Variant unlikely to have hold

Other than a single case of the XE Omicron subvariant caught at the border, no other new variants or subvariants have been detected in New Zealand to date but, as genome sequencing is limited at present, we cannot know for sure.

The Ministry of Health’s chief science adviser Dr Ian Town told the vast majority of recently sequenced Covid-19 cases in New Zealand were the BA.2 subvariant, and a small number were BA.1.

A single – the first known – case of XE was detected at the border and reported on April 23. To date, whole genome sequencing did not indicate that XE was established in Aotearoa at present, Town said. However, there are a couple of caveats to this: there is a time delay of at least ‘‘several’’ days between a case in the community being infected and genome sequencing for that case being potentially undertaken.

In addition, not all community cases can be sequenced. Most community cases are currently detected via rapid antigen tests (96% of 9047 positive results on Thursday were picked up via RAT), which are unable to be sent for sequencing.

So although there was no evidence that XE was present in the community – and such event was ‘‘unlikely’’ – this ‘‘cannot be excluded’’, Town said.

XE – a combination of BA.1 and BA.2 Omicron subvariants – had been spreading overseas and its arrival in New Zealand was ‘‘not unexpected’’, Town said.

There is some early evidence that it may be slightly more transmissible than BA.2, which is more transmissible than BA.1. Town said there was ‘‘no evidence to date’’ that XE caused more severe disease than other Omicron lineages – however, it’s worth noting that it took weeks or months to identify the severity of each new variant.

At this stage, public health settings in place to manage other Omicron variants were considered appropriate for managing XE, and no changes were required, he said.

At present, the majority of PCR-tested samples (which can be sequenced) are from hospitalised cases, healthcare workers, border workers and other essential workforces, and border arrivals.

According to ESR’s (the Institute of Environmental Science and Research) latest genomics report, 748 samples (the majority of which came from district health boards with the highest hospitalisation rates) underwent whole genome sequencing between April 6 and 13.

Of these, 91% were BA.2. The rest were BA.1 or ‘‘Omicron (unassigned)’’.

The Delta variant – at the centre of a lengthy lockdown in Auckland last year – has not been detected in New Zealand since March 2.

Town said the current priorities for whole genome sequencing were of border cases to identify the arrival of new variants, and in hospitalised patients to monitor severity of different variants.

Additionally, some Covid-19 treatments are effective for some variants but not others – Ronapreve, for example, does not work for Omicron – so sequencing also helps enable correct treatment for a patient.