Probing the mechanics of aerosol virus transmission
When the COVID-19 pandemic struck, and the SARS-CoV-2 virus’s method of infection was identified as respiratory — inhaling infectious liquid particles — the mechanisms of airborne transmission became a global concern. But even as “droplets” became a new buzzword, reaching peak popularity as a Google search term in April 2020, some scientists focused their attention on aerosols instead.
Aerosols can travel long distances and remain suspended in the air for hours or even days, a durability that poses significant infection risk for areas with poor ventilation, where infectious particles can accumulate.
“Medical dogma has long focused on droplets as the main transmission route for respiratory viruses, but airborne transmission via aerosols also plays a significant role in spreading disease, as evidenced by super-spreader events,” said Rommie Amaro, endowed chair and professor in the Department of Molecular Biology at the University of California San Diego. “Intervention and mitigation decisions, such as the relative importance of surface cleaning or when to wear a mask, have unfortunately hinged on a weak understanding of aerosol transmission — to the detriment of public health.”
The Amaro Lab is based at UC San Diego and develops and applies state-of-the-art computational methods to investigate the structure, function and dynamics of complex biological systems such as pathogen-bearing aerosols. A central challenge to understanding airborne transmission has been the inability of experimental science to reliably probe the structure and dynamics of viruses once they are inside respiratory aerosol particles. Simulations offer a way to predict these properties.
“Understanding the mechanisms behind the airborne transmission of disease is a crucial area of research for current and future pathogens. Computational microscopy is a powerful tool capable of overcoming the significant experimental limitations present in the study of submicron aerosols, particularly regarding those containing viruses,” Amaro said.
Although new experimental results have highlighted the importance of pH (how acidic or alkaline a substance is) in the airborne viability of SARS-CoV-2 and suggest that pH is the driving force behind its viral decay, these studies lack a clear mechanistic explanation of why it happens.
For its work on Summit, Amaro’s team ran all-atom molecular dynamics simulations of the Delta variant of SARS-CoV-2 within a submicron (280 nanometers) respiratory aerosol — a system comprising over 1 billion atoms. They were able to measure the immediate structural and morphological impacts of a rapidly increasing pH environment in the aerosol and evaluate the protective influence of respiratory fluid components in a pH 7 versus pH 12 environment.
“With our complementary smaller-scale simulations, this work will enable the study of aerosols across multiple scales of size, resolution, pH and time. Our work shows how leadership-class computing facilities will shed new light on scientific challenges that until now have been intractable,” Amaro said.
UT-Battelle manages ORNL for DOE’s Office of Science, the single largest supporter of basic research in the physical sciences in the United States. DOE’s Office of Science is working to address some of the most pressing challenges of our time. For more information, visit energy.gov/science. — Coury Turczyn
This Oak Ridge National Laboratory news article "Summit supercomputer’s bonus year of scientific achievement" was originally found on https://www.ornl.gov/news
