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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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How will the boosters help? Are they based on the "new" spike protein of Omicron, or the old ones?


I am another doctor (FP, 70 yo, retired 3 years ago, so not active in the COVID era) who agrees with the below comment - mostly. I got COVID in June 2020, before vaccines, not so sick. I went ahead with the vaccine in February, 2021, but I have not yet gotten a booster. I am pro-vaccine for the great majority of people over 40 or 50, but with the increasingly-likely realization that this virus will never go away, and will need a new-and-different shot every year (just like the flu, for which I also get a shot every year), I tend to think that it is better that NOT everyone (especially people under 20 without immune deficiencies) get the vaccine, as it probably tends to accelerate mutations.
But I am very opposed to vaccine and mask mandates and lockdowns. The ferocity with which these have been enforced worldwide and the social disruption this has caused is not a good thing. I worked in mission hospitals in Africa for 20 years; I care about the poor in the developing world. Many have been far more hurt by these social-governmental policies and the resulting economic impact than they were hurt/or will have been hurt by COVID itself.
I agree, of course, that our protests should be done with compassion and gentleness, but I am nevertheless delighted that some have been protesting!


I realize some of you will not agree with despite providing medical care for decades, no matter how many studies and articles I present related to covid, social distancing, masks and vaccines. Omicron will not be the only variant that will develop as the infection continues to spread, particularly among the unvaccinated, but as noted in the article, the shot (particularly the booster) will help. No matter how much I try to explain why some sources are more credible than others, and that not all "true" Christians are conservatives or Republicans, nor are all non-conservative news sources are untrustworthy with every story. No matter how much I try to explain that the people with the longer track record for character and medical competence like Fauci (with a deeply Catholic background, I do not know about his faith now) or Collins (who became saved in medical school and preaches science and his Christian faith still) deserve the benefit of the doubt (nobody is perfect) and more likely correct in their advice bout covid versus others that claim to be as competent. I can try to convince you that most of us doctors and medical personnel and researchers still do believe in shots, masks, and distancing, but I realize some of you still will believe that we are part of some grand conspiracy, even though a lot of us are Christians, to deceive you.
My concern even if you disagree with the above is whether we love others with the love of Christ on this issue and in general. Some of the words and tone here break my heart. Jesus does not say that we should not be in the public square, be involved in politics, and engaging on what is holy from the Bible. However, Jesus and Paul are two who do not make fighting the government the main focus, it is bringing others to Christ. That means loving our enemies, turning the other cheek, being meek and humble if that is what will win others to Christ. Sometimes we do need to fight, but my concern is we are turning to fighting and anger as our default mode, rather than being slow to anger, slow to speak.
Nurses and doctors are committing suicide, distraught by all of the patients dying or suffering long-term without recovering fully, some patients angrily denying that the medical people sacrificing for them have their best interest: that they are lying about them having covid, that they are trying to hurt them by denying them medicines like Ivermectin (as if doctors somehow know more than the patient except for covid, like doctors should be vending machines giving whatever patients want). We are losing many more nurses due to burnout from all of this hostility from patients and heartache from patients dying in unprecedented numbers, much more than loss from mandates. Public health officials (some of which are Christian) are being threatened (not just Fauci) with death threats and similar violence and even being run off the road. Scientists are being threatened in unprecedented levels now.
If you disagree with the concepts, fine. Just realize that standing on principle should not be rude, self-seeking, angry, mean. We are to be salt and light, we are to help those who are hurt, poor, lonely. We are not supposed to drive away the lost (which opinion polls, personal experiences tell me we clearly are) and we are not supposed to drive those in the Body of Christ away (which has happened way too many times). Consider if you truly love others as Christ did, and never let the fight for Christians and Christianity interfere with how we behave. There will always be persecution, and we should pray and fight for our brothers and sisters around the world in persecution now and the future, as well as here. However, these efforts (political, social, whatever) should never hinder the love of Christ:
2 Corinthians 2:14-17 "14 But thanks be to God, who always leads us as captives in Christ’s triumphal procession and uses us to spread the aroma of the knowledge of him everywhere. 15 For we are to God the pleasing aroma of Christ among those who are being saved and those who are perishing. 16 To the one we are an aroma that brings death; to the other, an aroma that brings life. And who is equal to such a task? 17 Unlike so many, we do not peddle the word of God for profit. On the contrary, in Christ we speak before God with sincerity, as those sent from God."
Please read I Peter 3 as a reminder for what we are called for, regardless of how the world responds, as we speak with "gentleness and respect". Please see the harvest for the Great Commission. Please see the poor, the downtrodden, those who need mercy, and not forget them.