Offshoot of Omicron variant could make global tracking more difficult

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

On account of a genetic quirk, Omicron, first identified in southern Africa, can be identified by a certain type of PCR test because 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 across South Africa, Australia and Canada no longer possesses this characteristic, meaning full genome sequencing is required to detect it. Researchers have classified the earliest identified form of Omicron as BA.1, while the offshoot has been labelled BA.2.

Experts have warned that the Omicron offshoot could prove more difficult to track as most countries have poor or non-existent genomic surveillance. But they stressed PCR tests would still be able to detect 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 critical to get that quick view in many different 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 more 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 hidden burden 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 immediate cause for concern.

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

Stuart added that countries with access 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 access to genomic sequencing — either because 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 change was “not going to help” scientists monitoring Omicron’s spread “in areas that are relying solely on S-gene target failure”. But he added 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 added that it highlighted “an argument 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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