Nearly 40 percent of U.S. adults are at least partially vaccinated against COVID-19, and herd immunity now seems within reach – at least, herd immunity for this iteration of the virus. Some troubling variants are picking up steam, with several exhibiting at least a partial ability to evade antibodies from prior infection, or even evade the immunity conferred by the most effective vaccines. Now, supercomputer-powered research from the Catholic University of America is exploring how those variants are able to escape.
“The UK, South Africa, and Brazil variants are more contagious and escape immunity easier than the original virus,” explained Victor Padilla-Sanchez, a research scientist at the Catholic University of America, in an interview with Faith Singer-Villalobos of the Texas Advanced Computing Center (TACC). “We need to understand why they are more infectious and, in many cases, more deadly.”
To do that, Padilla-Sanchez ran detailed analyses of the spike proteins of the variant viruses. The research was enabled by UC San Francisco’s Chimera molecular visualization and analysis software and molecular dynamics simulations run on TACC’s Frontera supercomputer. At 23.5 Linpack petaflops, Frontera remains the ninth most powerful publicly ranked supercomputer in the world.
The simulations helped Padilla-Sanchez assess which mutations were most important to the virus’ increased danger. “This N501Y mutation [in the receptor binding domain of the U.K. variant] provides a much higher efficiency of binding, which in turn makes the virus more infectious,” he said. “This variant is replacing the previous virus In the United Kingdom and is spreading in many other places in the world.” Vis-a-vis the South African variant, Padilla-Sanchez found that another mutation, E484K, was key to its immune escape.
On the heels of his in-depth research, Padilla-Sanchez is concerned about the efficacy of the current vaccines to adequately suppress these infectious, deadly and evasive variants. “The variants will require their own specific vaccines,” he said. “We’ll need as many vaccines for variants that appear.”
“This was a very fast project — the computational study lasted one month,” Padilla-Sanchez said. “There are many other labs doing wet lab experiments, but there aren’t many computational studies. That’s why I decided to do this important work now … The main computational challenge while doing this research was to find a computer powerful enough to do the molecular dynamics task, which generates very big files, and requires a great amount of memory. This research would not have been possible without the Frontera supercomputer.”
To read the reporting from TACC’s Faith Singer-Villalobos, click here.