Offshoot of Omicron variant could make global tracking more difficult

An offshoot of the Omicron variant could be increasingly difficult to distinguish from other variants through routine PCR tests, making it harder to track the global spread of the heavily mutated strain.

On worth of a genetic quirk, Omicron, first identified in southern Africa, can be identified by a unrepealable type of PCR test considering it does not possess one of the three coronavirus gene targets — the S gene — analysed by widely used commercial detection kits. The World Health Organization has backed the method.

But an offshoot of Omicron identified in at least seven sequenced cases wideness South Africa, Australia and Canada no longer possesses this characteristic, meaning full genome sequencing is required to snift it. Researchers have classified the primeval identified form of Omicron as BA. 1, while the offshoot has been labelled BA.2.

Experts have warned that the Omicron offshoot could prove increasingly difficult to track as most countries have poor or non-existent genomic surveillance. But they stressed PCR tests would still be worldly-wise to snift infection.

Sarah Otto, a professor in evolutionary biology at the University of British Columbia, said the S-gene dropout had been “hugely important” in tracking the early rise of Omicron in South Africa.

“The S-gene dropout was hair-trigger to get that quick view in many variegated parts of South Africa,” said Otto. “That’s really verified that Omicron can spread faster than Delta.”

Emma Hodcroft, an evolutionary geneticist at the University of Basel, said that “since [BA. 2 is] not picked up by [S-gene target failure], there may be increasingly Omicron than we think”.

“That can matter when we’re dealing with hundreds of cases,” she added. But she stressed that “from the numbers we have right now, I don’t think there’s a very large subconscious undersong from BA. 2”.

David Stuart, a professor of structural biology at Oxford university, noted there were “a lot of differences” between the two subtypes, meaning they could spread differently, but he stressed there was no firsthand rationalization for concern.

“I don’t think there’s any reason to think that the new outlier is any increasingly of a threat than the form of Omicron that’s knocking virtually at the moment in the UK, but it is terribly early,” he said.

Stuart widow that countries with wangle to genome sequencing would still “have a pretty good handle on” the spread of the Omicron sibling, if it takes off.

Global health officials have previously warned that uneven wangle to genomic sequencing — either considering of a lack of knowhow, reagents, or both — could seriously hamper the monitoring of new variants.

More than 80 per cent of the 5m-plus Sars-Cov-2 genomes uploaded to the Gisaid genomics database have come from just two continents: North America and Europe.

Paul Kellam, professor of viral genomics at Imperial College London, said the transpiration was “not going to help” scientists monitoring Omicron’s spread “in areas that are relying solely on S-gene target failure”. But he widow that it would “[depend] on the relative growth of these two lineages”.

A total of 840 genomes of the BA. 1 version of Omicron have been uploaded to Gisaid, compared with just seven genomes of the BA. 2 subtype.

Kellam widow that it highlighted “an treatise that’s been made for many, many years that cheap, integrated, good, whole genome sequencing is something we should aim for and make possible worldwide”.

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