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How is the Omicron variant different and why are scientists so concerned?


December 1st, 2021

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Scientists around the world are racing to learn more about the newly discovered B.1.1.529 coronavirus variant, now known as Omicron, to see how it compares to other variants of concern.

The important questions – like how transmissible it is, how good it is at evading immunity from vaccines or past illness, and whether it causes more severe illness – remain to be answered.

While some scientists say it will be weeks before we get a clear picture of how Omicron will impact the pandemic, the World Health Organization (WHO) said Wednesday it expects to have more information on the transmissibility of the variant within days.

What we do know about this variant is that it contains more than 30 mutations in the spike protein, which allows it to bind to human cells and gain entry to the body – a factor that has elevated concerns for some scientists.


First, it’s important to remember that mutations to SARS-CoV-2, the virus that causes COVID-19, have been expected since the early days of the pandemic. That’s because mutations always arise as viruses spread – it’s how they ensure their own survival.

According to researchers from Yale University, SARS-CoV-2 gains access to our cells using its “corona” – a layer of protein spikes that fit into our cells like a lock and key – where it makes copies of its genomes.

But during that process, errors are inevitably introduced into the code, causing a mutation or variant.

Sometimes those mutations are harmless. But other times, like in the case of the Delta variant, the virus can change to become more transmissible or cause more severe illness.

“What we have seen with other viruses is, over time, they mutate in various ways. And one of the ways that they can mutate is to actually get a little bit less severe because there’s a bit of a fitness cost to the virus,” Dr. Susy Hota, infectious disease expert at Toronto’s University Health Network told CTV’s Your Morning Wednesday.

“If it starts to kill off its hosts a little bit too early, it just won’t replicate. And that’s the goal of a virus, is to make more copies of itself and persist over time.”

Hota notes that COVID-19 has held its advantage with previous variants because it tends to have infections that last for quite a while, giving it plenty of opportunity to spread from person to person.


The variant’s genome, in total, has around 50 mutations, including those in the spike protein, according to the British Medical Journal (BMJ). Scientists say it hasn’t directly evolved from the Delta variant and contains characteristic changes found in the Alpha, Beta, Gamma and Delta variants.

“This variant carries some changes we’ve seen previously in other variants but never altogether in one virus. It also has novel mutations that we’ve not seen before,” Lawrence Young, a virologist and professor of molecular oncology at Warwick Medical School, told the BMJ in a briefing published Monday.

Another distinguishing note is that one of Omicron’s mutations leads to “S gene target failure” – also referred to as “S gene dropout” – meaning one of several areas of the gene that are targeted by PCR testing gives a false negative.

“In one PCR test, three different genes are monitored. However, one of the S gene targets is not detected due to the mutations,” Chris Richardson, Microbiology and Immunology professor at the University of Dalhousie, said in a release issued Tuesday.

“This is called S gene dropout or S gene target failure, which is actually helpful and is diagnostic of omicron. The dropout is a marker for this variant.”

According to the World Health Organization (WHO), Omicron has been detected at faster rates than previous surges in infection using this approach.

But researchers in South Africa first sounded the alarm over the B.1.1.529 variant after finding more than 30 mutations in the spike protein – a far greater number than what we’ve seen with any other variant.

Because the spike protein is the target of antibodies that our immune system produces to fight COVID-19, a high number of mutations raises concerns that Omicron may be able to evade the antibodies produced by a previous COVID-19 infection or vaccination.

“The spike protein of the virus is really important for entry into cells, as well as targets for antibodies that help to control infections. So, it’s possible, scientifically, looking at the virus that it could be more transmissible than what we’ve seen so far,” Hota explained.

“It also could result in what we call immune evasion — in other words, your immune system may not be able to control it as well, so you may be susceptible to more reinfections or vaccines maybe a little less effective.”

But Hota says these are merely hypotheses and we should be careful not to draw any conclusions from speculation or anecdotal reports about the severity of illness or transmissibility of Omicron at this stage.

“I think we need to see it in a larger number of people to get a good sense of how it compares to what we’ve seen so far with COVID 19,” she said.