Vietnamese scientist discovers hybrid variant between Omicron and Delta

When two SARS-CoV-2 variants meet inside a person's body, there is a risk of creating a hybrid variant like Frankenstein's monster.

On February 16, Scott Nguyen went hunting. What he found was a bit of a surprise: a SARS-CoV-2 variant with the head of the Omicron variant glued to the body of the Delta variant.

Scott Nguyen is a bioinformatician at the Public Health Laboratory in Washington, DC (USA). He tracks new SARS-CoV-2 virus variants emerging around the city.

Nguyen and a handful of scientists around the world have an interesting hobby: “We are variant hunters.”

Nguyen and other variant hunters search through millions of SARS-CoV-2 genetic sequences in a massive database, known as GISAID, to find strains that could change the course of the pandemic, helping scientists better understand how the virus evolves.

For example, in November 2021, a variant hunter found a very strange set of mutations in a variant in South Africa. It wasOmicron.

Then, in the early morning hours of February 2022, Nguyen discovered not just another variant, but a whole new class of variants: variants that mix together parts of Delta and Omicron. In some cases, the virus appears to be optimizing the combination—picking the best traits from each to infect and evade immunity.

Deltacron - Omicron spike protein and Delta stem

Nguyen found a variant that was mostly Delta but contained the Omicron spike protein.

So far, this variant, called XD, is rare. Scientists have detected XD in France, Denmark, Belgium, the Netherlands, Germany, the US, the UK... But there may be many more cases of this Deltacron out there.

Taking samples for testing at a French airport. Photo: NYTimes

Health officials, including those at the World Health Organization (WHO), are closely monitoring these hybrid variants. They show how viruses can combine their strongest elements into super viruses. This process is called reassortment, and it's how dangerous strains of flu are born.

“Reassortment is something that we are constantly faced with in terms of influenza pandemics, so we have to be very cautious,” said Dr Mike Ryan of the WHO.

For example, Omicron's spike protein has the ability to hide the virus from our immune system, specifically our antibodies. So XD is essentially the cloaked Delta variant of Omicron.

“This variant has the best points. It’s surprising that the virus can do this so well,” Nguyen said.

How are hybrid variations born?

First, the patient must be infected with Omicron and Delta at the same time, said Shishi Luo, a bioinformatician at Helix Gene Technology.

Luo and colleagues recently analyzed samples from nearly 30,000 Americans infected with SARS-CoV-2 during the Omicron outbreak, from November 2021 to February 2022. They found 20 people co-infected with both Delta and Omicron.

“Omicron emerged around Christmas and New Year’s, when there were a lot of gatherings. You go to one gathering and you get exposed to the Delta variant, then you go somewhere else and you get exposed to Omicron,” Luo said.

If both variants infect a cell, the viruses can complete the recombination process. During replication, one variant takes a piece of the gene from the other. In a way, Delta has taken part of Omicron's genetic code.

Recombination may hold the key to SARS-CoV-2's past and future

Scientists are just beginning to understand the importance of recombination in the evolution of SARS-CoV-2. "It's known that coronaviruses in general have a lot of recombination. For SARS-CoV-2, this is the first time we've seen a lot of evidence that it's happening," Luo said.

In fact, recombination may be the reason SARS-CoV-2 existed in the first place. Last month, scientists at the University of Glasgow published a new theory about the origins of SARS-CoV-2. Their analysis suggested that an animal at the Wuhan seafood market may have been co-infected with two viruses at the same time. These two viruses combined, just as Omicron and Delta are doing, to create the original version of SARS-CoV-2.

“You know, early on in the pandemic, we all hoped that SARS-CoV-2 wouldn’t mutate too much,” said Scott Nguyen. “But this virus has surprised us in every way.”

“So I think these recombinant variants provide some interesting clues about how this virus will evolve” — and how quickly the next variant might emerge.