Amplicon based MinION sequencing of SARS-CoV-2 and metagenomic characterisation of nasopharyngeal swabs from patients with COVID-19

  1. Shona C. Moore
  2. Rebekah Penrice-Randal
  3. Muhannad Alruwaili
  4. Xiaofeng Dong
  5. Steven T. Pullan
  6. Daniel P. Carter
  7. Kevin Bewley
  8. Qin Zhao
  9. Yani Sun
  10. Catherine Hartley
  11. En-min Zhou
  12. Tom Solomon
  13. Michael B. J. Beadsworth
  14. James Cruise
  15. Debby Bogaert
  16. Derrick W. Crook
  17. David A. Matthews
  18. Andrew D. Davidson
  19. Zana Mahmood
  20. Waleed Aljabr
  21. Julian Druce
  22. Richard T. Vipond
  23. Lisa F. P. Ng
  24. Laurent Renia
  25. Peter J. M. Openshaw
  26. J. Kenneth Baillie
  27. Miles W. Carroll
  28. Malcolm G. Semple
  29. Lance Turtle
  30. Julian A. Hiscox
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Abstract

COVID-19 is a complex disease phenotype where the underlying microbiome could influence morbidity and mortality. Amplicon and metagenomic MinION based sequencing was used to rapidly (within 8 hours) identify SARS-CoV-2 and assess the microbiome in nasopharyngeal swabs obtained from patients with COVID-19 by the ISARIC 4C consortium.

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