New Zealand officials announced on Saturday they had detected the first case of the new Omicron XE subvariant.
This and other subvariants had potential to help fuel an Omicron second wave, the University of Otago epidemiologist said.
The subvariant, first identified in the United Kingdom in January and a hybrid of the original Omicron subtype BA.1 and the faster-spreading, now-dominant BA.2, was detected in a traveller who arrived in New Zealand on April 19.
The person was tested the next day and was isolating at home, the Ministry of Health said.
There were 7930 new cases of Covid-19 in the community on Saturday and 19 new deaths with the virus announced - including two children aged under 9 and a person in their 20s. There were also 494 people in hospital, 15 in intensive care.
Because XE was another Omicron variant it wouldn't be fundamentally different from its parents BA.1 and BA.2, Baker said.
That meant being "ferociously infectious", good at evading immunity - especially for those who haven't had their booster - and unlikely to be any better than other Omicron lineages at seriously sickening or killing those it infected, the University of Otago epidemiologist said.
Omicron variants had similar virulence to the ancestral Covid-19 strain that emerged in Wuhan more than two years ago and killed millions before vaccines were developed.
It was too soon to be sure, but Baker thought XE would be slightly more infectious than BA.2, and could be among three drivers of the expected second virus wave in New Zealand, along with waning immunity and the easing of restrictions.
"I think we may be reaching a plateau [of case numbers] and we may be seeing the beginning of a second wave in New Zealand … [all the signs are] pointing towards more cases, rather than fewer.
"We're very unlikely to see numbers sit at one point, but now we're going to start seeing - and Auckland's the place to look [first] really - the equilibrium's starting to shift towards the case numbers rising."
The seven-day national rolling average of community cases today was 8475, up from 8283 a week ago.
There were 2241 new cases in Auckland on Friday.
It was likely only half or even a third of community cases were being recorded, but he expected official numbers to remain in the thousands a day "for the foreseeable future", Baker said.
"It might go up and down, it might be a waving pattern, for months because all these different factors are pushing the numbers in different directions."
Hospitals would likely, for the rest of the year, be caring for a large but not overwhelming number of people sickened with Covid-19.
Deaths would also reduce "very slowly", Baker said.
"Deaths may hover in that five to 15 a day range for months, which is sad."
He agreed with the Ministry of Health's comment that current public health settings were appropriate for managing XE - one of which was encouraging people to get their boosters.
"This isn't Delta, it's Omicron and you need three doses of the vaccine to give you protection. And there's still 900,000 or more New Zealanders who haven't had the booster, which is really quite shocking."
However, with New Zealand's border now open to many, including from next month to travellers coming from visa waiver countries, it was time for a national discussion on the circumstances when border quarantines would be re-introduced, he said.
He knew this wouldn't be a popular topic, but the discussion needed to happen - and transparently.
"Because there are definitely scenarios where we would, but I think we just need to be very explicit about it."
The deaths of two children with Covid-19 was "an awful reminder anyone can die from this infection", Baker said.
Usually, but not always, children who died from Covid-19 had a serious underlying illness, such as chronic lung and heart disease, diabetes, being an organ transplant recipient or undergoing chemotherapy, he said.
Vaccinating children protected their peers who were at more risk or couldn't be vaccinated, and it reduced the risk of children acquiring long Covid by at least half.
"It's a big gap [in our protection] that only 22 percent of children have had two doses. My biggest worry [for children] is long Covid.
"Death as an acute outcome is awful but it's very rare in children. The bigger problem will be, are some children going to get debilitating long-term chronic effects from Covid-19? I think the evidence is yes."
