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New omicron XE Covid variant first detected in the UK spreads to Japan as cases rise

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As of April 5 2022, 1,125 cases of XE — a new scombinant subvariant — have been identified in the U.K., up from 637 on March 25.
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Japan has reported its first case of omicron XE — a new Covid-19 strain first detected in the U.K. — just as British cases of the subvariant rise.

The XE variant was found in a woman in her 30s who arrived at Narita International Airport from the U.S. 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 U.K. Health Security Agency.

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

XE has since been detected in Thailand, India and Israel. It is suspected that the latter Israeli cases may have developed independently. The U.S. has not yet reported any XE cases.

What is omicron XE?

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

In the case of XE, it contains a mix of the previously highly infectious omicron BA.1 strain, which emerged in late 2021, and the newer “stealth” BA.2 variant, currently the U.K.’s dominant variant.

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

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

On Sunday, the U.K. reported 41,469 new Covid cases, with a seven-day average of 59,578 cases. As such, XE likely accounts for only a small percentage of total Covid cases currently.

How worried should we be?

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

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

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

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

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

XE contains spike and structural proteins from the same virus family, i.e. omicron, meaning that it should, theoretically at least, behave as omicron has done before. Existing vaccines and immunity should, therefore, provide some level of protection against infection.

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

However, other recombinants containing spike and structural proteins from different virus families continue to emerge. That 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 need to be closely monitored, especially in their early phases, to ensure they don’t evolve 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 takeaway is that for each of these variants and subvariants, risk of hospitalization and death appears to be, on average, lower where vaccination rates are higher, indicating that vaccination, including a third dose, should be effective in reducing risk for severe disease,” added Stephanie Silvera, professor of public health at Montclair State University.

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