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The cause of the second Covid-19 outbreak in Auckland remains a “frustrating” mystery, says New Zealand phylogeneticist James Hadfield.
“There is a real mystery about the revival and where it came from,” Hadfield said.
“Not knowing the source is frustrating from an academic point of view and it would be beneficial to the general response to know where it came from, but it will not prevent us from controlling this group in Auckland at this time.”
It has been more than two weeks since four members of a family in South Auckland tested positive for the coronavirus on August 11.
The new cases occurred after 102 days with no new cases of community transmission in New Zealand. With no known cause, the outbreak pushed Auckland into an alert level 3 lockdown.
Hadfield said it seemed likely that the virus had been brought to New Zealand by a person returning home from abroad, but genetic testing had been unable to prove it.
The scientists had genome sequences from about 60 percent of the people who had tested positive for Covid-19 while in controlled isolation. However, they were unable to obtain the genome sequences of the remaining 40 percent, making it difficult to know whether the outbreak is from the border or not.
“Testing and sequencing are different techniques,” Hadfield said.
“The test is incredibly amazing in being able to detect very, very small amounts of the virus. It can be positive with very few copies of the virus on the nasal swab.
“Unfortunately, sequencing technology needs a bit more genetic material to get started.”
He said it seemed unlikely that a person in administered isolation could have received false negatives from two tests and then spread the virus in the community after 14 days of isolation.
However, other possible scenarios were just as, if not more, unlikely, Hadfield said.
“One of the options is that there was a persistent, completely cryptic or hidden transmission in the community during those 100 days.”
This was unlikely because the virus would have been transmitted about 15 times without being detected, he said.
There was strong speculation that the virus could have entered through the Americold refrigeration store in Mt Wellington, where one of the people who suffered 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 in the United States who was staying at the Rydges Hotel in Auckland to a hotel worker, who then tested positive.
Recent cases at Mt Albert have also been traced through genetic testing to the main group in Auckland.
But the cause of the second wave continued to elude scientists, Hadfield said.
“Given that these are all low probability events and we have seen a resurgence in Auckland, one of them is likely to be true, but it would be a brave person to put their money into one in particular.”
Hadfield works on the open-source platform Nextstrain, which enables scientists around the world to compare genetic information about Covid-19 and track mutation and spread rates, in near real time.
Researchers from more than 100 countries around the world have compiled more than 80,000 coronavirus genomes in a public database. This helps New Zealand scientists investigate where the cases could have originated.
Scientists in New Zealand and the United States are testing wastewater for Covid-19, hoping they can give an early warning that the virus has affected a community.
“There is some evidence that it can give you a bit of a warning, because you can catch it before people go for a test.”
The virus generally mutates one out of every two times it is transmitted.
So far, it doesn’t seem like it is more or less harmful to people’s health. Levels of infectivity have also not changed substantially since scientists began investigating mutations, Hadfield said.
