Photo: Pete Linforth at Pixabay
Within hours of the Prime Minister giving us the bad news about a new Covid-19 cluster, scientists were at work trying to piece together the puzzle behind the latest outbreak.
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Genome testing used to be something that happened behind the scenes, in laboratories out of the spotlight. Now, it’s leading the news as the world tries to trace coronavirus cases back to their sources.
Today on The Detail, two of our genome detectives take time out from their extraordinarily busy jobs to explain how they’re trying to crack open the new cluster to stop its spread.
Otago University’s Jemma Geoghegan and Joep de Ligt, who is the head of bioinformatics at ESR in Wellington, are co-leaders in a year-long project that’s been given $600,000 from the government’s COVID-19 Innovation Acceleration Fund.
Their aim is to generate virus genomes from all of New Zealand’s confirmed positive cases. The information they gather is feeding into the interventions such as quarantine, travel restrictions and border closures.
It’s vitally important work but not glamorous - Geoghegan describes the lab work as tedious and says she spends all day looking at her computer at data gathered from positive testing samples.
But she says the rapid response globally to this virus has never really happened before – and it’s all happening in her specialist field of viral evolution.
“Currently there is a massive global effort to sequence genomes of coronavirus from positive patients,” she says. “And that information is being shared publicly all around the world.”
After a Covid-19 test, which gathers saliva from the back of the nose and throat, is found to be positive, the swab goes through several steps to separate the genetic material from the mucus that’s gathered.
Joep de Ligt explains extreme care is required not to destroy that material when it’s being handled. Then it goes into a sequencing machine that looks a bit like a printer cartridge. It contains thousands of little pores that the DNA flows through, and as that happens a current is measured.
That information can be captured and read on a computer, and compared to other genomes around the world. The more work a country has done on tracing its patients, the better the picture of the infection. New Zealand, England and Australia are among the top nations for this. So while our latest cluster has been linked to the same strain of the virus seen in England, part of this could be because of the huge amount of tracking and tracing that country has done.
There are also efforts being made here to speed up this work, with research happening now on how it could be done in hospitals.