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‘Deltacron’ variant discovery most likely lab error, health experts say

The discovery of a potential new COVID-19 variant dubbed “Deltacron” over the weekend has divided health experts, with some saying the findings are more likely due to a lab processing error or sample contamination.

Deltacron was first reported by Dr. Leondios Kostrikis, a professor of biological sciences and head of the laboratory of biotechnology and molecular virology at the University of Cyprus, who named the strain because of its genetic signature’s resemblance to Omicron and Delta.

Kostrikis reported 25 cases of the mutation, noting at that time it was too early to tell whether there were more cases of Deltacron or what its potential impact could be. That data was sent to the GISAID international database that tracks changes in the virus on Friday.

While it is possible for coronavirus variants to “recombine” their genomes to form new strains, in this case health experts are casting doubt on Kostrikis’ findings, instead positing that the new variant is more likely a lab error.

World Health Organization (WHO) COVID-19 technical team leader Dr. Krutika Kuppalli tweeted that “there is no such thing as #Deltacron,” saying it is “likely sequencing artifact,” which she explains to mean lab contamination of Omicron fragments in a Delta specimen.

When reached for comment Monday, a spokesperson for the WHO directed CTVNews.ca to a tweet posted Monday by Dr. Maria Van Kerkhove, Infectious Disease Epidemiologist and COVID-19 Technical Lead at the organization.

“Jumping in late here: Let’s not use words like deltacron, flurona or flurone. Please, “ Kerkhove’s tweet states, echoing Kuppalli. “These words imply combination of viruses/variants & this is not happening. ‘Deltacron’ is likely contamination during sequencing.”

Deltracron is not currently listed under the WHO’s “Variants of Concern” or “Variants of Interest” database.

Montreal-based bioethicist and geneticist at the Research Institute of the McGill University Health Centre and director of community outreach for the Coronavirus Variants Rapid Response Network Fatima Tokhmafshan says current data does not support the combined variant theory.

Comparing the evolution of the coronavirus to a piece of mail, Tokhmafshan said the sequencing of a variant is like a barcode that is scanned at each checkpoint it goes through.

“You can trace its steps and then you can draw a map… as its changes are introduced in its genome and it passes from one person to another,” she said in a telephone interview with CTVNews.ca Monday. “The genome is sort of scanned and we can create a family tree for it, and based on that family tree you can go back in time and place the mutations that have been introduced and build a history of when approximately these things emerged.”

Tokhmafshan said, based on this phylogenetic tree (a type of diagram that shows the evolution of different genes from a common ancestor) scientists are able to determine if a new variant has emerged.

“In the case of this particular Transformer variant,” she said in a reference to the online joke that Deltacron sounds like a TV villain, “Just getting a sequence that tells you that it has mutations that are both from Delta and Omicron isn’t enough for you to say this is a whole new recombination… the likelihood of this being a new variant is extremely low.”

Molecular biologist at the Scripps Research Translational Institute Eric Topol was even more firm in his rebuttal of Kostrikis’ findings, tweeting that “Deltacron is a scariant. One less thing to worry about.”

Virologist at Imperial College London Tom Peacock also took to Twitter to explain his belief that Deltacron is more likely lab error than new variant.

In a thread, Peacock posted that he believes Omicron has not circulated long enough to create any recombinants and that the “Deltacron sequences reported by several large media outlets look to be quite clearly contamination – they do not cluster on a phylogenetic tree.”

Peacock posted comparisons of the phylogenetic tree of the supposed Deltracron variant and a true recombinant variant of the Alpha and Delta variants previously discovered in Japan to show the difference in findings – mainly that in a true recombinant variant there are distinct clusters in the tree that show its shared material.

Peacock said it was most likely that all of the samples were “all sequences on the same sequencing run in the same lab on the same day which had a contamination issue,” but he could not be certain.

Despite rebuttals from peers and experts on his data, Kostrikis has doubled down on his discovery, telling Bloomberg in an emailed statement Sunday that his findings are not an error, and that Deltacron infection was found to be higher amongst patients hospitalized for COVID-19 than amongst non-hospitalized patients, which he says rules out the lab contamination theory.

Kostrikis also said that the same sequencing was found by a lab in Israel. He did not provide specifics or the name of the lab in his statement.

However, Tokhmafshan pointed out when asked about Kostrikis’ latest claims that if the samples he sent to the lab in Israel were the same potentially contaminated samples used in his lab in Cyprus, they will of course get the same result.

“If your original sample is not prepped properly, if you have some contamination and if I send it to 10 other labs, it’s the same sample, they’re going to get the same results,” she said. “I would be curious to know when they say a lab in Israel got the same thing, — is it that they found a new person with the same exact [mutation] in a totally different geographical location? If that’s the case, then I would be interested.”

CTVNews.ca reached out to Kostrikis but did not hear back by time of publication.

“I want to reassure Canadians that there is an entity of highly dedicated scientists, interdisciplinary scientists who are not paid by the government, not by any company who are doing this really, really gruelling work,” Tokhmafshan said of the Deltacron findings. “We’re monitoring the viral evolution and monitoring what’s happening here in Canada and also across the world… we will indeed sound the alarm should a Transformers style thing emerge.”

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