Lab contamination sparks false fears of new ‘deltacron’ Covid variant

British scientists have urged caution over a so-called "deltacron" variant which has been discovered in Cyprus.

The strain, which appeared to be a omicron and delta variant hybrid, is not a new form of coronavirus but the result of lab contamination, scientists believe.

A Cypriot academic raised the alarm after an analysis of 25 patients appeared to show they had been co-infected by two variants.

Prof Leondios Kostrikis, professor of biological sciences at the University of Cyprus and head of the Laboratory of Biotechnology and Molecular Virology, analysed the samples in his lab and suggested that two variants of the virus had amalgamated.

“There are currently omicron and delta co-infections and we found this strain that is a combination of these two,” Kostrikis said in an interview with Cypriot TV on Friday.

These 25 sequences were subsequently submitted to GISAID, the international database that tracks ongoing viral mutations.

Omicron is spreading all over the world

Analysis of these sequences revealed that the likelihood of it being a genuine recombination event is very slim.

Dr Thomas Peacock, a research associate at Imperial College London’s Department of Infectious Disease, regularly analyses new submissions on the database.

In November, he was the first to raise the alarm of a “very small cluster” of a new variant, which he said had a “really awful spike mutation profile”.

This variant went on to be called B.1.1.529, and later omicron. After taking a look at deltacron’s genetic profile, he said it “look[s] to be quite clearly contamination”.

In later tweets he said he and several colleagues had looked at the available sequences and determined it is “almost definitely contamination” and “doesn’t look like a real recombinant”.

‘New variants will continue to come along, but I don’t think this is one’

Dr Simon Clarke, associate professor in cellular microbiology at the University of Reading, told the Telegraph: “It’s perfectly possible for different versions of the virus that causes Covid-19 to combine sections of their genetic material, creating a recombinant, which is a genetic mosaic of the different variants with with altered characteristics, but they contain a number of telltale signs and ‘deltacron’ just doesn’t have any.

“Instead, its proposed genetic code looks more like what would happen if you contaminated one sample with another.

“That could have happened at any point between sampling and sequencing in the laboratory and I strongly suspect this is what has happened. New variants will continue to come along, but I don’t think this is one.”

Deltacron’s genetic code bore the scars of a notoriously faulty primer which is used in the process of sequencing. A primer allows scientists to sequence a virus, but one commonly used primer, called the V3 72 amplicon, doesn’t fully grab on to the delta spike protein due to a mutation.

As a result, it can throw up rogue results, and in this instance it likely resembled a handful of characteristic omicron signals, creating the confusion.

As of Sunday evening, the UKHSA has no new variants under surveillance and is not concerned about the reports from Cyprus, The Telegraph understands.

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