Omicron XE: What is it, how does it spread and what can NZ do?

By RNZ.co.nz and is republished with permission.

More than two years into the Covid-19 pandemic, new variants continue to emerge and it’s often not immediately clear what sorts of advantages – if any – it gives the virus or how much people ought to be concerned.

Sticker encouraging social distancing during the Covid-19 pandemic.
Sticker encouraging social distancing during the Covid-19 pandemic. (Source: Getty)

That’s the case for the XE variant of Omicron. While there are increasing numbers of people contracting it overseas, and with New Zealand finding its first case on Saturday, scientists say a lot of things about it aren’t yet clear.

Here’s what’s known so far.

What is Omicron XE?

University of Auckland computational biologist Dr David Welch says XE is a “recombinant” virus – made up of genetic material from multiple sources.

He says the variant emerged because someone contracted Omicron sub-variants BA.1 and BA.2 simultaneously. The two variants’ genetic material created the hybrid during an error in the virus’ copying process. This makes it different from the likes of Delta or Omicron, which emerged via mutation.

Though it’s a hybrid of Omicron sub-variants BA.1 and BA.2, with the latter about 30% more transmissible than the former, Welch says the way they combined was random.

“You can think of a virus having a genome which is an instruction manual for the virus, if you like. It’s basically a string of letters.”

During the recombination process those strings are cut and joined randomly, he says. Sometimes, the configuration doesn’t work. In XE’s case, the genetic code has been combined in a way that’s viable.

The World Health Organization (WHO) hasn’t classified it as a variant of concern or assigned a Greek letter to it yet.

“XE belongs to the Omicron variant until significant differences in transmission and disease characteristics, including severity, may be reported,” the WHO said in March.

Global public health specialist Peter Drobac says it remains to be seen if it will overtake BA.2. (Source: 1News)

More than a dozen recombinant strains of the SARS-CoV-2 virus have been classified to date.

Does XE cause more severe illness?

It’s early days and “there’s no evidence at the moment” that is the case, Welch says.

“XE is not very widespread anywhere in the world at the moment. So, the data on whether it causes more illness is just not in yet.”

But he says that because it is a hybrid of BA.1 and BA.2, the sickness XE may cause will probably be similar to those.

Omicron also tends to cause less severe disease than earlier variants, but is more easily spread.

Is XE more transmissible and how can we tell?

Early estimates from British modelling say XE, first detected in the UK in January, might have a growth rate 5-10% higher than the BA.2 Omicron variant. Growth rates are calculated by comparing the prevalence of the new variant in the number of infections in a sample of the population in relation to another circulating variant.

But the WHO cautions the findings need further confirmation because there are so few XE infections that it’s difficult to draw solid conclusions. Welch says it’s also “not clear” if XE’s UK spread will be replicated elsewhere.

The UK’s Health Security Agency notes XE has received most of its genetic code from BA.2, including the spike protein the coronavirus uses to invade host cells.

Consequently, it may mean XE’s transmissibility and severity eventually end up looking similar to that of BA.2. It also means people’s protection against XE – derived from a previous infection or Covid-19 vaccines – doesn’t appear to be significantly reduced compared to the earlier sub-variant.

What should we do now that XE has been found in New Zealand?

“I think if [XE] is a little bit more transmissible, we might see that it could produce a slightly longer tail to this outbreak,” Welch says.

But, he adds that other factors, such as winter helping the spread of respiratory viruses and the relaxation of pandemic restrictions will probably drive case numbers “in a much larger way than XE”.

Deputy Prime Minister Grant Robertson told Breakfast on Tuesday New Zealand was prepared for XE.

The Deputy PM says the variant’s arrival on our shores makes it even more important for people to get boosted. (Source: Breakfast)

“What we’ve put in place for other variants will still work when it comes to this new variant,” Robertson said of current public health measures.

University of Otago professor and epidemiologist Michael Baker says vaccination remains the best defence against XE and other new Covid-19 variants.

Should we keep paying attention to new variants? Why?

Welch says it’s important to keep an eye on new variants of concern in case they can evade current vaccines or re-infect people.

“Each time a major new variant comes through which has dangerous characteristics, we might get another wave. So, the earlier the warning we have about any new variants… the better we can prepare for that.

Immunologist Graham Le Gros warns that while rare, some people can be reinfected with Covid-19 as new variants continue to emerge.

Is New Zealand doing enough to detect new variants?

Welch told NZ Herald earlier in April he was concerned a new variant could go undetected for weeks because of patchy genomic sequencing and surveillance – but that’s improved in the past few weeks, more border cases being genomically sequenced.

He says there’s still room for improvement.

“The gold standard for genomic surveillance is to test everyone at the border, everyone who goes into hospital and tests positive with Covid, and then background surveillance testing where we have some sort of system where a random proportion of people who report a positive RAT get sent a [PCR] swab in the mail [for genome sequencing].”

Welch says sequencing at the border will give authorities a better idea about what new variants might be out there, and additional testing at hospitals can catch any that might have not been picked up through that process and help understand which variants are causing more severe illnesses.

New Zealand currently prioritises genomic sequencing for border cases; suspected reinfections; high-risk groups; or unusually severe illnesses, especially when the person has been vaccinated.

DHBs are also asked to send samples of randomly selected positive PCR swabs to the lab. This aims to provide a representation of how Covid-19 was spreading among different locations, age groups, ethnicities, and socioeconomic levels.

1News has contacted the Ministry of Health for comment.

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