Coronavirus: How quickly can scientists figure out where the new COVID-19 case came from?

Genomic testing is underway to find links between the new case and others.  

ESR, New Zealand's Crown Research Institute, is looking for potential links to managed isolation or other sources through genome sequencing.

ESR's lead for genomics Joep de Ligt told Checkpoint the organisation was frantically working to identify any link.

"What we do is whenever there is a sample like this in the community we try to process it as urgently as possible," he said. "And as we saw back in February that means that we typically are able to turn it around well within 24 hours.

"When the notifications came through that's when all the wheels started turning."

The Government has a database of previous cases seen in MIQ, and will compare the new community case against those to see if there are any links.

"But as we've seen in certain previous cases, there's not always a link found. That could be because that case might not have been picked up or the viral load was so low that we could not obtain a genome from it."

Genomic testing can determine how many people are between one infection and the next by the number of differences they see in the genome, which is about 30,000 letters long. 

"Each of those letters can change randomly because of the virus making mistakes when it copies itself. So we look at that to tell us a bit about how it is linked to other cases. 

"The thing is with COVID it doesn't always change, so sometimes there's genomes that we cannot distinguish. But that does indicate that those cases are more closely linked than if there's a number of mutations between." 

As a result of this new community case, genome sequencing will ramp up, but ESR is prepared for that with multiple sites and the ability to work within lockdowns. 

"Even if there's a larger number of cases, we can cope with that," de Ligt said. 

De Ligt is hopeful the testing will determine where this new case came from. 

"Since this case is recent, we hope we will get a good genome out."

ESR has been involved in genome sequencing for COVID-19 since the pandemic began last year. 

One hundred percent of the cases in MIQ during the last three weeks were the Delta variant, according to a Government report.

"Almost everything that we see is exclusively Delta, especially in the recent weeks," de Ligt said.  

"This is a reflection of Delta out-competing the older versions of the virus globally. 

"If we look at Europe and other places where we have travellers coming from, it's almost exclusively Delta what we're seeing there, and we also see that reflected in our travellers and the MIQ system and even the boats."