Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia

  1. Jessica E. Manning
  2. Jennifer A. Bohl
  3. Sreyngim Lay
  4. Sophana Chea
  5. Ly Sovann
  6. Yi Sengdoeurn
  7. Seng Heng
  8. Chan Vuthy
  9. Katrina Kalantar
  10. Vida Ahyong
  11. Michelle Tan
  12. Jonathan Sheu
  13. Cristina M. Tato
  14. Joseph L. DeRisi
  15. Laurence Baril
  16. Veasna Duong
  17. Philippe Dussart
  18. Erik A. Karlsson

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Abstract

Rapid production and publication of pathogen genome sequences during emerging disease outbreaks provide crucial public health information. In resource-limited settings, especially near an outbreak epicenter, conventional deep sequencing or bioinformatics are often challenging. Here we successfully used metagenomic next generation sequencing on an iSeq100 Illumina platform paired with an open-source bioinformatics pipeline to quickly characterize Cambodia’s first case of COVID-2019.

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  1. ScreenIT

    SciScore for 10.1101/2020.03.02.968818: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: Since clinical specimens are obtained from suspected COVID-19 cases as part of the national outbreak response, requirement for informed consent was waived for pathogen identification and characterization. mNGS libraries were prepared from the viral RNA extracted from the sample.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    No key resources detected.

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    The clear limitation in an mNGS approach is that low viral titers or high levels of host material demand greater read depth than may be available on instruments such as the iSeq100. To overcome this barrier, our follow-up steps included a target enrichment of SARS-CoV-2 while keeping the comprehensiveness of our mNGS pipeline intact.6 For an emerging threat, this strategy offers the flexibility to successfully recover the pathogen genome in question for subsequent phylogenetic analyses without compromising discovery. However, the other key factor in mNGS success is the accessibility to open-access, cloud-based metagenomics bioinformatics pipelines, such as IDseq which automates the process of separating host sequence characterizing the remaining non-host sequences.12 As recent as the Ebola epidemic, bioinformatics analyses were still mainly completed in the Global North.10 This newly available combination – more rugged, deployable sequencers plus user-friendly, globally accessible bioinformatics – represents an opportunity for responders in limited-resource settings; however, further proof-of-principle during outbreaks remains necessary. Overall, agnostic or unbiased metagenomic sequencing capabilities in-country provide the ability to detect and respond to a variety of pathogens, even those that are unanticipated or unknown. Bridging of existing local and global resources for sequencing and analysis allows for better real-time surveillance locally, while also enabling better...

    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:
    • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
    • 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.

    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.

  2. Version published to 10.1101/2020.03.02.968818v1 on bioRxiv