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Total Infectomes Characterization of Respiratory Infections in pre-COVID-19 Wuhan, China
Mang Shi; Su Zhao; Bin Yu; Wei-Chen Wu; Yi Hu; Jun-Hua Tian; Wen Yin; Fang Ni; Hong-Ling Hu; Shuang Geng; Li Tan; Ying Peng; Zhi-Gang Song; Wen Wang; Yan-Mei Chen; Edward C Holmes; Yong-Zhen Zhang.
Afiliação
  • Mang Shi; Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
  • Su Zhao; The Central Hospital of Wuhan, Wuhan, China
  • Bin Yu; Wuhan Center for Disease Control and Prevention, Wuhan, China.
  • Wei-Chen Wu; Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
  • Yi Hu; The Central Hospital of Wuhan, Wuhan, China
  • Jun-Hua Tian; Wuhan Center for Disease Control and Prevention, Wuhan, China.
  • Wen Yin; The Central Hospital of Wuhan, Wuhan, China
  • Fang Ni; The Central Hospital of Wuhan, Wuhan, China
  • Hong-Ling Hu; The Central Hospital of Wuhan, Wuhan, China
  • Shuang Geng; The Central Hospital of Wuhan, Wuhan, China
  • Li Tan; The Central Hospital of Wuhan, Wuhan, China
  • Ying Peng; Wuhan Center for Disease Control and Prevention, Wuhan, China.
  • Zhi-Gang Song; Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
  • Wen Wang; Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, China.
  • Yan-Mei Chen; Shanghai Public Health Clinical Center,, Fudan University, Shanghai, China.
  • Edward C Holmes; University of Sydney
  • Yong-Zhen Zhang; Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
Preprint em Inglês | medRxiv | ID: ppmedrxiv-21262865
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 - SARS-CoV-2. Herein, 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. Consequently, we identified 37 pathogen species, comprising 15 RNA viruses, 3 DNA viruses, 16 bacteria and 3 fungi, often at high abundance and including multiple co-infections (12.8%). However, 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.
Licença
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Texto completo: Disponível Coleções: Preprints Base de dados: medRxiv Tipo de estudo: Estudo observacional Idioma: Inglês Ano de publicação: 2021 Tipo de documento: Preprint
Texto completo: Disponível Coleções: Preprints Base de dados: medRxiv Tipo de estudo: Estudo observacional Idioma: Inglês Ano de publicação: 2021 Tipo de documento: Preprint
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