Update on the Omicron variant

 

 

By M.C.M. Iqbal- 2022/02/28

(mcmif2003@yahoo.com)

Scientists in South Africa announced on 25 November the discovery of a new variant of the Coronavirus. On 26 November, the WHO named this variant, Omicron. Although the virus originated in neighbouring Botswana, the media labelled South Africa as the country of origin.

Despite the WHO adopting a neutral system to identify new variants of the Coronavirus (using letters of the Greek alphabet), the Omicron variant is associated with South Africa. However, 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 last variant of the virus to emerge was the Delta variant, which surfaced in December 2020, in India. This article is an attempt to explain the latest findings on the Omicron variant.

Global status

Omicron has spread across countries faster than any of the previous variants of the Coronavirus. Within two months it spread to 151 countries on all the continents. Some experts believe it is the fastest spreading virus in human history. The figure below, from Nextstrain, shows the nearly total replacement of the then-dominant Delta variant by the Omicron variant by mid-February. Nextstrain is a global database depicting the real-time evolution of the genomes of the coronavirus and other globally significant pathogens. This interactive platform provides professionals and the public information to understand pathogens’ global spread and evolution, including information on individual countries. (https://nextstrain.org/ncov/open/global).

See figure:

Global distribution of Delta and Omicron variants on [A] 1^st January 2022 and [B] 11th February 2022 (Graphic: Fadil Iqbal/IUPUI. Data: Nextstrain)

What’s unique about Omicron?

Scientists are using hi-tech approaches to understand the unique structure of the Omicron variant. One such method is called cryo-electron microscopy, which has revealed the molecular structure of the spike proteins of the virus. Spikes on the Coronavirus, the flower-like protrusions on the surface, are the key to the virus’ design, which it uses to latch on to and enter our cells. Unlike the previous Alpha and Delta variants, the Omicron variant has over 30 changes (mutations) to its spike.

The initial Coronavirus and the earlier variants, Alpha and Delta, could infect our lungs, causing many complications. The virus turned the lungs into a battlefield reducing their capacity to provide oxygen to our body. Seriously ill patients were given oxygen. So, why is Omicron apparently causing a milder form of the disease? Omicron seems less efficient in infecting the cells in the lungs than those in our nose and throat. The changes in the spike of the Omicron have hindered its ability to enter the lung cells.

Changes in Omicron

The changes or mutations in the Omicron variant has enabled the virus to spread more quickly in the human population. Significant modifications identified by scientists are summarised below.

Evading defences

The immune system in our body is our defence system that destroys and eliminates any foreign disease-causing agents entering our body. A primary weapon of the immune system is antibodies. These are produced either due to previous infections or are induced by vaccines. They attach themselves to the virus and neutralise their ability to get into our cells. The vaccines for COVID-19 are based on spike proteins. Around half of the new mutations of Omicron are found on a region of the spike (called receptor binding domain), which binds with a protein on the surface of cells in our throat and lungs (called ACE2 receptor). This binding is crucial for the virus to enter the cell. These new mutations have changed the spikes of the Omicron variant so much so that our antibodies from vaccinations and previous infections cannot recognize the spike. Consequently, Omicron can escape some of the defences created by the vaccines. Fortunately, only some of our antibodies, called neutralising antibodies, are affected by this. Because of this, vaccination and boosters still provide us with protection, preventing severe infection.

The earlier variants too had spike mutations, but these were few and prevented only some of the antibodies from recognizing the spike. The changes on the Omicron spike are more numerous. Imagine a jigsaw puzzle with only a few pieces missing or changed, you can still make out the picture. But if many pieces are altered or missing, you would not recognize the picture.

Better spike to enter cells

Before latching onto the receptors on our cells in the throat and lungs, which are the doorway into our throat and lung cells, two parts (subunits) of the spike protein need to open or separate. In the previous variants, these subunits were weakly attached. Some separated too early and thus were not available to latch on to the receptors on the cells. In the Omicron variant these subunits are stabilised so that much more spikes are available, increasing the chances of the virus attaching to the receptors.

It begs the question, if the Omicron spike has changed, how can it bind to the cells at all? Scientists from the Universities of British Columbia and Washington say that the mutations have increased its ability to bind with our cells at a level on par with the Delta variant.

New route of entry

The previous variants needed the cooperation of two proteins on the surface of our cells, to enter (called ACE2 and TMPRSS2), and some cells do not have the second protein. Therefore, the virus could not enter cells that did not have the second protein. Omicron needs only the help of ACE2 to enter cells and now has a more extensive range of cells to enter.

Omicron spreads rapidly

The virus is quickly expelled into the air if it infects and multiplies in the throat. Further, since Omicron 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. Consequently, the obvious means of slowing or preventing the spread of the virus is to always wear a mask and avoid social gatherings.

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

Immediate concern

Scientists have two significant concerns. First, Omicron can spread rapidly, and second, it can bypass our immune system. Our immune system is our internal defence system, using antibodies and an arsenal of chemicals and cells. In addition, the available vaccines were designed by scientists based on the Coronavirus variants circulating in the population. Thus, major changes to the Coronavirus can reduce the efficiency of available vaccines. Health authorities observed both these concerns in the past month: Omicron can spread more rapidly than the earlier dominant Delta variant, and vaccination shows a reduced ability to prevent infection by Omicron, compared to the Delta variant. This has called for booster doses for people who have already received the two mandatory doses.

What can be done?

Vaccination is the primary tool we have to prevent the spread of the virus and curtail its opportunities to multiply. Besides the two mandatory doses of the vaccine, we also need to get the booster; this strategy has shown a marked reduction in severe disease and the need for hospitalisation. In addition, we should rigorously follow the simple rules we are familiar with – wearing a mask at all times when outside, maintaining social distance, and following hygienic practices by washing hands with soap and avoiding touching the nose and face with possibly contaminated hands.

Future

The Coronavirus is here for the long haul. New variants will keep emerging, and it seems unlikely we can eradicate it. The virus has only two major routes into our body: The nose and mouth, which we should always be mindful of, particularly in public spaces. All we need is a tight-fitting mask to prevent the entry of the virus. Media should help to counter vaccine hesitancy and the spread of misinformation. As individuals, we need to understand the biology of the virus (the purpose of this article), to avoid spreading the virus and infecting ourselves and others, and above all, to stop the spread of false information through social media. The underlying science of the Coronavirus is evolving rapidly, as seen by research published daily. Although the virus is also changing and producing unpredictable variants, the science should be supported, in a broad sense, for health authorities and policymakers to develop strategies to mitigate the spread and impact of the Coronavirus.