A Good Guide to the Omicron Variant

By M.C.M. Iqbal, PhD

Despite the WHO adopting a neutral system to name the variants of the coronavirus that keep emerging (using letters of the Greek alphabet), the Omicron variant is associated with South Africa. The last variant of the virus to emerge was the Delta variant, which surfaced in December 2020, in India. There are two more letters between Delta and Omicron in the Greek alphabet that the WHO decided not to use. These are ‘Nu’ and ‘Xie’, which the WHO thought could be confused with ‘new’ while Xie is a common surname in China.

The Omicron variant is spreading in many countries. With the number of infected persons rising and another wave expected, many countries in Europe have imposed the usual methods to arrest the spread, with immediate lockdowns. However, scientists are still collecting data to find out how bad Omicron is, since the data seems to indicate that in South Africa, the disease is not as bad as the Delta variant. At the same time, in Europe, there is no significant change in the number of persons hospitalized. Of immediate concern to health authorities are, is the Omicron variant spreading faster than the earlier variants, does it cause more or less severe disease, and can it bypass the vaccines available?

Discovery

Scientists in South Africa announced on 25 November the discovery of a new variant of the coronavirus. On 26 November, the WHO named it Omicron. Although South Africa has been labeled as the country of origin, the virus was identified in neighbouring Botswana. In addition, there are reports of an earlier detection of this variant in the Netherlands.

PCR tests look for four markers on the virus genome to identify it as the coronavirus. The tests in Botswana showed a reduced sensitivity because one of the four targets was not being detected. These samples were sent to South Africa, where scientists have state-of-the-art facilities to look for changes in the genome of the virus. Changes are found by reading the ‘letters’ of the virus genome (called sequencing) and comparing it to the already available genome of the virus. The new Omicron variant had many more changes than the Delta variant.

Global status

By 14th January, the Omicron variant had spread to 116 countries in all six continents since its discovery on 26 November 2021. The figure below shows the gradual replacement of the presently dominant Delta variant by the Omicron variant; at present global data on the coronavirus, maintained by Nextstrain (https:// nextstrain.org/ncov/open/global) shows a decline of the Delta variant from 88% on 30th October 2021 to 42% on 8th January 2022, while correspondingly the Omicron variant has increased from less than 1% to 56%. Nextstrain is a global database presenting a real-time view of the evolution of the genomes of the coronavirus and other globally important pathogens. The interactive platform provides information to professionals and the public to understand the spread and evolution of pathogens, including information on individual countries.

Distribution of Delta and Omicron variants on 1st January 2022 from Nextstrain. (Please see graph)

What’s unique about Omicron?

Unlike the previous variants of the coronavirus, this variant has over 30 changes (mutations) to its spike (a protein), the characteristic flower-like protrusion on its surface. It was these changes to the spike, one of the four targets of the PCR test that raised alarm bells in Botswana. This spike makes the coronavirus special – it is the key it uses to gain entry into the cells in our throat and lungs. The previous variants, Alpha and Delta also had changes in their spike protein, enabling them to enter cells more efficiently and thus making them more infectious. The vaccines against the virus are based on this spike, and the antibodies produced by our immune system are specific to the spike protein. Thus, any significant changes to the spike means the previous vaccines may not be effective against the newly changed spikes on the Omicron variant.

While the Omicron variant can spread rapidly, it appears to cause milder disease compared to the Alpha and Delta variants. Scientists believe this is because Omicron infects the upper airways or the throat, and not the lungs further down. Based on experiments done on hamsters and mice, scientists found the concentration of the virus was much lower in the lungs than in their throat. The earlier variants of the coronavirus caused severe damage to the lungs of the infected people, with extreme cases needing oxygen. This does not seem to be the case with Omicron. Scientists believe the changes to the spike enables the virus to enter cells in the throat more easily than in the lungs.

It can spread rapidly

The virus is quickly expelled into the air if it infects and multiplies in the throat. Since it causes a milder form of the disease, infected persons may be unaware that they carry the virus. They would be moving about socially and at work, spreading the virus. Thus, the obvious means of slowing or preventing the spread of the virus is to strictly wear the mask at all times, and avoid social gatherings.

Studies have suggested that the period between exposure to the virus and onset of symptoms has also reduced to three days for Omicron. At the pandemic’s beginning, this was more than five days, and for the Delta variant it was four days.

What is of immediate concern?

Of concern to scientists is the better ability of the Omicron to spread rapidly in the population and its suspected ability to bypass our immune system. Our immune system is our internal defense system, using antibodies and an arsenal of chemicals and cells. The available vaccines are designed on the coronavirus variants circulating in the population. Thus, major changes to the coronavirus can reduce the efficiency of the available vaccines. Both these concerns have been observed in the past month: Omicron can spread more rapidly than the presently dominant Delta variant, and observations on vaccinated people show a reduced ability by the vaccines to prevent infections, compared to the Delta variant. This has called for booster doses for people who have already received the two mandatory doses. In Israel, even a fourth vaccination is being administered.

How could the variant have evolved?

Variants of the coronavirus result from changes to the virus’s genome, called mutations. What is troubling about the Omicron variant is that it has many mutations in its spike. Mutations happen spontaneously as the virus multiplies in our bodies and spreads to others. Thus, the virus gradually accumulates small changes to its advantage. These advantages are infecting us more efficiently, spreading to others more easily, and multiplying more rapidly. Scientists believe that one possibility is that the virus circulated in a small isolated group of people (say a village), piling up the mutations over time, and then escaping into a broader population, and then eventually crossing borders.

Another possibility is that it developed in a single individual and spread to others. This happens when a person has low immunity, resulting in a prolonged infection because the immune system cannot eliminate the virus. This leads to the virus developing changes (mutating) to overcome the mild immune response. Answering this question needs scientists to painstakingly reconstruct the history of the virus, using tools from molecular biology. Unfortunately, locating patient zero is difficult since it is impossible to analyze the virus (or sequence its genome) of all the persons infected with the Omicron variant. What is usually possible is to determine a general area or community and the time of origin.

What can we do about it?

Vaccinate! This is the primary tool we have to prevent the spread of the virus and not give it opportunities to multiply. In addition, we should rigorously follow the simple rules we are familiar with – wear the mask when outside, physically distance ourselves, and follow hygienic practices by washing our hands with soap, and avoiding touching our nose and face with possibly contaminated hands.

The good news

The coronavirus has been with us for over two years. Many were infected and have recovered from the virus during this period, providing natural immunity. Others have acquired immunity through vaccinations. When a new variant infects these people, they will manifest a milder form of the disease. This may explain the reduced hospitalisation of Omicron patients.

A booster dose to those already vaccinated or were naturally infected by the coronavirus, appears to provide reasonable protection against the Omicron variant.

And the bad news

The Omicron variant can evade immunity from previous infections. A recent analysis of surveillance data from South Africa, involving over two million persons, indicated suspected reinfections of those previously infected. This is in contrast to Beta and Delta variants, which did not lead to reinfections on such a scale.

The Future

The coronavirus is here for the long haul. Variants will keep emerging, and it seems unlikely it can be eradicated. The media should help counter vaccine hesitancy and the spread of misinformation. As individuals, we need to understand the biology of the virus to avoid spreading the virus and infecting ourselves and others. Science has to be supported in a broad sense to develop strategies by the health authorities and policymakers.

Further reading

S. Wild. How the Omicron variant got so many scary mutations. Scientific American, 3rd December 2021.

Michael Chan Chi-wai.

G. Vogel and K. Kupferschmidt. Early lab studies hint Omicron may be milder. But most scientists reserve judgment. Science, 20th December 2021.

K. Kupferschmidt and G. Vogel. Omicron threats remain fuzzy as cases explode. Science, 7 January 2022.

(The writer is a scientist in Plant and Environmental Sciences, National Institute of Fundamental Studies, Hanthane Road, Kandy. He can be reached at iqbal.mo@nifs.ac.lk)