‘Deltacron’: Lab contamination likely responsible for Delta and Omicron hybrid, scientists say

An apparent coronavirus strain that combines mutations from both the Omicron and Delta variants is likely to be the result of laboratory contamination, scientists have said.

Fears emerged over the weekend that a new strain of Covid, dubbed ‘Deltacron’, had emerged from a so-called recombination event - when two variants co-infect a patient and exchange mutations to produce a new viral offspring.

Twenty-five sequences of Deltacron have been reported to date, but experts have insisted there is no evidence to suggest that Omicron and Delta have combined to generate a new variant.

“This is almost certainly not a biological recombinant of the Delta and Omicron lineages,” said Dr Jeffrey Barrett, director of the Covid-19 Genomics Initiative at the Wellcome Sanger Institute.

Instead, it’s been suggested that fragments of Omicron have accidentally been inserted into Delta’s genetic make-up during the sequencing process that takes place when attempting to identify a Covid variant infection.

This is a common error that can occur in any laboratory, said Aris Katzourakis, a professor of evolution and genomics at Oxford University.

He explained that, when sequencing a virus, its genome is divided into genetic fragments and then analysed before being put back together in a computer.

However, one particular fragment of Delta is prone to “dropping out” during the sequencing process and “sensitive to contamination”. In the case of the 25 ‘Deltacon’ samples, it appears this particular gap had been filled by a Omicron fragment, Prof Katzourakis said.

“This is a telltale sign of laboratory contamination giving the impression of recombination.”

Dr Barrett said the mutations of Deltacron that appeared to have derived from Omicron were located “precisely and exclusively” in the Delta genome fragment that is “affected by a technological artefact in certain sequencing procedures”.

The 25 samples reported to Gisaid, a global variant database, were processed in multiple sequencing procedures in more than one country, according to Leondios Kostrikis, a professor of biological sciences at the University of Cyprus who first identified Deltacron.

“These findings refute the undocumented statements that Deltacron is a result of a technical error,” Prof Kostrikis said.

However, Prof Katzourakis said the process of accidentally combining fragments of variants when sequencing lots of Covid samples in a lab was “a common error”. It “happens all the time,” he added.

“It’s not that it’s impossible for recombination between variants to happen. Just, this isn't evidence of it.

“If it was a real recombination event, when you make a tree of Delta and Deltracron sequences, the Deltacon sequences should form a distinct branch in that tree, indicative of their common ancestry.

“What you see instead, is a mix of the Deltacron sequences within the Delta tree. This means that they do not form a distinct lineage.”

Regardless of how it came to be, experts and officials are not concerned by Deltacron.

“It’s not one to worry about,” said Professor David Matthews, a virologist at the University of Bristol.

Cypriot health minister Michael Hadjipantela said on Sunday that Deltacron isn’t of concern, and that more details will be given at a news conference later in the week.

Professor Lawrence Young, a virologist at Warwick University, said the focus of the wider scientific community needed to be on how we “manage the inevitable emergence of new variants and how these are validated and reported.

“Variants will keep popping up as long as the virus continues to spread in under-vaccinated regions. That’s why global vaccination is so important.”