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Omicron causes and effects

Where did the coronavirus variant come from, and what does it mean for the pandemic?


Sandile Cele, a researcher at the Africa Health Research Institute in Durban, South Africa, works on the omicron variant of the coronavirus. Associated Press/Photo by Jerome Delay

Omicron causes and effects

The omicron variant of the coronavirus went from its first appearance in South Africa in mid-November to the strain responsible for at least 73 percent of all U.S. COVID-19 cases this week. The United States’ first omicron-related death was reported on Monday in Harris County, Texas. Omicron is the fifth variant to make the World Health Organization’s list of variants of concern. The rapid, global spread of omicron has raised numerous questions about whether it is possible to prevent variants and what they mean for the future of the pandemic.

Where did omicron come from? It might have originated in South Africa, where it was first detected in Pretoria, one of the country’s three capital cities. Dr. Peter Kasson, a virologist and biophysicist at the University of Virginia, entertains the possibility due to South Africa’s low vaccination rate (26 percent). The more a virus spreads and infects, the more opportunities it has to replicate, resulting in more mutations. “The best way to prevent variants is to give the virus fewer people it can infect,” Kasson said. He also pointed out that omicron cases that pre-date the South African report have now been identified, making it more difficult to pinpoint the variant’s origin. Omicron was already in the Netherlands a week before South Africa reported its first case, according to Dutch health authorities.

What causes the virus to mutate? Mutations, which occur when a virus copies its genetic material into a host cell, are inevitable. RNA-based viruses such the one that causes COVID-19, are made up of the nucleotide bases adenine (A), guanine (G), cytosine (C), and uracil (U). During the copying process, error is introduced when the wrong base is replicated, resulting in mutation. Base deletions and additions also cause mutations. Mutations can do one of three things: hurt the virus, help the virus, or nothing. “Helpful” mutations can make the virus more contagious or virulent. Dr. Laura Kramer, retired director of the Arbovirus Laboratory at New York State Department of Health’s Wadsworth Center, explained that a mutation’s effect depends on where the mutation occurs on the genome, and how important that spot is to the virus’ potency or transmissibility.

Omicron has more than 30 mutations in the spike protein, the region of the coronavirus that interacts with human cells. That’s more spike protein mutations than in any other known COVID-19 variant, even delta.

Is omicron more dangerous than other variants? It is more contagious. “[Omicron] is clearly being transmitted better, there’s no question about that,” said Kramer. The World Health Organization received its first report about omicron on Nov. 14, and the variant has already spread to at least 89 countries.

Omicron appears to be less deadly, based on initial data out of South Africa. Health Minister Joe Phaahla reported on Dec. 17 that hospitalizations in the second week of the omicron wave made up only 1.7 percent of COVID-19 cases, down from 19 percent in the same week of South Africa’s delta wave. Kramer cautioned that the strain’s virulence can’t be confirmed until more hospitalizations are observed in the coming weeks, but she doesn’t think anyone in the U.S. should feel panicked. “We have much better ways of handling people who are sick now,” she said. “The panic is being brought on by the way the media presents it.”

Do vaccines work against it? Vaccines available in the United States provide less protection against infection from omicron than from previous variants. Preliminary studies on the Pfizer vaccine indicate two doses are not sufficient to neutralize omicron. Studies done at Duke Health and the National Institutes of Health also showed less protection against infection for the Moderna vaccine. The same thing was true of natural immunity from a previous infection—studies by the Imperial College of London and the University of Texas Medical Branch found COVID-19 survivors had very few antibodies that could fight omicron.

Both Kasson and Dr. Richard Zimmerman, professor at the University of Pittsburgh’s Center for Vaccine Research, noted that booster shots could mitigate the effects of omicron. Kasson estimated that three doses of either the Pfizer or the Moderna vaccine give about 75 percent protection against the omicron variant compared to someone without a vaccine. 

The U.S. Food and Drug Administration also recently approved two new pills to treat COVID-19, Paxlovid and molnupiravir. Pfizer said Paxlovid should help prevent hospitalization and severe illness in people with COVID-19, and it appears to be effective against omicron. Molnupiravir targets the genetic material of the coronavirus and comes with warnings of possible birth defects. Harvard scientist William Haseltine has cautioned that molnupiravir tests in South Africa might have been involved in the emergence of the omicron variant because the drug induces mutations in the coronavirus.

Will the virus mutate again? Kasson anticipates more coronavirus variants to come. The only way to prevent new variants is to halt viral infections completely. He predicts the next variant will be highly contagious like omicron but said the severity is hard to foresee.


Heather Frank

Heather is a science correspondent for WORLD. She is a graduate of World Journalism Institute, the University of Maryland, and Carnegie Mellon University. She has worked in both food and chemical product development, and currently works as a research chemist. Heather resides with her family in Pittsburgh, Pa.

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