Omicron coronavirus variant raises questions among scientists

The fast-spreading Omicron coronavirus variant recently identified in South Africa has virologists and health authorities on edge because of its many mutations, but much about its infectiousness and virulence remains unknown.

Scientists said some of the roughly 50 mutations on the new variant, called B.1.1.529, could potentially render it more transmissible or reduce vaccine effectiveness. But it will take time for virologists and infectious-disease researchers to study the variant’s spread and the potential impact on vaccines and therapeutics.

“There are several aspects of concern here, but there are lots of unknowns," Sharon Peacock, director of the Covid-19 Genetics U.K. Consortium, said at a press briefing on Friday. “It’s so important to stress how much we don’t know at the moment about this new variant."

Researchers first detected B.1.1.529 in South Africa in early November, and the variant has fueled a jump in the country’s cases, albeit from a very low starting point. The variant also has been identified in Botswana, Hong Kong, Israel and Europe. Virologists said it isn’t known whether B.1.1.529 first emerged in South Africa or whether that was simply the first place it was detected. Many countries lack comprehensive genomic surveillance systems able to quickly flag new variants.

The World Health Organization on Friday designated B.1.1.529 a “variant of concern." A decision it said it based on evidence of “a detrimental change in Covid-19 epidemiology." The agency said preliminary evidence suggests the variant poses an increased risk of re-infection, compared with other variants of concern, and asked countries to increase surveillance and sequencing and to report initial cases or clusters caused by the variant, dubbed Omicron.

The WHO has identified four other variants of concern, including the Delta variant that was first identified in India, and two variants of interest. Delta is the dominant variant in the U.S., where 99.9% of sequenced Covid-19 cases were linked to the Delta variant as of Nov. 20.

The Centers for Disease Control and Prevention said Friday that Omicron hadn’t been identified in the U.S.

“The U.S. variant surveillance system has reliably detected new variants in this country," the CDC said. “We expect Omicron to be identified quickly, if it emerges in the U.S."

Scientists say it isn’t clear whether the new variant might be able to out-compete the Delta variant. Some variants of interest that have emerged, such as the Mu and Lambda variants, didn’t supplant the highly contagious Delta.

Several mutations on the B.1.1.529 variant have been linked in other variants to high transmissibility and the ability to more efficiently enter human cells. That, plus the rapid rise in variant-linked cases and positive tests in South Africa’s Gauteng province, have led some health officials and virologists to suspect that the variant might have heightened transmissibility.

“We don’t have definitive evidence at the moment that it is more transmissible," Dr. Peacock said. “There is enough evidence to make you concerned that transmissibility is higher."

More than 30 of the variant’s mutations are on the spike protein, the target of the authorized Covid-19 vaccines, according to the Network for Genomic Surveillance South Africa. Some mutations on B.1.1.529 also are associated with resistance to neutralizing antibodies or evasion of the immune response. The high number of mutations on the spike protein concerns virologists and health authorities, because of the potential that some of them could give the variant heightened transmissibility and immune escape.

The changes to the variant’s spike protein affect readings from some diagnostic tests but in a way that researchers can use to their advantage. The B.1.1.529 variant causes one part of some multipart viral tests called PCR tests not to work, so the tests can flag an infection and display a sort of glitch that makes the variant easier to track.

“It’s going to be incredibly useful as a tool for potentially tracking this variant," said Wendy Barclay, head of the G2P-UK National Virology Consortium that studies new Covid-19 variants and mutations. There are several other variants around the world that also cause that same fault in the test, she noted, so sequencing those samples to determine the specific variant will still be important.

It isn’t known whether or to what degree the variant is able to evade the immune response from prior infection or vaccination, Dr. Barclay said. Researchers and laboratories across the world will study the ability of neutralizing antibodies and vaccines to combat the new variant, she added.

The new variant might also dull the impact of monoclonal antibody treatment because of those same mutations, Dr. Barclay said. But there is currently no evidence that any of the mutations might affect the effectiveness of new antiviral treatments, or that the variant might cause more severe disease.

“We don’t have any evidence at the moment that this is a more severe virus," Dr. Barclay said.