, the null hypotheses were that: (i) antiseptic mouthrinses would not reduce salivary SARS-CoV-2 viral load compared with water; (ii) they would not alter salivary microbiome diversity or composition; and (iii) they would not modify the correlation patterns between SARS-CoV-2 gene targets and oral bacterial taxa.