Concern about Covid-19 variant Omicron centers on spike protein mutations


In the span of a little more than two weeks, a new Covid-19 strain advanced from its first known infection to classification as a variant of concern. Understanding the extent of the threat posed by the new variant Omicron and responding to it will take more time.

Analysis of Omicron so far found that this new variant, first identified in South Africa, has numerous mutations along the spike protein. The location of those mutations is significant because the virus uses the spike protein to latch onto a cell and infect it. This protein is also important because it is the target of the Covid vaccines that elicit an immune response. Scientists are concerned because spike protein mutations could make this new variant more transmissible and virulent. It’s also possible that the new variant may reduce effectiveness of the available diagnostics, drugs, and vaccines.

Speaking on a video that the World Health Organization posted on Twitter and YouTube on Friday, Maria Van Kerkove, the WHO’s technical lead on Covid-19, said that the large number of mutations in the new variant “have some worrying characteristics.” But she added that the studies needed to better understand this new variant could take weeks.

“There’s a lot of work that is ongoing in South Africa and in other countries to better characterize the variant itself in terms of transmissibility, in terms of severity, and any impact on our countermeasures, like the use of diagnostics, therapeutics, or vaccines,” Van Kerkove said. “So far, there is very little information, but those studies are underway.”

The WHO said the first known confirmed infection from this new variant came from a sample collected on Nov. 9. The new variant was reported to the organization on Nov. 24. Two days later, the WHO’s Technical Advisory Group on SARS-CoV-2 Virus Evolution, an independent body of experts that monitors and evaluates the evolution of the virus, met and concluded that there were enough changes in the virus to categorize it as a variant of concern. It joins the Alpha, Beta, Gamma, and Delta variants on this list.

According to a report in Nature, researchers in South Africa first identified Omicron in genome sequencing data from Botswana. The variant displayed more than 30 spike protein mutations. Penny Moore, a virologist at the University of the Witwatersrand, Johannesburg, whose lab is studying Omicron, told Nature that the mutations may help the virus evade antibodies produced by the body to stop the pathogen. She added that computer modeling suggests Omicron could also evade the immune system’s T cells.

The most important of the antibodies produced by the body to neutralize SARS-CoV-2 target three slightly different sites on the spike protein. Jesse Bloom, a virologist at the Fred Hutchinson Cancer Research Center, told the journal Science that Omicron’s mutations change the sites that antibodies recognize, making the antibodies less potent. Bloom said those who have recovered from Covid-19 or who have been vaccinated are unlikely to completely lose the ability to neutralize the virus.

“But I would expect, based on this particular combination of mutations, that the drop in neutralization is larger than for all the other major variants,” Bloom said.

It’s too soon to know for sure whether any of those things will happen. Like Omicron, the Beta variant was also first documented in South Africa. Despite characteristics that warranted its designation as a variant of concern nearly a year ago, Beta has not achieved the global spread reached by Delta, which has become the most dominant Covid-19 strain in the world.

In the meantime, vaccine companies are conducting their own tests. BioNTech said that it will take about two weeks to assess whether the messenger RNA vaccine it developed in partnership with Pfizer will work against Omicron. The German company added that the mRNA vaccine can be adapted to the new variant within six weeks and initial batches shipped within 100 days.

Moderna is also conducting similar tests. The company has been studying multi-valent versions of its mRNA vaccine as potential boosters that address the Beta and Delta variants. Omicron carries several mutations present in both Beta and Delta; Moderna said it will rapidly expand the blood sera testing from these studies to determine whether the multi-valent vaccine candidates are better able to protect against Omicron.

No Omicron cases have been reported in the U.S. so far, according to the Centers for Disease Control and Prevention. The CDC added that its variant surveillance system has reliably detected variants in the U.S., and the agency expects that this system will detect Omicron quickly.

Image: appledesign, Getty Images

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