Corona virus omicron variant contains many mutations in the spike protein, which facilitate the penetration of the virus into the cells
By: Soresh Kochipodi, Professor of Infectious Diseases and Epidemics, Penn State
A new variant of the corona virus named Omicron (B.1.1.529) was reported by researchers in South Africa on November 24, 2021, and was declared a “worrying variant” by the World Health Organization two days later. Omicron is unusual in that it is without a doubt the version that has undergone the heaviest mutation to date of SARS-CoV-2, the virus that causes COVID-19.
The omicron lorient has 50 mutations in total, 32 of them on the spike protein alone. The spike protein – which forms a kind of protruding “handles” on the outside of the SARS-CoV-2 virus – helps the virus to attach to cells so that it can enter and reproduce. It is also the protein that most vaccines available today use to cause the body to produce antibodies that will neutralize the virus if a loop enters. By comparison, the Delta Lorient has nine mutations. The greater number of mutants in the omicron variant may cause it to be more contagious and / or better in evading the immune system – the most worrying feature.
I am a virologist researching epidemics in the making in animals, to know how viruses emerge and an epidemic develops. My research group examined various aspects of the COVID-19 virus, including its leakage into animals.
Why new versions of SARS-CoV-2 Continue to perform?
While the unusually high number of mutations in the omicron variant is surprising, the appearance of another variant of SARS-CoV-2 is not unexpected.
Through natural selection, random mutations accumulate in each virus. This process is accelerated in RNA viruses, including SARS-CoV-2. If and when a group of mutations provides a survival advantage to a version over its predecessors, it will compete with all other existing variants of the virus.
Does the greater number of mutations in the omicron variant mean that it is more dangerous and transferable than the delta? We just do not know yet. The conditions that led to the emergence of the variation are still unclear, but what is clear is that the number and shape of the mutations in the omicron are unusual.
One possible explanation for how viral variants with multiple mutations are formed is through prolonged infection in a patient whose immune system is suppressed – a condition that can lead to rapid viral evolution. Researchers have suggested that some early SARS-CoV-2 variants, such as the alpha variant, may have been created this way. However, the unusual structure and the many mutations in the Omicron variant make it very different from all other SARS-CoV-2 strains, which raises questions about how it was formed.
Another possible source of variants could be animals infected with the human virus. The virus that causes COVID-19 can infect several species of animals, including mink, tigers, lions, cats and dogs. In a peer-reviewed study, an international team I lead recently reported widespread coronavirus infection in captive white-tailed deer in the U.S.
How the Delta version has become dominant around the world
The Delta variant infects 40% to 60% more than the alpha variant and almost twice as much as the original SARS-CoV-2 virus first identified in China. The increased transmission capacity of the Delta version is the main reason why researchers believe it has been able to compete on other versions to become the dominant strain.
A key factor in viral fitness is the rate of replication of the virus – or how fast a virus can make more copies of itself. The Delta variant replicates faster than previous versions of SARS-CoV-2, and a peer-reviewed study has estimated that it produces 1,000 times more virus particles than its predecessors.
In addition, people infected with the Delta variant are producing and spreading more viruses, which is another potential mechanism for its increased ability to spread. Studies suggest that a possible explanation for the increased ability of the delta variant to replicate is that mutations in the spike protein have led to more efficient binding of the spike protein to its host, using the ACE-2 receptor.
The Delta variant also acquired mutations that allowed it to evade neutralizing antibodies that play a critical role in protecting the body from invasive virus. This may explain why, as many reports have shown, COVID-19 vaccines were slightly less effective against the Delta variant. This combination of high transferability and immune evasion can help explain how the Delta variant has become 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 versions. One particular mutation in the Delta variant spike protein – the P681R mutation – is considered a key contributor to improving its ability to enter cells and cause more serious disease.
Will omicron replace Delta?
It is too early to say whether the omicron variant is more suitable than delta or it will become dominant. Omicron shares some mutations with the delta variant but there are also other quite different mutations. But one of the reasons we in the research community are particularly concerned is that the omicron lorient has ten mutations in the receptor linker – the part of the spike protein that interacts with the ACE-2 receptor and mediates cell entry – compared to only two in the delta version.
Suppose the combination of all the mutations in the omicron causes it to be more or better transmitted in immune evasion than in delta. In that case, we could see the spread of this version around the world. However, it is also possible that the unusually high number of mutations may damage the virus and make it unstable.
It’s very likely that Omicron is not the end of the game and more SARS-CoV-2 versions will appear. As SARS-CoV-2 continues to spread among humans, natural selection and adaptation will result in more variants that may be more contagious than Delta.
We know from flu viruses that the process of viral adaptation never ends. Lower vaccine rates in many countries mean that there are still many virus-susceptible hosts, and that it will continue to circulate and mutate as long as it can spread. The emergence of the omicron variant is another reminder of the urgency to vaccinate to stop the continued spread and development of SARS-CoV-2.
For an article in The Conversation
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