Has omicron XE arrived in California? Here’s what we know about the new coronavirus subvariant – San Francisco Chronicle

Omicron XE, which was first detected in the United Kingdom, has been found in the U.S. and, most recently, in Japan. While much is still unknown about the subvariant and what effect it will have on COVID-19s spread, heres what we know so far.

The XE variant is what experts call a recombinant of the BA.1 and BA.2 variants. Its name derives from the X prefix assigned for recombinants, said Stacia Wyman, senior genomics scientist at the Innovative Genomics Institute at UC Berkeley.

The coronavirus group of viruses make recombinants pretty readily, according to Shannon Bennett, chief of science at the California Academy of Sciences. However, whether the recombinant can be detected depends on whether the two parent strains are sufficiently different, she said.

Wyman said the XE subvariant likely arose from a person infected with both the BA.1 and BA.2 versions of the virus. When the virus was replicating, there was an error and the two viruses combined, she explained. Then the combined virus replicates and is spread to other people.

The first part of XEs genome sequence is BA.1, and then changes into BA.2 for the rest of the genome, she said. The S gene, or spike protein which latches onto healthy cells and causes infection comes from BA.2. However, Wyman said its not known yet if someone with a previous BA.2 infection would have some resulting protection from XE.

Since XE is a combination of both BA.1 and BA.2, it shares similarities and differences with both, Bennett said but from a public health standpoint, the variants infectiousness, the ability to evade prior immunity, and transmissibility are still being investigated.

According to a March 25 report from the U.K. Health Security Agency, XE has a growth rate 9.8% above that of BA.2, which Wyman said means it is 9.8% more transmissible. The World Health Organization has previously reported that figure may be 10%, though its still too early for a definitive conclusion.

The XE subvariant was first discovered in the U.K. in mid-January. As of April 5, 1,125 cases had been sequenced there.

In the U.S. so far, according to Wyman, two XE cases have been sequenced in Wisconsin and one in New York. She said Tuesday that she had learned about two unconfirmed cases in California. They had not yet been classified as XE on the international sequencing database GISAID, but have been on genome analysis tools UShER, out of UC Santa Cruz, and NextClade from Switzerlands University of Basel.

The subvariant has also been reported in Thailand, India and Israel, according to news reports. On Monday, Japan announced a traveler arriving from the U.S. was infected with the XE strain and was asymptomatic.

The BA.2 subvariant accounted for 86% of COVID cases in the U.S. for the week ending in April 9, according to the Centers for Disease Control and Prevention. It has quickly outstripped the original omicron variant, BA.1, which was last dominant during the week ending March 12 with 59% of sequenced cases, and led to the pandemics biggest surge so far.

The BA.2 subvariant is causing a spike in cases in the U.S., primarily on the East Coast, which prompted Philadelphia officials this week to reinstate the citys indoor mask mandate. U.S. officials on Wednesday extended the nationwide mask requirement for air travel and public transit, which was set to expire Monday, for another 15 days to allow more time to study and monitor BA.2.

Experts say any new variant that is more transmissible than others has a shot at eventually gaining dominance. Bennett said XE certainly could overtake BA.2, as every variant that takes over is likely to be a better spreader.

But Wyman said she is not too concerned yet about XE.

There is some early evidence that it may be more transmissible than BA.2, but the numbers are too small to draw any definitive conclusions at this time, she said. Its something to keep an eye on, but not for the general population to worry about.

She added that XE may die out completely regionally and never spread, which has occurred with other variants in different regions without clear explanations.

Wyman pointed to another variant, BA.2.12.1, that is being closely monitored in the U.S. According to data from CoV-Spectrum, a COVID variant monitoring platform using data from GISAID, there are 1,119 sequences in the U.S. so far, including 19 in California.

BA.2.12.1 been found in more than half of U.S. states, Wyman said.

We are seeing it spread quite rapidly in the U.S., particularly in New York, she said. The notable difference in this with respect to BA.2 is the addition of the S:L452Q mutation, which has been implicated in immune evasion.

The New York State Department of Health on Wednesday issued an announcement about BA.2.12.1 and another strain, BA.2.12 both sublineages of BA.2 saying they were contributing to a rise in infection rates in the central part of the state.

The Department's findings are the first reported instances of significant community spread due to the new subvariants in the United States, officials said.

The two subvariants are an estimated 23%-27% more transmissible than BA.2, officials said. While at this time, there is no evidence of increased disease severity by these subvariants, officials said, they are watching closely for any changes.

They urged New Yorkers to get fully vaccinated and boosted; mask up in public indoor spaces; get tested after exposure, symptoms or travel; stay home after a positive test and consult their health provider; and improve indoor ventilation or gather outdoors to reduce transmission risk during the Easter and Passover holidays.

Kellie Hwang is a San Francisco Chronicle staff writer. Email: kellie.hwang@sfchronicle.com Twitter: @KellieHwang

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Has omicron XE arrived in California? Here's what we know about the new coronavirus subvariant - San Francisco Chronicle