New Tool Monitors SARS-CoV-2 Mutations That Make It Difficult to Develop COVID-19 Vaccines and Drugs

Scientists have developed a new tool containing information about all the protein structures that coincide with the SARS-CoV-2 (COVID-19) genome, including every known genetic mutation and its resultant mutant protein structure, to monitor mutations that make it difficult to develop COVID-19 vaccines and drugs.

Ensuring treatments remain effective as the virus mutates is a huge challenge for researchers. The powerful new tool developed by scientists at the University of Melbourne (Melbourne, Australia) harnesses genomic and protein information about the virus and its mutations to aid COVID-19 drug and vaccine development. In order to develop the software tool and library, dubbed COVID-3D, the team analyzed the genome sequencing data of over 120,000 SARS-CoV-2 samples from infected people globally, including those that uniquely affect Australia, to identify mutations within each of the virus’ proteins. They tested and analyzed the mutations’ effects on their protein structure using computer simulations. This data was used to calculate all the biological effects of every possible mutation within the genome. To help researchers account for possible future mutations, the team analyzed mutations in the related coronaviruses SARS-CoV and Bat RaTG13.


Mutations or changes in an organism’s genetic material are natural ‘errors’ in the cell replication process. They can give the virus new ‘powers’ of survival, infectivity and virulence. Fortunately, the researchers found SARS-CoV-2 is mutating slower than other viruses such as influenza, with about two new changes in its genome every month. COVID-3D can help researchers recognize how mutations operate and identify more effective vaccine and drug targets. Several international universities and research institutions already use COVID-3D in vaccine and treatment development.

“Although the SARS-CoV-2 virus is a relatively new pathogen, its ability to readily accumulate mutations across its genes was evident from the start of this pandemic,” said University of Melbourne Associate Professor David Ascher. “In the context of therapeutic drug design and discovery, these mutations, and the patterns by which they accumulate within the virus’ protein structures, can affect the ability of vaccines and drugs to bind the virus, or to create a specific immune response against it. Because of this, scientists must not only try to control the virus, but outsmart it by predicting how it will change over time.”

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