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‘It is relentless, and it is exhausting’: Boston scientists race to find Omicron before it spreads too far

A Broad Institute employee walked down a hallway as trays holding tubes of COVID-19 tests lined the wall at the Broad Institute.Jessica Rinaldi/Globe Staff

CAMBRIDGE ― In a warren of labs and offices that stretch across three buildings here, scientists and machines work around the clock to prepare and analyze samples swabbed from the noses of people with COVID-19.

They have tracked the pandemic’s surges and patterns, fueled by every variant along the way. And now they are hot on Omicron’s tail.

The Broad Institute of MIT and Harvard has become the region’s powerhouse for monitoring shifts in the genetic makeup of the coronavirus. While the first Omicron case reported in Massachusetts on Saturday was sequenced by a different lab, many of the subsequent cases, when they arrive, will travel through this high-tech labyrinth.


The Broad sequences at least two-thirds of all the test samples in Massachusetts and also processes tests from across New England and from states as far away as Colorado, Texas, and Hawaii.

Tasha Smith, clinical lab lead for the viral sequencing team, held up a tube containing 384 positive COVID-19 samples at the Broad Institute. Jessica Rinaldi/Globe Staff

In just one 24-hour period this past week, couriers delivered more than 150,000 tests to the Broad, which on Friday boosted its sequencing capacity from about 7,500 to as many as 10,000 samples per week, to meet the urgent need posed by Omicron and a surge of tests from holiday travelers.

“It is relentless and it is exhausting, but we have been riding on adrenaline for the last 18 months,” said Bronwyn MacInnis, director of pathogen genomic surveillance at the Broad. “This is our responsibility to bring what we can to bear on this pandemic. So we just keep on keeping on.”

It is a critical race the United States and even Boston, a medical center of global significance, were barely part of in the pandemic’s early days. The United States was operating virtually blind to the threat from the novel coronavirus. Just a few academic labs across the country were conducting such genetic work and there was little coordination at the federal level, leaving the US largely defenseless as the number of COVID cases exploded.


But state health departments and more sequencing centers, including the Broad’s once-low-key sequencing operation, have since roared to life with new federal funding and palpable fears about potentially dangerous coronavirus strains. Collectively, the country’s COVID surveillance system is now sequencing roughly 80,000 samples a week, about 1 in every 7 positive cases, the Centers for Disease Control and Prevention said Tuesday. That’s a leap from about 8,000 a week even a year ago. Sequencing is crucial, alerting the country to dangerous shifts in the virus and giving hospitals, public health agencies, and drug makers time to switch into high gear and respond to protect the population.

It was scientists at the Broad who alerted the world to the alarming extent to which the February 2020 Biogen conference in a Boston hotel mushroomed into a global superspreader event. From about 100 cases among conference attendees and their contacts came as many as 300,000 infections across the nation and around the world likely traced back to the two-day event, the researchers concluded. They also tracked this summer’s Provincetown outbreak, with sleuthing that revealed that vaccinated people could just as easily spread the virus to others.

A Broad Institute employee wheeled an empty cart back to the area where COVID-19 tests are scanned into the system by process development associates at the Broad Institute. Jessica Rinaldi/Globe Staff

When scientists sequence a COVID sample, they decode and examine its genetic material, which appear as a string of thousands of letters across a computer screen. They scrutinize the long codes, comparing them with ones shared by scientists around the globe in open databases, to track mutations and the spread of new variants.


At the Broad, legions of white-coated technicians roll carts of test tubes down maze after maze of hallways. Thousands more samples in tubes line racks of metal shelves, labelled “overflow,” waiting for their bar codes to be scanned as they, too, are loaded into the system.

At long white benches, rows of machines add tiny drops of chemicals and heat to extract genetic material from each swab sample and break it up into smaller and smaller snips. That information is ultimately converted to digital data that MacInnis and her colleagues scrutinize for clues about how the virus is changing and whether those changes signal a more potent threat.

The Broad and other sequencing operations rely on nasal test swabs, known as PCR tests, that are processed in labs.

But on Thursday, President Biden unveiled a plan he hopes will tamp down transmission of the virus by making at-home rapid COVID-19 tests more widely available by requiring private insurers to cover their cost.

A machine used pipettes to withdraw tiny samples of liquid from only the samples in the tray that are positive for COVID-19 and meet a specific threshold of concentrated viral load, for testing at the Broad Institute. Jessica Rinaldi/Globe Staff

While the plan may make testing more accessible, it raises concerns about potentially weakening the country’s genomic surveillance system because at-home tests are typically discarded and aren’t reported to public health officials or sent to labs to be processed and sequenced.

Scientists are now working to address that concern. Michael Mina, a former Harvard epidemiologist and outspoken critic of the nation’s COVID testing system, recently left academia to become chief science officer at eMed, a biotech software company.


Mina said eMed has partnered with one at-home rapid testing company on a COVID test that would relay results to local health departments. Now, he envisions including a postage-paid envelope in the test kits for users to mail positive swab samples to nearby sequencing sites.

“One reason I moved [from Harvard] to eMed is to solve this sequencing problem,” he said.

The United States is catching up to other countries in the sheer volume of tests processed. But some public health experts worry that the system, which cherry-picks the samples with the highest concentrations of virus in them, may miss early warnings about local or regional outbreaks.

“We may be doing enough in total, but it’s not targeted in the right places,” said Dr. Kavita Patel, a nonresident fellow at the Brookings Institution and a primary care physician at community health centers in Maryland and Washington, D.C.

Patel said the surveillance system should regularly scrutinize samples from people who have been infected despite vaccination, because even though the amount of virus in their test samples might be lower than the threshold for sequencing, they may provide early warning about a strain that is more transmissible or evading protection from vaccines.

Dr. Nathan Grubaugh, an associate professor of epidemiology at Yale School of Public Health who is working with New England states on sequencing, worries the sampling is disproportionately lower in rural and other areas with lower rates of COVID testing, potentially missing important trends.


“We have been at this for so long, and it’s physically and mentally draining, and to expand it it’s more energy, something we don’t have,” Grubaugh said. “The public health system is so strained with just trying to treat and test.”

On Friday, amid COVID-19 case counts spiking in Massachusetts to numbers not seen since last winter’s surge, the Broad said it was adding more people to its sequencing operation to meet the demand, and aimed to shorten turnaround time to under a week from the time a test is taken.

“There wasn’t a mandate to bring genomic surveillance on for a bona fide response to COVID until ... early January with the [more contagious] Alpha and Beta variants first coming on to the scene,” MacInnis said. “We didn’t think it would become such a core part of the arms race as it has.”

Kay Lazar can be reached at Follow her @GlobeKayLazar.