Scientists use genome sequencing to track source of Auckland Covid-19 outbreak

Scientists are using genome sequencing as part of the ongoing efforts to trace the source of the latest Covid-19 outbreak in Auckland.

The Institute of Environmental Science and Research lab, in Porirua, is where scientists are working to trace Covid-19's footsteps.

Using high-powered cameras, scientists there can read the virus’ genetic material, revealing its origin.

"That genome actually contains the history of that particular virus,” Institute of Environmental Science and Research scientist Dr Joep de Ligt said.

As the virus spreads, it picks up mutations which are inherited by the next person. Each case contains the fingerprints of all previous cases, however, which scientists use to create a genetic family tree linking one case to another.

"We have been sequencing all the cases that have been coming through... and all the colours tell us a bit about of the history of where it might have come from," he said.

The lab is now looking into the cases from the recent Auckland outbreak, which is believed to be closely related to the ones found in England, Otago University scientist Dr Jemma Geoghegan said.

"We haven't found yet a match to the quarantine hotels, but by comparing them to the rest of the world, we found they're most closely related to ones that have been sequenced in England," she said.

Dr Ligt said the scientists are now investigating if the cold storage may have played a role in the discovery.

“We are investigating if the cold storage might have any implications, so by trying to get samples from those areas to see if we find the same virus there as we have found in this family,” he said.

Scientists have already sequenced the genomes of around 650 cases since New Zealand had its first case in February.

They found just 20 per cent led to a chain of transmission, with the origin for the cases most likely found in North America.

"It really highlights the prevalence in North America at the time, the fact that there are direct flights from North America into New Zealand and there were no travel restrictions," Dr Geoghegan said.