The new coronavirus strain, 'Deltacron' detected in Cyprus could just be contamination, virologist says

A researcher at Imperial College in London, which has driven much of the UK’s response to the Covid pandemic, says the ‘Deltacron’ variant Cyprus may have discovered “looks to be quite clearly contamination”.

In a Twitter thread, Dr Tom Peacock, a virologist, gave a technical explanation for his conclusion, saying “true recombinants don’t tend to appear until a few weeks/months after there’s been substantial co-circulation – we’re only a couple of weeks into Omicron – I really doubt there are any prevalent recombinants yet..”

The Cypriot ‘Deltacron’ sequences reported by several large media outlets “look to be quite clearly contamination” he said.

Peacock said there were lots of reports of Omicron sequences carrying Delta-like mutations such as P681R or L452R. “Although a subset of these might end up being real, the vast majority will most likely turn out to be contamination or coinfection. No clear signals of anything real or nasty happening (yet),” he added.

To be certain a signal like ‘Deltacron’ is real, he said “you really want multiple sequencing labs finding the same recombinant/homoplasy independently (or at least on different sequencing runs) – ideally you would look into the raw seq files as well and show no mixed bases”.

As far as he understands, such signals were appearing now for two reasons. One is that there is lots of Delta and Omicron circulating in the same areas, and secondly that some older sequencing primer sets were being less effective at picking up parts of Omicron “so low level contamination with Delta [is] being selectively picked up”.

“Finally its worth adding… much of what we understand about what makes Delta more transmissible/infectious, Omicron already possess – its currently unclear to me what Omicron could have to gain from Delta (with what we currently know at least),” he concluded.

Also, Greek virologist, Dr Gkikas Magiorkinis at the National and Kapodistrian University of Athens and a member of Greece’s scientific team weighed in, posting on Facebook: “Regarding the Deltacron (mix of Delta and Omicron) of Cyprus that was heard a lot in the Greek media recently, the first independent analyses show that this is a technical error of the laboratory in the process of reading the genome…”

On Saturday, Dr Leondios Kostrikis, who leads the team of scientists working at the University of Cyprus’ biotechnology and molecular virology lab, said a new coronavirus variant has been identified in the community.

Speaking to local media, Kostrikis explained that the new variant, which has been dubbed Deltacron, shares the genetic background of the Delta variant along with some of the mutations of Omicron.

He said his team had found a significant number of mutations only previously found in Omicron cases, which is different from other variants as it has 30 mutations. Ten of these were identified in these samples taken in Cyprus, he said.

Kostrikis said the variant was identified in 25 samples taken in Cyprus, 11 of which came from people hospitalised for coronavirus and 14 from the general population.

The frequency of the mutations was higher among those in hospital which could mean there is a correlation between Deltacron and hospitalisations, he said.

Kostrikis said that the sequences of the 25 samples have been submitted to the GISAID database, which will make them available to the global scientific community.

That being said, he concluded, it is still too early to predict whether Deltacron could overpower Delta and Omicron.

Kostrikis responded later on Sunday to the comment from the Greek professor, saying the statement was “incorrect and hasty”.

“They do not know the results we have,” he told Sigmalive.

At the same time, he stated that the said results of the research on Deltacron would be sent to Greece to a distinguished scientist, “in order to establish the truth of the matter”.

He said that in addition to the initial 25 individuals found in Cyprus they had found another 52.

The results showed that there was evolutionary pressure on a Delta ancestor to create polymorphisms like Omicron, and the Deltacron genealogy evolved, he concluded.

Source: Cyprus Mail