May 19, 2022
What is the hybrid ‘deltacron’ variant of the coronavirus?
A hybrid variant of the coronavirus that has characteristics of both the delta and omicron strains has been detected in the United States and several European countries, scientists say.The delta-omicron hybrid, informally dubbed "deltacron," is what's known as a recombinant virus, meaning it has melded-together genetic information from both variants. Cases are thought to be…

A hybrid variant of the coronavirus that has characteristics of both the delta and omicron strains has been detected in the United States and several European countries, scientists say.

The delta-omicron hybrid, informally dubbed “deltacron,” is what’s known as a recombinant virus, meaning it has melded-together genetic information from both variants. Cases are thought to be rare, but researchers say studying the hybrid and tracking other potential recombinants is crucial for understanding how the coronavirus is changing as the pandemic grinds on.

Here’s what to know about deltacron.

What is deltacron?

Recombinants can emerge when a cell is infected with two different strains of a virus at the same time — in this case, the delta variant and the omicron variant. As the viruses invade the cell and replicate, they can, in rare cases, swap parts of their genome and pick up mutations from each other.

“The genomes get a bit acrobatic, and pieces can jump and then recombine together,” said Jeremy Kamil, an associate professor of microbiology and immunology at Louisiana State University Health Shreveport. “It’s like if you had 70 printouts of an identical manuscript on your desk and then an office fan turns on and blows things around, and you’re trying to put everything back in order. Viruses are no different from that.”

Most of the delta-omicron hybrid samples found so far feature a genetic code that looks very similar to the original delta variant, but with one key addition.

“Delta basically grabbed omicron’s spike protein,” Kamil said. “This is essentially delta trying to hang on by plagiarizing from omicron.”

Recombinant viruses are not unheard of, and a few other coronavirus recombinants have been reported before, including one that involved the alpha variant. But in the same way that not all mutations will be beneficial to the virus and give rise to new variants, not all recombinant swaps will be advantageous and help a virus compete against the dominant strains circulating at the time.

The World Health Organization credited extensive genetic sequencing efforts around the world with detecting the hybrid variant and said it will continue to track its spread.

“As we look more, as we do more sequencing, it is possible that this recombinant virus will be detected in other countries, but it is circulating as we understand at very low levels,” Dr. Maria Van Kerkhove, the WHO’s technical lead on Covid-19, said Wednesday in a news briefing.

Recombinants can occur whenever more than one strain of the coronavirus is circulating widely within a population, Kamil said. For instance, deltacron likely emerged in places where the delta and omicron waves overlapped for a time.

Kamil likened deltacron to the delta variant getting a software upgrade. It’s thought that mutations to omicron’s spike protein, which covers the outside of the virus and is the main target of vaccines and treatments, helps the variant spread more easily and allows it to better evade protective antibodies. As such, the hybrid is essentially the delta variant borrowing omicron’s invisibility cloak, Kamil said.

Is it cause for concern?

It’s too soon to know for sure if deltacron affects humans differently than the delta variant or the omicron variant. Because the hybrid’s spike protein comes from omicron, Kamil said it’s likely that it would behave similarly to that variant.

“That’s not to say it’s not dangerous, because omicron is dangerous,” he said, “but my strong supposition is that it would match what we see with omicron.”

Deltacron cases are also thought to be rare, and there’s no indication yet that the hybrid is fueling big spikes in infection, said Scott Nguyen, a bioinformatician at the Washington, D.C., Public Health Laboratory, who was the first to piece together instances of the deltacron hybrid from European data.

“You wouldn’t expect this to be the next big wave because antibody responses and other immune responses against omicron should work on this recombinant, since it’s the exact same spike,” Nguyen said.

Researchers in France, where samples of deltacron were first identified, are conducting lab experiments on tissue cultures to assess how the hybrid affects human cells and to compare its severity to the delta and omicron strains.

Where has it been detected?

So far, samples of deltacron have been identified mostly in Europe. As of Wednesday, there have been 36 samples of deltacron reported in France, eight in Denmark and one each in Germany, Belgium and the Netherlands, according to GISAID.

An unpublished report by the genetic sequencing company Helix identified two deltacron cases in the U.S., as Reuters first reported.

Nguyen said he is also working to confirm potential deltacron cases in the U.S., separate to what has already been reported. He added that while he doesn’t expect deltacron to fuel a new wave of infections, it’s important to monitor and track these developments.

“Not only is it scientifically interesting to learn about these recombinants, but it also provides us clues about how the virus is changing over the course of the pandemic,” he said.

How was deltacron found?

Nguyen said he first took note of potential deltacron cases in mid-February and began sifting through GISAID, a public repository of coronavirus genomes, to find samples with characteristics from both the delta and omicron variants. He found a small cluster of potential recombinants that had been reported in January in France, along with a few in Denmark and one in the Netherlands.

“What struck me was that they were all genetically very, very similar,” Nguyen said, suggesting that researchers across the three countries were picking up on real recombinants rather than laboratory anomalies.

He posted what he found to an online forum known as cov-lineages, which allowed other researchers to investigate the claim. Etienne Simon-Loriere, a virologist at the Institut Pasteur in Paris, whose lab had submitted some of the genetic sequences identified by Nguyen, was subsequently able to check his raw data to confirm that these were real recombinants.

Nguyen said this is likely the first time recombinants have been discovered between two major coronavirus variants, unlike the three previous recombinants that involved mostly lesser known variants and petered out quickly.

Identifying a true recombinant requires a stringent burden of proof, he added. A supposed delta-omicron hybrid that was reported by researchers in Cyprus in January wound up being the result of contamination in the lab.

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