New omicron XE variant detected in Japan as UK cases rise

As of April 5, 2022, 1,125 cases of XE – a new combinative subvariant – have been identified in the UK, up from 637 on March 25.

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Japan has reported its first case of omicron XE – a new strain of Covid-19 first detected in the UK – just as UK cases of the sub-variant are rising.

The XE variant was found in a woman in her 30s who arrived at Narita International Airport from the United States on March 26. The woman, whose nationality was not immediately disclosed, was asymptomatic, Japan’s health ministry said Monday.

It comes as cases of the new strain have almost doubled in Britain, according to the latest statistics from the UK Health Security Agency.

As of April 5, 1,125 cases of XE had been identified in the UK, up from 637 on March 25. The first confirmed case has a specimen date of January 19 this year, suggesting it could have been circulating in the population for several months.

XE has since been detected in Thailand, India and Israel. These latest Israeli cases are suspected to have developed independently. The United States has yet to report any cases of XE.

What is omicron XE?

XE is what is known as a “recombinant”, a type of variant that can occur when an individual is infected with two or more variants at the same time, resulting in a mixture of their genetic material in a patient’s body.

In the case of XE, it contains a mixture of the previously highly infectious omicron strain BA.1, which emerged in late 2021, and the new “stealth” variant BA.2, currently the dominant variant in the UK.

Such recombinants are not uncommon, having occurred several times during the coronavirus pandemic. However, health experts say it’s too early to draw conclusions about the severity of the new subvariant or its ability to evade vaccines.

“We continue to monitor cases of the recombinant XE variant in the UK, which currently accounts for a very small proportion of cases,” Meera Chand, director of clinical and emerging infections at UKHSA, said in a statement.

On Sunday, the UK reported 41,469 new Covid cases, with a seven-day average of 59,578 cases. As such, XE probably only represents a small percentage of total Covid cases currently.

How worried should we be?

Early estimates suggest that XE may be more transmissible than earlier strains, having so far demonstrated a slightly higher growth rate than its predecessor.

UKHSA data shows that XE has a growth rate of 9.8% higher than BA.2, while the World Health Organization has so far put this figure at 10%.

However, experts say they expect it to decrease in severity even though it spreads more easily. XE has so far not been declared a variant of concern.

“XE appears to be moving in the same direction as BA.2, having increased transmissibility to BA.1 but being less severe,” Jennifer Horney, a professor of epidemiology at the University of Delaware, told CNBC.

“It’s the devil we know, so to speak. [It is] essentially a reworking of the same deck of cards,” added Mark Cameron, associate professor at Case Western Reserve University School of Medicine.

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XE contains advanced and structural proteins from the same family of viruses, i.e. omicron, which means it should, in theory at least, behave like omicron did before. Existing vaccines and immunity should therefore provide some level of protection against infection.

“Recombinants that contain the spike and structural proteins of a single virus (like XE or XF) are quite likely to act similarly to [their] parental virus,” wrote Tom Peacock, a virologist in the Department of Infectious Diseases at Imperial College London, in a tweet thread in mid-March. XF refers to another recombinant previously detected in the UK in February.

However, other recombinants containing spike and structural proteins from different virus families continue to emerge. This includes the XD subvariant, recently discovered in Germany, the Netherlands and Denmark, which contains delta structural proteins and omicron spike proteins and which Peacock described as “a little more concerning”.

As such, all new emergences should be closely monitored, especially in their early stages, to ensure that they are not developing into something more serious.

“The virus is still capable of evolving, recombining and developing a new branch of its family tree,” Cameron said.

“The key finding is that for each of these variants and subvariants, the risk of hospitalization and death appears to be, on average, lower where vaccination rates are higher, indicating that vaccination, including including a third dose, should be effective in reducing the risk of severe illness,” added Stephanie Silvera, professor of public health at Montclair State University.