Omicron becomes dominant variant in Mass., already ‘straining the system’

Data from the Broad Institute show Omicron surpassed Delta last Friday; CDC reports Omicron accounts for 73 percent of U.S. cases

Salem Board of Health members Jeff Barosy, left, and Elizabeth Gagak, center, hand out COVID-19 Antigen Rapid Test kits to residents, in the Jean A. Levesque Community Life Center.Pat Greenhouse/Globe Staff

The Omicron variant has swiftly overtaken Delta as the dominant form of the coronavirus in Massachusetts, according to a new analysis by scientists at The Broad Institute of MIT and Harvard, now accounting for the majority of the cases here.

“We are in the Omicron wave,” said Bronwyn MacInnis, director of pathogen genomic surveillance at the Broad. “It is circulating widely in Massachusetts and appears to be continuing to amplify.”

The announcement from the Broad comes as the US Centers for Disease Control and Prevention reported that Omicron accounted for 73 percent of new coronavirus cases in the United States between Dec. 12 and 18, up from 12.6 percent during the week ending Dec. 11. In New England, Omicron made up 37.7 percent of cases, the CDC estimates.

It remains unclear how long the Omicron wave will last or how much harm it will do.

“We need to prepare for the possibility that this could have substantial impact,” said Jacob Lemieux, an infectious disease specialist at Massachusetts General Hospital and co-leader of the viral variants program at the Massachusetts Consortium on Pathogen Readiness.

Early evidence suggests that Omicron replicates quickly in the upper airway, but is less likely to spread deep into the lung, said Dr. Jeremy Luban, chairman in AIDS research at the UMass Chan Medical School. That could explain why some Omicron infections have appeared milder.

In South Africa, Omicron cases have proved less severe than previous variants, but experts emphasize that there’s no guarantee that it will play out the same way in the United States, already in the grips of a massive surge of the Delta variant.

“The data out of the UK was a sobering contrast,” MacInnis said. Hospitalizations are up 10 percent with no evidence that Omicron causes less severe illness than Delta.

In any case, she said, “With the transmission levels we’re seeing, even a small percentage of severe cases will still be a large number.” And as the virus spreads, it will continue to mutate, risking the rise of a new variant.

Broad scientists, in partnership with the Massachusetts Department of Public Health tested 1,108 specimens collected throughout Massachusetts Dec. 13 through 16, using a new technology called mCARMEN. They found that 45 percent of samples showed strong evidence of the Omicron variant. Based on the trends observed during this time period, the team estimates Omicron crossed the 50 percent mark on Friday and has continued to soar in prevalence.

Developed at the Broad, mCarmen can rapidly differentiate among variants, providing what officials called a “provisional look at the rising prevalence of Omicron in the state.” The technology allows researchers to hunt for Omicron’s fingerprint by quickly analyzing snippets of the viral genome.

In experiments, it was shown to be as accurate as full genome sequencing 97 percent of the time. But because it only analyzes snippets, this method produces results in a day rather than the week or more that full genomic sequencing takes. Researchers are examining samples from across the state, rather than using those from just one hospital or region, capturing a more representative cross-section of infections.

Although the technology was developed two years ago, Omicron’s arrival marks the first time when a variant increased exponentially at such a pace that results from genomic sequencing came in too late to guide the public health response.

The Broad is using this technique on about 1,000 samples a day, performed by graduate student Nicole Welch.

“We have a pretty good sense of where this is going to go,” MacInnis said.

Around New England, states reported a smattering of Omicron cases — three in New Hampshire, 40 in Connecticut, one each in Rhode Island and Maine, about three in Vermont — but current case counts give little indication of current infections. Massachusetts has not released the state’s Omicron case counts.

“If someone tells you today that the most recent data is that Omicron is 15 percent of all cases, it’s safe to say the real number is twice that,” said Dr. Bruce Walker, director of the Ragon Institute of MGH, MIT, and Harvard.

“I don’t think there is any lab in the world that can keep up with the number of cases we are going to be seeing, even in terms of testing, because it’s already straining the system,” Walker said.

“If you look at what’s going on today, it’s actually what already happened 10, 14 days ago,” said Salim Abdool Karim, clinical infectious disease epidemiologist and director of the Centre for the AIDS Program of Research in South Africa. “Time is not on your side.”

Karim, Lemieux, and Luban spoke at an online briefing Monday sponsored by the Massachusetts Consortium for Pathogen Readiness.

Vermont, the most vaccinated state in the country, reported its first Omicron case Saturday, and a state spokesman said there have been several more confirmed through genomic sequencing since then, but declined to say the precise number. At the same time, Vermont is reporting a slight decline in COVID cases overall and hospitalizations in the past two weeks, but that followed a large spike that lasted for weeks.

“This would be great if we weren’t looking at the potential of an Omicron surge,” said Ben Truman, spokesman for Vermont’s health department.

But in New Hampshire, New England’s least-vaccinated state, the Dartmouth-Hitchcock Medical Center saw the largest number of patients on ventilators since the start of the pandemic last week, driven largely by unvaccinated patients with COVID-19, according to Dr. Michael Calderwood, the hospital’s chief quality officer.

Now the hospital is girding for the Omicron wave.

Right now, the variant makes up about 3 percent of all COVID cases in the hospital, according to Calderwood. But he expects that share to increase quickly. To prepare, Dartmouth-Hitchcock is asking smaller hospitals to take on the care of less-sick COVID patients so the larger hospital can expand its capacity to treat the seriously ill.

“Our biggest focus right now is making sure that we are able to increase critical care capacity to serve the needs of northern New England,” he said.

He added that the vast majority of his hospitalized patients are unvaccinated, and that information about the safety and effectiveness of vaccines and boosters is still not reaching the right people. He recalled seeing a patient recently who had decided to put off their booster shot until after the holidays so they wouldn’t have to tell their anti-vaccine family about it. “This is a person at very high risk,” said Calderwood. “We need to figure out how to change that dialogue and try to get that correct info out there. That is the hardest thing, and sometimes it feels like we’re shouting into a vacuum and the people who most need to hear that info aren’t hearing it.”