The omicron coronavirus variant

Guesses about the new variant abound, but only time will tell if it can compete with delta

As a result of the emergence of yet another coronavirus variety, a new wave of anxiety and unanswered questions have been sparked. Even vaccine manufacturers are at odds with each other, and we’re in a prognostication whirlwind for days after the news emerged. It will take time to discover whether immunizations can prevent the emergence of new strains. A coronavirus variety with numerous alterations was discovered late last week by researchers in South Africa and Botswana, and many of them occur in the component of the virus that aids in its entry and infection of cells. The World Health Organization (WHO) promptly assigned the significantly mutated variation the Greek letter omicron, officially designating it as a variant of worry. During a special session of the World Health Assembly on November 29, WHO Director-General Tedros Adhanom Ghebreyesus observed, “Omicron’s very emergence is another reminder that although many of us might think we are done with COVID-19, it is not done with us. South African and neighboring governments were enraged by the wave of dubious travel prohibitions that followed Omicron’s discovery. However, these snap judgments are based more on anxiety than fact.
There is no doubt in our minds. Only a few facts are known about omicron at this time. From fewer than 300 cases per day at the beginning of November to more than 2,000 by the end of the month, we know that COVID-19 cases have increased dramatically in South Africa. Omicron is being tested as a possible cause of some of those infections. The variation has been found in Israel, the United Kingdom, Hong Kong, and Australia, among other places. On December 1, a vaccinated Californian who had just returned from South Africa became the first case in the United States.

According to Müge evik, an infectious diseases physician and virologist at the University of St. Andrews in Scotland, cases of omicron have been reported in the United Kingdom and Europe that have not been linked to travel to southern Africa. This suggests that the variant may have spread person-to-person in the community for around a month. We first learned that the coronavirus was moving outside of China in early 2020, and this is eerily similar. Scientists are finding what they’re looking for now that they know what they’re looking for.

There is a great deal we don’t know about omicron. For the time being, most information is based on conjecture. Is this a more transmissible form of the virus? How effective are virus-fighting antibodies? We don’t know. If it causes a more serious condition or if the symptoms are lesser, we don’t know yet. Omicron’s origins remain a mystery. With a well-established monitoring program, South Africa was one of the first places to catch wind of this new strain. It’s not true in every country.) Vaccines against it are unknown. Re-infections aren’t something we can predict with any degree of certainty. In the end, we don’t know how omicron will compete with delta. In the future, Omicron may replace Delta as the main variation worldwide. No one knows for sure what will happen. It’s difficult to draw inferences from what’s happening on in South Africa because cases there were already low when omicron ignited a rise, meaning there wasn’t much delta around to compete with. It also depends on local conditions whether a version gains traction in a given area.

A lack of instances in South Africa may have aided in the discovery of omicron, according to evik, a researcher in the field. Detecting and analyzing clusters is easier when there are fewer infections than when there are many. There are a lot of unknowns, so patience and caution are essential. For example, we won’t be able to answer questions about immunological evasion for at least a few weeks. Other answers, such as the severity of the condition, may take months to come to light. In the interim, we have public health tools at our disposal to control the spread of any new variations that may arise. Masks, social isolation, ventilation, testing, and contact tracing are all variant-proof methods of coping. Regardless of how the virus evolves, these procedures will continue to be effective.

Why omicron is causing anxiety among scientists
Omicron, however, is a source of concern for scientists. It raises some red flags on a molecular level. A distinct set of mutations is responsible for these characteristics. Omicron’s spike protein, which the virus uses to break into cells, contains roughly 30 alterations, many of which have been discovered in or are related to other worrying variants, such as the highly infectious alpha and the world-dominant delta. About 20 more viral changes are found in other proteins that perform functions such as aiding the virus’s ability to proliferate inside cells or disrupting early immune responses. Scientists can make early assumptions about the effects of some of the spike mutations in omicron based on previous investigations on other variants. Omicron, for example, shares a mutation known as P681H with the alpha variation that may improve the virus’s ability to spread from person to person when paired with two additional modifications. Q498R and N501Y may assist the virus better connect to the protein ACE2 (the virus’s doorway into host cells), according to studies in cell dishes. The N-terminal domain of the spike is also missing several amino acids. Mutations in this section of the spike can help the virus evade the immune system’s detection, as it is a popular target for immune proteins known as neutralizing antibodies. Even yet, these are only educated assumptions at this point. We don’t know if the combination of these mutations would have the same impact. The virus’s abilities may be harmed as a result of so many alterations, compared to previous varieties. It’s possible they won’t. It’s too early in the process to make an assessment. Yiska Weisblum, a virologist at Rockefeller University in New York City, says it’s difficult to picture this virus taking over because it has so many mutations in important places of the spike protein. Many of omicron’s alterations, however, have been shown to assist it avoid sections of the immune system. In the event that it infects people who have had vaccinations, “it might take over,” according to Weisblum. In addition, it’s too early to determine how the virus acquired so many mutations. People with compromised immune systems have been proven to be infected for months in previous investigations (SN: 12/22/20). Viruses can develop to resist certain of the immune system’s weapons, such as antibodies, when the immune system is unable to remove the infection. This could be what happened to omicron. It’s also possible that the virus has mutated while flying under the radar in a country that doesn’t have the resources to do extensive genetic monitoring. It wasn’t until omicron spread to South Africa, where the country’s monitoring apparatus was already in place, that researchers realized it was a problem.

Isn’t it strange to see a virus so mutated? According to Weisblum, “However, if you have millions of sick individuals, something that is unlikely becomes reality.” Weisblum, virologist Fabian Schmidt of Rockefeller University, and others were curious about how the immune system might respond to a variation with a lot of mutations months before omicron surfaced. Using an animal virus that doesn’t infect humans, researchers generated a coronavirus spike with 20 mutations. Antibodies were then tested to see if they could prevent the virus from invading cells. People who had recovered from COVID-19, those who had been vaccinated, and those who had both recovered and been vaccinated were all screened for antibodies by the researchers. Recovered and vaccinated individuals’ antibodies could still neutralize the virus (SN: 8/19/21). There was a problem with neutralizing antibodies from people who had received two doses of an mRNA vaccination or had been infected only. Nature appears to have mimicked the team’s experiment with omicron. Nature’s results will be revealed in due time. Though Weisblum, Schmidt, and his colleagues’ experiment found that neutralizing antibodies failed to recognize the virus, it is good news that the body has more than only neutralizing antibodies at its disposal to combat infection. There are other antibodies that can recognize the coronavirus and alert the body’s immune system to its presence. T cells, which are immune cells, can either kill infected cells or activate other immune cells, such as B cells, into action. According to Schmidt, the immunizations should still be able to protect humans from the coronavirus in the future. There’s a chance that our bodies may not be able to entirely prevent the virus from entering cells.

What is the significance of vaccines?
The use of boosters may be beneficial. Scientists have no idea. It’s too early to tell whether or if the additional doses will help people produce neutralizing antibodies that can still recognize even severely altered forms like omicron, adds Weisblum. As we get vaccinated or become infected, our bodies are constantly updating their arsenal of antibodies to better fight off the disease. It’s possible that booster doses could become necessary if omicron spreads worldwide. On November 29, the Centers for Disease Control and Prevention (CDC) issued a new recommendation that all adults receive a booster vaccination (previously, it suggested that those 18 to 49 may get one, but now the agency has upped the sense of urgency). Omicron-specific vaccines are being prepared by several vaccine producers, notably Pfizer and its German partner BioNTech and Moderna, but they won’t be ready for months. Getting immunizations to folks who haven’t had a single dose is more crucial than boosters. For the vast majority of people in Africa and other parts of the world, immunization rates are far lower than those in other regions and continents. Inequities in the provision of vaccines could assist the virus by exposing big groups of individuals to the disease (SN: 2/26/21) for months. As I have said many times, the more time we allow the pandemic to drag on—by failing to address vaccine inequity or to implement public health and social measures in a tailored and consistent manner—the more opportunity we give this virus to mutate in ways we cannot predict or prevent,” the WHO’s Tedros said November 30 at a WHO member state information session. It’s a waiting game for the time being. If omicron rises to the top like delta or fades away like alpha and beta, we’ll know soon enough. We have no choice except to wear our masks and wait.


S. Leary et alGeneration of a novel SARS-CoV-2 sub-genomic RNA due to the R203K/G204R variant in nucleocapsid. bioRxiv. Posted April 14, 2021. doi: 10.1101/2020.04.10.029454.

D. Benvenuto et alEvolutionary analysis of SARS-CoV-2: how mutation of Non-Structural Protein 6 (NSP6) could affect viral autophagyJournal of Infection. Vol. 81, July 2020, p. e24. doi: 10.1016/j.jinf.2020.03.058.

S. Yu et alContribution of single mutations to selected SARS-CoV-2 emerging variants Spike antigenicity. bioRxiv. Posted August 4, 2021. doi: 10.1101/2021.08.04.455140.

J. Zahradník et alSARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolutionNature Microbiology. Vol. 6, September 2021, p. 1188. doi: 10.1038/s41564-021-00954-4.

F. Schmidt et alHigh genetic barrier to SARS-CoV-2 polyclonal neutralizing antibody escape. Nature. Published online September 20, 2021. doi: 10.1038/s41586-021-04005-0.

Categories: Clinical