17 Aug 2021

Scientists race to find source of Covid-19 community case

From Checkpoint, 6:40 pm on 17 August 2021

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

Scientists are working hard to find the source of this latest community case of Covid-19.

Machine sorts positive Covid-19 samples for genome testing.

Genome testing being carried out at ESR.  Photo: RNZ / Dom Thomas

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


This is an official COVID-19 ALERT.

From 11:59pm tonight 17 August, ALL OF NEW ZEALAND moves to COVID-19 Alert Level 4. 

 The Alert Level will be reviewed after 3 days for all areas EXCEPT Auckland & Coromandel Peninsula which is likely to remain at Level 4 for an initial period of 7 days.

A community case of COVID-19 has been identified. 

STAY HOME where possible & follow the Alert Level 4 guidelines. This will stop the spread of COVID-19 and SAVE LIVES.

Everyone is asked to: 
    Wear a mask and keep a 2 metre distance from others whenever you leave your home
    If you are sick, call your doctor or Healthline on 0800 358 5453 for advice about getting tested
    Keep on scanning QR code's whenever you leave your home
    Practice good hygiene - wash hands often.

Services including supermarkets, pharmacies, clinics & petrol stations will stay open at Alert Level 4. 

For more information on Alert Level 4 go to www.covid19.govt.nz.

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