Coronavirus variants: Here’s what we know

By CNN

Published November 27, 2021 3:07 PM

CNN

By Maggie Fox, CNN

Omicron, the newest coronavirus variant, is also the quickest to be labeled a “variant of concern” by the World Health Organization and the US Centers for Disease Control and Prevention because of its seemingly fast spread in South Africa and its many troubling mutations.

Its emergence has already led to travel restrictions, high-level government meetings and promises by vaccine makers to start working on strain-specific vaccines just in case.

But it has a long way to go to take over from Delta, the variant that dominates all over the world. And the long list of variants that at first frightened the world before falling off the map can be a reminder that viruses are unpredictable.

Here’s a look at the named coronavirus variants.

Variants of concern

WHO designates coronavirus variants as either variants of concern — meaning they look dangerous enough to bear close scrutiny and continual updates — or as variants of interest, or variants under monitoring. Only five currently meet the definition for variants of concern: Alpha, Beta, Gamma, Delta and Omicron.

Omicron

The first sample of the Omicron or B.1.1.529 lineage was taken November 9, according to WHO. It got noticed because of a surge of cases in South Africa.

“This new variant, B.1.1.529 seems to spread very quick!” Tulio de Oliveira, director of South Africa’s Center for Epidemic Response & Innovation, and a genetics researcher at Stellenbosch University, said on Twitter.

Also, genetic sequencing showed it carried a large number of troubling mutations on the spike protein — the knoblike structure on the surface of the virus that it uses to grapple onto the cells it infects.

Some of those mutations were already recognized from other variants and were known to make them more dangerous, including one called E484A — a slighly altered version of a mutation called E484K that may make the virus less recognizable to some antibodies — immune system proteins that are a frontline defense against infection and that form the basis of monoclonal antibody treatments.

It also carries a mutation called N501Y, which gave both Alpha and Gamma their increased transmissibility. Just last week, Scott Weaver of the University of Texas Medical Branch and colleagues reported in the journal Nature that this particular mutation made the virus better at replicating in the upper airway — think in the nose and throat — and likely makes it more likely to spread when people breathe, sneeze and cough.

Like Delta, Omicron also carries a mutation called D614G, which appears to help the virus better attach to the cells it infects.

“Early evidence suggests that fully vaccinated people who become infected with the Omicron variant can spread the virus to others. All FDA-approved or authorized vaccines are expected to be effective against severe illness, hospitalizations, and deaths,” the CDC says on its website.

“The number of mutations per se does not mean that the new variant will cause any problems; although it may make it more likely to look different to the immune system,” Dr. Peter English, former chair of the British Medical Association’s Public Health Medicine Committee, said in a statement.

What worries scientists is the number of mutations affecting the spike protein. That’s because most of the leading vaccines target the spike protein. Vaccines made by Pfizer/BioNTech, Moderna, Johnson & Johnson, AstraZeneca and other companies all use just small pieces or genetic sequences of the virus and not whole virus, and all of them use bits of the spike protein to elicit immunity. So a change in the spike protein that made it less recognizable to immune system proteins and cells stimulated by a vaccine would be a problem.

So far, there’s no evidence this has happened but there is no way of knowing by looking at the mutations alone. Researchers will have to wait and see if more breakthrough infections are caused by Omicron than by other variants.

The other fear is that the mutations might help make the virus less susceptible to monoclonal antibody treatments. However, WHO says it’s unlikely these mutations would affect other Covid-19 treatments, including antiviral drugs in development and the steroid dexamethasone.

Omicron has been detected in multiple countries, including South Africa and Botswana, and among travelers to the US, Belgium, the Netherlands, Australia, Canada, the UK, Italy, Israel and Austria, according to the GISAID database and local officials. The first US case was in a fully vaccinated traveler from South Africa who arrived in California on November 22 and who tested positive after experiencing mild symptoms.

It takes an extra layer of testing above and beyond standard tests to detect infection to tell which variant of coronavirus has infected someone. Genetic sequencing must be conducted and that takes longer than a quick antigen test or a PCR test.

It’s also too soon to tell whether Omicron causes more severe disease, although one doctor who treated some patients in South Africa told Reuters her patients had only mild symptoms. “The most predominant clinical complaint is severe fatigue for one or two days, with then the headache and the body aches and pain,” Dr. Angelique Coetzee, a private practitioner and chair of the South African Medical Association, said.

But doctors agree that vaccination is likely to provide a great deal of protection against Omicron and urge people to get vaccinated if they are not already. Of note: Just under 24% of South Africa’s total population is vaccinated. Just 35% of adult South Africans are fully vaccinated, the country’s president, Cyril Ramaphosa, said Sunday. And South Africa has many people infected with HIV — which suppresses the immune system — who are currently unable to get treatment, and who may be more susceptible to infection.

Those factors may influence the rise of the variant in South Africa as opposed to countries where more people are vaccinated and fewer have immunocompromising conditions.

Physical barriers also will work against any mutant virus. These include masks, handwashing, physical distancing and good ventilation. “Much uncertain but we know what works vs. CoV-19: – improving indoor ventilation – quality masks/respirators – avoid indoor crowds – distancing – test, isolate, quarantine – vax + booster now for Delta,” Dr. Jeffrey Duchin, health officer for Seattle & King County, tweeted Sunday.

While experts say they’re watching closely, several have said they are not especially worried about Omicron just yet.

“I don’t think we should panic,” Robert Garry, a professor of microbiology and immunology at Tulane University School of Medicine, told CNN.

“The sky is not falling,” Dr. Peter Hotez, dean of the School of Tropical Medicine at Baylor, told CNN. “We’ve not seen any evidence that Omicron causes any more severe disease than any other variants.”

Delta

The Delta variant of coronavirus is the dominant lineage in the US and much of the world. The Delta variant accounts for 99.9% of cases in the US, according to the US Centers for Disease Control and Prevention.

Also known as B.1.617.2, it is clearly more transmissible than other variants, but it is still unclear if it causes more severe disease.

It quickly took over from the B.1.1.7, or Alpha, variant in most countries.

Delta also carries a cluster of mutations on the spike protein. It can also evade the immune system, which may mean people who have been infected once with an older variant may be more likely to catch it again. It also eludes the effects of a monoclonal antibody treatment called bamlanivimab, made by Eli Lilly and Company, but is vulnerable to the protection offered by other monoclonal antibody treatments.

Alpha

First identified as a variant of concern last December, the B.1.1.7 or Alpha variant of coronavirus was worrying public health officials last spring. It swept across England quickly and then out into the world, quickly becoming the dominant lineage in the United States. It has now been demoted to “Variant Being Monitored” by the CDC because of its low impact in the US.

It was shown to be at least 50% more transmissible than older lineages. It carries 23 mutations, including one called N501Y that increases transmission.

It’s fully susceptible to monoclonal antibody treatments and vaccines.

Beta

First seen in South Africa, the B.1.351 or Beta variant has both an E484K mutation that is linked with immune escape and the N501Y mutation suspected of helping make many other variants more contagious. It has been shown to be 50% more transmissible than older strains and evades Lilly’s dual monoclonal antibody treatment, but not others.

Blood tests and real-life use both suggest it can infect people who have recovered from coronavirus and also people who have been vaccinated against Covid-19.

Vaccine makers trying to get out ahead of the new variants by developing booster shots had focused on B.1.351, as it’s the variant scientists most fear could elude vaccine protection. But partial escape doesn’t mean full escape, and vaccines are still expected to protect people to some degree.

It was overtaken by Delta in South Africa and have never gained much of a foothold in the US, despite the worry it caused, and is now designated a Variant Being Monitored by the CDC.

Gamma

The P.1 or Gamma variant that swept Brazil also never gained much ground elsewhere and is also now a CDC Variant Being Monitored.

Gamma carries both E484K and N501Y mutations, with more than 30 others. It has been demonstrated to evade the effects of Lilly’s monoclonal antibody treatment but not one made by Regeneron. Blood tests show it might partly escape both natural and vaccine-elicited immune responses.

WHO Variants of Interest

Lambda: Lambda or C.37 was designated a WHO Variant of Interest in June. The CDC doesn’t mention it.

Mu: Mu or B.1.621 caused a flurry of fear when it was declared a WHO Variant of Interest in August, but it soon fizzled out. It’s now designated Variant Being Monitored by the CDC.

Variants Being Monitored by CDC

All of the following variants are listed by the CDC as Variants Being Monitored.

Epsilon: The B.1.427 and B.1.429 variants are usually lumped together and known as Epsilon. First seen in California, this one has the same L452R mutation carried by Delta, but not some of its other mutations and has not taken off in the way Delta has.

Iota: First seen in New York last November, the B.1.526 or Iota variant spread at first, accounting for as many as 9% of samples last April, but it’s now virtually disappeared. It has what’s called a 484 mutation that should help the virus attach more easily to the cells it infects and makes the virus less recognizable to the immune system.

Eta: First seen in the UK and Nigeria, Eta, also known as B.1.525, carries an E484K mutation. It has also virtually disappeared.

Zeta: Circulating in Brazil since last year, this variant, also known as P.2, also carries the E484K mutation and has not been found widely globally. It’s almost disappeared in the US, according to the CDC.

There are no variants designated Nu or Xi. WHO decided “Nu” sounded too much like the English word “new” and Xi is a common last name.

This story has been corrected to show that Omicron carries a mutation called E484A, which is similar to but not exactly the same as E484K.

CNN’s John Bonifield contributed to this report.

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