Two COVID Variants Just Combined Into a ‘Frankenstein’ Virus

Authors: David Axe Published  Apr. 07, 2022 4:49AM ET 

The first subvariant of Omicron, the latest major variant of the novel coronavirus, was bad. BA.1 drove record cases and hospitalizations in many countries starting last fall.

The second subvariant, BA.2, was worse in some countries—setting new records for daily cases across China and parts of Europe.

Now BA.1 and BA.2 have combined to create a third subvariant. XE, as it’s known, is a “recombinant”—the product of two viruses interacting “Frankenstein”-style in a single host.

With its long list of mutations, XE could be the most contagious form of the coronavirus yet. “From the WHO reports, it does appear to have a bit more of an edge in terms of transmissibility,” Stephanie James, the head of a COVID testing lab at Regis University in Colorado, told The Daily Beast.

But don’t panic just yet. The same mix of subvariants that producedXE might also protectus from it. Coming so quickly after the surge of BA.1 and BA.2 cases, XE is on track to hit a wall of natural immunity—the antibodies left over from past infection in hundreds of millions of people.

Those natural antibodies, plus the additional protection afforded by the various COVID vaccines, could blunt XE’s impact. For that reason, many experts worry less about XE and more about whatever variant or subvariant might come after XE.

And rest assured, that future subvariant is coming. “COVID-19 continues,” Eric Bortz, a University of Alaska-Anchorage virologist and public health expert, told The Daily Beast.

Testers first detected XE in the United Kingdom back in mid-January. Six weeks later U.K. authorities had identified 600 XE infections. Those cases are a proverbial drop in the bucket in light of the millions of BA.1 and BA.2 cases the U.K. has tallied in the past three months. But XE stood out.

According to the World Health Organization, XE is 10 percent more contagious than BA.2, which itself is up to 80 percent more contagious than BA.1, a subvariant epidemiologists described as the most transmissible respiratory virus they’d ever seen when it first appeared in South Africa back in November.

There’s a lot of uncertainty about XE. The WHO stressed that its own finding about the subvariant “requires further confirmation.” But given what we think we know, it seems XE evolved in someone with overlapping BA.1 and BA.2 infections, when two separate but related viruses swapped genetic material.

“We don’t have a roadmap.”

XE isn’t the first COVID recombinant—there have been at least two others, including the so-called “Deltacron” subvariant that sprang from simultaneous Delta and BA.1 infections. But with two highly contagious parent viruses, XE stands a chance of being the fastest-spreading recombinant. Health officials have also detected XE in Thailand.

The subvariant hasn’t shown up in U.S. tests yet. But that doesn’t mean it hasn’t reached U.S. shores. “It might not be detected by the standard analysis pipeline,” Rob Knight, the head of a genetic-computation lab at the University of California, San Diego, told The Daily Beast. Major new forms of SARS-CoV-2 can require tweaks to testing methods.

XE is a nasty bug, owing to potentially dozens of mutations to its spike protein, the part of the virus that helps it grab onto and infect our cells. And it’s a strong reminder that the pandemic isn’t over. Even with widespread natural immunity and highly effective and safe vaccines, SARS-CoV-2 keeps finding pockets of unprotected people—and opportunities to evolve.

But it’s not 2020 anymore. The novel coronavirus has changed, but so have we. Each successive wave of infections—Alpha then Delta then both major forms of Omicron—has seeded the population with natural antibodies that offer strong, albeit temporary, protection against the worst effects of future infection by a related form of the virus.

The leading vaccines, meanwhile, have stood up to each new variant and subvariant, especially when you add one or two booster doses.

Even as more and more countries fully reopen schools, businesses and borders, the peak death rate from a COVID wave keeps dropping in a lot of countries. Cases might go up as some new subvariant outcompetes an earlier subvariant and becomes dominant. But deaths don’t necessarily increase in the same proportion—a phenomenon epidemiologists call “decoupling.”

Decoupling is partially a function of the time between waves. Natural antibodies from past infection can begin fading after three months. But if two variants or subvariants strike within a few months of each other, the second strain collides with the immunity left over from the firs strain—especially if the strains are related. Meanwhile, the second strain produces antibodies that could mitigate the worst outcomes of the next strain, assuming it arrives fast enough.

That’s why Omicron has infected more people than the previous variant, Delta, but has killed fewer. And why many experts consider XE less frightening than BA.2 or BA.1. “Immune responses to XE should be similar to that of Omicron,” Bortz said. “Those with prior Omicron infection and vaccination are going to be mostly immune.”

By the same token, a big gap between separate variants—that is, a long reprieve from COVID—might actually be more dangerous to a population than back-to-back-to-back waves of related strains.

There’s another risk. We were lucky with the major variants and subvariants before XE, in that the leading vaccines worked really well against all of them. Experts are cautiously optimistic that the jabs hold up against XE, too. “XE is, as you say, supposed to be more contagious than BA.2 [or] BA.1,” Edwin Michael, an epidemiologist at the Center for Global Health Infectious Disease Research at the University of South Florida, told The Daily Beast, “but it seems not to be more severe or immune-evasive.”

But if some new variant, perhaps even a recombinant of XE and some other strain, eventually mutates in a way that helps it evade the vaccines and arrives three months or longer after the previous surge in cases, we could be in trouble.

“While thus far mutants that are more transmissible have emerged and spread, there is also the possibility of one that is both more transmissible and immune-evasive to emerge,” Michael said. In that case, neither of our approaches to building population-level immunity–vaccines and natural antibodies—would be able to prevent a devastating spike in deaths.

COVID cases rise again in half the states

Change in reported COVID-19 cases per 100k people in the last two weeks

March 23 to April 5, 2022

Half of the states are seeing COVID case numbers rise again while nationwide totals continue to fall.

The big picture: The Omicron subvariant known as BA.2 is the dominant strain circulating around the U.S., accounting for almost three out of every four cases.

By the numbers: Overall, cases dropped 5% across the U.S. to an average of about 28,700 cases from an average of more than 30,000 cases two weeks ago.

  • Three states — Alaska, Vermont and Rhode Island — had more than 20 new cases per 100,000 people.
  • Nine states — Utah, Montana, South Dakota, Kansas, Louisiana, Iowa, Arkansas, Indiana and Tennessee — had three or fewer new cases per 100,000 people.

Between the lines: Deaths fell to an average of 600 a day, down 34% from just over 900 a day two weeks ago.

What we’re watching: While U.S. officials have said they aren’t expecting a significant rise in hospitalizations or deaths, there have been signs of hospitalizations rising among older individuals in the U.K., the Guardian reported.

  • Since those numbers lag behind new cases, we won’t have a clear view of that impact in the U.S. for a few weeks.
  • The highly contagious subvariant surged through parts of Europe but probably will spare many Americans, thanks in part to this winter’s Omicron surge.

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New Mutant “XE” Omicron Variant May Be The Most Transmissible Version Of Covid Yet, According To WHO

Authors:  Tom Tapp March 31, 2022 4:46pm Deadline Breaking News Alerts

The CDC announced this week that the BA.2 Omicron variant, which is reportedly 30% more transmissible than the original BA.1 Omicron strain — has become dominant among new cases sequenced in the United States. That’s a startling rise for a variant that was less than 1% of all sequences as recently as January. But, just as Americans are hearing about BA.2, there’s already a newer, even more transmissible variant on the rise.

There are actually three new variants that have been given designations. According to a recently-released report from the UK Health Services Agency, the two being called XD and XF are combinations of Delta and BA.1, or so-called “Deltacron” strains, which have been talked about for months but made no significant inroads in any country.

XD is present in several European countries, but has not been detected in the UK, according to the report. XF caused a small cluster in the UK but has not been detected there since February 15. The variant of greater concern, it seems, is the one dubbed XE.

Like the other two new arrivals, XE is a recombinant strain, meaning it is made up of two previously-distinct variants. But it is not a Deltacron mix. XE is actually made up of the original Omicron (BA.1) and the newer Omicron (BA.2) which has taken over in the U.S.

Omicron BA.2 Variant Now Dominant In U.S.; Hitting Northeast Hard

The World Health Organization issued a report yesterday with some preliminary findings about XE.

“The XE recombinant was first detected in the United Kingdom on 19 January and >600 sequences have been reported and confirmed since,” reads the WHO document. “Early-day estimates indicate a community growth rate advantage of ~10% as compared to BA.2, however this finding requires further confirmation.”

Further confirmation is getting more difficult by the day, according to WHO, which registered concern this week at what it calls “the recent significant reduction in SARS-CoV-2 testing by several Member States. Data are becoming progressively less representative, less timely, and less robust. This inhibits our collective ability to track where the virus is, how it is spreading and how it is evolving: information and analyses that remain critical to effectively end the acute phase of the pandemic.”

Covid BA.2 Omicron Variant Likely Now Accounts For Majority Of New Cases In Los Angeles

Last week’s briefing from the UK Health Services Agency reinforces some of the WHO report’s assertions and urges caution about jumping to conclusions. One difference between the two documents is that the WHO data and analysis seems to be more recent.

From the UK HSA briefing:

XE shows evidence of community transmission within England, although it is currently less >1% of total sequenced cases. Early growth rates for XE were not significantly different from BA.2, but using the most recent data up to 16 March 2022, XE has a growth rate 9.8% above that of BA.2. As this estimate has not remained consistent as new data have been added, it cannot yet be interpreted as an estimate of growth advantage for the recombinant. Numbers were too small for the XE recombinant to be analysed by region.

To be clear, XE only accounts for a tiny fraction of cases worldwide. That may change, given that XE is thought to be about 10% more transmissible than the already more-transmissible BA.2. That means it may be roughly 43% more transmissible than the original Omicron that savaged the globe last winter.

But a new wave of infections from the now-dominant BA.2 has not materialized, even as restrictions have been eased. So hopefully the trend with XE, should it out-compete BA.2, will be similar. Only time — and good surveillance — will tell.