Total infectome characterization of respiratory infections in pre-COVID-19 Wuhan, China

  1. Mang Shi
  2. Su Zhao
  3. Bin Yu
  4. Wei-Chen Wu
  5. Yi Hu
  6. Jun-Hua Tian
  7. Wen Yin
  8. Fang Ni
  9. Hong-Ling Hu
  10. Shuang Geng
  11. Li Tan
  12. Ying Peng
  13. Zhi-Gang Song
  14. Wen Wang
  15. Yan-Mei Chen
  16. Edward C. Holmes
  17. Yong-Zhen Zhang

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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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  1. Version published to 10.1371/journal.ppat.1010259
  2. ScreenIT

    SciScore for 10.1101/2021.08.30.21262865: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    EthicsIRB: Ethics statement: The sampling and experimental procedures for this study were reviewed by the ethics committees of the Central Hospital of Wuhan and the National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention.
    Consent: Written informed consents were taken from all patients and volunteers recruited in this study.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    For each of the sequencing results generated, we removed adaptor sequences, non-complex reads, as well as duplicated reads using the BBmap software package.
    BBmap
    suggested: (BBmap, RRID:SCR_016965)
    Human and ribosomal RNA (rRNA) reads were subsequently removed by mapping the de-duplicated reads against the human reference genome (GRCh38/hg38) and the comprehensive rRNA sequence collection downloaded from SILVA database30.
    SILVA
    suggested: (SILVA, RRID:SCR_006423)
    For virus identification, the reads were directly compared against reference virus databases using the blastn program and against the non-redundant protein (nr) database using diamond blastx31, with an e-value threshold set at 1E-10 and 1E-5 for blastn and diamond blastx analyses, respectively.
    blastn
    suggested: (BLASTN, RRID:SCR_001598)
    These genomes were then aligned with related reference virus sequences downloaded from NCBI/GenBank using MAFFT program34.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2021.08.30.21262865v1 on medRxiv