Frontiers in Microbiology (Sep 2022)
Microbial and human transcriptional profiling of coronavirus disease 2019 patients: Potential predictors of disease severity
- Hairun Gan,
- Hairun Gan,
- Hairun Gan,
- Jiumeng Min,
- Jiumeng Min,
- Haoyu Long,
- Haoyu Long,
- Haoyu Long,
- Bing Li,
- Xinyan Hu,
- Xinyan Hu,
- Xinyan Hu,
- Zhongyi Zhu,
- Zhongyi Zhu,
- Luting Li,
- Luting Li,
- Luting Li,
- Tiancheng Wang,
- Tiancheng Wang,
- Tiancheng Wang,
- Xiangyan He,
- Xiangyan He,
- Jianxun Cai,
- Jianxun Cai,
- Jianxun Cai,
- Yongyu Zhang,
- Jianan He,
- Luan Chen,
- Luan Chen,
- Dashuai Wang,
- Jintao Su,
- Jintao Su,
- Ni Zhao,
- Weile Huang,
- Jingjing Zhang,
- Ziqi Su,
- Ziqi Su,
- Hui Guo,
- Xiaojun Hu,
- Xiaojun Hu,
- Xiaojun Hu,
- Junjie Mao,
- Junjie Mao,
- Junjie Mao,
- Jinmin Ma,
- Pengfei Pang,
- Pengfei Pang,
- Pengfei Pang
Affiliations
- Hairun Gan
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Hairun Gan
- Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Hairun Gan
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Jiumeng Min
- BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, China
- Jiumeng Min
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
- Haoyu Long
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Haoyu Long
- Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Haoyu Long
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Bing Li
- Department of Ophthalmology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Xinyan Hu
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Xinyan Hu
- Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Xinyan Hu
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Zhongyi Zhu
- BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, China
- Zhongyi Zhu
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
- Luting Li
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Luting Li
- Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Luting Li
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Tiancheng Wang
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Tiancheng Wang
- Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Tiancheng Wang
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Xiangyan He
- BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, China
- Xiangyan He
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
- Jianxun Cai
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Jianxun Cai
- Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Jianxun Cai
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Yongyu Zhang
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Jianan He
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Luan Chen
- BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, China
- Luan Chen
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
- Dashuai Wang
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Jintao Su
- BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, China
- Jintao Su
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
- Ni Zhao
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Weile Huang
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Jingjing Zhang
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Ziqi Su
- BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, China
- Ziqi Su
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
- Hui Guo
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Xiaojun Hu
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Xiaojun Hu
- Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Xiaojun Hu
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Junjie Mao
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Junjie Mao
- Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Junjie Mao
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Jinmin Ma
- BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, China
- Pengfei Pang
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Pengfei Pang
- Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Pengfei Pang
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- DOI
- https://doi.org/10.3389/fmicb.2022.959433
- Journal volume & issue
-
Vol. 13
Abstract
The high morbidity of patients with coronavirus disease 2019 (COVID-19) brings on a panic around the world. COVID-19 is associated with sex bias, immune system, and preexisting chronic diseases. We analyzed the gene expression in patients with COVID-19 and in their microbiota in order to identify potential biomarkers to aid in disease management. A total of 129 RNA samples from nasopharyngeal, oropharyngeal, and anal swabs were collected and sequenced in a high-throughput manner. Several microbial strains differed in abundance between patients with mild or severe COVID-19. Microbial genera were more abundant in oropharyngeal swabs than in nasopharyngeal or anal swabs. Oropharyngeal swabs allowed more sensitive detection of the causative SARS-CoV-2. Microbial and human transcriptomes in swabs from patients with mild disease showed enrichment of genes involved in amino acid metabolism, or protein modification via small protein removal, and antibacterial defense responses, respectively, whereas swabs from patients with severe disease showed enrichment of genes involved in drug metabolism, or negative regulation of apoptosis execution, spermatogenesis, and immune system, respectively. Microbial abundance and diversity did not differ significantly between males and females. The expression of several host genes on the X chromosome correlated negatively with disease severity. In this way, our analyses identify host genes whose differential expression could aid in the diagnosis of COVID-19 and prediction of its severity via non-invasive assay.
Keywords
