Omicron: What We Know About the New Coronavirus Variant

Posted on by Matt Kristoffersen

The New York Times, January 3, 2022 (with Andrew Jacobs)

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What is the Omicron variant?

First identified in Botswana and South Africa in November, the Omicron variant has surged around the world over the past few weeks, faster than any previously known form of the coronavirus. While there’s a lot that scientists have yet to understand about Omicron, the variant is already causing a rise in new cases that may push some hospital systems to the breaking point.

Scientists first recognized Omicron thanks to its distinctive combination of more than 50 mutations. Some of them were carried by earlier variants such as Alpha and Beta, and previous experiments had demonstrated that they could enable a coronavirus to spread quickly. Other mutations were known to help coronaviruses evade antibodies produced by vaccines.

Based on those mutations, along with a worrying rise in Omicron cases in South Africa, the World Health Organization designated Omicron a “variant of concern” on Nov. 26, warning that the global risks posed by it were “very high.” Since then, the variant has been identified in more than 110 countries. At the beginning of December, a California resident who returned home from South Africa was identified as the first American infected with Omicron. By Dec. 25, the Centers for Disease Control estimated that it made up 58 percent of all new infections in the United States. Omicron is quickly surging to dominance in many parts of the world, living up to the potential that scientists recognized when it was first discovered.

Yes. It is two to three times as likely to spread as Delta.

The earliest evidence for Omicron’s swift spread came from South Africa, where Omicron rapidly grew to dominance in one province after another. In other countries, researchers have been able to catch Omicron earlier in its upswing, and the picture is the same: Omicron cases are doubling every two to four days — a much faster rate than Delta.

For a closer look at how well Omicron spreads, British researchers also observed what happened in the households of 121 people who had been infected with the variant. They found that Omicron was 3.2 times as likely to cause a household infection as Delta was.

Scientists don’t yet know what makes Omicron so good at spreading, but a few clues have emerged from preliminary research. A team of British scientists found that Omicron is particularly good at infecting cells in the nose, for example. When people breathe out through their noses, they can release new viruses. Omicron is also adept at dodging antibodies produced by vaccines and previous infections.

Some symptom differences have emerged from preliminary data. For instance, one possible difference is that Omicron may be less likely than earlier variants to cause a loss of taste and smell.

Data released last week from South Africa’s largest private health insurer, for instance, suggest that South Africans with Omicron often develop a scratchy or sore throat along with nasal congestion, a dry cough and muscle pain, especially low back pain.

But these are all symptoms of Delta and of the original coronavirus, too. It’s likely that the symptoms of Omicron will resemble Delta’s more than they differ.

“There’s probably a huge amount of overlap between Omicron and the prior variants, because they are essentially doing the same thing,” said Dr. Otto O. Yang, an infectious disease physician at the University of California, Los Angeles. “If there are differences, they’re probably fairly subtle.”

While it likely provides protection against severe disease, immunity from previous infections does little to hinder infections with Omicron. The first clues that Omicron could evade immunity came from South Africa, where scientists estimate that at least 70 percent of people have had Covid-19 at some point in the pandemic. An unexpectedly large fraction of Omicron cases involved people who had previously been infected.

When Omicron surged in England, British researchers similarly found that many people infected with the new variant had already survived Covid. The researchers estimated that the risk of reinfection with Omicron was about five times that of other variants.

Similar results came from Denmark, where scientists compared more than 2,200 households where someone got infected with Omicron to some 6,300 Delta-infected households. Omicron was 3.6 times more likely to infect people with boosters sharing the same house than Delta. But it was barely more likely to infect unvaccinated people.

For a deeper understanding of this increased risk of reinfection, a number of teams of scientists have studied the antibodies produced by people who recover from Covid-19. If they mix those antibodies in a dish with other variants, the antibodies do a good job of preventing the viruses from infecting human cells.

But if they mix those antibodies with Omicron, it still manages to get inside the cells much of the time. That means that the mutations carried by Omicron are changing the shape of its surface proteins, where antibodies lock onto the coronavirus.

Several studies indicate that full vaccination plus a booster shot provides strong protection against infection with Omicron. Without a booster, however, two doses of a vaccine like Pfizer-BioNTech’s or Moderna’s provide much less protection. (Still, two doses of a vaccine do appear to protect against severe disease from Omicron.)

Scientists drew blood from fully vaccinated people and mixed their antibodies with Omicron in a petri dish loaded with human cells. Every vaccine tested so far has done a worse job at neutralizing Omicron than other variants. And antibodies from people who received two doses of the AstraZeneca or one dose of Johnson & Johnson vaccines don’t seem to do anything at all against Omicron.

But when researchers tested antibodies from people who had received boosters of Moderna or Pfizer-BioNTech vaccines, they saw a different picture. Boosted antibodies blocked many Omicron viruses from infecting cells.

Researchers found a similar response when they looked at people who had been fully vaccinated with two doses after a Covid-19 infection: Their antibodies were extremely potent against Omicron.

Real-world studies support the results of these experiments. In South Africa, researchers found that two doses of the Pfizer-BioNTech vaccine had effectiveness against Omicron infection of just 33 percent. Against other variants, they found its effectiveness is 80 percent.

In Britain, researchers found that people who had received two doses of the AstraZeneca vaccine enjoyed no protection at all from infection from Omicron six months after vaccination. Two doses of Pfizer-BioNTech had effectiveness of just 34 percent. But a Pfizer-BioNTech booster had effectiveness of 75 percent against infection.

Results like these have reinvigorated vaccination efforts and have spurred widespread booster campaigns in many countries to prepare for Omicron surges in the weeks to come.

Yes. In a large study of more than a million cases of Covid, British researchers found that people who had received booster doses were 81 percent less likely to be admitted to the hospital, compared with unvaccinated people. The risk of being admitted to a hospital for Omicron cases was 65 percent lower for those who had received two doses of a vaccine.

The protection that vaccines afford against severe disease with Omicron is leaving its mark on hospitals. As Omicron fuels a new surge of cases, the people coming to hospitals in New York City are overwhelmingly unvaccinated.

Vaccinated people are at risk of infection with Omicron because the variant can evade antibodies produced by vaccines and start multiplying in the nose and throat. But vaccines do more than just trigger the production of antibodies against coronaviruses. They also stimulate the growth of T cells that help fight a particular disease. T cells learn to recognize when other cells are infected with specific viruses and then destroy them, slowing the infection.

Scientists are starting to examine the T cells produced by Covid-19 vaccines to see how well they fare against Omicron. Preliminary studies suggest that these T cells still recognize the Omicron variant.

This preliminary evidence suggests that Omicron infections cannot get past the T-cell line of defense. By killing infected cells, T cells may make it harder for Omicron to reach deep into the airway, where it can cause serious disease.

While Omicron can cause deadly infections in some people, it is less severe overall than the Delta variant.

Scientists measure the severity of a coronavirus variant by examining how many people infected by it end up in the hospital. The Delta variant turned out to be substantially more severe than earlier variants. But the reverse is true for Omicron. A British study found that the risk of hospitalization due to Omicron is half that of Delta.

When the Omicron variant began surging in the United States, hospitals observed the same reduced risk. Despite record-breaking new cases, new hospitalizations rose at a much slower rate. Although it’s a relief that Omicron is not as severe as Delta, the new variant may still put tremendous strain on hospitals, thanks to its extraordinary contagiousness.

The lower severity of Omicron likely has several causes. Many of the people that Omicron is infecting are vaccinated or recovered from previous infections. Their immunity lowers their chances of ending up in a hospital with Covid.

But preliminary studies on animals and cells also suggests that Omicron has a different biology than other variants. Its strategy for infecting cells works well in the upper airway, but not in the lungs.

Yes. In late December, the Food and Drug Administration authorized two new antiviral pills for Covid, called Paxlovid and molnupiravir. Preliminary experiments indicate that both treatments should work against Omicron. People who are at high risk of developing severe Covid can be prescribed either drug in the first few days after a diagnosis.

Another effective treatment is a drug called sotrovimab, made by GSK and Vir. It is a monoclonal antibody that can attach to the Omicron variant and prevent it from infecting cells. Unlike Paxlovid and molnupiravir, which are packaged as pills, sotrovimab has to be given as an infusion in a hospital or clinic.

Two other widely used monoclonal antibodies, made by Regeneron and Eli Lilly, won’t work because Omicron is resistant to them. As Omicron comes to dominate the United States, the federal government is scrambling to secure more doses of sotrovimab.

Another option for people infected with Omicron is an antiviral drug called remdesivir. Like sotrovimab, it is effective at preventing severe Covid.

For people hospitalized with Omicron infections, a wide range of other treatments are also available. For example, a steroid called dexamethasone has been demonstrated to be very effective at reining in lung-damaging inflammation.

Researchers are creating mathematical models to figure out what Omicron will do in the months to come. These models, by necessity, are based on assumptions about the variant, and those assumptions may need to be altered as more evidence comes to light. But scientists can already see that Omicron is very transmissible and is adept at evading immune defenses.

Even if Omicron does turn out to be milder than other variants, it could still push hospitals to their limits. A smaller fraction of Omicron cases may require hospitalization, but if the number of Omicron cases is much bigger than in previous surges, there will still be more seriously ill patients to treat. And in the United States, those Omicron cases will stack on top of already high levels of hospitalizations driven by the Delta variant.

A team of modelers who run a project called the Covid-19 Scenario Modeling Hub issued a statement on Dec. 22 making it clear that even as they fine-tuned their projections, the writing was already on the wall.

“The best information we have at the moment indicates the threat posed by Omicron is substantial and imminent, and individuals and governments should be prepared to respond accordingly,” they warned.

The warning contains an important message: Disease projections are not carved in stone. The variables can change if more people get vaccinated and practice safety measures in public like social distancing and mask-wearing that help contain the spread. Boosters will create an even stronger wall of defense.

When the W.H.O. began to name emerging variants of the coronavirus, they turned to the Greek alphabet — Alpha, Beta, Gamma, Delta and so on — to make them easier to describe. The first “variant of concern,” Alpha, was identified in Britain in late 2020, soon followed by Beta in South Africa.

But veterans of American sorority and fraternity life might have noticed that the system has skipped the next two letters in the alphabetical order: Nu and Xi.

Officials thought Nu would be too easily confused with “new,” but the next letter, Xi, is a bit more complicated. W.H.O. officials said it was a common last name, and therefore potentially confusing. Some noted that it is also the name of China’s top leader, Xi Jinping.

A spokesman for the W.H.O. said the organization’s policy had been designed to avoid “causing offense to any cultural, social, national, regional, professional, or ethnic groups.”

Next in line? Omicron. (Here’s how it’s pronounced, and here.)

Copyright 2022 The New York Times Company. Reprinted with permission.