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Siouxsie Wiles said if they did have a genuine reason for leaving the city they needed to take alert level 3 precautions with them and act as if they could already be infectious.
The expert has sounded the alert to anyone who has left or is planning to leave the city since the Government's announcement last night.
In a tweet this morning, which has been retweeted hundreds of times, the expert has told Aucklanders to act as if they are in alert level 3, no matter where they go to next, as they could be already incubating the virus.
"Hey, all you Aucklanders leaving the city during the night to spend the week at your bach... you better bloody well take level 3 with you," she wrote on Twitter.
"You do realise this is a s****y thing to do? If you are incubating the virus you run the risk of spreading it outside Auckland."
According to the microbiologist, people should adhere to level 3 rules if they have left Auckland, regardless of whether or not they show Covid-19 symptoms.
"I know you all feel fine and don't think you have the virus, but that's how everyone incubating Covid-19 starts off," she warned.
"You could be setting off chains of transmission and potentially in places with far less healthcare capacity than Auckland."
Speaking to The New Zealand Herald, Wiles said the advice to take alert levels with them applied to Aucklanders fleeing to their out-of-town baches as well as anyone who had been visiting Auckland and was now leaving the city to return home.
"There are definitely people with legitimate reasons for leaving," she said, referring to those visitors who need to get home elsewhere in the country.
"But because they have been in Auckland during the last week, it is advisable for them to conduct themselves as if they were at level 3."
"There are also anecdotal reports of people leaving Auckland who shouldn't be leaving, perhaps because they'd rather spend the week somewhere more comfortable. Those people should not be doing that, for starters, regardless of whether they leave now or left after the announcement [last night]," she added.
"People should not be going to their baches. That is not within the spirit of moving alert levels."
"These people have to be mindful that they might be infectious" and, as such, the expert warns they should behave as if they are in alert level 3, wherever they are.
It is also important that people who leave Auckland keep in mind that they might be in regions with less healthcare capacity than Auckland.
Wiles says the Government's decision to move alert levels was "absolutely the right thing to do" considering the new case and explained that the difference in time between the press conference at 9pm on Saturday and the alert level kicking in at 6am on Sunday was merely so legal processes could be put in place.
"That doesn't mean people have a few hours to do as they please," she added.
Auckland is now in alert level 3, for a minimum period of seven days. The rest of New Zealand is at alert level 2.