Abstract
BACKGROUND: SARS-CoV-2 and COVID-19 are still active in the population. Some patients remained PCR-positive for more than 4 weeks, called "persistently PCR-positive". Recent evidence suggests a link between the gut microbiota and susceptibility to COVID-19, although no studies have explored persistent PCR conditions. We aimed to evaluate the relationship between persistent positive SARS-CoV-2 RT-PCR, the gut microbiome, and individual host determinants. METHODS: A shotgun metagenomic analysis was conducted on fecal samples from 28 individuals affected by COVID-19. Patients were divided into two groups: those who had cleared the virus within 30 days (designated as the control group) (n = 15), and those who remained PCR-positive beyond 30 days (called the PCR+ group) (n = 13). We also investigated the correlation between prolonged viral clearance and several additional factors, including clinical parameters, immune responses, microbial metabolites, and dietary habits. RESULTS: The composition and functionality of the microbiome varied based on the duration of positivity as determined by PCR. Compared to the control group, the persistent PCR+ group exhibited elevated pathogen levels and augmented diversity in functional gene families (p-value < 0.05). A multi-omics analysis integrating metagenomics, metabolites, and metadata also revealed the specific contribution of certain blood markers in this group, including basophils, IgM, IgG (both general and specific for SARS-CoV-2), and markers of liver damage. Unhealthy diet was identified as a significant factor influencing the duration of PCR positivity. CONCLUSIONS: These findings indicate that the gut microbiome may play a role in delayed viral clearance and persistent positive RT-PCR results. Our study also contributes to the understanding of the role of host factors as mediators linking the gut microbiota and disease outcomes. Further large-scale studies must confirm these data; however, they suggest the relevance of monitoring microbiome changes in the early post-viral years to control SARS-CoV-2 and providing individual healthcare support.