Scientists have detected cases of a new variant of SARS-CoV-2, which is the virus that causes COVID-19, in a number of countries. Omicron (B.1.1.529) has an unprecedentedly large number of mutations in the part of its genome that encodes a key section of its spike protein, which the virus uses to infect host cells. This suggests that Omicron may be able to evade some of the immune protection afforded by vaccines, many of which are based on the original spike protein, and past infections.

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Travelers looking at a flight notice board displaying canceled flights at OR Tambo International Airport in Johannesburg, South Africa, on November 27, 2021. PHILL MAGAKOE/Getty Images

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On November 16, 2021, there were 136 daily recorded cases of COVID-19 in South Africa. By November 25, 2021, that number had risen to over 1,200.

More than 80% of these cases were in the densely populated province of Gauteng, which includes Johannesburg and Pretoria.

Researchers estimated that the R-value, which is the average number of new cases caused by each infection, was 1.47 for South Africa as a whole.

If R is more than 1, an outbreak will grow exponentially. In Gauteng province, R was 1.93.

Scientists at the Centre for Epidemic Response and Innovation (CERI) in Stellenbosch, South Africa, believe that a new variant of the virus known as Omicron (B.1.1.529) is responsible for these worrying figures.

There have been three previous peaks of infection in South Africa during the course of the pandemic, with the third due to the Delta variant. The latest surge coincides with the first detection of Omicron by scientists.

Scientists have sequenced around 100 confirmed cases of Omicron infection in South Africa. Most of the cases have been in Gauteng.

The new variant is also present in Botswana, Hong Kong, Europe, Canada, Israel, Japan, the United States, and elsewhere.

“The main message today is that you have to know the enemy in order to fight,” said Prof. Tulio de Oliveira, Ph.D., the director of CERI, at a virtual news briefing on November 25, 2021.

He went on to say that the variant’s genome contains “a very unusual constellation of mutations.” Many of these are confirmed or predicted to either help the virus evade the immune system or increase its transmissibility.

He said that there are around 50 mutations across the entire genome of the virus and more than 30 in the part that codes for its spike. This is the protein that allows the virus to invade its host cells.

A particular part of the spike called the receptor-binding domain (RBD) binds to a receptor called ACE2 in the membrane of human cells.

Prof. Oliveira said that there is an exceptionally large number of changes within the RBD of the new variant.

Antibodies that bind to the RBD can prevent the virus from infecting cells. So, the RBD is a crucial target for COVID-19 vaccines, which provoke the immune system to make antibodies against particular protein sequences.

The Beta variant has three mutations in the RBD part of its genome, and the Delta variant has two, said Prof. Oliveira. However, according to the European Centre for Disease Prevention and Control, Omicron has 15 mutations there.

The concern among scientists is that the changes due to the mutations may prevent antibodies, which are generated through vaccination or an encounter with an older variant of the virus during an infection, from neutralizing the virus.

Dr. Richard Lessells, Ph.D., an infectious disease specialist based at the Africa Centre for Health and Population Studies, told the news briefing that Omicron’s genome has several mutations associated with resistance to neutralizing antibodies.

These include not only antibodies generated through vaccination or natural infection but also therapeutic monoclonal antibodies.

Dr. Lessells said that the Omicron genome also has a cluster of mutations associated with more efficient entry into host cells and enhanced transmissibility.

In addition, it has a mutation associated with resistance to the body’s first line of defense against newly encountered pathogens, known as the innate immune system.

“All these things are what gives us some concern that this variant might have not just enhanced transmissibility, to spread more efficiently, but might also be able to get around parts of the immune system and the protection that we have in our immune system,” he said.

However, he emphasized that the combined effect of the mutations was unknown. There is even a possibility that Omicron may cause more mild symptoms than previous variants.

“We will only know for real by doing the studies in the laboratory […]. [T]hat work is already ongoing,” he added.

“We can make some predictions about the impact of the mutations, but the full significance remains uncertain, and the vaccines remain the critical tool to protect us.”

– Prof. Tulio de Oliveira, Ph.D.

On November 26, 2021, the World Health Organization (WHO) designated B.1.1.529 a variant of concern and gave it the name Omicron (the 15th letter of the Greek alphabet).

Over the next few days, several countries around the world imposed additional restrictions on travelers returning from southern African countries.

Dr. Daniel Griffin, Ph.D., a virologist at Columbia University in New York City, told Medical News Today that the number of changes in the Omicron variant is very high compared with previous variants of SARS-CoV-2.

He speculates that the new variant may have evolved in an unvaccinated individual with a compromised immune system. This would have given the virus an unusually long time to develop adaptations to the human immune system.

“It is really not surprising that this variant is now being described, as we continue to have so many parts of the world with low vaccination coverage, giving the virus millions of opportunities to replicate and select for more fit variants,” said Dr. Griffin.

“We currently have limited data on this virus, but we can look at some of the spike protein changes, and, based on what we know about this virus, it is very appropriate to be concerned about immune evasion and potentials for this variant to replace the Delta variant,” he added.

Over the next few weeks, he said, the critical questions for scientists to answer will be:

  • How well will the different vaccines work against this variant?
  • What will its impact be on rates of reinfection?
  • Has Omicron already spread widely?
  • What is the relative fitness of Omicron compared with the Delta variant?

Sharon Peacock, the director of the COVID-19 Genomics UK Consortium and a professor of public health and microbiology at the University of Cambridge in the United Kingdom, told the Science Media Centre in London that several changes in Omicron are consistent with enhanced transmissibility.

“Mutations are also present that have been associated in other variants with immune evasion,” she explained.

“But the significance of many of the mutations detected, and the combination of these mutations, is not known.”

She emphasized that there are currently no data on how much protection the current vaccines will provide against Omicron.

However, a recent small-scale study, which is yet to be peer-reviewed, adds some new information about vaccine effectiveness.

A series of small experiments with the Pfizer-BioNTech COVID-19 vaccine has found a drop in protection against the new Omicron variant.

The researchers compared the immune responses of six people who had received the vaccine and six who first developed COVID-19 before receiving the vaccination.

They found that, overall, there was a 41-fold reduction in neutralization against Omicron. However, five of the participants, all of whom had developed COVID-19, maintained “relatively high neutralization [levels] with Omicron.”

The study suggests that people who have had COVID-19 before this vaccine are likely to be better protected. The researchers expect this to be similar for people who have received a booster dose.

Although the findings are worrisome to an extent, scientists point out that looking solely at antibodies paints an incomplete picture of the body’s immune response to SARS-CoV-2, the virus that causes COVID-19 — especially against hospitalization or death.

However, as Prof. Peacock concludes, “In the meantime, vaccination should continue to proceed at pace.”