Explained: Why ‘Kraken’ hasn’t caused another big Covid-19 wave in NZ

If you’ve had Covid-19 lately, it’s more likely than not to have been caused by the now-dominant “Kraken” Omicron variant, XBB1.5. Image / AP

If you’ve had Covid-19 lately, it’s more likely than not to have been caused by the now-dominant “Kraken” Omicron variant, XBB1.5. Why isn’t it causing another major wave? Jamie Morton explains.

What do we know about this variant?

Being one of the most immune-evasive variants of Omicron we’ve seen to date, it’s perhaps unsurprising that some creative scientists decided to name New Zealand’s currently-dominant XBB1.5 after a multi-tentacled mythical sea monster.

But “Kraken” came not from the darkest depths of the ocean, but from the very lineage that washed over New Zealand in last year’s first Omicron wave: BA.2.

From BA.2 came BA.2.75 and another sub-lineage, BA.2.10.1 - both of which combined to make the immune-evasive hybrid, XBB.

This “recombinant” variant went on to cause a surge in cases in Singapore and Bangladesh, before turning up here in January.

As at last week, XBB turned up in about half of clinical samples, making it the first time New Zealand has had a single dominant variant since BA.5 powered our winter wave last year.

And most of those XBB sequences happened to be its offshoot XBB1.5, set apart by a specific mutation in its spike protein that helped it better bind to the receptor that gave the virus entry to our cells.

Singled out by the World Health Organisation (WHO) as the most transmissible Omicron strain seen to date, Kraken went on to cause a whopping nine in 10 cases in the US over February.

New #COVID19 insight: The XBB variant, particularly XBB.1.5, is causing >50% of all sequenced cases in Aotearoa New Zealand, matching its growth in other countries. #Wastewater testing confirms the most common variants found, incl. CH.1.1 & BA.2.75*
See https://t.co/8ucqpIBEWh pic.twitter.com/fJyMjJxhvD

— Rhys White 🧬 (@RhysTWhite) April 7, 2023

But already, however, XBB.1.5 itself may be pushed aside by another XBB type - XBB.1.16 - which, amid a sharp case jump, has shot up to become India’s number-one variant.

“It has one additional mutational mutation in the spike protein which in lab studies shows increased infectivity, as well as potential increased pathogenicity,” WHO’s Covid-19 technical lead Maria Van Kerkhove told a press conference late last month.

“So, it’s one that we are monitoring and we’re monitoring it because it has potential changes that we need to keep a good eye out on.”

ESR’s pathogen genomics technical lead Dr David Winter said XBB.1.16 had been detected in New Zealand, as had XBB.1.9.1, which similarly appeared to have a higher growth advantage over Kraken.

“Both of those are present here at lower levels [than XBB1.5], but we expect them to grow over time.”

Does Kraken make us sicker?

They may be more transmissible, but there’s no sign yet that XBB variants are hitting people any harder relative to the 600-odd other Omicron types.

The WHO found Kraken itself didn’t “carry any mutation known to be associated with potential change in severity”, with symptoms similar to other variants Kiwis would’ve already encountered over the past year.

These ranged from typical cold symptoms like cough and congestion to shortness of breath, fever, fatigue, body aches and nausea.

While data was still being gathered on the newer XBB types, Van Kerkhove said there’d been no change in severity seen with XBB.1.16.

The other piece of good news was that, while XBB variants had a knack at dodging immunity built up from prior infection or vaccination, our vaccines still held up well at preventing severe illness.

“There’s been a consistent picture for a while that [XBB1.5] is growing, but not fast enough to create a wave,” said Professor Michael Plank, of Covid-19 Modelling Aotearoa. Photo / Supplied

The updated bivalent Covid-19 shot - now available to everyone aged over 30, provided it’s been at least six months their last vaccination or infection – has been shown to be more effective against Omicron types than the previous booster.

Oral antivirals like Paxlovid – free to those most at risk of severe infection – were also expected to be effective against XBB as they didn’t function by boosting antibodies, which the variants tried to evade, but by hindering the virus’ ability to replicate within us.

Why haven’t we seen an XBB wave like other countries?

While reported cases have been gradually creeping upwards over recent weeks, there’s no obvious signal that Kraken and its cousins have the legs to make waves like we saw last Christmas and winter.

“There’s been a consistent picture for a while that [XBB1.5] is growing, but not fast enough to create a wave,” said Professor Michael Plank, of Covid-19 Modelling Aotearoa.

“It may be that it’s contributed a little bit to the rise in cases we’ve seen over the last two or three months, although schools and universities going back will have been an element in that, too.”

One obvious reason for Kraken’s somewhat slower take-off was the sheer amount of background immunity it was meeting in the population – particularly with our most recent wave having been only several months ago.

Similar to other countries, New Zealand now had a high degree of “hybrid immunity” from widespread vaccine uptake and exposure to the virus.

“A lot more people will have had Covid in the last six to nine months since BA.5 arrived, and that definitely makes it harder for new variants to get established, or at least grow at the kind of speed you’d need to produce a large wave,” Plank said.

Although we know reported cases are capturing just a portion of infections at a given time, scientists can turn to other indicators to be confident there’s no hidden “Kraken wave” occurring.

One was hospitalisation rates, which showed no alarming spikes relative to case numbers.

Is #COVID19 up or down in NZ and which variant is most prevalent? Find out which🦠are swimming in your region's 💩 in our latest COVID-19 #Wastewater Surveillance Report 👉 https://t.co/MUMkzVQeYF pic.twitter.com/uMhJxOJ3Vm

— ESR - Science and research (@ESRNewZealand) April 2, 2023

Another was data gathered from wastewater collected around the country, and which was also telling a similar story to official case reporting.

ESR science leader Dr Joanne Hewitt said that, in line with clinical sampling, the latest wastewater surveillance showed XBB as the dominant variant.

“Where we’ve got successful sequencing, XBB has been detected in most, if not all, of the sites over the last few weeks,” she said.

“But although we’ve seen an increase in proportion of XBB nationally, that hasn’t translated to an increase in cases overall.”

Plank was hopeful that New Zealand’s XBB experience could be a sign of things to come with future waves.

“There’s definitely been a pattern where, although this virus continues to evolve, the impact of new variants has been getting smaller over time as our population has built greater immunity,” he said.

“Of course, there’s also the possibility that a completely new variant can come out of nowhere, which we have to hope doesn’t happen.”