Omicron accounts for 95 percent of COVID-19 cases in Massachusetts

The Broad Institute processes tens of thousands of COVID-19 tests a day and then scrutinizes as many as 5 thousand a week for signs of worrisome variants.Jessica Rinaldi/Globe Staff

New data from the Broad Institute of MIT and Harvard shows Omicron has displaced the once-dominant Delta variant in Massachusetts.

Omicron now accounts for 95 percent of the COVID-19 cases analyzed by Broad researchers through January 2, said Bronwyn MacInnis, director of pathogen genomic surveillance at the Broad.

That’s up significantly from Dec. 23, when the researchers found that Omicron accounted for about 75 percent of the COVID cases in Massachusetts.

“We have been over 90 percent Omicron since around Dec. 28th,” MacInnis said.

Broad researchers have been using new technology, called mCARMEN, that allows them to greatly speed up the process, analyzing snippets of the virus for Omicron’s fingerprint from a few hundred samples at a time. This method produces results in a day rather than the week or more that full genomic sequencing takes.

“One question we have is, will Omicron completely replace Delta, or will there be residual Delta?,” MacInnis said. “Are there isolated cases here and there or particular populations that are somehow more susceptible?’

Omicron is similarly muscling out Delta across the country, the latest data from the Centers for Disease Control and Prevention show. Omicron accounts for more than 90 percent of cases in all regions of the country, except for the heartland — Iowa, Kansas, Missouri, and Nebraska — where it accounts for 77 percent, and in the six New England states, where it makes up 82 percent of cases sequenced through Jan 1.

Nathan Grubaugh, an epidemiologist at the Yale School of Public Health who tracks Omicron through outpatient samples at Yale New Haven Hospital, has also seen the variant rise to about 95 percent of cases in the New Haven area. In a series of Tweets, he predicted that Omicron would eventually push out Delta in his region but that Delta was still hanging on, “likely due to the very high transmission through the holidays.”

2022.01.05 update

Omicron 95% from 885 positive tests conducted on Jan-4, and estimated Omicron infections are still 📈 by >1000/day.

Delta is still hanging on, likely due to the very high transmission through the holidays. pic.twitter.com/sdv7vAvzzV

— Nathan Grubaugh (@NathanGrubaugh) January 5, 2022