COVID-19 managed isolation and quarantine facilities in our largest cities is an ongoing concern, according to public health expert Michael Baker, who says it opens the door for people who want to escape.

He believes having clear rules around the use of masks will help dampen down the threat of community transmission and avoid another lockdown. 

Professor Baker told Sunday Morning it was too early to say if Auckland was safe from further community transmission just yet.

"We really have to wait a couple of weeks before we can sound the all-clear."

He said having MIQ facilities in large cities was a concern.

"That always creates a potential for people staying in these facilities to... maybe break... bend the rules or even escape. There are so many staff working in shifts in these facilities, again there's potential for errors to occur. 

"We're really only always a few days away from having a major outbreak if something goes wrong in these facilities in our cities."

He has been pushing for mandatory use of masks on public transport for months.

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"We all want to do everything we can to avoid a lockdown. This is one of the big benefits of masks - we know that they are effective at reducing virus transmission and they're not particularly disruptive of normal activities, people can still take public transport, they can go to work and school."

He also said people needed to be given clear guidance on taking sick leave if they came down with cold or flu symptoms without fear of job security.

"We have to have a workplace environment which makes it very easy for people to take time off when they're sick and no questions asked."

Baker said genome sequencing "was a real standout success for New Zealand that we have gone from not having the capability at the start of the year now to the point where we're sequencing all off our detected cases".

Genome sequencing for the latest Auckland community case was completed overnight.

New Zealand was advancing the science in this area, he said.

The government has also confirmed that it would be looking to make mask-wearing mandatory on all public transport in the Auckland region from Monday.