#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol

  1. Abigail Dommer
  2. Lorenzo Casalino
  3. Fiona Kearns
  4. Mia Rosenfeld
  5. Nicholas Wauer
  6. Surl-Hee Ahn
  7. John Russo
  8. Sofia Oliveira
  9. Clare Morris
  10. Anthony Bogetti
  11. Anda Trifan
  12. Alexander Brace
  13. Terra Sztain
  14. Austin Clyde
  15. Heng Ma
  16. Chakra Chennubhotla
  17. Hyungro Lee
  18. Matteo Turilli
  19. Syma Khalid
  20. Teresa Tamayo-Mendoza
  21. Matthew Welborn
  22. Anders Christensen
  23. Daniel G. A. Smith
  24. Zhuoran Qiao
  25. Sai Krishna Sirumalla
  26. Michael O’Connor
  27. Frederick Manby
  28. Anima Anandkumar
  29. David Hardy
  30. James Phillips
  31. Abraham Stern
  32. Josh Romero
  33. David Clark
  34. Mitchell Dorrell
  35. Tom Maiden
  36. Lei Huang
  37. John McCalpin
  38. Christopher Woods
  39. Alan Gray
  40. Matt Williams
  41. Bryan Barker
  42. Harinda Rajapaksha
  43. Richard Pitts
  44. Tom Gibbs
  45. John Stone
  46. Daniel Zuckerman
  47. Adrian Mulholland
  48. Thomas Miller
  49. Shantenu Jha
  50. Arvind Ramanathan
  51. Lillian Chong
  52. Rommie Amaro

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Abstract

We seek to completely revise current models of airborne transmission of respiratory viruses by providing never-before-seen atomic-level views of the SARS-CoV-2 virus within a respiratory aerosol. Our work dramatically extends the capabilities of multiscale computational microscopy to address the significant gaps that exist in current experimental methods, which are limited in their ability to interrogate aerosols at the atomic/molecular level and thus ob-scure our understanding of airborne transmission. We demonstrate how our integrated data-driven platform provides a new way of exploring the composition, structure, and dynamics of aerosols and aerosolized viruses, while driving simulation method development along several important axes. We present a series of initial scientific discoveries for the SARS-CoV-2 Delta variant, noting that the full scientific impact of this work has yet to be realized.

ACM Reference Format

Abigail Dommer 1† , Lorenzo Casalino 1† , Fiona Kearns 1† , Mia Rosenfeld 1 , Nicholas Wauer 1 , Surl-Hee Ahn 1 , John Russo, 2 Sofia Oliveira 3 , Clare Morris 1 , AnthonyBogetti 4 , AndaTrifan 5,6 , Alexander Brace 5,7 , TerraSztain 1,8 , Austin Clyde 5,7 , Heng Ma 5 , Chakra Chennubhotla 4 , Hyungro Lee 9 , Matteo Turilli 9 , Syma Khalid 10 , Teresa Tamayo-Mendoza 11 , Matthew Welborn 11 , Anders Christensen 11 , Daniel G. A. Smith 11 , Zhuoran Qiao 12 , Sai Krishna Sirumalla 11 , Michael O’Connor 11 , Frederick Manby 11 , Anima Anandkumar 12,13 , David Hardy 6 , James Phillips 6 , Abraham Stern 13 , Josh Romero 13 , David Clark 13 , Mitchell Dorrell 14 , Tom Maiden 14 , Lei Huang 15 , John McCalpin 15 , Christo- pherWoods 3 , Alan Gray 13 , MattWilliams 3 , Bryan Barker 16 , HarindaRajapaksha 16 , Richard Pitts 16 , Tom Gibbs 13 , John Stone 6 , Daniel Zuckerman 2 *, Adrian Mulholland 3 *, Thomas MillerIII 11,12 *, ShantenuJha 9 *, Arvind Ramanathan 5 *, Lillian Chong 4 *, Rommie Amaro 1 *. 2021. #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy ofDeltaSARS-CoV-2 in a Respiratory Aerosol. In Supercomputing ‘21: International Conference for High Perfor-mance Computing, Networking, Storage, and Analysis . ACM, New York, NY, USA, 14 pages. https://doi.org/finalDOI

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  1. ScreenIT

    SciScore for 10.1101/2021.11.12.468428: (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: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    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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  2. Version published to 10.1101/2021.11.12.468428v1 on bioRxiv