New COVID-19 genomic ‘radar’ to track outbreaks
Jill Margo

Australia has begun setting up the equivalent of a national radar system to track COVID-19 as it moves across the country.

It will capture the genetics of positive cases and track the disease nationally, rather than state-by-state.

The first national implementation of pathogen surveillance has the potential to reveal information that would otherwise be missed, including rapid insights into the behaviour, spread and evolution of COVID-19.

If vaccines for COVID-19 become available it could be useful for tracking viral mutations and provide early warnings of emerging strains.

“This will address the urgent need for national implementation of COVID-19 genomics,” says Professor Bill Rawlinson.  Kate Geraghty

This vast genomic network will also be an early warning system for future pandemics, epidemics and other medical threats to the country, such as antibiotic resistance.

Australia’s public health laboratory organisations are leading this initiative with industry partner, Illumina, a leader in DNA sequencing technologies. Other partners will likely join as the project proceeds.

Australia’s Medical Research Future (MRFF) has provided a $3.3 million grant through UNSW Sydney’s School of Medical Sciences to establish the network. Illumina has contributed more than $2 million worth of genomic sequencing systems and related consumables.

Similar national genomic tracking systems are underway in countries such as the UK and France.

These systems are quite different to national notification systems for infectious diseases, such as measles, which register where and when cases appear.

This genomic system characterises individual cases. It specifies the whole genome and names it, allowing public health officials to trace which viruses are running though the population, where they come from and what the future risks look like.

Real-time data

Australia’s Communicable Disease Genomics Network will use next-generation genomic sequencing technology to enable real-time data sharing and integration to improve understanding of the transmission and spread of the virus.

This should provide immediate application in investigating outbreaks, identifying emerging outbreaks and transmission events. Data on mutations could also help to improve the design of treatments and vaccines.

Importantly, for healthcare and frontline workers, it should expand the capacity precisely to identify persistent infection versus reinfection or inactive infection.

“It will address the urgent need for national implementation of COVID-19 genomics in Australia,” says Bill Rawlinson, professor at University of NSW and Senior Medical Virologist at NSW Health Pathology.

“While we’ve been doing all this already, the network allows us to do it at a greater level and build up skills and resources in States that haven’t had many cases.”

Illumina’s systems are expected to be delivered next week to Melbourne’s Doherty Institute, Sydney’s Westmead Hospital, The Prince of Wales Hospital at University of NSW and Queensland’s Health Forensic and Scientific Services.

This will expand capacity of four major public health laboratories in three states. The MRFF grant, with some support of the states, will create capacity in other public health laboratories.

Chief medical officer of Illumina, Dr Phil Febbo, says vital data will be shared through bioinformatics so the sequencing information will not be limited to pandemic management, but will continue to expand in academic research and in public health system management.

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Jill Margo is the health editor. She writes about medicine and health from the Sydney office. Jill has won multiple prizes, including two Walkley Awards and is an adjunct associate professor of the University of NSW, Sydney. Connect with Jill on Twitter. Email Jill at jmargo@afr.com

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