"Each of these waves saw large numbers of cases, hospitalisations and deaths.
"If we see another wave rising, which seems very likely, and whether it's BQ.1.1 or one of the other subvariants that are starting to become dominant, we're going to see more cases and all the things that go with that."
The two main Covid restrictions still in place are requirements to self-isolate for seven days if positive, and mask wearing is required in health and aged care facilities.
Although the traffic light system was scrapped in September, Baker said he believed there was still a need for some kind of alert level.
"What I do think we need is that we have a system that when the risk of infection rises we have the equivalent of an alert level system that describes the level of risk in a way that people really understand.
"We have alert level systems for fires, for earthquakes, for all these other threats. I think we need one again for the pandemic."
Baker said such a system could have simple measures that kick in when cases reach a certain level, such as mask mandates for public transport.
"I think at the moment, unfortunately, government and other groups are quite worried as being seen to do anything systematic.
"I think we need that leadership with the pandemic."
On Monday, the Government announced 11,205 new community cases of Covid-19 in the country in the past week, up from under 10,000 new cases the prior weeks.
The BQ.1.1 variant is already causing cases to surge in Europe.
"The list of new subvariants appearing within New Zealand is lengthy and growing," the ministry said in a statement yesterday.
"So far, most Omicron variants have not demonstrated a change in severity of the disease. Early evidence overseas suggests the BQ.1.1 has a growth advantage relative to BA.5, the dominant variant currently circulating in New Zealand."
Baker said each subvariant of Omicron is unique.
"These subvariants are often very different than those that have come before.
"In a way the mere fact that they're becoming more common overseas and causing waves of infection means they're more likely to do the same in New Zealand.
"They're surviving or thriving by escaping our existing immunity.
"Personally I know people who have had [Covid] three times. ... and in some cases they say it was not milder when they got it again."
University of Auckland computational biologist David Welch said there appeared to be a slow rise in cases.
"Cases have been rising recently, pretty much since the beginning of October.
"I think at the moment that that's caused by the relaxation of protective measures that we saw about a month ago now.
"If that's all it's caused by then we'd expect to see kind of a small increase in cases and then come back down."
Baker said about 10 per cent of new Covid cases were reinfections, but in reality it was probably higher than that.
Welch said a new subvariant such as BQ.1.1 could drive cases up.
"If one of those really gets a foothold here - they're already circulating - then we could see a more significant wave."
Watching how subvariants were spreading overseas, "BQ.1.1 seems to be the one that is increasing most widely and most rapidly," he said.
Welch said that booster shots can be an important tool in preventing cases getting worse.
"There's two ways to get immunity: you either get infected which can be very unpleasant or sometimes outright dangerous, or you can get a vaccine. Like natural immunity, vaccine-induced immunity does wane."
University of Auckland vaccinologist Helen Petousis-Harris told RNZ earlier this week that most people should have enough immunity from three boosters and not need a fourth.
Welch said while he was not a vaccinologist, he was not sure he agreed.
"I think we should be regularly having boosters. At the moment a booster twice a year looks like it would be very sensible because we're getting waves more frequently than that."
Baker said there was less worry about the hospital system being overwhelmed, thanks to improved treatment and antivirals.
"It really pushed the health system but basically workers in the system now can manage this infection very effectively."
However, he said dealing with Covid-19 patients was still having a knock-on impact on people who may need medical care for other reasons, "and it is putting a real burden on the system".
