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‘Deltacron is non-variant of no concern’: Why experts aren’t worried about Delta-Omicron ‘hybrid’

Cypriot researchers claimed 'variant' contained mutations that appeared to be a combination of Delta and Omicron, but many virologists globally refute 'deltacron' being a variant.

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Bengaluru: There has been a flurry of news articles about a supposed new SARS-CoV-2 variant, of the name B.1.640.2 or ‘Deltacron’, being reported by a team of researchers in Cyprus. The sequences, which were first reported as early as November last year, have gained renewed attention of late, primarily because of fresh writing on it.

While Cypriot researchers had claimed that the variant contained mutations that appeared to be a combination of Delta and Omicron variants, many virologists globally refute ‘deltacron’ being a variant, stating that it is most likely the result of laboratory contamination.

Some virologists have even taken to Twitter to explain the science behind what might have happened in the Cyprus lab, and how the limited number of sequences available indicates contamination.

A Twitter post Tuesday claimed the Cypriot researcher who had first uploaded the sequences on a collaborative database used by the World Health Organization (WHO), GISAID, has asked them to be removed from the platform.

Contaminated and amplified

Laboratory contamination can occur at any time in any facility owing to mixing of fluids at a microscopic level when sequencing viruses. Contamination of a sequence occurs if it contains fragments from a different sequence, which takes place commonly in labs. It can occur through residues from previous PCR amplifications carried over into the current batch of samples, or when samples are not carefully handled.

Amplicons are fragments of genome sequences that are used as originals to make copies in amplification processes like PCR. Primers are short, single-strand segments of DNA that attach to regions of the DNA segment that needs to be amplified in these processes. The region called Amplicon 72 is not easily picked up by some primers that are used in PCR processes.

This has previously caused confusions where some mutations in Delta were also not detected by some primers, but were by others.

As a result, when there is even a minor change introduced by contamination during sequencing, which causes it to then get picked up, the changes or contamination get exponentially amplified in the regular PCR process. The resulting sequence makes the original look like a hybrid sequence with characteristics from two different variants.

Phylogenetic trees are visual representations of evolution of the virus, and as the virus branches off into a new variant, subsequent sequences uploaded of the variant fall within the branch, based on characteristics and mutations. With the supposed ‘deltacron’ variant, the sequences are found randomly across multiple trees instead of together like with every other variant.

Furthermore, virologists have also noted that the supposed variant pre-dates Omicron. Its sequences were first uploaded to GISAID back in early November. The first Omicron sequence appeared three weeks later.

But since November, until today, there are a total of only 24 sequences of the B.1.640.2 (‘deltacron’), while there are over 120,000 sequences of the Omicron variant. As a result, experts say that there is no risk from B.1.640.2 yet, as it doesn’t appear to be spreading.

Cyprus scientist asks sequences to be removed from GISAID

The Cypriot scientist Leonidos Kostrikis — who had been the first to upload the sequences — and his team have meanwhile reportedly asked GISAID to remove the sequences from their database.

Kostrikis had previously defended his findings, telling Bloomberg in an interview published Sunday that the cases identified “indicate an evolutionary pressure to an ancestral strain to acquire these mutations and not a result of a single recombination event”.

He had claimed the sequences were also reported from multiple countries including France and Israel, which refute that it’s a technical error.

Detailed analysis of the sequences, in the absence of additional data is, however, indicative of deltacron just being a contamination and not a variant by itself. At the moment, health experts and virologists are not worried about B.1.640.2.

WHO’s Covid technical lead, Maria Van Kerkhove, too, had said Monday that deltacron is likely the result of contamination during sequencing and asked to avoid portmanteaus when commenting on Covid co-infections.

(Edited by Poulomi Banerjee)

Also read: ‘IHU’ or B.1.640.2 — the new Covid variant detected in France which has 46 mutations


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