Covid 19 coronavirus: Geneticist James Hadfield on mapping and tracking the virus in NZ

By RNZ

The cause of the second outbreak of Covid-19 in Auckland remains a "frustrating" mystery, says New Zealand phylogeneticist James Hadfield.

"There's a real mystery about the re-emergence and where it came from," Hadfield said.

"Not knowing the source is frustrating from an academic point of view and it would be beneficial for the overall response to know where it came from, but it's not going to stop us controlling this cluster in Auckland at the moment."

More than two weeks have passed since four members of a family in South Auckland were tested positive for the coronavirus on 11 August.

The new cases came after 102 days without any new cases of community transmission in New Zealand. With no known cause, the outbreak pushed Auckland into a level 3 lockdown.

Hadfield said it seemed likely the virus had been brought into New Zealand by a person returning home from overseas, but genetic testing had been unable to prove this.

Scientists had genome sequences for about 60 percent of people who had tested positive for Covid-19 while in managed isolation. However, they had been unable to get genome sequences for the remaining 40 percent, making it difficult to know if the outbreak came from the border or not.

"The test and the sequencing are different techniques," Hadfield said.

"The testing is incredibly amazing at being able to detect very, very small amounts of the virus. It can return a positive test with very few copies of the virus in the nose swab.

"Unfortunately, sequencing technology needs a bit more genetic material to start from."

He said it seemed unlikely a person in managed isolation could have received false negatives from two tests and then gone on to spread the virus in the community after 14 days in isolation.

However, other possible scenarios were equally - if not more - improbable, Hadfield said.

"One of the options is there was lingering onward, completely cryptic or hidden transmission in the community for those 100 days."

This was unlikely because the virus would have been transmitted about 15 times without being detected, he said.

Mobile Covid-19 testing station st up behind the Ranui Library in West Auckland. Photo / Dean Purcell

There had been strong speculation that the virus could have entered through the Americold cool store in Mt Wellington where one of the people suffering from Covid-19 in the latest outbreak worked.

"That seems to be largely off the table now," Hadfield said.

Genome sequencing has helped trace the virus from a person from the United States who was staying at Rydges Hotel in Auckland to a worker at the hotel, who later tested positive.

Recent cases in Mt Albert have also been traced through genetic testing to the main Auckland cluster.

But the cause of the second wave continued to evade scientists, Hadfield said.

"Given they're all low probability events and we have seen a re-emergence in Auckland, it's probable one of them is true but it would be a brave person to put your money on any particular one."

Hadfield works on the open source Nextstrain platform, which allows scientists around the world to compare genetic information about Covid-19 and to track mutation rates and spread, almost in real time.

Researchers from more than 100 countries around the world have collected more than 80,000 coronavirus genomes in a public database. This helps New Zealand scientists investigate where cases might have originated.

Scientists in New Zealand and the United States are testing wastewater for Covid-19, in the hope it might give early warning that the virus has struck a community.

"There's some evidence it can give you a bit of forewarning, because it can detect it before people might go get a test."

The virus typically mutates once every two times it is transmitted.

So far, it does not appear to be growing more or less harmful to people's health. The levels of infectiousness have also not substantially changed since scientists began research on mutations, Hadfield said.