First Complete COVID-19 Coronavirus Model Shows Cooperation – “They Work Together”

The COVID-19 virus holds some mysteries. Scientists remain in the dark on aspects of how it fuses and enters the host cell; how it assembles itself; and how it buds off the host cell. Computational modeling combined with experimental data provides insights into these behaviors. But modeling over meaningful timescales of the pandemic-causing SARS-CoV-2 virus has so far been limited to just its pieces like the spike protein, a target for the current round of vaccines.

A new multiscale coarse-grained model of the complete SARS-CoV-2 virion, its core genetic material and virion shell, has been developed for the first time using supercomputers. The model offers scientists the potential for new ways to exploit the virus’s vulnerabilities.

“We wanted to understand how SARS-CoV-2 works holistically as a whole particle,” said Gregory Voth, the Haig P. Papazian Distinguished Service Professor at the University of Chicago. Voth is the corresponding author of the study that developed the first whole virus model, published November 2020 in the Biophysical Journal.

“We developed a bottom-up coarse-grained model,” said Voth, “where we took information from atomistic-level molecular dynamics simulations and from experiments.” He explained that a coarse-grained model resolves only groups of atoms, versus all-atom simulations, where every single atomic interaction is resolved. “If you do that well, which is always a challenge, you maintain the physics in the model.”