Visualization of the spike protein (cyan), surrounded by mucus molecules and calcium ions (yellow). The purple color is the viral membrane. Credit: UC San Diego’s Lorenzo Casalino and the Amaro Lab.
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 Amaro, along with partners across the U.S. and around the world, has modeled the delta virus inside an aerosol for the first time.
This work was selected as a finalist for this year’s Gordon Bell Prize. The prize is awarded 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 modeling the all-atom SARS-2 virus and its spike protein, to understand how it behaves in human cells.
“It is 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 of this work to deepen our understanding on how viruses can be transmitted via aerosols. These impacts could transform our perception of airborne diseases. “
Aerosols have a very small size. 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. She has extensively studied ocean aerosols and sea spray. Amaro was contacted by Prather several years ago, pointing out that aerosols contained more than seawater.
Delta SARS-CoV-2 is visualized in a respiratory aerosol. The virus is shown in purple and the spike proteins are in cyan. The mucins are in red, the albumin proteins are green, and deep lung fluid oils lipids are in ocher. Credit: UC San Diego’s Abigail Dommer and the Amaro Lab.
” The common belief was that ocean aerosols contained only salt water.” Prather said. Prather stated that the common belief was that ocean aerosols only contained salt water. But, we found a lot of ocean-biology in them–living organisms such as proteins and viruses. Rommie was interested in this study, and I thought her work could be very beneficial to us in understanding aerosol composition and movement as well as airborne survival. “
Amaro began developing computer models of aerosols using Prather’s sea spray work. These simulations allowed Amaro and her team to develop computer models of aerosols using Prather’s sea spray work.
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. Amaro combined the aerosol work that 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 part of the lungs, which can prove to be devastating,” Amaro said. There is no way to see particles in such detail with an experimental microscope or microscope. But this computational microscope lets us see how the virus behaves during flight, and what it does to our bodies. It is very powerful to be able to see how something looks, and how it works together. This fundamentally changes the types of questions that people 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 the few supercomputers capable of large-scale simulations. This allowed researchers to view aerosols at a staggering one billion atoms.
These simulations included more intricate details of the virus’s membranes, as well as visualizations 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 cover most surfaces of the body that have water, 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.
Now that the models are complete, Amaro plans to create an experiment that will verify the 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 virus aerosols.
Aside from the immediate need to learn as much as possible about SARS-CoV-2’s operation, computer models of aerosols have wide-ranging effects, including on climate science and human healthcare.
“What we learned during the pandemic is that aerosols were one of the main drivers in spreading the virus and that their importance in the transmission of many other respiratory pathogens has been systematically underappreciated,” said Dr. Robert “Chip” Schooley, a professor in the Department of Medicine at UC San Diego School of Medicine. The more we know about aerosols and the pollutants they can host, like viruses and pollen, the better we can create effective mitigation and treatment measures. This is good for the health and well-being of all people. “
This work appears in The Proceedings of SC21, Virtual Event, November 14-19, 2021
COVID gets airborne: Team models delta virus inside an aerosol for the first time (2021, November 22)
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