Oral microbiome-based noninvasive diagnostic model for patients reinfected with SARS-CoV-2 omicron variants

In April 2023, there was a wave of patients reinfected with the omicron variant (ORs) in China. The characteristics of the oral microbiome in ORs and the potential of the oral microbiome as a noninvasive biomarker for ORs were still unknown. Increased abundance of 13 genera, including Prevotella, and decreased abundance of 12 genera, including Neisseria, were observed in ORs. Then, we constructed a diagnostic model based on the oral microbiome for ORs, and high AUC values were achieved in one independent validation phase, two cross-regional validation phases and three cross-disease validation phases. This study is the first to characterize the oral microbiome of ORs. Moreover, an efficient and specific microbial diagnostic model for ORs that successfully achieved cross-region and cross-disease validation was constructed that might compensate for the shortcomings of high false-negatives in SARS-CoV-2 nucleic acid detection and the inability to determine virus variant subtypes.