Why genome sequencing is crucial to this outbreak

Author
Jamie Morton, NZ Herald,
Publish Date
Thu, 19 Aug 2021, 10:38AM
Results from genome sequencing could make a crucial difference to the scale of this outbreak and how long New Zealand stays in lockdown. (Photo / Dom Thomas/RNZ)
Results from genome sequencing could make a crucial difference to the scale of this outbreak and how long New Zealand stays in lockdown. (Photo / Dom Thomas/RNZ)

Why genome sequencing is crucial to this outbreak

Author
Jamie Morton, NZ Herald,
Publish Date
Thu, 19 Aug 2021, 10:38AM

Results from genome sequencing could make a crucial difference to the scale of this outbreak and how long New Zealand stays in lockdown. Science reporter Jamie Morton explains.

What is genome sequencing?

Genome sequencing creates a "genetic fingerprint" of a virus that has infected a person, and can help public health officials untangle different cases involved in an outbreak through their genetic sequences.

We can think of a whole genome as a box of jigsaw pieces, all of which make up the genetic puzzle of any organism on the planet.

Within our own box is 22 paired chromosomes, along with a 23rd that sorts our sex.

It's formed as a double helix of DNA, or deoxyribonucleic acid, and packs about 30,000 genes, along with three billion chemical bases that help hold the strands of DNA together.

Even the SARS-CoV-2 virus that causes Covid-19 has its own jigsaw puzzle.

But it's different in that it's comprised of ribonucleic acid, or RNA, so is single-stranded rather than double-stranded like DNA.

Unsurprisingly, it's much less complex than us: it contains just 30,000 bases, making up 15 specific genes.

Scientists piece these puzzles together through a process called sequencing - or figuring out the order of bases in a genome, then assembling them at once to get a complete picture of an organism's DNA.

How has genome sequencing helped us so far?

In New Zealand's first wave of Covid-19, for instance, scientists sequenced the genomes of 649 separate cases to reveal nearly 300 different introductions from different parts of the world.

Later, in Auckland's August outbreak, genome sequencing - together with other tools like contact tracing - swiftly helped officials tie together chains of infections in real-time.

Because of our relatively low number of positive cases to date, scientists have been sequencing samples of every positive case that's come into the country through MIQ.

That's helped link back any cases that have managed to get into the community.
In this case, so far, it's already told us we're dealing with the Delta variant - and that the strain came from New South Wales, where much sequencing has also been done.

Scientists will also be sequencing the genomes of positive cases that emerge from this outbreak, to aid tracing.

What results are we waiting on?

Just three positive cases from Sydney went through MIQ in New Zealand in August and scientists have been quickly carrying out genome sequencing on samples from these cases.

For rapid or urgent samples, ESR can typically have a result within 24 hours.

If one of these cases is linked to the current outbreak, that will give officials a clear link to the border - and narrow down the search for chains of infection.

"If contact tracing and genome sequencing can identify when the virus first leaked into New Zealand from New South Wales, we'll be in a better position to estimate how far down the chain of transmission these new cases are and how many additional community cases might be out there," Te Punaha Matatini modeller Dr Rachelle Binny said.

Fellow modeller Professor Shaun Hendy said a best-case scenario would be a firm genomic link to MIQ - or to another border point like a port.

"That will tell us something about the chain of transmission and then maybe we are just looking at a handful of cases."

Otherwise, the situation would remain uncertain - potentially pointing to a tip-of-the-iceberg scenario and raising worrying questions about how the virus entered the country.

Had the original incursion been a traveller who arrived in New Zealand from New South Wales before the transtasman bubble closed last month, for instance, that would mean the virus had been circulating here since then.

Yet, so far, indicators like community testing and wastewater surveillance for Covid-19 - all showing no positives - hadn't suggested a large hidden outbreak.

The Government was meanwhile contacting all travellers from Australia into New Zealand during the relevant timeframe to find whether the first case is linked to them.

Prime Minister Jacinda Ardern said the Government would leave "no stone unturned" in identifying a case that at some point originated in Australia.