'Deltacron', the reportedly new variant of COVID-19, which derives its name from a combination of the Delta and Omicron mutations, and which is said to combine viral material from both, may just be the result of a contamination.
A researcher at Imperial College in London, who worked extensively on the UK’s response to the Covid pandemic, says the so-called 'Deltacron' variant that was discovered on the island of Cyprus “looks to be quite clearly contamination”.
In a a series of tweets, Dr Thomas Peacock, a virologist with the College, said that “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.”
Small update: the Cypriot 'Deltacron' sequences reported by several large media outlets look to be quite clearly contamination - they do not cluster on a phylogenetic tree and have a whole Artic primer sequencing amplicon of Omicron in an otherwise Delta backbone.
— Tom Peacock (@PeacockFlu) January 8, 2022
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.”
Delta and Omicron together
These signals are now appearing because "there is lots of Delta and Omicron circulating in the same areas." Secondly, he argues, 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 possesses.Its currently unclear to me what Omicron could have to gain from Delta (with what we currently know at least),” he concluded.
(With wires)
