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When news broke Thursday of a new community Covid-19 case in Auckland with no known link to the border, anxiety took hold across the country.
Health officials launched an investigation, interviewing the woman at the center of the case to trace her contacts and whereabouts.
Meanwhile, the swab used to diagnose it was being transferred from Auckland to Wellington in a biohazard bag, inside a container, inside a box, to ESR, the government scientific agency, to trace if it was related to any existing cases. .
THINGS
Covid-19 Response Minister Chris Hipkins provides an update on Auckland’s new Covid-19 case.
Overnight, complete genome sequencing directly linked the student and the shop assistant to a Defense Forces worker who spent time in places close to where she worked. But establishing that was no easy task.
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So how was it done?
Dr. Joep de Ligt, ESR Bioinformatics Leader, leads the small team for genome sequencing of Covid-19 positive samples.
Genome sequencing consists of developing a complete image of the RNA of a virus.
It involves generating a complete RNA sequence of that virus from a positive sample. The entire viral genome (about 30,000 nucleotides, the building block of DNA and RNA) is extracted and sequenced, allowing scientists to read the genome of viruses.
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ESR Lead Bioinformatician Dr Joep de Ligt, left, and scientist Matt Storey.
ESR work begins after a PCR test comes back positive, de Ligt said Things a few hours after the government announced that a link had been found.
A sample is packaged in three or four different layers of biohazard protection before it is sent to a laboratory.
The Auckland sample took off from the airport around 1.30pm and arrived at ESR via a dedicated courier service at around 3.15pm.
All eyes were on this test as Auckland residents hoped to know if a change in alert level was likely.
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One of the machines used in the genome sequencing process.
After verifying that it was the correct sample, it was taken to an area accredited to handle dangerous pathogens, with special conduits to ensure that no viral material spread.
The first step is to extract the RNA (which carries genetic codes in some viruses) and break the virus particles, which means that the sample is no longer infectious.
After about an hour, the scientists, or in this case, just one, working late into the night, have the intact RNA ready for the next step: investing the RNA into ‘copy’ DNA (called cDNA), which takes another two or three hours. .
Once they have the cDNA, they amplify the virus to get the bits they want to sequence.
There are hundreds of “sticky parts” that are the same as small parts of the virus. These are attached and made a copy, which takes about another two hours.
The scientists then prepare the tiny molecules they have created, all copies of the virus, to place in the sequencing machine, which resembles a printer cartridge.
The machine reads the material, which comes out as a “scribble,” before translating it back into letters of genomic code.
Once they have the code, scientists can look for mutations that differentiate it from other sequences in the genome, or match it to others.
“It’s a bit like a unique barcode,” de Ligt said.
“If two people have the same barcode, it is very likely that they have been infected by the same person, the same event or the same chain of transmission.”
This can take anywhere from 30 minutes to up to 10 hours, depending on how many samples are being processed.
“Last night was our personal best.”
NEXTSTRAIN
This map, from Nextstrain, shows how COVID-19 genome sequences trace transmission routes. (file photo)
The person had a high viral load, which means that the scientists had a lot of material to work with, allowing them to “shorten” some stages to reduce the process on time.
At approximately 10.30pm, seven hours after receiving the sample, ESR scientists knew that the genome was consistent with the same source as a positive case in a defense worker and notified the ministry of their findings.
De Ligt said the case was suspected to be related in some way to MIQ, so the scientists initially compared the sequence to a much smaller group of 169 genomes, rather than the 1,084 genomes sequenced to date.
After making comparisons against all genome sequences overnight, they were able to confirm, around 8 am, that the case was “identical” to an existing sequence, issuing their final report.
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ESR scientists have now sequenced 1,085 Covid-19 genomes.
When the ESR began sequencing the Covid-19 genomes, the process took 24 hours.
They have been able to “push that further and further”, and can now complete the sequencing in about 10 hours.
There was added pressure on the team knowing that all eyes were on them, and the sequence was needed “as quickly as possible,” he said.
“Pushing as hard as we could,” they cut it down to seven hours Thursday night.
If there is any material left after all that, it is destroyed. But the work is not done.
The findings go into a national surveillance system, which ESR monitors to see how outbreaks develop or if something “adverse” is happening.
ESR chief scientist Dr. Brett Cowan said this case is proof that genomics is playing a “crucial role” in supporting case investigations.
Cowan said determining the source of infection was crucial, as it helps the government make informed decisions about levels of lockdown and helps minimize risk to others.
“I would like to applaud the work of our staff, not only for this result, as they worked through the night, but for all 1085 genomes that ESR has successfully sequenced to date, often working late and into the weekends. week”.
