Identification of a polymorphism in the N gene of SARS-CoV-2 that adversely impacts detection by a widely-used RT-PCR assay

  1. Manu Vanaerschot
  2. Sabrina A. Mann
  3. James T. Webber
  4. Jack Kamm
  5. Sidney M. Bell
  6. John Bell
  7. Si Noon Hong
  8. Minh Phuong Nguyen
  9. Lienna Y. Chan
  10. Karan D. Bhatt
  11. Michelle Tan
  12. Angela M. Detweiler
  13. Alex Espinosa
  14. Wesley Wu
  15. Joshua Batson
  16. David Dynerman
  17. CLIAHUB Consortium
  18. Debra A. Wadford
  19. Andreas S. Puschnik
  20. Norma Neff
  21. Vida Ahyong
  22. Steve Miller
  23. Patrick Ayscue
  24. Cristina M. Tato
  25. Simon Paul
  26. Amy Kistler
  27. Joseph L. DeRisi
  28. Emily D. Crawford

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Abstract

We identify a mutation in the N gene of SARS-CoV-2 that adversely affects annealing of a commonly used RT-PCR primer; epidemiologic evidence suggests the virus retains pathogenicity and competence for spread. This reinforces the importance of using multiple targets, preferably in at least 2 genes, for robust SARS-CoV-2 detection.

Article Summary Line

A SARS-CoV-2 variant that occurs worldwide and has spread in California significantly affects diagnostic sensitivity of an N gene assay, highlighting the need to employ multiple viral targets for detection.

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  1. ScreenIT

    SciScore for 10.1101/2020.08.25.265074: (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

    No key resources detected.

    Results from OddPub: Thank you for sharing your code and 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.

    About SciScore

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  2. Version published to 10.1101/2020.08.25.265074v1 on bioRxiv