No, ‘Deltacron’ Is Probably Not Real

A scientist in an island country discovers that in dozens of COVID-19 patients, the Delta and Omicron viral variants have fused genetically to form a third variant, more powerful and deadly than any before.

If it seems like science fiction, that’s because it probably is.

Reports over the weekend set the internet abuzz with news of a new variant known as “Deltacron,” discovered in Cyprus by Leondios Kostrikis, PhD, of the University of Cyprus Laboratory of Biotechnology and Molecular Virology. Bloomberg first reported that Kostrikis, speaking on the Cypriot station Sigma TV, said the new strain combined elements of Delta and Omicron and could have come from patients with “coinfection” of both variants of SARS-CoV-2 at the same time

But other experts, responding on Twitter, said that this alleged mega-variant was likely just a result of lab contamination. Tom Peacock, PhD, of the Barclay Laboratory of Imperial College London, wrote that this kind of contamination isn’t uncommon in labs. He tweeted that “very, very tiny volumes of liquid can cause this” kind of sequencing contamination, but “usually these fairly clearly contaminated sequences are not reported by major media outlets.”

In other words, a lab that had been sequencing samples of Delta and then got started sequencing samples of Omicron could pick up traces of the older genetic material in their new analyses, which would then mistakenly show a variant with elements of both variants. In this case, genetic mutations normally found in Delta would appear on an Omicron “backbone.”

Peacock also explained that in a phylogenetic tree of SARS-CoV-2, which lays out the lineage of variant genomes like a family tree, a true recombinant variant would appear to be “clustered” within the same branch of the tree. In contrast, trees from Nextstrain posted by Alexis Verger, a molecular biologist with the French National Centre for Scientific Research, showed the uploaded genomes of the supposed Deltacron variant distributed all over the tree in different branches, which Verger characterized as a sign of contamination.

Peacock also tweeted that the samples had all likely come from the same lab, strengthening the case for a misleading result. “True” recombinant variants, he wrote, would be found in more than one sequencing lab.

But in a subsequent Bloomberg piece, Kostrikis refuted the arguments and said that there was evidence the same variant has been found in other countries, citing at least one sequence from Israel that appears in a global database.

And although Kostrikis told Bloomberg that the 25 cases he identified with this genetic signature “indicate an evolutionary pressure to an ancestral strain to acquire these mutations and not a result of a single recombination event,” Peacock and others on a Twitter thread debated the evolutionary advantage Omicron would gain by adopting elements of Delta. One commenter suggested its ability to replicate more quickly in the lungs. But recombinant variants aren’t always more “successful.” For example, Japanese researchers identified one recombinant variant of Alpha and Delta, but it didn’t appear to have any genetic advantages related to infectivity or immune escape.

According to Bloomberg, these 25 supposed Deltacron sequences were sent to GISAID, the Germany-based sharing service tracking SARS-CoV-2 strains, on January 7.

MedPage Today was unable to reach Peacock, Verger, and Kostrikis for further comment by the time of publication.