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Will Omicron beat out Delta and the vaccines?

'Vaccine might be slightly less effective, but highly unlikely it will be a complete failure’

As the new Omicron coronavirus variant emerges in a growing number of countries, it likely will soon be detected in the United States, Northwestern Medicine experts say.

How well will current vaccines protect against it? Is it more infectious and virulent than Delta? Will Omicron overtake the Delta variant, and why is that concerning?

Northwestern experts address these questions based on accruing knowledge of the variant first discovered in South Africa. 

The experts

Ramon Lorenzo Redondo is a molecular virologist who studies the evolution of SARS-CoV-2, the coronavirus that causes COVID-19. He is the bioinformatics director of the Center for Pathogen Genomics and Microbial Evolution in the Havey Institute for Global Health and a research assistant professor of medicine in infectious diseases at Northwestern University Feinberg School of Medicine.

Dr. Egon Ozer is a microbiologist who studies the genetic sequences of SARS-CoV-2, the coronavirus that causes COVID-19. He is the director of the Center for Pathogen Genomics and Microbial Evolution in the Havey Institute for Global Health, an assistant professor of medicine in infectious diseases at Feinberg and a Northwestern physician.

Lori Post is the Buehler Professor of Geriatric Medicine and director of the Buehler Center for Health Policy and Economics at Feinberg. She also developed and coordinates a SARS-CoV-2 Global Surveillance System which provides standardized surveillance and forecasting metrics on the state of the pandemic for 217 countries daily, including the basic speed of the pandemic, whether that speed is accelerating, and compared to the previous week, whether the acceleration is jerking upwards.

Dr. Robert Murphy is executive director of the Institute for Global Health at Feinberg and a Northwestern Medicine infectious disease specialist. 

Why is Omicron alarming?

Dr. Robert Murphy: “Delta took over the world in a matter of months. It’s much more contagious, and it reduces the protection from getting infected in vaccinated people. Serious disease, hospitalization and death were not so affected, though. If Omicron outcompetes Delta, we are at its mercy. It appears to be more contagious, and the vaccines may be less effective at preventing infection, severe disease and death. It’s basically a new ballgame. If we have to make a new vaccine, it’s December 2020 all over again.”

Ramon Lorenzo Redondo: “Omicron has the highest number of mutations we have seen so far in the spike protein. This is the protein the virus uses to attach to the cell and infect it. Omicron has a unique combination of mutations, some of which have been already tested alone or in small combinations because they appear in other variants. Some of these mutations have been shown to confer higher transmissibility or a lower recognition by the immune system. However, we still don’t know their combined effect.

“In immunity generated by natural infection, people with some of these mutations seen in Omicron are more likely to be reinfected. The mutations also render monoclonal antibodies less effective. However, most of these mutations don’t seem to significantly lower the recognition by vaccine-generated immunity. The vaccine drops its effectiveness to a certain degree with some of these mutants but not in a way that renders vaccines ineffective so far.”

Egon Ozer: “You might need to be exposed to less of the virus for infection to take place. There are 32 mutations in the spike gene of Omicron compared to just nine or 10 in Alpha and Delta. Many of these mutations occur in regions of the gene we know are important for the virus to infect our cells. That makes us concerned they could have arisen because they give the virus an advantage.

“As one example, Omicron has a set of three mutations in a region called the furin cleavage site. When the spike protein binds to cells, it must be cleaved or split by a protein in the human cell that allows it to be taken up by the cells, so infections can occur. The mutations may allow it to split more easily and could make it more likely for the virus to get into cells.” 

Do you expect Omicron to outcompete Delta? What is the significance of that? 

Ozer: “Usually you see these new variants move in when case counts are low, because they don’t have much competition. In South Africa, case counts were very low in late summer and early fall when this took hold. Here in the U.S., we still have high case counts. Omicron may have a higher threshold to overcome to become dominant here. If its advantages are much greater than Delta, it still might be able to take over.”

Will the vaccines protect against Omicron? 

Lorenzo Redondo: “We need to test the virus with all the mutations to see if the vaccine works with this variant. The vaccines could still be efficacious, because this variant has been successful in an area with low vaccination rates. There has not been pressure for the virus to evolve to escape against the vaccine. It might have adapted a little bit, but it shouldn’t be able to completely escape. 

“The vaccine has been working well with most of the variants. We present the body with the original virus with the vaccine. The body recognizes that and generates memory and immunity against that. When a new variant comes, if it is very different, the body might be a little confused and won’t recognize it as fast as something familiar. But it will still respond.  

“Why do we vaccinate every year against the flu? The flu changes so much at the end of the year your immune system doesn’t recognize it at all. But that has not been the case with the COVID-19 variants.”

How worried should we be? 

Ozer: “We are doing science a lot more quickly than we have done in the past in terms of studying this virus and understanding how changes affect its behavior. We’ve had several variants come and go. Some that seemed worrisome turned out to be a regional problem and didn’t spread widely or cause severe disease. That said, the rate of new COVID-19 cases in South Africa over the last week has been alarmingly high, and the surge there currently appears to be driven mostly by this new variant. There is reason to be concerned. 

“Omicron may not be quite as virulent. Some early data from South Africa said the first cases were detected in students and younger people and — from what they observed — it didn’t seem like the kids were that sick. They weren’t necessarily going to hospitals. We’ll see if that remains true as it spreads, especially in older people who have been at higher risk for severe illness with past versions of the virus. There are too many unknowns currently. 

“Until we know more, redouble your efforts to get the vaccine or booster, mask and social distance.” 

What is the status of global pandemic cases? Can you decipher the effect of Omicron? 

Lori Post: “I track the expansion and contraction of the pandemic by country. I also look for countries with exponential or problematic growth. On Tuesday of last week, South Africa was not on my radar. The daily new transmissions were less than 1 person per day per 100,000 population. Over four days, it went from less than one case per 100,000 people to nearly 7.04 cases in 100,000. This rate of acceleration and speed is unprecedented since we began tracking the pandemic. South Africa went from not appearing on my surveillance maps to now setting off an alarm. 

“There was no warning, no upward slope, just an unexplainable leap in cases. 

“While I cannot comment on why cases are accelerating in South Africa, it coincides with the debut of Omicron. Some underlying cause is responsible for the clustering of cases this week based on novel transmissions from seven days earlier.

“Four days into the alarming growth within South Africa, the speed continues to accelerate, and this week’s acceleration is bigger than last week, meaning South Africa will surpass the threshold of an outbreak in a matter of days. 

“Also alarming, a week ago Omicron was not considered a variant of concern and this week, we have identified Omicron in Israel, Hong Kong, Italy, United Kingdom, Swaziland and Botswana. 

More countries are having outbreaks, and cases per day exceed prior outbreaks

“Not only are we seeing more countries having an outbreak on our surveillance, the number of cases per day in these countries exceed prior outbreaks," Post said. "Europe is now the epicenter of the pandemic, and the outbreaks are escalating higher and higher. Now there are 66 countries having an outbreak; the top used to be 63 countries during any surge of cases. And outbreaks are affecting so many more people than before. Slovenia leads the globe at 203.11 cases per 100,000; the Czech Republic has 172.65 cases per 100,000 population; and Belgium and Austria’s outbreaks are at 140.08 and 143.13 cases per 100,000 population respectively.” 

Post is concerned that the longer countries remain in an outbreak and the more defused the cases become, the more likely there will be disruptions to the food supply chain. The pandemic has resulted in increased violence, particularly against women and children at home and abroad. 

What is the global solution?

Lorenzo Redondo: “If we don’t vaccinate the entire world, it doesn’t matter if we have high vaccination rates in Europe and the U.S. If you get a flow of mutated viruses from regions that are unvaccinated, the virus will keep evolving and new variants will keep appearing.

“More importantly, we don’t want the virus to adapt and generate outbreaks in countries with weaker health systems that could lead to a public health system failure in those countries. We must help countries with lower resources vaccinate and test, as well as provide economic help if other countries are shutting down their borders to travelers from these regions.”