Experts have warned the new Omicron subvariant could become widespread and dominant within weeks.
New Zealand's first case of BQ.1.1 was recorded this week in Southland and it was also detected in Te Waipounamu wastewaters.
Senior Scientist David Winter says overseas data suggests BQ.1.1 will replace BA.5 as the dominant strain of Covid.
"There's actually a great deal of uncertainty of how it will behave in New Zealand because we have a different background in terms of immunity."
More than three million cases of Covid were reported in the last week alone, but the World Health Organization (WHO) has warned this is a conservative number.
The WHO's Covid-19 technical lead Dr Maria Van Kerkhove says there are likely many more cases due to a drop off in testing and reporting.
Epidemiologist Michael Baker says the new subvariant is "out-competing the other subvariants".
"That means it's effectively infecting more people and it will cause a wave of infection," he said.
The arrival of the new subvariant comes after the Government ditched masks, mandates and most other Covid measures in September.
Baker has called for a return to the Covid alert system as cases grow overseas.
"I'd really like to see all our politicians getting together to have a joined up agreed strategy for how we're going to manage this threat."
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