In:
PLOS Pathogens, Public Library of Science (PLoS), Vol. 18, No. 2 ( 2022-2-17), p. e1010259-
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.
Type of Medium:
Online Resource
ISSN:
1553-7374
DOI:
10.1371/journal.ppat.1010259
DOI:
10.1371/journal.ppat.1010259.g001
DOI:
10.1371/journal.ppat.1010259.g002
DOI:
10.1371/journal.ppat.1010259.g003
DOI:
10.1371/journal.ppat.1010259.g004
DOI:
10.1371/journal.ppat.1010259.g005
DOI:
10.1371/journal.ppat.1010259.s001
DOI:
10.1371/journal.ppat.1010259.s002
DOI:
10.1371/journal.ppat.1010259.s003
DOI:
10.1371/journal.ppat.1010259.r001
DOI:
10.1371/journal.ppat.1010259.r002
DOI:
10.1371/journal.ppat.1010259.r003
DOI:
10.1371/journal.ppat.1010259.r004
Language:
English
Publisher:
Public Library of Science (PLoS)
Publication Date:
2022
detail.hit.zdb_id:
2205412-1
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