Prevalence of Anelloviruses in Nasopharyngeal Samples from SARS- CoV-2 Screened Individuals: A Cross-sectional Study

The human virome encompasses both pathogenic and commensal viruses, with small circular DNA viruses such as Anelloviruses and Redondoviruses (ReDoVs). The objective of this study was to determine the prevalence of Anelloviruses and ReDoVs in nasopharyngeal samples, and to evaluate their potential clinical and oral health associations. In this cross-sectional study, 412 samples were collected. Demographic, clinical, and oral health data were obtained through interviews and clinical records. Viral DNA was extracted and ReDoVs were amplified by PCR targeting a conserved Capsid/Rep intergenic region. Anelloviruses were detected through a two-stage nested-PCR. Statistical analyses included chi-square, Fisher’s exact test, logistic regression, and ROC curve modeling to assess associations between viral positivity, clinical symptoms, and oral health indicators. SARS-CoV-2 was detected in 26.5% and ReDoV in 22.1%. Anelloviruses were highly prevalent (TTV: 81.6%, TTMV: 47.8%, TTMDV: 43.9%). SARS-CoV-2 infection was associated with symptoms including fever, headache, and cough (p < 0.0001). ReDoV and TTMV were independently associated with self-reported gum problems (p < 0.0001 and p = 0.015, respectively). ReDoV showed intra-viral co-detection with TTMV and TTMDV. Logistic regression confirmed fever and gum problems as the only robust predictors of SARS-CoV-2 and ReDoV infection, respectively. Predictive models for these two viruses demonstrated good discrimination (AUC = 0.81-0.83). These findings highlight the ubiquity of Anelloviruses and the distinct clinical association of ReDoVs with oral health indicators. The results underscore the complexity of the respiratory virome and its potential as a biomarker of host–microbe interactions.