Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study

  1. Luke W Meredith
  2. William L Hamilton
  3. Ben Warne
  4. Charlotte J Houldcroft
  5. Myra Hosmillo
  6. Aminu S Jahun
  7. Martin D Curran
  8. Surendra Parmar
  9. Laura G Caller
  10. Sarah L Caddy
  11. Fahad A Khokhar
  12. Anna Yakovleva
  13. Grant Hall
  14. Theresa Feltwell
  15. Sally Forrest
  16. Sushmita Sridhar
  17. Michael P Weekes
  18. Stephen Baker
  19. Nicholas Brown
  20. Elinor Moore
  21. Ashley Popay
  22. Iain Roddick
  23. Mark Reacher
  24. Theodore Gouliouris
  25. Sharon J Peacock
  26. Gordon Dougan
  27. M Estée Török
  28. Ian Goodfellow

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Abstract

No abstract available

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  1. Version published to 10.1016/s1473-3099(20)30562-4
  2. ScreenIT

    SciScore for 10.1101/2020.05.08.20095687: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: It therefore did not require individual patient consent or ethical approval.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Amplicon libraries were sequenced using MinION flow cells v9.4.1 (Oxford Nanopore Technologies, Oxford, UK).
    MinION
    suggested: (MinION, RRID:SCR_017985)

    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:
    We acknowledge several limitations to our study. Firstly, we were unable to sequence all of the genomes from samples that were collected during the study period. We may therefore have missed the opportunity to investigate all potential transmission events. Furthermore, we only had main ward location data for most of the HCW and could have overlooked potential epidemiological links with patients with whom they had contact on other wards. Similarly, we were unable to track HCW movements outside their main ward location to identify potential contact with patients on other wards or HCW within shared communal areas. Finally, due to the recent introduction of SARS-CoV-2 into the human population, highly similar genomes are not sufficient evidence to infer a recent transmission, in the absence of confirmatory epidemiological data. However, our experience indicates that further investigation of genomic clusters with highly similar genomes can uncover previously unknown epidemiological links. Furthermore, we were able to use rapidly generated genomic data to investigate HCAI within the hospital setting. The next initiative is to expand this platform into a more detailed analysis of infections in HCW and in community settings, such as residential homes. As the practical challenges associated with implementing real-time genome sequencing during epidemics are overcome, unlocking the real power of genomic epidemiology will require its integration with clinical and public health systems to...

    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

    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 10.1101/2020.05.08.20095687 on medRxiv