Genome sequencing has revealed a cleaner at a managed isolation hotel who tested positive for Covid-19 has the UK variant B117, and their infection is a close match to that of a recent returnee.

The cleaner worked at the Grand Millennium managed isolation hotel in Auckland where the returnee stayed from 13 to 15 March. The guest had tested positive on 'day zero-one' testing.

Director-General of Health Ashley Bloomfield says that ruled out the infection having come from the community.

It's also before the worker had their their second Covid-19 vaccination on March 16, says Bloomfield.

Repeat testing and serology testing of a household member - who initially tested weak positive for the coronavirus - have returned negative results, he said.

"Whilst we're keeping that as a case under investigation for the moment, and we will do some retesting in the next day or two, we're not worried that that is an active case, and also that there was no ability to get full genome sequencing on that initial very weak test.

"It rules out that the household member was the initial case because it has shown that link through the whole genome sequencing to a guest who was at the hotel."

The household case remains "a bit of a puzzle" and will be monitored over the next few days.

The MIQ worker had had the first of two vaccination jabs, and Bloomfield says that may have meant any infection was passed on in a less severe form.

"Our case has remained asymptomatic throughout, and we know that one of the great impacts of the vaccination is for many people it prevents them becoming infected in the first place, then for those who are vaccinated - even partially vaccinated - does provide some protection, so if they do get infected the illness is much more mild.

"It's very effective, this vaccine, at preventing serious illness, hospitalisation and death.

"So it may well be that our initial case was shedding less virus."

There were no further places of interest to add to Countdown Mt Roskill on Sunday 20 March.

"We've had reports the person was a very meticulous user of the Covid tracer app, again that's very helpful, it's meant we've been able to put out the push notification to others who had scanned in to the Countdown at a similar time."

-RNZ.