Why Omicron is a Major Threat: An Evolutionary Virology Perspective in Simple English

Saltation evolution, a rare type of evolution that results in jumps of evolution, probably gives rise to Omicron.

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Microbial Instincts

7 min readNov 27, 2021

Photo by Fusion Medical Animation on Unsplash

A new Covid-19 variant first identified early November this year in Botswana has spread all over South Africa, and it has been added to WHO’s variants of concern. Its scientific name is SARS-CoV-2 B.1.1.529, and it was assigned a Greek letter ‘Omicron’ variant by WHO’s board.

Although a lot is yet to be researched about the variant, a few facts are already known. However, what everyone might want to know is Why?. Why is the virus a threat when not much has been researched? In this article, I will translate into simple English the Virology which makes Omicron a major threat. Some of the ideas are linked to this article I wrote 2 months ago.

A Spike protein of SARS CoV 2(red) attaching onto the human ACE 2 receptor (blue) (Source: qps, labels by author)

A brief intro

Since May 2021, the Delta variant has been the predominant variant in circulation globally. The Delta variant was first identified in late 2020, and it has a range of 13–17 mutations on its Spike protein. Mutations are changes that occur on the genetic material (DNA/RNA) of an organism (not limited to viruses). These changes are due to errors that sometimes result in a more fit virus or, in some cases, a weaker virus.

It is these new mutants that are called variants. The more ‘fit’ the virus, the better chance of surviving, hence more predominant in a population. The Spike protein is the ‘key’ used by the Coronavirus to enter the human cell through binding to the ACE2 receptor (the ‘lock’). In the southern part of Africa, the Delta caused the third COVID19 wave and the Beta variant first identified in South Africa caused the second COVID19 wave.

Because human antibodies target these Spike proteins, mutations in the spike might decrease binding between the Coronavirus and antibodies, hence enabling the virus to evade the host immune response.

Now enters the Omicron variant

Omicron has been found to have more than 30 mutations, as published in an article by Nature. What this means is that there are 30 changes on the spike protein of the omicron variant compared to the ‘wild’ type or the first Wuhan Hu 1 coronavirus. The mutations observed in the Delta variant are also part of > 30 mutations in the omicron variant spike protein.

But these are just numbers that might mean nothing when not explained carefully. The Alpha variant has 10 mutations compared to the original Coronavirus isolated in the Wuhan Hu 1 patient (wild type) in December 2019. Only these 10 mutations caused the transmissibility (readiness to be transmitted to the next person) of the Alpha variant to increase by 40–80%. If, for example, the transmissibility increases by 50%, it means if it took 2 days for the wild type to infect 2 more people, then with Alpha variant it would infect 3 more people in the same time frame of 2 days.

By adding some compounding effect, it means if 10 000 people infected with the wild type could infect 20 000 more people in two days, then with the Alpha variant, the same 10 000 people can infect 30 000 more people in two days. All this originates from only 10 mutations. Imagine the threat Omicron would cause with >30 mutations.

Another way of understanding this is that, with only 3 more mutations on the Delta variant compared to the Alpha variant, the Delta variant became more transmissible, of course, but here is an additional fun fact, the Delta variant could now take 4 days to show symptoms compared to 6 days by other variants … only from 3 mutations. Compare that with over 30 mutations (with Delta mutations included in those mutations) to understand why the omicron variant is a major threat.

Of course, it depends on where the mutations occurred and the biological function of such a site. Some mutations might not have an impact if they happen on a less functional part of the protein. But still, 30 is a lot of mutations, over double the mutations on the Delta variant that predominated the COVID19 cases in Mid-2021.

One more possible threat of Omicron, perhaps the major threat…

Now the world was starting to return to normal again with less stringent conditions like sanitising and wearing masks, mostly because of COVID19 vaccination. One more threat of Omicron, perhaps the most bigger threat I should have mentioned earlier in the article, is that the variant has capabilities of reinfection.

In normal circumstances, when the body learns how to fight a foreign pathogen, it stores that information in its memory cells such that upon reinfection by the same pathogen, there is quick immune response to eradicate this pathogen. The body can learn how to fight this pathogen through the entry of the real pathogen (naturally) or by introduction of the weakened or dead pathogen (artificially). The latter is the basis of vaccination, at least the body learns to fight the pathogen without developing the disease in most cases.

Because the omicron variant has also been identified in patients who received vaccines, this means nobody is safe whether naturally or artificially vaccinated. The mutations changed the shape of the Spike protein such that the available human antibodies can not fit tightly to the Spikes, hence making evasion of the immune system by the virus inevitable.

This might cause re-introduction of stringent conditions like tight lockdowns, which from an economic view is not good for business, especially when global markets are starting to rise again from ashes.

Evolutionarily speaking, it's not proper that the omicron variant had developed >30 mutations in this short period. So what happened?

I will take you through an evolutionary biology crash course in this paragraph. From Charles Darwin research, Evolution is a gradual change in an organism. Keyword there is ‘gradual’. Usually, organisms evolve to adapt to new conditions, and this process takes a lot of time and generations until the advantageous trait has been achieved.

It also follows that the evolved organism is the one that survives in a given ecosystem. That process is called selection. Selection occurs naturally or artificially; cases like breeding are what we call artificial selection. One of the reasons some ancient organisms like Dinosaurs or mammoths could not survive up to today is because they could not adapt to changing conditions of their Ages. This can be summarised by my favorite statement, ‘Survival of the fittest’. If an organism cannot adapt, then it deserves to die, also new fit species emerge to replace the old unfit species, that’s just nature.

Now, remember the part I wrote that when the human body is re-infected by the same pathogen, there is a quick immune response to wade off the pathogen. Upon reinfection, in most cases, the body might not show any symptoms caused by the pathogen because of less time taken by the immune system to garner a counter-response.

The reason I am saying this is because I want to point out that time is very important in immunity. The difference in disease severity between vaccinated and unvaccinated people is only because the pathogen of interest is eradicated quicker in vaccinated than unvaccinated people.

Back to the Omicron variant…

Photo by National Cancer Institute on Unsplash

Omicron is the second ‘variant of concern’ to be first identified in the Southern part of Africa. Before the entry of the Coronavirus, there has been another nasty virus which has been flourishing in this region. If you guessed HIV, well you are right.

In South Africa, around 8.1 million people are living with HIV. Well like I said, numbers sometimes mean nothing unless well explained. What this means is that if it was a country like Zimbabwe, which has a population of ~14 million, it means more than half of the Zimbabwean population would be living with HIV. Zimbabwe is a beautiful country😀.

Because HIV attacks white blood cells, which are the soldiers of the body, it also means such individuals will have a weaker immune system. The term for that condition is immunocompromised.

Adaptive evolution is, like you guessed, evolution to adapt in unfavourable conditions. There is yet another type of evolution I would like to point out called saltation evolution. This is a very rare type of evolution that results in jumps of evolution, like what is being observed in the omicron variant.

If one mutation per given time is allowed in normal circumstances, then it would be 10 mutations per given time when it comes to saltation. However, for saltation evolution to be complete, there is a need for a favourable environment that supports such jumps without interference of the immune system. Immunocompromised individuals offer such a perfect environment for saltation. COVID19, as expected, has been noticed to cause prolonged illnesses in immunocompromised patients. This gives time and favourable environment for the Coronavirus to evolve. Because there is a huge population of people living with HIV in Sub-Saharan Africa, it also means a lot of COVID19 variants will be expected to originate here.

This is my account of COVID19 omicron variant Virology which I hope was not too technical but rather understandable to anyone who can read English.

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