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Total infectome characterization of respiratory infections in pre-COVID-19 Wuhan, China.
Shi, Mang; Zhao, Su; Yu, Bin; Wu, Wei-Chen; Hu, Yi; Tian, Jun-Hua; Yin, Wen; Ni, Fang; Hu, Hong-Ling; Geng, Shuang; Tan, Li; Peng, Ying; Song, Zhi-Gang; Wang, Wen; Chen, Yan-Mei; Holmes, Edward C; Zhang, Yong-Zhen.
  • Shi M; Zhongshan Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
  • Zhao S; Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia.
  • Yu B; Department of Pulmonary and Critical Care Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
  • Wu WC; Wuhan Center for Disease Control and Prevention, Wuhan, China.
  • Hu Y; Zhongshan Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
  • Tian JH; Department of Pulmonary and Critical Care Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
  • Yin W; Wuhan Center for Disease Control and Prevention, Wuhan, China.
  • Ni F; Department of Pulmonary and Critical Care Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
  • Hu HL; Department of Pulmonary and Critical Care Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
  • Geng S; Department of Pulmonary and Critical Care Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
  • Tan L; Department of Pulmonary and Critical Care Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
  • Peng Y; Department of Pulmonary and Critical Care Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
  • Song ZG; Wuhan Center for Disease Control and Prevention, Wuhan, China.
  • Wang W; Zhongshan Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
  • Chen YM; Zhongshan Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
  • Holmes EC; Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, China.
  • Zhang YZ; Zhongshan Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
PLoS Pathog ; 18(2): e1010259, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1690683
ABSTRACT
At the end of 2019 Wuhan witnessed an outbreak of "atypical pneumonia" that later developed into a global pandemic. Metagenomic sequencing rapidly revealed the causative agent of this outbreak to be a novel coronavirus denoted SARS-CoV-2. To provide a snapshot of the pathogens in pneumonia-associated respiratory samples from Wuhan prior to the emergence of SARS-CoV-2, we collected bronchoalveolar lavage fluid samples from 408 patients presenting with pneumonia and acute respiratory infections at the Central Hospital of Wuhan between 2016 and 2017. Unbiased total RNA sequencing was performed to reveal their "total infectome", including viruses, bacteria and fungi. We identified 35 pathogen species, comprising 13 RNA viruses, 3 DNA viruses, 16 bacteria and 3 fungi, often at high abundance and including multiple co-infections (13.5%). SARS-CoV-2 was not present. These data depict a stable core infectome comprising common respiratory pathogens such as rhinoviruses and influenza viruses, an atypical respiratory virus (EV-D68), and a single case of a sporadic zoonotic pathogen-Chlamydia psittaci. Samples from patients experiencing respiratory disease on average had higher pathogen abundance than healthy controls. Phylogenetic analyses of individual pathogens revealed multiple origins and global transmission histories, highlighting the connectedness of the Wuhan population. This study provides a comprehensive overview of the pathogens associated with acute respiratory infections and pneumonia, which were more diverse and complex than obtained using targeted PCR or qPCR approaches. These data also suggest that SARS-CoV-2 or closely related viruses were absent from Wuhan in 2016-2017.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Pneumonia / Respiratory Tract Infections / Disease Outbreaks / SARS-CoV-2 / COVID-19 Type of study: Cohort study / Observational study / Prognostic study / Randomized controlled trials Limits: Adolescent / Adult / Aged / Female / Humans / Male / Middle aged / Young adult Country/Region as subject: Asia Language: English Journal: PLoS Pathog Year: 2022 Document Type: Article Affiliation country: Journal.ppat.1010259

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Pneumonia / Respiratory Tract Infections / Disease Outbreaks / SARS-CoV-2 / COVID-19 Type of study: Cohort study / Observational study / Prognostic study / Randomized controlled trials Limits: Adolescent / Adult / Aged / Female / Humans / Male / Middle aged / Young adult Country/Region as subject: Asia Language: English Journal: PLoS Pathog Year: 2022 Document Type: Article Affiliation country: Journal.ppat.1010259