Researcher creates computer reconstruction of a virus

An Aston University researcher has created a computer reconstruction of a virus, including its complete native genome, in what has been described as a world first. Although other researchers have created similar reconstructions, this is understood to be the first to replicate the exact chemical and 3D structure of a ‘live’ virus.

The research was conducted by Dr Dmitry Nerukh using existing data of virus structures measured via cryo-electron microscopy and computational modelling which took almost three years using supercomputers in the UK and Japan. His work has been published in the journal Faraday Discussions.

The breakthrough should open the way for biologists to investigate biological processes that can’t currently be fully examined because the genome is missing in the virus model. This includes finding out how a bacteriophage, which is a type of virus that infects bacteria, kills a specific disease-causing bacterium.

At the moment it is not known how this happens, but this new method of creating more accurate models will open up further research into using bacteriophages to kill specific life-threatening bacteria. This could lead to more targeted treatment of illnesses that are currently treated by antibiotics, and therefore help to tackle the increasing threat to humans of antibiotic resistance.

“Up till now, no one else had been able to build a native genome model of an entire virus at such detailed (atomistic) level,” Nerukh said.

“The ability to study the genome within a virus more clearly is incredibly important. Without the genome it has been impossible to know exactly how a bacteriophage infects a bacterium.

“This development will now help virologists answer questions which previously they couldn’t answer.

“This could lead to targeted treatments to kill bacteria which are dangerous to humans, and to reduce the global problem of antibiotic-resistant bacteria which are over time becoming more and more serious.”

The team’s approach to the modelling has many other potential applications. One of these is creating computational reconstructions to assist cryo-electron microscopy — a technique used to examine life forms cooled to an extreme temperature.

Image caption: Segment of reconstructed genome model (red to green to blue), placed over the cryo-EM backbone (white). Image has been cropped from the original and is courtesy of Faraday Discussions (2022) under CC BY 3.0.