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The Air NZ crew member arrived in Auckland on a flight from Tokyo on February 28 - they tested negative after a Covid test that day, but positive after a routine test yesterday.
They have been moved to the Auckland quarantine facility at Jet Park. The individual's three household family members have already been tested today and the results were all negative, said the Ministry of Health.
Fourteen other air crew on the same journey as the latest case were being contacted, isolated and retested, the ministry said tonight.
Anyone who was at the Auckland Airport Countdown store last Wednesday, March 3, between 12.07pm and 1.22pm is asked to monitor their health for the next 10 days (until March 17).
If they feel unwell or develop symptoms, they should contact Healthline on 0800 358 5454, and get tested and stay at home until a negative test result is received.
The ministry said there was also a health appointment that the case made that was being assessed. "All those attending the same clinic at the same time are being identified and will be contacted and provided specific health advice."
Air New Zealand chief medical officer Dr Ben Johnston tonight confirmed the case.
"The aircrew member tested negative for Covid-19 on 23 and 28 February as part of the regular surveillance testing programme in place for international aircrew. Their last duty was flight NZ90 from Tokyo to Auckland on 28 February, after which they returned a negative Covid-19 test.
"On 6 March (yesterday) they were tested again in Auckland as part of their regular surveillance testing and returned a positive test. The aircrew member is now isolating following advice from the Ministry of Health."
Johnston said all other aircrew who were considered close contacts were being advised and would be isolated and tested according to Ministry of Health's requirements.
"There are significant precautions in place for our crew operating to international destinations set out by the Ministry of Health, and we are confident that our people are following the protocols diligently," said Johnston.
"For Japan these include taking private transport to and from their hotel, isolating in the hotel while on layover and wearing PPE while travelling to and from the hotel, through the airport and on board. Aircrew are also subject to regular surveillance testing where they are tested up to once every seven days."
Countdown general manager health and safety Kiri Hannifin said they were contacted by the Auckland District Health Board this evening about a visit to Countdown's Auckland Airport store.
"The customer visited our store on Wednesday, 3 March from 12.37pm for approximately 30 minutes.
"The Ministry of Health has advised us that this visit is deemed low risk and casual contact exposure. Any customers who shopped in the store at this time aren't required to self isolate, but should get a test if they develop any symptoms.
"We are now going through our own processes, including giving the store a deep clean overnight as an extra precaution."
The Ministry of Health said the case had been identified today after a swab was taken as part of routine surveillance testing.
"The person has today moved to Auckland's quarantine facility," said the ministry.
"The Public Health initial assessment is there is low risk to the public due to Auckland being at Alert Level 3 for the period in which this case was back in New Zealand and were either in isolation or at home for most of that time," the Ministry of Health said.
For members of the public, testing is available at six community testing centres (CTCs) throughout Auckland as well as at general practices and urgent care clinics.
"There is currently good capacity in the testing system, and the CTCs in Otara (South Auckland) and Wiri (West Auckland) have additional staff available to meet any increase in demand. Visit arphs.health.nz/covid19test for testing locations," said the ministry.
The ministry said the air crew member was a frequent user of the Covid tracer app, which was helping staff "to identify potential exposure events and assess any risks from their activities".
"Specific advice will be provided to individuals identified as contacts by public health staff about the steps they need to take.
"Results from genome sequencing are expected on Tuesday and will help rule out any local transmission."
No Government press conference is scheduled for tonight. A further update would be provided tomorrow.
Johnston said the airline was making "excellent progress" with the rollout of the vaccine for its frontline employees. It looked "forward to the added layer of protection this will offer to our aircrew on international duties".
Under Covid rules, air crew members are required to undergo Covid-19 testing every seven days.
All Air New Zealand aircrew returning to New Zealand after flying on "higher-risk" routes need to self-isolate in a prearranged hotel for 48 hours. Los Angeles and San Francisco are currently designated as higher risk routes.
Once they have returned a negative test, they can leave the hotel.