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The application of genomic technologies in public health responses has been present for some time, though previously this was primarily utilised for confirmation after the fact. Through AusTrakka, linkages between inter-jurisdictional cases can be identified prospectively and inform where investigators should be looking, allowing for the comprehensive visualisation of outbreaks as data is uploaded enabling jurisdictions to view their sequences in the national context. The national coordination and reporting from the AusTrakka system complements local analysis already being performed by jurisdictional genomic epidemiologists and bioinformaticians and connects the genomics expertise across Australia.

Australia has consistently contributed SARS-CoV-2 sequences to global data sharing platforms throughout the pandemic. This was proportionally higher in the early days of 2020, when the context of a relatively low number of cases of COVID-19 in Australia meant that nearly every case could be genomically sequenced, a key factor in the global push to better understand the virus and keep track of the spread.

To have rapidly established genomics capacity across the country and generated over 200,000 sequences in just two years is a testament to the support of local governments, public health laboratories and units and health care providers across the various jurisdictions in partnership with the Commonwealth Government.

To capture the scale of this achievement, it is important to outline the process of collecting a single successful sequence.

From sample to sequence

When a sample is first collected, it goes through a series of identification and referral steps prior to physically arriving at the relevant Public Health Laboratory. The sample undergoes the relevant laboratory processes to be sequenced, with the successful outputs simultaneously analysed by bioinformaticians and epidemiologists at the local level and uploaded to AusTrakka. Here is where it is included in the national analysis and interpretations from the AusTrakka epidemiology team help to inform the national response. It should also be noted that there are rigorous quality checks undertaken at multiple steps throughout the process, further reducing the number of samples that are successfully sequenced by the end.

What does this milestone represent?

In terms of the impact this number of sequences has had, Mathilda Wilmot, Genomic Epidemiologist of the AusTrakka National Analysis Team notes, “the significance of the 200,000-sequence milestone does not necessarily lie in just the number, but the collective moments of combined data sharing, learning, knowledge base development and collaboration.”

AusTrakka has brought together key genomics experts across Australia, strengthened by the integration and governance under the Communicable Diseases Genomics Network. Some jurisdictions across the nation initially had greater capacity than others, and the collaboration has had a focus on democratising access to sequencing capacity, empowering smaller/less-resourced jurisdictions, now meaning that everyone across the country has the capability to genomically sequence.

Effectively, the collaborative network means that a genomic epidemiologist in Victoria can consult with a bioinformatician in Queensland about potential outbreaks taking place across jurisdictional borders in the country, and work with local representatives to coordinate a response. Looking towards how we can share this knowledge overseas and build capacity elsewhere, the understanding of the implications, severity and scale of sampling and sequencing in response to outbreaks gained in those 200,000 successful sequences is invaluable.

Where to from here?

Whilst the focus of the last several years has been around the response to SARS-CoV-2, there are broader applications for the platform as we look towards the future.

“AusTrakka’s biggest potential lies in multi-jurisdictional surveillance, in particular food-borne outbreak investigation,” says Mathilda Wilmot. “Previously, you might need 3-5 cases in a single jurisdiction to realise there was an outbreak. Now, 3-5 cases nationally can be linked, allowing for the implementation of public health actions before we see an impact in the population.”

“Not only does this allow for the detection of an outbreak with far fewer cases, it can streamline the investigative process by definitively informing you when cases are not linked.”

Evidence of this can be seen in the Coffin Bay oyster outbreak from November 2021, wherein a series of cases of gastro across multiple states were able to be genomically linked to the Coffin Bay region. This allowed health authorities to rapidly implement measures to limit the export of oysters from the region and limit the impact of the outbreak.

“Interestingly, there was a simultaneous outbreak occurring in New Zealand, however as their sequence data is also uploaded to AusTrakka we were able to quickly determine that these were in fact not linked to each other. Without genomics, the investigators would have spent time pursuing possible pathways connecting the disparate situations, which may have delayed the employment of any public health measures.”

Read more about AusTrakka here.