Thread by @sailorrooscout

Just a heads up. Regarding “Deltacron” or the “new variant” out of Cyprus. Please be aware those sequences being reported by media outlets right now appear to be due to contamination. It is NOT a new variant.

Per @PeacockFlu “they do not cluster on a phylogenetic tree and have a whole artic primer sequencing amplicon of Omicron in an otherwise Delta backbone.”

When processing several COVID samples at the same time, procedural failures can occur, and contaminations between samples with different variants occur. As @wanderer_jasnah says, it is PCR recombination due to contamination. Usually computational analysis can detect these flaws.

There had been reports of Omicron sequences carrying Delta-like mutations (such as P681R or L452R) with the vast majority of those likely being results of contamination or coinfection. But what you see here is just PCR recombination due to contamination of samples.

If needed, GISAID is always accessible and can be found here: gisaid.org

Regarding the number of samples. When you do a PCR run, with contamination present in your original sample, and your samples are on that same run you are simply replicating that contamination. As @STEMthebleeding so cleverly put it, think of xeroxing a piece of paper with an

ink spot on it. Every copy made will have that same ink spot. Per @PeacockFlu, the “Deltacron” sequences reported look to be quite clearly contamination and appear to have been sequenced by the same lab (possibly even on the same run as well) so they're not independent samples.

Here is proof if needed. USHER build for the 24 samples out of Cyprus. All Delta with NO monophyletic source. nextstrain.org/fetch/genome.u… This is clearly contamination. H/T: @PeacockFlu and @shay_fleishon

Great example. H/T: @Alexis_Verger

Left: Recombination with variants, the sequences are found in a cluster. 🔴 nextstrain.org/fetch/genome.u…

Right: “Deltacron.” With contamination, the distribution is found everywhere. 🔴 nextstrain.org/fetch/genome.u…

Per @YYCist: Failure of amplicon 72 in the ARTIC primer scheme, as all Omicron-like in these sequences (i.e. A67V, H69_V70del,T95I,G142D,V143_Y145del) are in that amplicon. Low level contam from other samples then fills the gaps. Likelihood of recombining JUST this amplicon ~0.

WHO COVID expert Dr. Krutika Kuppalli: "Deltacron is not real and is likely due to sequencing artifact (lab contamination of Omicron sequence fragments in a Delta specimen).”
•walesonline.co.uk/news/uk-news/s…
•qz.com/2110931/deltac…
•cyprus-mail.com/2022/01/09/cor…
•kxan.com/news/internati…