Co-infection with SARS-CoV-2 Omicron and Delta variants revealed by genomic surveillance

  1. Rebecca J. Rockett
  2. Jenny Draper
  3. Mailie Gall
  4. Eby M. Sim
  5. Alicia Arnott
  6. Jessica E. Agius
  7. Jessica Johnson-Mackinnon
  8. Winkie Fong
  9. Elena Martinez
  10. Alexander P. Drew
  11. Clement Lee
  12. Christine Ngo
  13. Marc Ramsperger
  14. Andrew N. Ginn
  15. Qinning Wang
  16. Michael Fennell
  17. Danny Ko
  18. Linda Hueston
  19. Lukas Kairaitis
  20. Edward C. Holmes
  21. Matthew N. O’Sullivan
  22. Sharon C.-A. Chen
  23. Jen Kok
  24. Dominic E. Dwyer
  25. Vitali Sintchenko

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Abstract

Co-infections with different variants of SARS-CoV-2 are a key precursor to recombination events that are likely to drive SARS-CoV-2 evolution. Rapid identification of such co-infections is required to determine their frequency in the community, particularly in populations at-risk of severe COVID-19, which have already been identified as incubators for punctuated evolutionary events. However, limited data and tools are currently available to detect and characterise the SARS-CoV-2 co-infections associated with recognised variants of concern. Here we describe co-infection with the SARS-CoV-2 variants of concern Omicron and Delta in two epidemiologically unrelated adult patients with chronic kidney disease requiring maintenance haemodialysis. Both variants were co-circulating in the community at the time of detection. Genomic surveillance based on amplicon- and probe-based sequencing using short- and long-read technologies identified and quantified subpopulations of Delta and Omicron viruses in respiratory samples. These findings highlight the importance of integrated genomic surveillance in vulnerable populations and provide diagnostic pathways to recognise SARS-CoV-2 co-infection using genomic data.

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  1. Version published to 10.1038/s41467-022-30518-x
  2. ScreenIT

    SciScore for 10.1101/2022.02.13.22270755: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    No key resources detected.

    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.

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  3. Version published to 10.1101/2022.02.13.22270755 on medRxiv