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Newswise — In May 2021, the Centers for Disease Control officially recognized that SARS-CoV-2–the virus that causes COVID-19–is airborne, meaning it is highly transmissible through the air.

Now University of California San Diego Professor and Endowed chair of Chemistry and Biochemistry Rommie, together with other partners from around the U.S. and the world, have created the first aerosol model of the delta virus.

This work was selected for the Gordon Bell Prize. The prize is awarded each year by the Association for Computing Machinery to recognize exceptional achievement in high-performance computing. Amaro was the leader of the team that won last year’s prize for their work on modeling the all-atom SARS/CoV-2 virus, and its spike protein, to understand how it behaves. .

” It’s an honor to be a finalist in the Gordon Bell Prize for the second year running,” said Amaro. “But we are more excited than that about the potential this research has to deepen understanding of viruses transmitted via aerosols. The impacts could change the way we view airborne diseases.”

Aerosols are tiny. A human hair is approximately 10 microns in width. A droplet–think of the spray that come out of your mouth and nose when you sneeze–can be up to 10 microns wide. Aerosols have a width of less than 1 micron. Whereas droplets fall to the ground in under 30 seconds, aerosols, because of their small size, can float in the air for hours and travel long distances.

Kim Prather is a Distinguished Chair in atmospheric Chemistry and the Director of the Center for Aerosol Impacts on Chemistry of the Environment. He has extensively studied ocean aerosols and sea spray. Amaro was contacted by Prather several years ago to inform her that aerosols contained more than just seawater.

” It used to be believed that ocean aerosols contained only salt water,” Prather said. “But, we discovered that there was ocean-biology within–living organisms such as proteins and viruses. I not only thought Rommie would be interested in studying this, but also thought her work could be really beneficial in helping us gain a better understanding of aerosol composition and movement and airborne survival.”

Amaro’s lab began to develop computer models of what aerosols looked like using Prather’s work in sea spray. These simulations allowed Amaro and her team to better understand aerosol research tools and methods, and to create a framework for building, simulating, and analysing complex aerosol models.

When SARS-CoV-2 came on the scene in early 2020, she began modeling the virus and was able to show how it infects host cells through a sugary coating called a glycan that covers the spike proteins.

Aerosol researchers always suspected that SARS-CoV-2 is airborne. Therefore, studying the virus in an aerosol gave them an opportunity to prove their suspicions. Amaro combined the aerosol research her lab had done and the virus work she was doing, and put them together.

“These fine aerosols can travel the furthest and reach the deepest lungs, which can prove to be devastating,” Amaro said. The only way to see particles in such detail is with an experimental microscope. But this computational microscope lets us see how the virus behaves during flight, and what it looks like. There is something very powerful about being able to see what something looks like, seeing how components come together–it fundamentally changes the kinds of questions people even think to ask.”

To better understand how the virus moves and lives inside aerosols, Amaro worked with a team of 52 from around the globe, including Oak Ridge National Laboratory, using their Summit supercomputer to simulate the models. Summit is one of the few supercomputers in the world capable of performing these large-scale simulations, which allowed researchers to see aerosols at an unprecedented one billion atoms.

These simulations provided more detailed information about the virus’s membranes as well as visualisations of aerosols. These sub-micron respiratory aerosols contained not only the SARS-CoV-2 viruses, but also mucins and lung surfactant, as well as water and ions.

Mucins, polymers that line the majority of the body’s wet surfaces, including the respiratory tract, may help protect the virus against harsh external elements such as sunlight. Amaro’s group is investigating whether the delta variant SARS-CoV-2 may be more transmissible, in part due to its interaction with mucins.

Amaro is now working on a formal experiment to test her predictions about aerosolized virus movement. Amaro is also working on tools to study how wind, humidity and other environmental conditions impact the transmission and longevity of the virus in aerosols.

Aside from the immediate need to learn as much as possible about SARS-CoV-2’s operation, computer models of aerosols have broad-ranging effects on climate science, human health, and climate science.

” What we discovered during the pandemic was that aerosols played a major role in spreading the virus, and their importance in transmitting other respiratory pathogens, has been systematically underestimated,” stated Dr. Robert “Chip” Schooley from the Department of Medicine at UC San Diego School of Medicine. This is good news for the public health and wellbeing of people around the world. This benefits the public health and wellbeing of people around the world.”

This work appears in The Proceedings of SC21, Virtual Event, November 14-19, 2021. Full video presentation available on Rommie’s YouTube channel .

This work was supported by the NSF Center for Aerosol Impacts on Chemistry of the Environment (CAICE), National Science Foundation Center for Chemical Innovation (NSF CHE-1801971), NIH GM132826, NSF RAPID MCB-2032054, Oak Ridge Computing Facility at Oak Ridge National Laboratory (DOE DE-AC05-00OR22725), Texas Advanced Computing Center Frontera (NSF OAC-1818253), Argonne Computing Facility (DOE DE-AC02-06CH11357), and Pittsburgh Supercomputer Center ( NSF TG-CHE060063). Additional funding provided by RCSA Research Corp. and a UC San Diego Moore’s Cancer Center 2020 SARS-CoV-2 seed grant.

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