Tracking the COVID-19 pandemic in Australia using genomics

September 2, 2020

This research has been published in Nature Communications

Using genome sequencing to identify genetic mutations in SARS-CoV-2 cases in Victoria, researchers have identified clusters and transmission networks which has helped limit the spread of the virus, painting an important picture of transmission in Victoria.

Whole genome sequencing of pathogens in real-time is an important tool in managing public health responses to infectious diseases outbreaks.

A dedicated SARS-CoV-2 multidisciplinary genomic response team from the Peter Doherty Institute for Infection and Immunity (Doherty Institute) public health laboratories (including APPRISE collaborators), and the Victorian Department of Health and Human Services (DHHS) was formed to link epidemiological and genomic data of Victoria’s COVID-19 cases and assess the impact of social restrictions.

University of Melbourne Professor Benjamin Howden, Director of the Microbiological Diagnostic Unit Public Health Laboratory at the Doherty Institute, said the team sequenced 80 per cent of Victoria’s cases between 6 January and 14 April.

“Our sequencing showed that Victoria’s cases were representative of the global diversity of SARS-CoV-2. Consistent with epidemiological findings, we found that most of Victoria’s cases were imported with limited onward transmission,” Professor Howden said.

“Sequencing allowed us to identify large clusters from social venues, healthcare facilities and cruise ships, and importantly see how enforced social restrictions impacted transmission.

“Finally, we are able to demonstrate how the application of genomics will become critically important to rapidly identify SARS-CoV-2 transmission chains as social restrictions ease globally.”

Victoria’s Chief Health Officer, Professor Brett Sutton said public health responses to emergent cases of SARS-CoV-2 must be swift, highly focused and effective.

“Genomic sequencing is an incredibly powerful tool for our disease detectives to identify SARS-CoV-2 cases and clusters, which will be an ongoing challenge in Victoria and Australia,” Professor Sutton said.

“Working so closely with the team at Doherty Institute, who rapidly shared the sequences they found has had a huge, positive impact on Victoria’s successful response to limiting transmission of SARS-CoV-2.”

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