A research team led by University of California San Diego Professor and Endowed Chair of Chemistry and Biochemistry Rommie Amaro (PhD, '05) has modeled for the first time the delta variant of the SARS-CoV-2 virus inside an aerosol.
Amaro was an Illinois chemistry graduate student in the research group of Zaida (Zan) Luthey-Schulten and completed her bachelor's degree in 2000 in the Department of Chemical and Biomolecular Engineering at Illinois.
The work of Amaro's team, which included researchers across the United States and the world, was featured in The New York Times, and was a finalist for the Gordon Bell Prize, given by the Association for Computing Machinery each year to recognize outstanding achievement in high-performance computing. Amaro also led the team that won that same prize in 2020 for modeling an all-atom SARS-CoV-2 virus and the virus's spike protein to understand how it behaves and gains access to humans.
In a news release from UCSD, Amaro said the team is excited about the potential of this work to help us better understand how viruses are transmitted through aerosols.
"The impacts could change the way we view airborne diseases,” Amaro said.
Aerosols are tiny, smaller than the diameter of a human hair. Despite their size, the aerosols that humans produce by breathing and speaking can float in the air for hours and travel long distances. Kim Prather, Distinguished Chair in atmospheric chemistry and director of the Center for Aerosol Impacts on Chemistry of the Environment (CAICE), has studied sea spray and ocean aerosols extensively. She contacted Amaro several years ago noting that these aerosols had much more than seawater in them.
“The common thinking used to be that ocean aerosols only contained salt water,” Prather stated. “But we discovered there was a ton of ocean-biology inside—living organisms including 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 paved the way for Amaro and her group to understand the experimental methods and tools used to study aerosols, generally, as well as develop a useful framework to build, simulate and analyze 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 scientists always suspected SARS-CoV-2 was airborne, so studying the virus inside an aerosol provided an opportunity to back those suspicions with evidence. Taking the work her lab was already doing with aerosols and the work her lab was also doing with the virus, Amaro put two and two together.
Visualization of delta SARS-CoV-2 in a respiratory aerosol, where the virus is depicted in purple with the studded spike proteins in cyan. Mucins are red, albumin proteins green, and the deep lung fluid lipids in ochre.
“It’s these fine aerosols that can travel the farthest and move into the deep lung, which can be devasting,” Amaro said. “There is no experimental tool, no microscope that allows people to see the particles in this much detail, but this new computational microscope allows us to see what happens to the virus—how it moves, how it stays infectious during flight. 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.
These simulations included more intricate details of the virus’s membranes, as well as visualizations of aerosols. In addition to the SARS-CoV-2 virus, these sub-micron respiratory aerosols also contained mucins, lung surfactant, water and ions.
Mucins are polymers that line most of the surfaces of the body that are wet, including the respiratory tract and they may work to protect the virus from harsh external elements like sunlight. One of the hypotheses that Amaro’s team is exploring is whether the delta variant of SARS-CoV-2 is more transmissible in part because it seems to interact so well with mucins.
Now that the models have been built, Amaro hopes to formally create an experiment that will test the predictions of aerosolized virus movements. She is also developing tools that will investigate how humidity, wind and other external conditions affect the transmission and life of the virus in aerosols.