Vietnamese-born scientist finds hybrid variation between Omicron and Delta

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

On February 16, Scott Nguyen went hunting. What he found was a bit of a surprise: the SARS-CoV-2 variant had 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 the new SARS-CoV-2 virus variants emerging around the city.

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

Sampling at the French airport. Photo: NYTimes

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

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

Then, in the early morning of February 2022, Nguyen discovered not just another variant, but a whole new class of variants: variations that mixed parts of Delta and Omicron together. In some cases, viruses appear to be optimizing combinations – picking out the best traits from each to infect and evade immunity.

Deltacron – Omicron spike protein and Delta body

Nguyen found a variant that is predominantly Delta but contains Omicron’s spike protein.

So far, this variant, known as XD, remains rare. Scientists have detected XD in France, Denmark, Belgium, the Netherlands and Germany, the US, UK… But there may be more cases of this Deltacron infection out there.

Health officials, including those at the World Health Organization (WHO), are closely monitoring these hybrid variants. They show how viruses can combine the most powerful elements into super viruses. This process is called recombination, and that’s how dangerous strains of flu are born.

Dr Mike Ryan of the WHO said: “Frequent recombination exposes us to pandemics of influenza. So we have to be very cautious.”

For example, Omicron’s spike protein has the ability to hide viruses from our immune system, especially our antibodies. Thus, the XD is essentially a Delta variant wearing the invisibility cloak of Omicron.

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

How are hybrid variants born?

Shishi Luo, a bioinformatics officer at Helix Gene Co., said that the patient had to be infected with Omicron and Delta at the same time.

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

“Omicron appears around Christmas and New Year, when there are many gatherings. You go to one meeting and are exposed to the Delta variant, then you go to another place and expose the Omicron,” Luo said.

If both variants infect a cell, the virus can complete recombination. During replication, one variant takes a gene fragment from another variant. In a way, Delta took part of Omicron’s genetic code.

Recombination may be key to the past and future of SARS-CoV-2

Scientists are just beginning to understand the importance of recombination for the evolution of SARS-CoV-2. “It’s well 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 that’s happening,” Luo provided.

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

“You know, right from the start of the pandemic, we all wanted SARS-CoV-2 not to 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 as to how this virus will evolve” – ​​and how quickly the next variant could emerge.

An Yen (According to NPR)