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Heavily mutated Omicron variant puts scientists on alert

People wearing personal protective equipment pick up a suspected COVID-19 patient

Medics at an infectious-disease unit in South Africa, where a new strain of COVID is spreading quickly.Credit: Alet Pretorius/Gallo Images/Getty

Researchers in South Africa are racing to track the concerning rise of a new variant of the SARS-CoV-2 coronavirus that causes COVID-19. The variant harbours a large number of the mutations found in other variants, including Delta, and it seems to be spreading quickly across South Africa.

A top priority is to follow the variant more closely as it spreads: it was first identified in Botswana earlier this month and has since turned up in a traveller arriving in Hong Kong from South Africa. Scientists are also trying to understand the variant’s properties, such as whether it can evade immune responses triggered by vaccines and whether it causes more or less severe disease than other variants do.

“We’re flying at warp speed,” says Penny Moore, a virologist at the University of the Witwatersrand in Johannesburg, South Africa, whose lab is gauging the variant’s potential to dodge immunity from vaccines and previous infections. There are anecdotal reports of reinfections and of cases in vaccinated individuals, but “at this stage it’s too early to tell anything”, Moore adds.

“There’s a lot we don’t understand about this variant,” Richard Lessells, an infectious-diseases physician at the University of KwaZulu-Natal in Durban, South Africa, said at a press briefing organized by South Africa’s health department on 25 November. “The mutation profile gives us concern, but now we need to do the work to understand the significance of this variant and what it means for the response to the pandemic.”

On 26 November, the World Health Organization (WHO) designated the strain, known as B.1.1.529, as a variant of concern and named it Omicron, on the advice of scientists who are part of the WHO’s Technical Advisory Group on SARS-CoV-2 Virus Evolution. Omicron joins Delta, Alpha, Beta and Gamma on the current WHO list of variants of concern.

Researchers also want to measure the variant’s potential to spread globally — possibly sparking new waves of infection or exacerbating ongoing rises being driven by Delta.

Changes to spike

Researchers spotted B.1.1.529 in genome-sequencing data from Botswana. The variant stood out because it contains more than 30 changes to the spike protein — the SARS-CoV-2 protein that recognizes host cells and is the main target of the body’s immune responses. Many of the changes have been found in variants such as Delta and Alpha, and are linked to heightened infectivity and the ability to evade infection-blocking antibodies.

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Nature 600, 21 (2021)

doi: https://doi.org/10.1038/d41586-021-03552-w

Updates & Corrections

  • Update 27 November 2021: The story now includes that the World Health Organization has named the variant Omicron and designated it as a variant of concern.

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