New Omicron Variants Are Here–What We Know So Far

New Omicron Variants Are Here–What We Know So Far

The Omicron family, which is responsible for COVID, now has some menacing members At the end of the week ending October 29, data from the U.S. Centers for Disease Control and Prevention showed that two variants–BQ.1 and BQ.1.1–account for nearly 17 percent of viral samples genetically sequenced in the country. This was a significant increase from a month ago when the variants were almost invisible in the data. It suggests that they will soon outcompete BA.5 or BA.4.6, the dominant strains in America. A variant called XBB is causing a significant infection wave in Southeast Asia.

The three new variants are likely to spread quickly because they bypass immune defenses that have been developed through previous infections or vaccinations. They could also render monoclonal antibodies treatments ineffective. These features warrant attention–especially as the country heads into the fall and winter–but not panic. Scientists believe that the COVID vaccines are likely to continue to protect against death and hospitalization. And Paxlovid, an oral antiviral pill, is also expected to remain effective. The mixed news means that variants “have potential to create a wave but it’s unlikely to be a tsunami,” says Katelyn jetelina, an epidemiologist at UTHealth who is also the publisher of “Your Local Epidemiologist”.

Omicron was first created in the latter half of last year. The original version, known as BA.1, was previously known as B.1.1. 539) overtook the Delta variant and caused more than 800,000 U.S. cases per day during its January peak. BA.1 was only one of many Omicron subvariants. BA.2 was the successor to BA.1 and caused a surge during spring. BA.5 beat out BA.2 and caused an increase in the summer. Now it appears that BQ.1, BQ.1.1 and XBB –or some combination thereof–will cause a surge in the fall and winter. For the record, BQ.1.1 is identical to BQ.1, but with an additional mutation. Many scientists believe that the race will be between BQ.1 and BQ.1.1 or XBB. However, how this race will play out and whether it will cause an increase in disease incidence depends on three key metrics: how fast these variants spread; if the severity of the disease is greater; and if they can bypass our immune protection or evade immune focused treatments.

There is no doubt that these variants are growing at a rapid pace. BQ.1.1, for example, currently accounts for 7,000 cases per day and appears to be doubling every nine days, says Trevor Bedford, a virologist at the Fred Hutchinson Cancer Center who models COVID evolution. It is surpassing BA.5–the current dominant variant in the U.S. This is because each person infected with BQ.1.1 has an average of 1.4 others, while BA.5 has an average of one person infected. This so-called reproduction rate can be very telling. For example, BA.1 had a staggering reproduction number of 3. BA.1 had a reproduction number 3. Bedford predicts that the U.S. will see a wave similar in size to the BA.5 surge earlier this summer but not on the same scale as the Omicron surge last year. It is too early to predict whether BQ.1.1 will drive a greater percentage of infections or XBB, but Bedford predicts that either BQ.1.1 will hit first and suppress the circulation of XBB (which has been detected in the U.S. but not widely circulating) or both. Depending on what comes into play, Bedford predicts the U.S. will see 100,000 to 200,000 COVID cases per day–much higher than today’s average of fewer than 40,000 cases per day.

How many cases will result in hospitalizations or deaths is a big question. BQ.1, BQ.1.1 and XBB all carry mutations in the spike protein–the studs on the pathogen’s surface that it uses to recognize and infect cells. These mutations make it more difficult for the immune system recognize the virus and to kick into action quickly. Indeed, a few preliminary studies (neither of which have been peer-reviewed) have shown that antibodies from vaccination and earlier infections are less able to block infection from these new variants in a lab dish. This sounds alarming, but our immune system includes additional defenses beyond antibodies such as T and B cells. Justin Lessler, an epidemiologist from the University of North Carolina Gillings School of Global Public Health, says that laboratory tests can provide us with powerful and important information but they don’t tell all the story. While the risk of reinfections will increase due to the new subvariants it won’t necessarily lead to more severe diseases.

To answer this question, scientists combine lab data with real-world information. Hospitalizations appear to be increasing in Germany, but scientists cannot say if that is a result of BQ.1.1 or behavioral changes since Oktoberfest just occurred. The same is true in New York, which has the highest proportion of BQ.1.1 and an uptick in hospitalizations. This could be due to behavioral changes, as the weather cools down and children return to school. Scientists are optimistic that vaccines will continue to be effective against new variants. Scientists chose a bivalent booster to target both the original and current circulating strains BA.4 or BA.5. This would allow for a wider immune response to future and current variants. “The whole idea behind the bivalent booster was to protect against exactly that situation here, which has been the rapid evolution of SARS-Cov-2,” states Sam Scarpino, a viral surveillance expert at Rockefeller Foundation’s Pandemic Prevention Initiative.

Another tool to combat infection is a bigger cause for concern. These new variants could disarm monoclonal antibodies treatments such as Evusheld that have played an important part in protecting immunocompromised patients and those at high risk for serious illness. They target a specific virus shape and have simply mutated. Jetelina states that many of the tools we have to protect our most vulnerable population members are being lost. Jetelina states that Paxlovid, which has been effective in preventing serious cases, especially in older people, does not target a specific virus shape and should continue to work well.

All of this will likely increase the fall and winter surge. That’s particularly worrisome when pediatric hospitals are overflowing with respiratory syncytial virus (RSV), influenza is ticking up and there are very few mitigation measures in place. The booster vaccine is still expected to do a good job in keeping people safe from severe infections, hospitalization, and death. However, there is very little enthusiasm for it. As of late October, only about 20 million people in the U.S. The updated bivalent shot had been administered to approximately 8 percent of those eligible. Scarpino states that now is the time to act, for both flu vaccines as well as for the bivalent booster. “I wouldn’t wait.”

Scientists are also recommending dusting off those N95 or other high-quality masks, opening the windows at large gatherings and taking advantage of rapid tests–especially if you are going to see someone who is at high risk of severe disease. Jetelina states, “I believe everyone should be laser-focused this winter on protecting those who are vulnerable.” She believes that if we can do this, it will save lives as well as greatly reduce the pressure on our fragile healthcare system.



    Shannon Hall is an award-winning freelance science journalist based in

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