New Zealand has recorded its first case of a new Covid-19 subvariant, the Ministry of Health has confirmed.

ESR confirmed it has sequenced the country's first case of the Omicron subvariant BQ.1.1 in a person who tested positive for Covid.

BQ1.1 was also detected in Te Waipounamu (South Island) wastewater samples.

The ministry said the list of new subvariants appearing within New Zealand is "lengthy and growing".

"Many of these new subvariants are identified by their mutations, many of which are shared across several subvariants, but it can take weeks or months to determine whether these mutations will allow a subvariant to out-compete others circulating in the community.

"At the early stage of a new variant being identified in New Zealand, it is difficult to predict whether and when it will become established in the community."

So far, most Omicron variants had not demonstrated a change in the 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. In recent weeks in the Northern Hemisphere the colder weather, waning immunity, timing of last vaccinations and other behavioural factors, are likely to have contributed to an increase in BQ.1.1 cases," the ministry said.

"Evidence is still evolving as to how BQ.1.1 would compete against BA.5 in a New Zealand context and whether this could affect the level of Covid-19 circulating in the community in the coming months."

The Herald reported this week that the reign of an Omicron subvariant that fuelled our last Covid-19 surge could be over within weeks, with two other fast-spreading lineages quickly on the rise – and another potential wave-maker waiting in the wings.

The latest ESR surveillance showed community prevalence of BA.5 - which helped push daily reported cases past 10,000 in mid-July – had fallen to about 75 per cent of sequenced genome samples.

At the same time, two sub-variants – BA.4.6 and BA.2.75 - now accounted for 15 and 10 per cent of community sampling.

While these two offshoots appeared to be quickly on track for domination, ESR bioinformatics and genomics lead Dr Joep de Ligt said their apparent rise could be partly explained by a drop-off in PCR testing, following changes to our border settings.

"These two have sort of been slumbering in the background, but do now appear to be picking up," he said.

"It's not scary just yet, but they clearly are creating a longer tail to our winter wave."

Still, he expected BA.5 could soon be overtaken by one or several subvariants that have been causing fresh Covid-19 waves overseas.

Meanwhile, the ministry said that relative to many other parts of the world, New Zealand had a high level of immunity based on high vaccine uptake and widespread relatively recent infection, predominantly with BA.2 and BA.4/5 variants.

Vaccines were still expected to provide robust protection against severe disease, particularly in those who have received boosters. People were encouraged to get their vaccine and booster doses when they fall due.

"The recent increase in cases nationally falls within our expected modelling of a slow rise in cases from now to the end of the year, although this may still change.

"We would expect regions to experience increases and decreases in Covid-19 cases at different times depending on a range of conditions. Local factors that could impact case numbers include levels of immunity in the community related to immunisation, previous infections, large events and indoor gatherings.

"At this stage, there is no evidence that BQ.1.1 is driving an increase in cases but Manatū Hauora - the Ministry of Health, and Te Whatu Ora – Health New Zealand, alongside ESR, are closely monitoring the development of Covid-19 subvariants overseas and in New Zealand, including BQ.1.1."

The ministry carried out regular Covid-19 public health assessments and updated its advice to Government on appropriate public health measures based on the latest evidence.