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Scientists Confirm New US COVID Variant With Hybrid Delta-Omicron Spike Protein


Dr. Katie Spalding

Katie has a PhD in maths, specializing in the intersection of dynamical systems and number theory.

Freelance Writer

delta omicron

So far, the recombinant lineage doesn’t seem to be spreading all that quickly. Image: CKA / Shutterstock

Have you heard of the “Deltacron” variant? Half Delta, half Omicron; originally French before it took off in the US, and with a delicious portmanteau of a name, it truly is the Cronut of COVID-19 variants.

When this hybrid virus – or to use the scientific term, recombinant – first turned up, it was put down to a lab mix-up. The two lineages hadn’t mixed in the real world, but a petri dish. But now, just two months later, Delta-Omicron recombinants are really out there – and a paper, published Monday as a preprint on the BioRxiv server, has the evidence.


“Given the divergence of Delta and Omicron genomes, as well as Omicron’s known immune escape properties, a Delta-Omicron recombinant strain could alter the landscape of vaccine and therapeutic efficacy,” explains the paper.

“In this report, we identify candidate Delta-Omicron recombinant genomes from CDC’s national genomic surveillance … We show that these genomes are likely the result of recombination within the Spike gene, containing substitutions common to Delta lineages … and Omicron lineages[.]”

But what does all this actually mean? Well, before we get into it, it’s important to remember that the emergence of recombinants isn’t surprising. COVID-19, like any virus, is constantly mutating, and “when two related viruses infect the same cell (ie, during a coinfection) the viral replication machinery can accidentally switch from one genome to the other resulting in a mixed genome,” explained preprint co-author Tom Peacock.

“This is viral recombination,” he wrote in a Twitter thread introducing the findings. “[SARS-CoV-2, the virus responsible for COVID-19] has been doing this all of the way through the pandemic – however it’s only easy to see when the two parental viruses are distantly related.”


Basically, you should try to ignore any headlines suggesting the Delta-Omicron recombinants are extra dangerous purely because of their hybrid nature – COVID-19 has been doing this all along. In fact, an Alpha-Delta recombinant cropped up back in October, and it barely made a blip outside of the virology community.

That said, how worried should we be about a variant with both Omicron and Delta as its parents? Using detailed sequence analysis – and having made sure that this wasn’t another case of lab error – the researchers confirmed that the new lineages had a Spike protein with characteristics from both the Delta and Omicron variants.

Importantly, there were no extra amino mutations in the receptor binding domain (the bit of the Spike protein that latches on to human cells and lets the virus particle get inside it) that hadn’t already been seen in the Omicron variant. That’s likely good news, according to Peacock.

“I would think (but would like to see evidence to prove it!) that it should be antigenically more like [Omicron],” he wrote. “[So the] vaccine works similar to against [Omicron].”


And here’s another hopeful sign: so far, the recombinant lineage doesn’t seem to be spreading all that quickly.

“Despite being detected over the course of 6 weeks, the number of cases resulting from these hybrid Spike recombinant viruses remains low,” notes the preprint. “Additionally, the majority of cases were identified within the mid-Atlantic region of the United States.”

Nevertheless, recombinant lineages aren’t going to disappear any time soon. We may have got lucky with this particular hybrid variant, but researchers know that the next one – and there will be a next one – could be much worse.

“Emerging variants of SARS-CoV-2, the virus that causes COVID-19, are characterized and monitored closely via national genomic surveillance,” remarks the paper.


“Given the potential public health consequences of new variants emerging from recombination, investigations involving laboratory and bioinformatic components, such as the one presented here, are critical to correctly identify and track these viruses.”


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