Genomic leaders collaborate to create Australia’s first national COVID-19 tracking system

Australian public health laboratories will aim to sequence the virus genomes of all positive COVID-19 tests in Australia and track COVID-19 using genomics across the country, rather than state by state, under a ground-breaking initiative spearheaded by Australia’s public health laboratory organisations and leading industry partners.

The Communicable Disease Genomics Network (CDGN) and Illumina are collaborating to track COVID-19 using next-generation genomic sequencing technology, which enables real-time data sharing and integration to better understand the transmission and spread of the virus. Coordinated by the CDGN, this will be the first national implementation of pathogen surveillance and a critical step forward in Australia’s pandemic response.

The Australian Government has provided a $3.3 million Medical Research Future Fund (MRFF) grant through UNSW’s School of Medical  Sciences.  As part of the research project, Illumina has further contributed more than  $2 million worth of its genomic sequencing systems and related consumables.

UNSW Conjoint Professor Bill Rawlinson, Senior Medical Virologist, said the research project will address the urgent need for national implementation of COVID-19 genomics in Australia.

“This research will provide us with a better understanding of the behaviour, spread and evolution of COVID-19, thanks to the precision of next-generation sequencing technology. The project will enable us to measure the impact of using this technology not only for the COVID-19 pandemic, but also for future responses,” Prof. Rawlinson said.

Illumina’s systems are expected to be delivered next week to the Doherty Institute, Westmead Hospital, UNSW at the Prince Of Wales Hospital and Queensland Health Forensic and Scientific Services, expanding the capacity of the four major public health laboratories in New South Wales, Victoria and Queensland to sequence pathogens, including COVID-19 samples.

The Medical Research Future Fund grant will also help to build support in other jurisdictional public health laboratories and, with the added support of State and Territory Governments, will aim to sequence virus genomes of all positive COVID-19 tests in Australia.

“This is a leading global example that will demonstrate the unique value of genomics surveillance in understanding and helping to control the COVID-19 pandemic and Illumina is thrilled to be an instrumental partner of this effort,” Dr Phil Febbo, Illumina’s Chief Medical Officer, said. “The program will allow sharing of vital pathogen data with the use of bioinformatics across states and territories assuring that the sequencing of viral and other pathogens is not limited to this pandemic but will continue to expand in both academic research and the public health systems going forward.”

Pathogen genomics can reveal information that would otherwise be missed, including rapid insights into the behaviour, spread and evolution of COVID-19. This project will have an immediate application in the investigation of outbreaks, including identification of emerging outbreaks and transmission events as part of efforts to reduce community transmission.

Other benefits of genomics include the ability to identify mutations of COVID-19 in the Australian population to inform the design of treatments and vaccines, and the capacity to precisely identify persistent infection versus reinfection or inactive infection. This holds particular significance to healthcare workers and can help protect the capacity of the frontline workforce and vulnerable patients.

“The CDGN has been working to establish a nationally integrated pathogen genomics initiative that will facilitate the rapid implementation of this project, ensuring national access and consistency in genomics analyses. Information on the national transmission of the virus that causes COVID-19 will be important to informing future public health responses in Australia,” said University of Melbourne Professor Ben Howden, Co-chair of the CDGN and Director of the Microbiological Diagnostics Unit Public Health Laboratory at the Doherty Institute.