Omicron variant of COVID — some initial facts about vaccines

Just when we thought we might be seeing the light at the end of the tunnel for the COVID-19 pandemic, a new Omicron variant was discovered in Africa. Although many countries shut down travel from Africa, it’s probably too late — it probably was being spread before the Omicron variant was found.

Like when the Delta variant was first observed, there was a lot of confusion about how serious it was going to be and whether vaccines would be effective. It caused a surge in cases and deaths worldwide over the summer.

Although it’s very early, I think there is enough information to, at a minimum, understand what may be upcoming. Of course, as with everything about this pandemic, stay tuned because what we know today may be superseded by what we discover tomorrow.

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Photo by Fusion Medical Animation on Unsplash

What is the Omicron variant?

On 25 November 2021, the World Health Organization had detected a new variant with a high level of mutations that could make it more easily transmissible. On 25 November 2021, they labeled it a “variant of concern” and gave it the Greek letter designation of “omicron.” The variant is also known as “B.1.1.529” by the CDC.

As of 1 December 2021, the new variant has been found in 23 countries (and I’m sure as soon as I push publish, it’ll be in a few more), not all directly linked to South Africa.

On 23 November 2021, scientists in South Africa made public data on the variant. Noticing the distinct sequences on the spike protein, a virologist at Imperial College London, Tom Peacock, raised alarms about the “really awful Spike mutation profile.”

Right now, there is too little research into the variant, so what we don’t know vastly overwhelms what we do know. Both the CDC and WHO announcements on the Omicron variant were very light in detail. So right now there is too little information to conclude.

However, it is probably the most problematic variant since Delta appeared last spring.

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What do we know about the new variant?

The variant’s genetic profile is unique from other variants (such as Delta), which means it represents a new lineage of the virus. The most important distinction of the Omicron variant compared to previous variants is that there are a greater number of mutations. There are more than 30 mutations in the spike protein, which is the part of the virus that binds to human cells, allowing it to infect those cells.

Other variants including Alpha, Beta, Gamma, and Delta have around eight to 10 mutations in the spike protein, and that’s largely what’s given them their advantageous phenotype. Omicron comes with 30 mutations, which could make it more dangerous.

Although we don’t have enough information to be certain, it is possible that the Omicron variant could be more transmissible. And it could be better at evading the body’s immune defense, making current vaccines less effective in preventing in. The WHO stated that preliminary evidence appeared to show an “increased risk of reinfection” compared to the Delta variant.

Also, early data seems to show that it might be spreading 3X faster than was observed with the Delta variant.

Scientists have noted that some of the mutations could make it more elusive to the antibodies produced through COVID-19 vaccines or a previous infection. A drop in antibody neutralization will cause significant consternation about the danger of this new variant. This could make the variant not only more transmissible but also better at evading the immune system.

Yes, that is scary. But again, this is preliminary information, and epidemiologists need more time to give us better information about this variant.

woman applying hand sanitizer omicron variant
Photo by Anna Shvets on Pexels.com

What’s being done to halt the spread of omicron?

As opposed to what happened with previous variants, many countries began imposing restrictions on flights to and from South Africa and its closest neighbors. For example, Israel closed its borders to “foreigners from all countries.” Australia, Britain, Japan, Thailand, the USA, and the EU have introduced travel bans or quarantine rules for air passengers.

The U.S. restrictions will apply to travelers from South Africa, Botswana, Zimbabwe, Namibia, Lesotho, Eswatini, Mozambique, and Malawi. They do not apply to American citizens and lawful permanent residents. President Biden, in a statement, said the move is “a precautionary measure,” and urged Americans to get vaccinated and get booster shots.

I worry about travel bans because they seem to be panic moves rather than scientifically sound public health measures. I think, in our interconnected world, unless you completely stop all travel, eventually, a new variant is going to get around borders. Even the exceptions, for citizens and permanent residents, may allow the disease to get across borders before it can be stopped.

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Photo by Nataliya Vaitkevich on Pexels.com

Let’s talk about vaccines and the Omicron variant

I need to remind you that everything I am about to write is based on speculation — educated speculation, fact-based speculation, and scientific speculation, but we are lacking evidence to support anything I write.

  1. Even if our current vaccines have lowered effectiveness against the Omicron variant, it will not completely eliminate the protections that the vaccines provide. It is possible that the vaccines will reduce hospitalizations and deaths from the new variant. It is highly unlikely that the variant will completely escaped antibody neutralization, so there will be some positive effect of vaccines against this variant.
  2. Researchers in South Africa have noticed a higher level of breakthrough infections of the new variant in vaccinated individuals. However, the sample size is small and it has not been published anywhere. So, this could be at the level of good science or just anecdotes.
  3. Vaccine manufacturers have whole teams of scientists who watch for new variants and quickly test their vaccines against it. One of the great things about the mRNA and adenovirus vaccines being used against COVID-19, they can be quickly adjusted to any new variant. If this variant is dangerous, then expect that a new set of booster vaccines will be necessary. And this may be our way of life for a long time.

What this tells me is that you need to get fully vaccinated to lower the risk of contracting the new variant and to improve your outcomes if you do catch it. Also, this is more evidence that we should be careful with large gatherings, and you should always wear a mask.

One other important point I’d like to make. Viruses can only mutate if they reproduce and infect new people. South Africa has a vaccination rate lower than 25%, so the virus remains endemic throughout southern Africa. And as long as the virus circulates, new, and likely more dangerous variants can arise. We need to increase vaccine uptake in all parts of the world, or we’re going to be dealing with more and more variants until the WHO runs out of Greek letters.

Update on vaccines and Omicron

Dr. Anthony Fauci, one of the heroes of our battle against this persistent pandemic, has stated that vaccination with a booster dose of COVID vaccine is expected to offer “some degree of cross-protection” against the Omicron variant. That’s not overwhelming endorsement, but remember the endpoints that we want to see from vaccines is reduced risk of hospitalization and death.

Fauci also said:

Although we haven’t proven it yet, there’s every reason to believe that if you get vaccinated and boosted that you would have at least some degree of cross protection, very likely against severe disease, even against the Omicron variant.

I like Dr. Fauci’s confidence — the one way we stop the spread of the Omicron variant is by vaccination. However, everything is measured here, because we don’t know enough to say with certainty about how the vaccines will deal with Omicron.

woman in blue shirt sitting beside man in blue shirt
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What about COVID-19 treatments?

Again, like with vaccines, what we don’t know far outweighs what we do know about COVID-19 treatments against the Omicron variant.

So, here are more speculations:

  1. The variant could have an impact on how monoclonal antibody treatments work.
  2. The anti-viral treatments that are targeted against COVID-19, Merck’s molnupiravir, (Lagevrio) and the Pfizer’s PF-07321332 (Paxlovid) probably would be unaffected by this mutation. However, we don’t have enough information to determine what the effectiveness would be.

What does this new variant mean to us?

I know, we are all sick and tired of nearly two years of bad news about this pandemic. However, the virus, being without a brain or emotions, couldn’t care less about how exhausted we are.

We don’t know how serious this new variant is. We don’t know how effective our vaccines are. And we don’t know how fast it will transverse the world.

But we can only do what is within our power. Make sure you get vaccinated because it does appear that it lowers the risk of catching the disease and improves outcomes. But even that we can’t be sure.

But the worst news is that the Omicron variant couldn’t have worse timing — it’s showing up just when we’re opening up our doors to friends and families. My thinking is that any relative or friend who refuses to be vaccinated is quickly uninvited. You cannot take that risk.

And when you’re out in public, mask up. I do, and I will for the foreseeable future. I don’t think this is the last of the variants that are going to scare us.


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The Original Skeptical Raptor
Chief Executive Officer at SkepticalRaptor
Lifetime lover of science, especially biomedical research. Spent years in academics, business development, research, and traveling the world shilling for Big Pharma. I love sports, mostly college basketball and football, hockey, and baseball. I enjoy great food and intelligent conversation. And a delicious morning coffee!