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First omicron subvariant case detected in Illinois

Will BA.2, thought to be more transmissible, halt decline of cases?
Scientists say case numbers have plateaued in countries where BA.2 is more prevalent.

The first omicron BA.2 subvariant case has been detected in Illinois by Northwestern Medicine’s Center for Pathogen Genomics and Microbial Evolution (CPGME). The subvariant was detected over the weekend from an individual who was tested for COVID-19 on Jan. 18.

The arrival of BA.2 is no surprise, scientists said. 

“Now the question is whether the new subvariant will extend the tail of cases infected with omicron,” said Ramon Lorenzo-Redondo, the bioinformatics director at CPGME, which is part of Northwestern University Feinberg School of Medicine.

Cases in much of the U.S. have peaked and are declining, but scientists said the case numbers have plateaued in countries where BA.2 is more prevalent.

“If BA.2 follows the same pattern in the U.S. as observed in countries like the United Kingdom, Denmark or India, we could observe a slowing of the current decline in new cases. In this case, the number of new cases could stabilize for a while before starting to decrease again,” Lorenzo-Redondo said. “It is still too soon to know because there are still very few BA.2 cases in the U.S.” 

“BA.2 is a specific variant of omicron that carries a number of additional mutations that are thought to make it even more transmissible,” said Judd Hultquist, associate director of CPGME. “It is unclear if the arrival of this new variant will result in a surge of local cases, but it is an important reminder that we are still in the middle of an ongoing pandemic. Vaccinations, booster shots and the proper use of face masks are still the best ways to protect yourself and your loved ones from this virus.”

Preliminary data show full vaccination and a booster are similarly effective in preventing symptomatic cases of BA.1 (the most widely spread omicron subvariant) and BA.2. Vaccination without the booster, however, is not as effective against either version of omicron, Lorenzo-Redondo said.

A team of scientists at CPGME at Feinberg’s Havey Institute for Global Health, including Lorenzo-Redondo, Hultquist, CPGME director Dr. Egon Ozer and scientist Lacy Simons, among others, has sequenced thousands of samples to identify SARS-CoV-2 variants circulating in the Chicago region in near real-time since the beginning of the pandemic in March 2020. CPGME team members have worked over the last several months and through the recent holidays to provide up-to-date data for the region during this recent surge.  

“Understanding which variants are circulating in a community is critical to inform the best practices in public health and clinical care,” Hultquist said. “For example, the omicron variant has been found to be resistant to a couple different monoclonal antibody treatments, which now can no longer be considered part of our effective therapeutic toolbox.”

From the end of November through the end of December, the population of viruses shifted from nearly 100% delta to nearly 100% omicron in Chicago, a remarkable change in a very short period of time, Hultquist said.

Although experience in other countries suggests that omicron BA.2 is more transmissible than other versions of the virus, there is no data yet showing that the new subvariant causes more severe disease, Ozer said. Still, he cautioned, we can't rule out the possibility of a slower decline or a new surge in infections with BA.2.  

Center scientists collaborate with Northwestern Memorial Hospital and the Ann & Robert H. Lurie Children’s Hospital of Chicago, reporting their findings to the Chicago Department of Public Health, the CDC and to the public through online repositories.

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