New variant, omicron (B.1.1.529) appeared

29 November 2021. Cellspect Co., Ltd.

Here comes a new coronavirus variant Omicron (B.1.1.529). This variant was first detected in South Africa on November 12 and in just two weeks, WHO judged that this variant had adversely changed the epidemiology, so it decided to change B. 1.1.529 into a Variant of Concern (VOC), named Omicron.

Why does the Omicron make scientists particularly worried?

It is because Omicron contains 32 mutations on the spike protein (S protein) which combines the mutation characteristics of various previous variants, including mutations related to virus entry into cells, immune escape, or increased infectivity, etc.. It carries mutations P681H and N679K which are 'rarely seen together' and could make it yet more resistant to vaccines. These two mutations, along with H655Y, may also make it easier for the virus to sneak into the body's cells. And the mutation N501Y may make the strain more transmissible and was previously seen on the Alpha and Beta among others. Two other mutations (R203K and G204R) could make the virus more infectious, while a mutation that is missing from this variant (NSP6) could increase its transmissibility. It also carries mutations K417N and E484A that are similar to those on the Beta variant that made it better able to dodge vaccines. Moreover, it also has the N440K, found on Delta, and S477N, on the New York variant — which was linked with a surge of cases in the state in March — that has been linked to antibody escape. Other mutations it has include G446S, T478K, Q493K, G496S, Q498R and Y505H, although their significance is not yet clear.

Omicron variant was first discovered in South Africa and Botswana, and the number of confirmed cases in Gauteng province in northeastern South Africa rose rapidly in the past two weeks, becoming the dominant variant now, showing that its transmission ability cannot be underestimated.


Figure 1. X-ray crystal structure analysis diagram of S protein and ACE2 receptor complex.

The mutation site of S protein found in the Omicron variant is indicated by purple spheres.

Can current PCR detect Omicron variant?
The current PCR test can detect this variant without problems. Several labs have indicated that for widely used PCR test, usually three main genes would be tested. For Omicron, it can be tested positive but one of genes will not be detected (called S gene dropout or S gene target failure), and this result can therefore be used as a marker for Omicron variant.

Will Omicron be more likely to cause severe disease?
The initial report in South Africa showed that the majority of cases were mild, but the virus was only detected for the first time in South Africa on November 12, and at the beginning it infected mostly young people. Therefore, it may take several weeks to accumulate more clinical information to analyze whether there is a higher risk for severe disease in the elderly or those who have not been vaccinated. Previously, it took about two months for this information in the case of Alpha or Delta variant.

Is the vaccine still useful for Omicron? How about oral drugs for monoclonal antibodies?
Almost all existing COVID-19 vaccines target against the S protein of the virus, however, there are 32 mutations on the S protein of Omicron variant. According to previous information on Beta, Delta variants, etc., the vaccine effectiveness should be affected more or less. Vaccine companies have already started laboratory research, and preliminary results should come out in about two weeks. The South African NICD estimates that there may be some immune escape, but the vaccine should still provide high protection against severe disease and death. Omicron variant has many mutations in the receptor-binding domain (RBD) that the monoclonal antibody acts on. Therefore, monoclonal antibodies may indeed decrease their effectiveness, which requires follow-up research. As for oral medicine, because its mechanism is completely different from that of vaccines, it does not act on S protein, so it is likely to be less affected. But this also needs to be confirmed by follow-up research.

Israel is to ban the entry of visitors from all countries due to the Omicron variant. The United States began restricting the entry of travelers from eight countries including South Africa on November 29, and urged the public to administer additional vaccines as soon as possible. The European Union proposes to impose travel restrictions on people from seven countries in southern Africa. And just now, prime minister Kishida has announced that all new entry to Japan will be suspended due to the worldwide expansion of the new COVID-19 variant Omicron.


  1. WHO“Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern”

  2. 27 Nov, 2021, “Why is Omicron so scary?” Mail Online News

  3. 26 Nov, 2021, “CDC Statement on B.1.1.529 (Omicron variant)”

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