Omicron variant

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The Omicron variant of the coronavirus causing COVID-19 first appeared in South Africa in November 2021.

This variant now represents 90% of coronavirus infections in South Africa and has spread to more than 100 countries. After arriving in a country, the Omicron variant is expected to replace the Delta variant in about 3-4 weeks.

This variant has changes or mutations in its DNA with respect to previous coronavirus variants. Some of these mutations have allowed it to remodel the Spike protein (S) to be more efficient at infecting cells through the AC-2 receptor, a protein on the plasma membrane of human cells.

One of the main differences between this and previous variants is its contagiousness. The transmission rate of the Omicron variant is the highest of the variants found so far. The R number (the average number of people an infected person passes the disease on to) for this variant is calculated to be 10. As well as infecting unvaccinated people, this variant also infects a significant number of people already vaccinated.


This variant has a number of changes, also called mutations, in its external structure and DNA, compared with previous variants. Some of the advantages these mutations provide for the virus are:

  • More efficient entry into human cells (of the respiratory system). This gives it greater infectivity.
  • It replicates more in the upper respiratory tract, that is, in the bronchi rather than the lungs. This causes a higher viral load in the upper respiratory tract which makes infected people more contagious.

The methods used so far to diagnose coronavirus variants are as effective in diagnosing the Omicron variant.

Image showing a vial and the instrument for taking the sample and do the antigen test

Commercial antigen tests available in chemists detect the N protein of the nucleus and not the S, which is what the mutations have. Therefore, these tests detect all the variants, as they all have the N protein.

Nasopharyngeal swab

The PCR test amplifies coronavirus genes common to all variants, including those of the Omicron variant which have not mutated, so persons infected with the Omicron variant will still test positive. The only exception is the Thermo Fisher TaqPath Kit. This detects the coronavirus S protein, which the Omicron variant does not have; so the test cannot detect this variant and will give a negative result for it.

Microscopy and viral DNA or RNA detection blood test

The PCR test amplifies or detects more than one coronavirus gene and there are more than 40 different types of PCR tests. Only 8 of these detect the gene that provides the information to make the S protein, and one of these is the Thermo Fisher TaqPath Kit, which detects 3 genes: ORF1AB and the S and N (of the nucleus). Therefore, if this PCR test does not detect the S gene but does find the other two genes, then this is indicative of the Omicron variant; this variant accumulates so many mutations in the S gene that it is not detectable. Therefore, this test can detect this new variant.

The Omicron variant has a faster infection rate. The incubation period (the time from infection to when the person shows symptoms) is much shorter than for other variants: 2 days instead of 4-6 days.

Some of the different symptoms of this variant with respect to previous ones are:

Person with itchy inside of mouth and throat

Itching and discomfort in the throat.

Reduced sense of taste and smell

It usually does not cause loss of smell or taste.

Old person with a respiratory infection

The fact that the virus grows more in the bronchi instead of the lungs makes it a milder disease; with symptoms more akin to bronchitis than pneumonia.

Hospital building

The probability of hospitalisation is much lower than with other variants.

There are 3 main antiviral treatments shown to be effective against the Omicron variant. These are Remdesivir, approved in Spain, Molnupiravir and Nirmatrevir. The latter two are in the process of being approved by the European Medicines Agency (EMA).

Most monoclonal antibodies (with the exception of Sotrovimab) and the plasma of already immunised people are not very effective in treating patients infected with this coronavirus variant.

The effectiveness of complete vaccination (two doses) against COVID-19 decreases markedly at 6 months, and has been shown to protect little from infection by the Omicron variant, as antibody levels are very low after this time.

However, the cellular immunity produced probably protects people from severe disease. That is why a third dose should be given to the elderly and those with comorbidities. 2-4 weeks after a 3rd dose (of mRNA vaccines, i.e. Pfizer or Moderna), immunity is very high, its efficiency increases up to 60-70%. However, preliminary data from the UK say that protection is significantly reduced after 3 months and it is not known whether farther booster doses will be needed later.

As a result of these investigations, the need to produce a new generation of vaccines containing a combination of the variants that have already appeared has become evident. Fortunately, there are already over 300 research projects working on COVID-19 vaccine updates, including the project carried out in Catalonia with Hipra

Substantiated information by:

Antoni Trilla
Eduard Vieta Pascual
Gema Maria Lledó Ibáñez
Jacobo Sellarés Torres
Josep M. Miró Meda
Josep Maria Peri
Maica Rubinat
Mariona Violan

Published: 12 March 2020
Updated: 12 March 2020

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