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March 25, 2022

Deltacron: How does a 'Frankenstein' virus happen?

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    Writing for NPR's "Goats and Soda," Michaeleen Doucleff explains how the delta and omicron variants combined to create a "Frankenstein virus" with "the head of the omicron variant stuck onto the body of the delta variant."

    How was 'deltacron' detected?

    In February, Scott Nguyen, a scientist with the Public Health Laboratory in Washington, D.C., was analyzing coronavirus samples from the Global Initiative on Sharing Avian Influenza Data (GISAID) when he "detected not simply another variant but a whole new class of variants: variants that mix together parts of delta and omicron," Doucleff writes. "And not just any parts, randomly put together. In some instances, the virus seems to be optimizing the combinations—picking the best traits from each for infectiousness and immune evasion."

    In particular, Nguyen identified a "Frankenstein virus" that was mostly made up of delta but contained the spike protein of the omicron variant, characterized by tiny points on the surface of the virus that induce infection, Doucleff writes. "It has the head of the omicron variant stuck onto the body of the delta variant," she adds.

    "So a good chunk of the virus' spike protein is omicron but the body of the virus is still delta," Nguyen said. "So yes, that's the best way to describe it."

    Initially, the cases Nguyen identified were believed to be a coinfection of both variants—but he suspected that the samples were actually a recombinant virus.

    Typically, "recombinants arise when more than one variant infects and replicates in the same person, in the same cells," said Lawrence Young, a virologist at the University of Warwick.

    Recombinant viruses "demonstrate how the virus can take its most successful parts and combine them quickly into a supervirus," Doucleff writes.

    Currently, this variant, known as XD, is rare. So far, scientists have detected it in France, Denmark, Belgium, the Netherlands, and Germany. However, "there are likely many of these deltracrons out there," Doucleff adds.

    In fact, scientists in San Mateo, California, have already identified a handful of them across the United States, and at least one has been detected in the United Kingdom and Brazil.

    Health officials, including those at the World Health Organization (WHO), are closely monitoring these hybrid variants. "So very often recombination is the way in which we get pandemics of influenza," said WHO's Mike Ryan. "So we have to be very cautious ... we have to watch these recombinant events very, very closely."

    "From the variant's perspective, it has the best of worlds," Nguyen said. "It's surprising that the virus can really do this, and do it very well, as well."

    How is a 'Frankenstein hybrid' created?

    To create a hybrid variant, a person must contract both omicron and delta at the same time, according to Shishi Luo, a bioinformatician at the genomics company Helix. "So a person has to be exposed to both variants in a short enough time frame so that they have both of them in this system," Luo said.

    In a preprint paper that has not yet been peer-reviewed, Luo and her colleagues analyzed samples from almost 30,000 Americans infected with SARS-CoV-2 between November 2021 and February 2022. During that time, they identified 20 people who were co-infected with both delta and omicron.

    "Omicron happened around Christmas and New Year, when there were many social gatherings," Luo explained. "So you can imagine, you go to one social gathering and got exposed to delta, and then you go to a different social gathering, and you catch omicron."

    According to Luo, if both variants infect the same cell, at the same time, recombination can occur. "In essence, during replication, one variant steals a chunk of genes from another variant. So the delta variant, in way, plagiarized part of omicron's genetic code," Doucleff writes.

    "If you're writing a document, you can have typos where you change a single letter," Luo said. "But you can also copy and paste and move big chunks of text. That's recombination, where one variant, in this case delta, takes a big chunk of text from omicron."

    Because the virus can take chunks of code instead of just single letters, it is more malleable, Luo said, which means it can quickly evolve new variants, including those that can evade immune protection. "It just shows how SARS-CoV-2 has many tools in its kit for changing itself." (Doucleff, "Goats and Soda," NPR, 3/23)

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