Macquarie University Professor leads CSIRO team in development of a novel analysis of COVID-19 in race for a vaccine

20 April 2020

Honorary Associate Professor at Macquarie University’s Department of Biomedical Sciences, Dr Denis Bauer is leading a team of bioinformatics researchers from the CSIRO, who have collaborated with virologists and unveiled a new approach to analysing the genetic codes, or the blueprint, of the SARS-CoV-2 virus that causes COVID-19.

The findings will help researchers better understand how strains of the virus evolve and identify new clusters of the virus.

Analysing global data on the published genome sequences of this novel coronavirus will help fast track our understanding of this complex disease.

The researchers developed a novel visualisation platform, underpinned by bioinformatics algorithms originally used to analyse the human genome, to pinpoint differences among the thousands of genetic sequences of the SARS-CoV-2 virus.

Dr Bauer, who is also the Bioinformatics Team Leader at CSIRO, and lead author of the paper, said: “As the virus evolves, this blueprint becomes increasingly important, effectively because it holds instructions about the behaviour of the virus and what kind of disease it can cause.”

“Globally, there is now a huge amount of individual virus sequences,” says Dr Bauer.

“Assessing the evolutionary distance between these data points and visualising it helps researchers find out about the different strains of the virus – including where they came from and how they continue to evolve.”

CSIRO Chief Executive Dr Larry Marshall said knowing the genetic code was vital.

“The more we know about this virus, the better armed we’ll be to fight it.”

“This highly complex analysis of the genome sequence of the SARS-CoV-2 virus has already helped to determine which strains of the virus are suitable for testing vaccines underway at the Australian Centre for Disease Preparedness in Geelong – the only high biocontainment facility of its kind in the Southern Hemisphere,” says Dr Marshall.

As part of the research the first 181 published genome sequences from the current COVID-19 outbreak were analysed to understand how changes in the virus could affect its behaviour and impact.

The CSIRO says it is important information to monitor as preclinical and clinical studies progress in the search to develop a vaccine.

The research team is calling on the international research community to share de-identified details of case severity and outcome, and other relevant meta-data such as co-morbidities and smoking status, alongside the genomic sequences of the virus.

The work shows the importance of cross-collaboration between the established and emerging disciplines of bioinformatics, genomics, vaccinology and virology.

“The advantage of the data visualisation platform is that it highlights evolving genetic mutations of the virus as it continues to change and adapt to new environments,” says Dr Bauer.

“The more informed we are about the genetic differences and their likely consequences on the progression of the disease, the better we can tackle the disease with diagnostics and treatments.”

The peer-reviewed research paper, “Supporting pandemic response using genomics and bioinformatics: a case study on the emergent SARS-CoV-2 outbreak”, was accepted for publication by the Transboundary and Emerging Diseases journal on 7 April 2020.

The COVID-19 genome visualisation platform can be found here.

 

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