Dataset Information

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

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.

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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.

SUBMITTER: Dommer A

PROVIDER: S-EPMC8609898 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature

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

Dommer Abigail A Casalino Lorenzo L Kearns Fiona F Rosenfeld Mia M Wauer Nicholas N Ahn Surl-Hee SH Russo John J Oliveira Sofia S Morris Clare C Bogetti Anthony A Trifan Anda A Brace Alexander A Sztain Terra T Clyde Austin A Ma Heng H Chennubhotla Chakra C Lee Hyungro H Turilli Matteo M Khalid Syma S Tamayo-Mendoza Teresa T Welborn Matthew M Christensen Anders A Smith Daniel G A DGA Qiao Zhuoran Z Sirumalla Sai Krishna SK O'Connor Michael M Manby Frederick F Anandkumar Anima A Hardy David D Phillips James J Stern Abraham A Romero Josh J Clark David D Dorrell Mitchell M Maiden Tom T Huang Lei L McCalpin John J Woods Christopher C Gray Alan A Williams Matt M Barker Bryan B Rajapaksha Harinda H Pitts Richard R Gibbs Tom T Stone John J Zuckerman Daniel D Mulholland Adrian A Miller Thomas T Jha Shantenu S Ramanathan Arvind A Chong Lillian L Amaro Rommie R

bioRxiv : the preprint server for biology 20211115

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 trans ...[more]

PMID: 34816263

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Project description:This study analyzes the reasons the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant of concern (VOC) spreads so rapidly. Novel topics such as universal conditions for the rapid spread of respiratory viruses, minimum viral loads for viral aerosol generation, effects of vaccination on viral aerosol generation, and viral aerosol clouds were studied. The analyses were based on experimental results and analytic model studies. Four universal conditions, namely asymptomatic host, high viral load, stability of viruses in air, and binding affinity of viruses to human cells, need to be satisfied for the rapid spread of respiratory viruses. SARS-CoV-2 and its variants such as the Alpha VOC and Delta VOC satisfy the four fundamental conditions. In addition, there is an original principle of aerosol generation of respiratory viruses. Assuming that the aerosol-droplet cutoff particle diameter for distinguishing potential aerosols from earthbound respiratory particles is 100 μm, the minimum viral load required in respiratory fluids to generate viral aerosols is ~106 copies mL-1, which is within the range of the reported viral loads in the Alpha VOC cases and the Delta VOC cases. The daily average viral loads of the Delta VOC in hosts have been reported to be between ~109 copies mL-1 and ~1010 copies mL-1 during the four days after symptom onset in 1848 cases of the Delta VOC infection. Owing to the high viral load, the SARS-CoV-2 Delta VOC has the potential to effectively spread through aerosols. COVID-19 vaccination can decrease aerosol transmission of the SARS-CoV-2 Alpha VOC by reducing the viral load. The viral load can explain the conundrum of viral aerosol spreading. The SARS-CoV-2 Delta VOC aerosol clouds have been assumed to be formed in restricted environments, resulting in a massive numbers of infected people in a very short period with a high spreading speed. Strong control methods against bioaerosols should be considered in this SARS-CoV-2 Delta VOC pandemic. Large-scale environmental monitoring campaigns of SARS-CoV-2 Delta VOC aerosols in public places in many countries are necessary, and these activities could contribute to controlling the coronavirus disease pandemic.

Dataset Information

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

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Publications

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

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