Why Omicron quickly became a variant of concern

Enlarge / There are many mutations.

On Friday, the World Health Organization officially appointed a new version of the SARS-CoV-2 virus, a worrying variant, and attached the Greek letter omicron to the designation. The Omicron variant is notable for the large number of mutations in the spike protein of the virus. While Omicron appears to have started to spread in Africa, it has already appeared in European countries such as Belgium and the United Kingdom, which are working to limit its spread through surveillance and contact tracing.

As of now, data on the variant is very limited; We currently do not know how easily it spreads compared to other variants, nor do we understand the degree of protection against Omicron offered by vaccines or past infections. However, the new designation will likely help focus resources on studying Omicron’s behavior and tracking its spread.

Many changes

While the peak version of the Delta variant has nine changes compared to the virus that started the pandemic, Omicron has 30 differences. While many of these have not been previously identified, several of these have been seen in other strains, where they have a variety of effects. These include increasing the infectivity of the virus, as several of the changes increase the affinity between the spike protein and the protein in human cells that it targets when a new infection begins.

Other changes in the peak occur in areas of the protein that are frequently attacked by antibodies that neutralize the virus. The changes here may mean that an immune response generated to vaccines or older versions of the virus are less capable of attacking Omicron.

While these mutations are suggestive, understanding how they and previously undescribed mutations in Omicron alter their behavior will depend on obtaining real-world data on their spread. Right now though, we just don’t have much of it.

We are lucky in the sense that Omicron is relatively easy to spot. According to the WHO, some of the large collection of mutations in the gene encoding the spike protein interfere with recognition of the gene using common versions of PCR tests. Those tests continue to recognize the presence of the virus by targeting other areas of the genome as well. So a PCR test that returns a negative but positive peak for the virus suggests the presence of Omicron, which can then be confirmed by genome sequencing.

These tests have shown that Omicron is spreading rapidly in several southern African countries, although total cases in Botswana and South Africa remain relatively low at this time, so the significance of this spread is unclear. Vaccination rates in these countries also remain low, making it difficult to determine how much risk Omicron poses to those who have been immunized.

Some constants

The cases identified outside of southern Africa so far have all been in travelers who spent time in this region. Public health authorities in those countries are currently involved in contact tracing to try to limit the spread of the variant outside of those already infected. and several countries (including the US) already have limited trips from countries in the region.

Testing and contact tracing are part of the now familiar set of public health measures that can limit Omicron’s impact as we learn more about him. TO CDC statement provides a reminder of the rest: social distancing, mask when indoors, and get vaccinated if eligible. While we do not know how much protection vaccines provide against Omicron, it is quite certain that their effectiveness against it is considerably greater than zero.

Listing image by Aurich Lawson / Getty

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