Omicron variant accounts for 3% of U.S Covid-19 infections

Cases caused by the Omicron variant started cropping up in the U.S. after Thanksgiving, and as of Dec. 11 account for an estimated 2.9% of infections, according to data the Centers for Disease Control and Prevention released on Tuesday. The estimates range regionally from less than 1% of cases in some areas to more than 13% of cases in the region including New York and New Jersey.

The U.S. has markedly improved its ability to sequence the genetic material of virus samples and keep track of circulating variants, but the amount of sequencing still varies by state and community. The CDC estimates variant proportions using sequencing data and modeling.

The agency says that about 97% of recent U.S. cases were estimated to be caused by Delta. Because Omicron has shown in other countries that it can take over rapidly, its true share of new cases is likely higher, said Nathan Grubaugh, an associate professor of epidemiology at Yale University’s School of Public Health.

“I don’t think we get out of December without Omicron being the most common variant in a lot of places in the U.S.," Dr. Grubaugh said.

As Omicron gains ground, Delta is already fueling case and hospitalization surges in parts of the country including the Northeast and Midwest where the weather is turning colder, sending people back indoors where the virus can most easily spread. Nationally, the seven-day average for new U.S. cases is near 120,000, according to Johns Hopkins University, up from a recent dip to around 71,000 in late October, when the Delta-fueled surge cooled in southern states.

The continuing case surge is prompting some renewed restrictions, including indoor mask rules in New York and California. The variant has been identified in at least 30 states and Washington, D.C., according to the CDC. The agency said preliminary evidence suggests that Omicron is more transmissible than the Delta variant.

“I think this is the beginning of that exponential growth," said William Lee, vice president of science at Helix OpCo., a population genomics company involved with Covid-19 testing and sequencing.

Public-health experts said precautions and tools developed throughout the pandemic, such as masking, testing and vaccination, can help fight all known variants, including Omicron.

“This is not March of 2020," said Michael Merson, visiting professor of global health at the New York University School of Global Public Health.

The Omicron variant, also called B.1.1.529, has been spreading rapidly in South Africa and parts of Europe and is also circulating in the U.S. since being identified by scientists in southern Africa in November. The U.K. has said that Omicron represents more than one in five Covid-19 cases there and that the number of cases from that variant is doubling every two to three days.

Researchers are racing to figure out the variant’s transmissibility, severity and ability to evade the immune response from vaccination and prior infection. A study from a large private health insurer in South Africa recently found that two shots of the Pfizer Inc. and BioNTech SE Covid-19 vaccine lowered the risk of hospitalization by 70% for patients infected with the variant.

The study also found that adults infected with the Omicron variant were 29% less likely to need hospitalization than during the country’s first wave and that the disease appeared less serious for those admitted. But the researchers also said that the lower hospitalization rate could be the result of high levels of immunity in the population from either prior infection or vaccination and that they couldn’t determine whether Omicron is inherently less virulent than earlier strains.

Epidemiologists have warned that a highly transmissible variant still poses risks. Hospitals in some states, including New Hampshire and Michigan, are already managing record numbers of Covid-19 patients due to Delta, federal data show.

“Even if as a population level we are more protected from disease, if you just increase that number of infections, that’s an easy way to get more people into the hospital," Dr. Grubaugh said.