Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and SARS-CoV-2 variants

  1. N.L. Welch
  2. M. Zhu
  3. C. Hua
  4. J. Weller
  5. M. Ezzaty Mirhashemi
  6. S. Mantena
  7. T.G. Nguyen
  8. B.M. Shaw
  9. C.M. Ackerman
  10. S.G. Thakku
  11. M.W. Tse
  12. J. Kehe
  13. M.R. Bauer
  14. M-M. Uwera
  15. J.S. Eversley
  16. D.A. Bielwaski
  17. G. McGrath
  18. J. Braidt
  19. J. Johnson
  20. F. Cerrato
  21. B.A. Petros
  22. G.L. Gionet
  23. S.K. Jalbert
  24. M.L. Cleary
  25. K.J. Siddle
  26. C.T. Happi
  27. D.T. Hung
  28. M. Springer
  29. B.L. MacInnis
  30. J.E. Lemieux
  31. E. Rosenberg
  32. J.A. Branda
  33. P.C. Blainey
  34. P.C. Sabeti
  35. C Myhrvold
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Abstract

The COVID-19 pandemic has demonstrated a clear need for high-throughput, multiplexed, and sensitive assays for detecting SARS-CoV-2 and other respiratory viruses as well as their emerging variants. Here, we present microfluidic CARMEN (mCARMEN), a cost-effective virus and variant detection platform that combines CRISPR-based diagnostics and microfluidics with a streamlined workflow for clinical use. We developed the mCARMEN respiratory virus panel (RVP) and demonstrated its diagnostic-grade performance on 533 patient specimens in an academic setting and then 166 specimens in a clinical setting. We further developed a panel to distinguish 6 SARS-CoV-2 variant lineages, including Delta and Omicron, and evaluated it on 106 patient specimens, with near-perfect concordance to sequencing-based variant classification. Lastly, we implemented a combined Cas13 and Cas12 approach that enables quantitative measurement of viral copies in samples. mCARMEN enables high-throughput surveillance of multiple viruses and variants simultaneously.

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