Metagenomic Sequencing To Detect Respiratory Viruses in Persons under Investigation for COVID-19

  1. Ahmed Babiker
  2. Heath L. Bradley
  3. Victoria D. Stittleburg
  4. Jessica M. Ingersoll
  5. Autum Key
  6. Colleen S. Kraft
  7. Jesse J. Waggoner
  8. Anne Piantadosi

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Abstract

Broad testing for respiratory viruses among persons under investigation (PUIs) for SARS-CoV-2 has been performed inconsistently, limiting our understanding of alternative viral infections and coinfections in these patients. RNA metagenomic next-generation sequencing (mNGS) offers an agnostic tool for the detection of both SARS-CoV-2 and other RNA respiratory viruses in PUIs. Here, we used RNA mNGS to assess the frequencies of alternative viral infections in SARS-CoV-2 RT-PCR-negative PUIs ( n  = 30) and viral coinfections in SARS-CoV-2 RT-PCR-positive PUIs ( n  = 45).

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  1. ScreenIT

    SciScore for 10.1101/2020.09.09.20178764: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    A convenience sample set was selected from 75 PUIs who were tested for SARS-CoV-2 in the Emory Healthcare system between February 26th and April 23rd 2020 (spanning the first detection of SARS-CoV-2 infection in Georgia on March 2nd and in the Emory Healthcare system on March 3rd).
    Emory Healthcare
    suggested: (One Mind Biospecimen Bank Listing, RRID:SCR_004193)
    ., Carlsbad, CA), BioFire® FilmArray® Biofire Respiratory pathogen and BioFire® FilmArray® Pneumonia panel (BioFire Diagnostics, LLC, Salt Lake City, UT) had been performed at the discretion of treating physicians.
    BioFire®
    suggested: None
    In some cases, reads were assigned to a virus by KrakenUniq but failed to align to the reference; these reads underwent classification by BLASTn.
    BLASTn
    suggested: (BLASTN, RRID:SCR_001598)

    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:
    Limitations of our study include the testing of banked samples which may degrade over time with freeze-thaw cycles, and the use of clinical tests (such SARS-CoV-2 RT-PCR) as an imperfect gold standard. Nevertheless, our results offer several valuable insights regarding molecular testing for respiratory viruses among SARS-CoV-2 PUIs. First, we found a low rate of viral co-infection in patients with SARS-CoV-2, with only one co-infection (with RSV) among 45 patients (2%). Our results are concordant with a systematic review of 16 studies and 1,014 patients, which found a 3% rate of viral co-infection, with RSV and Influenza A being the most common (8). Thus, viral co-infections may be less common than initially reported (9); nevertheless, it is imperative to continue to monitor for them in the setting of the upcoming respiratory virus season and ongoing waves of COVID-19. Second, our results illustrate key considerations about the potential use of mNGS as a diagnostic tool. Notably, mNGS detected all viruses that were identified by routine clinical workup, as well as five viruses that were not identified by clinical workup. Three of these five had not been tested for clinically, underscoring the importance of routine broad-spectrum molecular testing for respiratory viruses among PUIs. However, two of the viruses were tested for and not identified by multiplex PCR, suggesting that mNGS may offer improved sensitivity. Additional advantages of mNGS have been reviewed elsewhere (10)...

    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.

    About SciScore

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  2. Version published to 10.1128/jcm.02142-20
  3. Version published to 10.1101/2020.09.09.20178764v1 on medRxiv