Mystery at heart of city’s second wave

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.’’

Four members of a family in South Auckland were tested positive for the coronavirus on August 11. 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 per cent 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 per cent, 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.

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.

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.

– RNZ

Two new cases of coronavirus were announced yesterday, both in the community and linked to the Auckland August cluster.

The first case is part of a household cluster of a Covid19-positive Finance Now worker, while the second case is a Tokoroa healthcare worker who had contact with an existing case in the same town.

The medical centre where the positive case works has been closed for a deep clean but had been operating under alert level 4 conditions.

Contact tracing is under way, including of staff and patients at the Tokoroa medical centre, director of public health Dr Caroline McElnay said yesterday.

The potentially infectious period for this case was August 25-27.

The case, who lives alone and has no household contacts, has been in isolation since August 27.

Two testing sites were available in Tokoroa yesterday. The first is at Tokoroa Hospital and is open until 3pm. The second is at South Waikato Pacific Islands Community Services and is open until 5pm.

‘‘If you are in Tokoroa and have concerns about whether you need to be tested, please contact Healthline,’’ McElnay said.

She said 2475 contacts of cases were self-isolating and 138 people were now in Auckland quarantine facility JetPark Hotel due to their connection to the cluster.

There were 10 people in hospital and two of these people were in intensive care, she said.

Two were considered to have recovered yesterday.

There remain 137 active cases, 20 of which are from overseas and are in isolation facilities.

On Saturday, 10,487 tests were conducted and the total is now 750,808 tests.