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. Elena Martinez
  9. Alexander P Drew
  10. Clement Lee
  11. Christine Ngo
  12. Marc Ramsperger
  13. Andrew N Ginn
  14. Qinning Wang
  15. Michael Fennell
  16. Danny Ko
  17. Linda Huston
  18. Lukas Kairaitis
  19. Edward C Holmes
  20. Matthew N O’Sullivan
  21. Sharon C-A Chen
  22. Jen Kok
  23. Dominic E Dwyer
  24. Vitali Sintchenko
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Abstract

We identified the co-infection of the SARS-CoV-2 Omicron and Delta variants in two epidemiologically unrelated patients with chronic kidney disease requiring haemodialysis. Both SARS-CoV-2 variants were co-circulating locally at the time of detection. Amplicon- and probe-based sequencing using short- and long-read technologies identified and quantified Omicron and Delta subpopulations in respiratory samples from the two patients. These findings highlight the importance of genomic surveillance in vulnerable populations.

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