COVID Omicron Variant: How Did It Emerge and Is It More Contagious Than Delta? A Virus Evolution Expert Explains

A new variant named omicron (B.1.1.529) was reported by researchers in South Africa on November 24, 2021, and designated a “variant of concern” by the World Health Organization two days later. Omicron is very unusual in that it is by far the most heavily mutated variant yet of SARS-CoV-2, the virus that causes COVID-19.

The omicron variant has 50 mutations overall, with 32 mutations on the spike protein alone. The spike protein – which forms protruding knobs on the outside of the SARS-CoV-2 virus – helps the virus adhere to cells so that it can gain entry. It is also the protein that all three vaccines currently available in the U.S. use to induce protective antibodies. For comparison, the delta variant has nine mutations. The larger number of mutations in the omicron variant may mean that it could be more transmissible and/or better at evading immune protection – a prospect that is very concerning.

I am a virologist who studies emerging and zoonotic viruses to better understand how new epidemic or pandemic viruses emerge. My research group has been studying various aspects of the COVID-19 virus, including its spillover into animals.

The omicron variant possesses numerous mutations in the spike protein, the knob-like protrusions (in red) that allow the virus to invade other cells.

Why do new SARS-CoV-2 variants continue to emerge?

While the unusually high number of mutations in the omicron variant is surprising, the emergence of yet another SARS-CoV-2 variant is not unexpected.

Through natural selection, random mutations accumulate in any virus. This process is sped up in RNA viruses, including SARS-CoV-2. If and when a set of mutations provides a survival advantage to a variant over its predecessors, the variant will out-compete all other existing virus variants.

Does the omicron variant’s greater number of mutations mean it is more dangerous and transmissible than delta? We simply don’t know yet. The conditions that led to the emergence of the variant are not yet clear, but what is clear is that the sheer number and configuration of mutations in omicron is unusual.

One possible explanation for how viral variants with multiple mutations emerge is through prolonged infection in a patient whose immune system is suppressed – a situation that can lead to rapid viral evolution. Researchers have hypothesized that some of the earlier SARS-CoV-2 variants, such as the alpha variant, may have stemmed from a persistently infected patient. However, the unusual constellation and numerous mutations in the omicron variant make it very different from all other SARS-CoV-2 strains, which raises questions about how it came about.

Another possible source of variants could be through animal hosts. The virus that causes COVID-19 can infect several animal species, including mink, tigers, lions, cats and dogs. In a study that is not yet peer-reviewed, an international team that I lead recently reported widespread infection by SARS-CoV-2 in free-living and captive white-tailed deer in the U.S. Therefore, we also cannot rule out the possibility that the omicron variant emerged in an animal host through rapid evolution.

White-tailed deer have recently been identified as a significant reservoir for SARS-CoV-2, the virus that causes COVID-19.

How the delta variant became dominant worldwide

Delta is between 40% and 60% more transmissible than the alpha variant and nearly twice as transmissible as the original SARS-CoV-2 virus first identified in China. The delta variant’s heightened transmissibility is the primary reason why researchers believe it was able to out-compete other variants to become the dominant strain.

A key factor in viral fitness is its replication rate – or how quickly a virus can make more copies of itself. The delta variant replicates faster than previous SARS-CoV-2 variants, and a not-yet-peer-reviewed study estimated that it produces 1,000 times more virus particles than its predecessors.

In addition, people infected with the delta variant are making and shedding more virus, which is another potential mechanism for its increased ability to spread. Research suggests that a possible explanation for the delta variant’s heightened ability to replicate is that mutations in the spike protein led to more efficient binding of the spike protein to its host, via the ACE-2 receptor.

The delta variant has also acquired mutations that would allow it to evade neutralizing antibodies that serve a critical role in the body’s defense against an invading virus. This could explain why, as multiple reports have shown, the COVID-19 vaccines have been somewhat less effective against the delta variant. This combination of high transmissibility and immune evasion could help explain how the delta variant became so successful.

Studies also show that people infected with the delta variant have a higher risk of being hospitalized compared to those infected with the original SARS-CoV-2 and early variants. One particular mutation on the spike protein of the delta variant – the P681R mutation – is thought to be a key contributor to its improved ability to enter cells and to cause more severe disease.

Will omicron replace delta?

It is too early to say if the omicron variant is fitter than delta or if it will become dominant. Omicron shares some mutations with the delta variant but also possesses others that are quite different. But one of the reasons why we in the research community are particularly concerned is that the omicron variant has 10 mutations in the receptor-binding domain – the part of the spike protein that interacts with the ACE-2 receptor and mediates entry into cells – compared with just two for the delta variant.

Suppose the combination of all the mutations in omicron makes it either more transmissible or better at immune evasion than delta. In that case, we could see the spread of this variant globally. However, it is also possible that the unusually high number of mutations could be detrimental to the virus and make it unstable.

It is highly likely that the omicron variant is not the endgame and that more SARS-CoV-2 variants will emerge. As SARS-CoV-2 continues to spread among humans, natural selection and adaptation will result in more variants that could plausibly be more transmissible than delta.

We know from influenza viruses that the process of viral adaptation never ends. Lower vaccination rates among many countries means that there are still a lot of susceptible hosts out there for the virus, and that it will continue to circulate and mutate as long as it can spread. The emergence of the omicron variant is yet another reminder of the urgency to vaccinate to stop the further spread and evolution of SARS-CoV-2.

Written by Suresh V. Kuchipudi, Professor of Emerging Infectious Diseases, Penn State University.

This article was first published in The Conversation.

COVID-19Infectious DiseasesPenn State UniversityPopularPublic HealthThe ConversationVirology
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  • Alex

    Yadda-yadda. I take exception to articles of this sort, which purport to answer abiding questions but skirt their “instructive” purpose and “devolve” to the official Chapter and Verse. These articles are typically accompanied by “spikey” artist’s conceptions, which have more in-common with SCIFI than Good Science.

    Beyond the gobbledygook the process is simple: Virus “punches” a hole through the cell membrane (utilizing a chemistry similar to that contained in the head of a spermatozoon), injects its errant (in both the “aberrant” sense and “purposeful” sense of the word) RNA, to “pollute” the process of cell division to produce copies of itself.

    But this “encapsulation” is OFF the point: Historically speaking, the distinction between “vaccination” (generic term) and “vaccination” (as in THE VAC) have been blurred, often with drastic consequences. The Poliomyelitis vaccine is a case in point:
    Dr. Jonas Salk had developed what he believed to be a “viable” vaccine, but deferred from promoting it as such, advising a testing period of 3-5 years before widespread utilisation. He was overruled by his government “sponsors”, his lab was commandeered, his cultures and proto-vaccines confiscated and, shortly thereafter, a MIRACLE was put to use.

    It’s effects were in deed miraculous: Children (primarily) and adults were freed from the “iron lung” within days of their injection. Ain’t SCIENCE GREAT! 1953 FADE OUT…

    FADE IN: 30 years later (as some contend: ALLEGEDLY) The due bill for expediency: Lupus surfaces PRIMARILY in those female “subjects” vaccinated in the first round. Inoperable Glial tumors surface in the same group, primarily affecting males.

    CAUSE AND EFFECT (as some ALLEGE):
    GLIAL TUMORS: Some of the first Polio VAC batches were contaminated with tumor cells extracted from the blood of a donor along with the polio “titre”. This form of cancer can have an “incubation” period of +20-30 YEARS. Right on schedule. Lyle Alzado, Defensive Lineman for the Denver Broncos, was perhaps its most famous victim. He passed away in 1992, from “complications”. One TOUGH CUSTOMER, particularly if one was opposite him On the Line.

    LUPUS (a general term applied to a syndrome involving the failure of the auto-immune system, one result of which, among others, is a body turned against its connective tissue). Can’t say CAUSE here, but the effect stuck two women, known to me, separated by 1,800 miles.
    #1) A woman who was confined to an iron lung for more than a year before vaccination.
    #2) A cousin who did not develop full-blown Polio but, like the above recipient, was among the first children to be vaccinated.
    COMMON THREADS: Same age. Both had their Thymus gland (integral to the auto-immune response) irradiated during puberty to eliminate virulent Subaceous Acne.

    Cause and Effect are difficult to assess 50+ years after the fact. COVID is current and, despite caution(s) advised by individuals far more versed than I in such subjects, THE VAC was rushed to MARKET. BAD SCIENCE. Profitable, perhaps, but irresponsible.

    I defer to one of my instructors’ caution for those who might “tinker” with the Human body for gain of any kind: for Fortune or Fame. THIS IS THE WISDOM OF A FOOL, OR THE “METHODOLOGY” OF A CRIMINAL. Such “types” DO NOT belong anywhere near a Human Body.

    A PARAPHRASE. But one gets the point: It is gun to the head of the unwary or undereducated.
    👉🤑

  • Howard Jeffrey Bender, Ph.D.

    All the coronaviruses and all their variants have different protein spikes, with Delta having one that’s more efficient at getting around the vaccines. Perhaps Omicron will, too. But the real problem is in the virus itself, not its protein shell, and why the most dangerous (MERS, SARS, and Covid-19) are so infectious. My independent research has found multiple one-in-a-million nucleotide sequence matches between all the coronaviruses and the human genome. Those sequences are the same as some of the loops of human tRNA. Using those loops and their amino acid code matches, viruses may be able to fool the nucleus membrane in cells to allow the virus to enter and associate with the human DNA, creating more opportunities for further infection. Our immune system may be compromised and may no longer be able to stop the virus and other diseases from attacking organs throughout the body. Vaccines that attack the virus protein shells while ignoring their contents are doomed to failure from the Darwin effect, but recognizing these loops suggests a possible approach to successful coronavirus vaccines. Only the infection process is considered in my work, not the innate virulence of the virus. For more info, check out this YouTube, Coronavirus – Using Your DNA Against You. https://www.youtube.com/watch?v=8dOIzD6ch8s

  • Herrnhut

    If it is no worse than the Spanish flu (1918-1920), it will disappear at the end of two full years.

  • john campbell

    Precisely, Claire!
    We are expected to believe that this variant, which appeared in Nigeria, has been isolated and analysed to the point where politicians can assert how virulent or problematic it is and that it has had the time to spread around the globe- all in the space of a month- DESPITE the draconian restrictions currently placed on global travel, the vaccinations, the masks and solcial distancing, and the fact that very few Nigerians ordinarily go globe-trotting by plane in normal circumstances, let alone in the midst of a pandemic restriction regime!

    People need to take the blinkers off and realise this is all political scam.