Dynamic changes of Bacterial Microbiomes in Oropharynx during Infection and Recovery of COVID-19 Omicron Variant

• DOI: 10.1371/journal.ppat.1012075
• Publication Date: 2024-04-03T17:25:46Z
• Authors: Guangying Cui; Ying Sun; Yawen Zou; Ranran Sun; Yanxia Gao; Xiaorui Liu; Yongjian Zhou; Donghua Zhang; Xueqing Wang; Yonghong Li; Liwen Liu; Guizhen Zhang; Benchen Rao; Zujiang Yu; Zhigang Ren
• Keywords: Cross Infection; Bacteria; QH301-705.5; SARS-CoV-2; Microbiota; Humans; COVID-19; Immunologic diseases. Allergy; RC581-607; Biology (General); Research Article

Oropharyngeal microbiomes play a significant role in the susceptibility and severity of COVID-19, yet these for development COVID-19 Omicron variant have not been reported. A total 791 pharyngeal swab samples were prospectively included this study, including 297 confirmed cases (CCO), 222 case who recovered (CCOR), 73 original strain (CCOS) 199 healthy controls (HC). All completed MiSeq sequencing. The results showed that compared with HC, conditional pathogens increased CCO, while acid-producing bacteria decreased. Based on six optimal oropharyngeal operational taxonomy units (OTUs), we constructed marker microbial classifier to distinguish between patients people, achieved high diagnostic efficiency both discovery queue verification queue. At same time, introduced group cross-age infection cohort subtype XBB.1.5 branch, which can be accurately distinguished by model. We also analyzed characteristics two subgroups disease group—severity vaccination times, found change may affect efficacy vaccine. In addition, some genera differences gradually or decreased recovery infection. Spearman analysis 27 OTUs closely related 6 clinical indexes CCO HC. Finally, had different characterization from strain. Our research characterizes rehabilitation cases, successfully verified non-invasive model variant, described correlation indexes. It was microbiomes.