Researchers have completed the first functional computational model of the entire virus behind the COVID-19 illness — and they are making the new model widely available, with aims to help advance global research in efforts to curb the pandemic, according to a recent study published in Biophysical Journal.
Scientists created first-ever model of entire virus behind COVID-19
"If you can understand how a virus works, that's the first step towards stopping it," said Professor Gregory Voth, whose team developed the indispensable model described in the study. "Each thing you know about the virus' life cycle and composition is a vulnerability point where you can hit it."
Voth and his University of Chicago team used their earlier experience to discern the most significant characteristics of every discrete component of the COVID-19 virus — and let the "less important" aspects slide. This allowed them to build a comprehensive computational model simple enough to run on a computer, but not too complex to exhaust computing capabilities.
The U of C team helped to pioneer this method — called "coarse-graining" — which made the new COVID-19 computational model possible.
Modeling how COVID-19 virus interacts with host bodies
This simplified approach helped to overcome a crucial issue in health research: while viruses are comparatively simple among the world of biological entities, creating a computational system capable of modeling them accurately is extremely challenging — especially when the goal is to model how the virus interacts with a host body — adding billions of atoms to the simulated scenario.
"You could try running an atom-level model of the actual entire virus, but computationally it would bog you down immediately," said Voth, Phys.org reports. "You might be able to manage it long enough to model, say, a few hundred nanoseconds worth of movement, but that's not really long enough to find out the most useful information."
'Gestalt' theory of virus modeling
This limitation is why researchers have focused on making models of discrete proteins of the virus. But while this piece-meal process has its pros, it also loses out on the big picture, said Voth who is a computational scientist, in addition to a Haig P. Papazian Distinguished Service Professor of Chemistry.
"The virus itself is a holistic thing," Voth added. "In my opinion, you can't assume you can look at individual parts in isolation. Viruses are more than just the sum of their parts."
COVID-19 virus parts are interactive
The U of C lab has worked on modeling numerous viruses for years — including HIV — according to Voth. One of the insights the team gained into viruses is how multiple parts of them collaborate.
For example, a drug capable of binding to spike proteins on a virus' surface — to prevent them from attaching to host cells — can hit a snag.
COVID-19 virus model open for research to fight pandemic
"One of the main things you might want to know is, do you need to dose every spike protein for it to work?" said Voth. "If not, how low a percentage can you get away with? This is a key question when you're trying to create drugs or antibodies, and it's something you can best understand by looking at the entire virus."
Voth and his team hope their new model will help scientists develop useful coronavirus drugs — while also lending insight into mutations of the virus, like the ones recently detected from the U.K. and South Africa. As of writing, the model is open for anyone to download for research purposes, which means the model is already helping global healthcare efforts to fight the pandemic.