Canberra team maps genomic sequencing of ACT's outbreak

One of the analysts said Canberra's outbreak could be separated into two main genomic sequences - the initial introduction and the post-party era.

A team at the Australian National University has mapped almost every single case of COVID-19 in the territory.

ANU biologist Benjamin Schwessinger said the team approached ACT health authorities in early 2020 and offered to undertake sequencing for any local cases.

Dr Schwessinger said he received a call form ACT Health early in the morning of August 12 to say the territory had recorded its first locally-acquired COVID-19 case in more than a year.

He said once they picked up the sample it took about 13 hours to determine the case was linked to NSW.

Throughout the ACT's outbreak, the lab was processing virus samples seven days a week. It has only recently cut back to six days.

More than 85 per cent of all cases in the ACT have been successfully sequenced by the team.

"ACT Health does the case interviews and we support them with the genomics and we try to match up the genomics with the contact tracing and the interviews," Dr Schwessinger said.

One of the most interesting discoveries is that cases associated with a recent superspreader house party in Wanniassa had a different sequence to the dominant outbreak in the ACT.

"You can trace these waves, so everybody knew about the party recently and we can see this in the genomics that basically most of the new cases suddenly were like a new lineage of the strain," Dr Schwessinger said.

"Of course we have had the initial introduction and now we kind of have the post-party era if you would like.

"The event basically gives it a different fingerprint... so the party had a different fingerprint than everything else which was before."

The party took place in Wanniassa on the night of October 30. The party was attended by up to 150 teenagers, at the time public health orders only allowed a maximum of 10 guests at a house.

There have been 44 cases linked with the house party cluster and it has been deemed responsible for generating a series of clusters across Canberra schools and colleges.

While the genomic sequencing of the virus is different to the dominant one found in most cases in the ACT, Dr Schwessinger said it was not more infectious.

It is also not a different strain of the virus, like the recent Omicron variant that has emerged in South Africa.

As restrictions have eased across Australia, different introductions and genomic sequences of the virus will enter the territory.

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Genomic sequencing works by extracting the RNA of a positive case and then it builds a genetic profile.

The Canberra lab was essential, otherwise the tests would have needed to be sent to a Sydney or Melbourne lab, which were already overwhelmed with demand from the outbreaks in the respective cities.

The shorter turnaround time from the ANU lab meant the ACT's epidemiological investigation could be completed quicker. This help in understanding chains of transmission.

"It was really hard to get in contact with anybody, even at NSW Health because they were so overwhelmed with their own cases that it basically would not have happened," Dr Schwessinger said.

"Also just having that short turnaround time is especially important.

"If you're in a hospital setting, for example, you want to know if you have an outbreak in the hospital and you probably want to know how often there was an introduction to the hospital, was it one person or was it multiple times.

"It informs your public health decision, basically, how you manage the outbreak."

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