Researchers at the Commonwealth Scientific and Industrial Research Organisation (CSIRO) have developed a new visualization platform, underpinned by bioinformatics algorithms originally used to analyze the human genome, to pinpoint differences among the thousands of genetic sequences of SARS-CoV-2, a novel coronavirus that causes the COVID-19 disease.
“The more we know about this virus, the better armed we’ll be to fight it,” said Dr. Larry Marshall, Chief Executive of CSIRO.
“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.”
“As the virus evolved, the genome becomes increasingly important, effectively because it holds instructions about the behavior of the virus and what kind of disease it can cause,” said Dr. Denis Bauer, CSIRO’s bioinformatics team leader and a researcher at Macquarie University.
“Globally there is now a huge amount of individual virus sequences. Assessing the evolutionary distance between these data points and visualizing it helps researchers find out about the different strains of the virus — including where they came from and how they continue to evolve.”
The first 181 published SARS-CoV-2 genomes were analyzed to understand how changes in the virus could affect its behavior and impact.
“This RNA virus is expected to evolve into a number of distinct clusters that share mutations, which is what we have confirmed and visualized,” said Professor S.S. Vasan, CSIRO’s dangerous pathogens team leader and a researcher at the University of York.
“At this time, we do not expect it will affect the development and evaluation of COVID-19 vaccines, therapies and diagnostics, but it is important information to monitor as preclinical and clinical studies progress.”
“To enable this, we are 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.”
This study shows the importance of cross-collaboration between the established and emerging disciplines of bioinformatics, genomics, vaccinology and virology.
“Following the scientific process of peer-reviewed open publication such as this one is a vitally critical component of the CSIRO’s response,” said Dr. David Hansen, CSIRO’s Australian e-Health Research Centre CEO.
The team’s paper was published in the journal Transboundary and Emerging Diseases.
Denis C. Bauer et al. Supporting pandemic response using genomics and bioinformatics: a case study on the emergent SARS-CoV-2 outbreak. Transboundary and Emerging Diseases, published online April 19, 2020; doi: 10.1111/tbed.13588
This article is based on text provided by CSIRO.
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