Supercomputers Could Hasten COVID-19-like Vaccine Development

The world’s most powerful supercomputers are used to calculate and solve some of our most complex problems. This ranges from maximizing traffic flow to mathematical probabilities involving chemical compounds. These machines are capable of solving calculations that would take our home PCs months or years to solve.

Related articles:

World’s Supercomputers To Unite Against Coronavirus

NVIDIA Announces New ARM Based CPU

Researchers at the Los Alamos National Laboratory in the US are running supercomputer simulations to study the dominant G form variant of COVID-19. It differs from the initial D614 due to the mutation of the spike protein. The D614G mutation is occurs because of the switch between amino acids at position 614 of the SARS-coV-2 genome from aspartic acid (D) to glycine (G).

Using large scale simulations, researchers were able to study its mechanism of infection as well the ability of our antibodies to resist it. Gnana Gnanakaran, the author of the paper published in Science Advances, says that the basic build blocks of the spike protein is more symmetrical for the G variant of the virus.

This allows it to bind to our cells easier than the original D variant, which is what was used to develop the current crop of vaccines. But, researchers also found that this symmetry, meant that it would expose its receptors more often, which would allow our antibodies to attack it more easily than the original strain.

D614G is far more infectious than previously known strains of COVID-19 but could still be neutralized by our antibodies. The problem was, researchers didn’t know how and why this happened. That is where a supercomputer earns its keep. By simulating more than a million individual atoms, they were able to attain molecular-level detail about the variant’s behavior.

The virus’s spike protein, which is what determines its characteristic corona, binds to specific receptors of our cells through spike binding domains, which causes the infection. This requires the virus’ receptor binding domain to transition from a closed confirmation to an open one. D614G’s spike protein’s symmetry leads to more viral spikes in the latter phase, which is why it’s more infectious.

This new understanding of the G variant through computer simulations at the atomic level, could serve as a backbone to the development of future vaccines. Instead of having to wait for months or years for the completion of extensive research, a supercomputer could do a lot of the heavy lifting in a fraction of the time.

Source:
Los Alamos National Laboratory News Release

The Paper: “The SARS-CoV-2 Spike variant D614G favors an open conformational state,” Science Advances. Rachael A. Mansbach, Srirupa Chakraborty, Kien Nguyen, David C. Montefiori, Bette Korber, S. Gnanakaran. DOI: 10.1126/sciadv.abf3671

The Funding: The project was supported by Los Alamos Laboratory Directed Research and Development project 20200706ER, Director’s Postdoctoral fellowship, and the Center of Nonlinear Studies Postdoctoral Program at Los Alamos.