Multicohort oral microbial analysis contributes to non-invasive diagnosis for patients reinfected with SARS-CoV-2 omicron variants
Description
Infection with SARS-CoV-2 can lead to alterations in human oral microbiome. Recently, there was a wave of patients reinfected with SARS-CoV-2 omicron variant (ORs) in China. Alterations in the oral microbiome in ORs were still unknown. A total of 2046 participants were enrolled and provided tongue-coating samples, and 1637 samples were ultimately used for sequencing and analysis, including 702 ORs, 184 omicron variant primary-infected patients, 50 wild-type strain primary-infected patients (WTPs), 154 common cold patients and 547 heathy controls (HCs). The results showed that no significant difference in the α diversity of the oral microbiome between the OR and HC groups. Compared with HCs, increased abundance of 13 genera, including Prevotella and Veillonella, and decreased abundance of 12 genera, including Neisseria and Actinomyces, were observed in ORs. Then, 5 OTUs were identified to construct a diagnostic model. In the discovery phase, the training set and test set obtained AUC values of 97.25% and 97.07%. Importantly, the independent validation phase achieved 89.61%. Strikingly, two cross-regional validation phases showed 70.90% and 73.97%. In addition, 92.34%, 95.46 and 85.10% were identified in three cross-disease validation phases. Furthermore, we found although SARS-CoV-2 continued to mutate, the overall composition of the oral microbiome changed little. Among them, the microbial community of WTPs was most disturbed, while that of ORs was least disturbed. This study is the first to characterize the oral microbiome of ORs. A diagnostic model which achieved cross-region and cross-disease validation for ORs may help the diagnosis of OR. The data uploaded include the original clinical data of the participants of this study (Table S1) and the data generated during the analysis process and placed in the supplementary materials of the paper (Table S2-24). Please find the title in the first row of each sheet.