Title Total infectome characterization of respiratory infections in pre-COVID-19 Wuhan, China.
Author 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
Journal PLoS Pathog Publication Year/Month 2022-Feb
PMID 35176118 PMCID PMC8853501
Affiliation + expend 1.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.

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.

StrainID RV Species Serotype Length(nt) Country Year Strain Name
CNM01210 C 6 7038 China 2016 S0679ZYY
CNP01212 C 7 7073 China 2016 S0590XDY
CNS01213 C 31 6966 China 2016 S0425ZDP
CNZ01211 C 19 7148 China 2016 S0595YZY
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