High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs

  1. J. E. Gorzynski
  2. H. N. De Jong
  3. D. Amar
  4. C. Hughes
  5. A. Ioannidis
  6. R. Bierman
  7. D. Liu
  8. Y. Tanigawa
  9. A. L. Kistler
  10. J. Kamm
  11. J. Kim
  12. L. Cappello
  13. N. F. Neff
  14. S. Rubinacci
  15. O. Delaneau
  16. M. J. Shoura
  17. K. Seo
  18. A. Kirillova
  19. A. Raja
  20. S. Sutton
  21. C. Huang
  22. M. K. Sahoo
  23. K. C. Mallempati
  24. G. Montero-Martin
  25. K. Osoegawa
  26. N. Watson
  27. N. Hammond
  28. R. Joshi
  29. M. A. Fernández-Viña
  30. J. W. Christle
  31. M.T. Wheeler
  32. P. Febbo
  33. K. Farh
  34. G. P. Schroth
  35. F. DeSouza
  36. J. Palacios
  37. J. Salzman
  38. B. A. Pinsky
  39. M. A. Rivas
  40. C.D. Bustamante
  41. E. A. Ashley
  42. V. N. Parikh
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Abstract

During COVID19 and other viral pandemics, rapid generation of host and pathogen genomic data is critical to tracking infection and informing therapies. There is an urgent need for efficient approaches to this data generation at scale. We have developed a scalable, high throughput approach to generate high fidelity low pass whole genome and HLA sequencing, viral genomes, and representation of human transcriptome from single nasopharyngeal swabs of COVID19 patients.

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