The Omicron variant

Omicron has an unusually high number of mutations. There are more than 50 total and about 35 in the spike protein, which is a critical part of the virus.

Dr. David Beckham is a virologist and a specialist in infectious diseases. He does research at UCHealth University of Colorado Hospital and has a laboratory on the University of Colorado Anschutz Medical Campus. Right now, he and his colleagues are researching the tricks that variants use to copy and spread.

“The spike protein is important both for the virus’ ability to spread and our body’s ability to fight the virus,” Beckham said. “There’s a mutation in the spike protein that primes the virus to cause infections more easily. The delta variant has one mutation in this region and omicron has three mutations.”

According to the CDC, the omicron variant spreads more easily than the original virus that causes COVID-19 and the delta variant. The CDC expects that anyone with omicron infection can spread the virus to others, even if they are vaccinated or don’t have symptoms.

Yet, a CDC report published in January 2022 says that ICU admittance and death have been “lower than during previous pandemic peaks” even though omicron has caused a record number of cases.

As of mid-March 2022, about 1,000 Americans were dying each day from COVID-19, according to the CDC’s COVID Data Tracker.

Although that number is much lower than the daily death toll of about 2,300 earlier in the year, researchers wonder why so many Americans are still dying from omicron even though 60% of the population is fully vaccinated.

A CDC analysis found that unvaccinated Americans, most of them in their 30s and 40s with no underlying conditions, made up at least 75% of the deaths. The CDC found that unvaccinated people were 20 times more likely to die of the virus than fully vaccinated people.

Early reports from South Africa, one of the first countries affected by omicron, showed that most cases had mild symptoms such as a sore throat and upper respiratory congestion, and often with severe fatigue (feeling very tired).

Unlike earlier variants, omicron did not seem to cause a loss of taste or smell.

According to the CDC, many factors can make a difference in how severe omicron symptoms are, and if the symptoms happen. These factors include vaccination status, having had an infection before, age and other health conditions.

Getting fully vaccinated and keeping up to date with COVID-19 booster shots, offers the highest degree of protection against omicron infection.

Because of omicron’s high number of mutations, it may be more resistant than earlier variants were to the antibodies created by vaccines.

In December 2021, early data from South Africa showed that the two-dose Pfizer vaccine was only 33% effective at preventing infection but was 70% effective at preventing hospitalization.

In January 2022, the CDC reported that a “booster” dose of the Pfizer vaccine was “highly effective” at restoring some of the lost protection and lowering the chance of visits to urgent care facilities and hospitalization.

The agency warned that breakthrough infections are likely to happen in vaccinated people. But it also reported that some, but not all, monoclonal antibody treatments are effective against omicron.

In December 2021, researchers discovered that the original omicron variant had split into two subvariants: BA.1 and BA.2.

The two subvariants arose around the same time and come from the same ancestor strain. They have many mutations in common, but around 20 mutations differ between the two subvariants. The differences between the subvariants can be seen in the spike protein of the virus.

Some researchers started calling BA.2 a “stealth” variant because they believed it might be more difficult to track than the original omicron variant.

Between Jan. 30 and Feb. 5, BA.2 cases only made up about 1% of the new coronavirus cases in the United States. But BA.2 cases increased to about 7% at the end of February and then doubled to about 14% by the first week in March.

By mid-March 2022, the CDC estimated that BA.2 caused 23.1% of all cases in the United States while BA.1 caused 10.8% of cases. Another subvariant (BA.1.1) was the cause of the remaining 66.1% of cases.

According to the WHO, BA.2 is about 30% more infectious than BA.1.

It has a distinct genetic sequence, including some amino acid differences in the spike protein and other proteins which may make it more transmissible than the original omicron.

Some data shows that BA.2 may be more likely than BA.1 to spread between people who live in the same home.

BA.2’s increased transmissibility is why it is able to overtake and replace BA.1, not because it can avoid the body’s immune defenses. BA.2 is only slightly better than BA.1 at staying away from the antibodies created by vaccines, natural infection or both.

The evidence is mixed. Some research shows that it’s not associated with an increased risk of serious illness or hospitalization compared to BA.1.

For example, the WHO looked at clinical data from countries with high rates of immunity from vaccination or natural infection, such as South Africa, the United Kingdom and Denmark. The data shows no significant difference in the severity of disease caused by the 2 subvariants.

There’s evidence that an earlier infection with BA.1 gives “strong protection” against reinfection with BA.2, at least in the short term, according to the WHO. That’s good news for the millions of people worldwide who were infected during the first omicron surge between November 2021 and February 2022.

However, research shows that people with no immunity to SARS-CoV-2 may have an increased risk of severe disease. In Japan, animal studies show that BA.2 is more likely than BA.1 to infect and damage cells deep inside the lungs.

Hong Kong may be a textbook example of what can happen to countries with low vaccination rates — especially among elderly residents — where strict quarantine and other measures have kept COVID-19 cases extremely low.

After two years of “zero tolerance” COVID-19 policies, Hong Kong suddenly found itself overwhelmed by omicron BA.2. By mid-March 2022, the Chinese territory with a population of 7.5 million had seen more than 700,000 cases and more than 4,000 deaths. The outbreak gave Hong Kong the unfortunate record of having the world’s highest COVID-19 death rate.

After weeks of having coronavirus numbers go down, many European countries also experienced an increase in BA.2 cases and hospitalizations. In just one week, the highly vaccinated United Kingdom saw a 48% increase in cases and a 17% increase in hospitalizations.

During previous outbreaks, hospitalizations lagged behind cases in the U.K. Now they seem to be increasing together, which hasn’t happened before.

In an interview with CNN, Dr. Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases, said this double whammy is likely caused by three factors:

• The BA.2 variant itself, which is more transmissible than the original omicron.
• The opening of society, with people spending more time together indoors without wearing masks.
• Decreasing immunity from vaccination or being infected before.

No one expects BA.2 to affect the United States as drastically as it has Hong Kong. But some experts believe that a “stealth” variant surge may happen in the United States, like it already has started to do in Europe.

By mid-March 2022, BA.2 was the cause of 68.6% of cases in the United Kingdom and more than 50% of cases in several other European countries. Daily cases were rising in more than half of the countries in the European Union.

Some experts believe that a 50% rate can be seen as a “tipping point.” A tipping point is the rate where a subvariant (such as BA.2) starts to cause more widespread, serious disease.

Up to 28 million American seniors are at high risk of severe COVID-19 illness. That’s because they are either unvaccinated or partially vaccinated, or that at least five months have gone by since they got their second vaccine or booster dose.

More than two years into the pandemic, an estimated 1/3 of Americans ages 65 and older still haven’t gotten the recommended booster dose. That means an estimated 15 million older adults have decided not to get the extra protection that could save their lives.

The effectiveness of two-dose vaccines goes down quickly over time. If at least six months have gone by since the second dose, vaccines are only 10% effective against omicron infection, 35% against hospitalization, and 70% against death, according to the UK’s Health Security Agency.

A booster shot restores protection against symptomatic disease from both variants, to 69% for BA.1 and 74% for BA.2.

But how much protection the booster gives also goes down over time. After four to six months, among all adults, boosters are only 40% to 50% protective against omicron infections, and 75% to 85% against hospitalizations.

CDC data shows that vaccine effectiveness against emergency room or urgent care visits drops from 78% right after getting a booster shot to 66% after 4 to 5 months.

It’s not clear how long natural COVID-19 infections (such as those caused by BA.1) protect against BA.2.

Pharmaceutical companies hope to one day make a vaccine that’s effective against all variants of concern—including omicron—that would be given once a year.

Meanwhile, the SARS-CoV2 virus keeps doing what it does best: mutate and evolve. In several Europe countries, a new variant has been found that combines parts of the delta and omicron variants. Called “deltacron,” it has not infected enough people yet to be designated as a variant of concern.