‘It’s relentless and it’s exhausting’: Boston scientists rush to find Omicron before it spreads too far

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

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

In a single 24-hour period last week, couriers delivered more than 150,000 tests to Broad, which on Friday increased its sequencing capacity from about 7,500 to 10,000 samples per week, to meet the urgent need posed by Omicron and a wave of holidaymakers’ tests.

“It’s relentless and exhausting, but we’ve been on the adrenaline rush for 18 months,” said Bronwyn MacInnis, director of genomic pathogen surveillance at Broad. “It is our responsibility to provide what we can to fight this pandemic. So we just keep on going.

It’s a critical race that the United States and even Boston, a globally significant medical center, were barely a part of when the pandemic began. The United States was operating virtually blindly from the threat of the novel coronavirus. Only a few university labs across the country were performing such genetic work and there was little coordination at the federal level, leaving the United States largely defenseless as the number of COVID cases skyrocketed.

But state health departments and more sequencing centers, including Broad’s once-covert sequencing operation, have since come back to life with new federal funding and palpable fears about potentially dangerous coronavirus strains. Collectively, the country’s COVID surveillance system is now sequencing about 80,000 samples per week, about 1 in 7 positive cases, the Centers for Disease Control and Prevention said Tuesday. That’s a jump of about 8,000 a week even a year ago. Sequencing is crucial, alerting the country to dangerous developments in the virus and give hospitals, public health agencies and drug manufacturers time to step up a gear and take action to protect people.

It was scientists on the Broad who alerted the world to the alarming extent to which the February 2020 Biogen conference at a Boston hotel has turned into a large-scale global event. Out of around 100 cases among conference attendees and their contacts, as many as 300,000 infections across the country and globally are likely due to the two-day event, the researchers concluded. They have also been tracking the Provincetown outbreak this summer, with detectives who revealed that those vaccinated can just as easily pass the virus on to others.

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

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

On the Broad, legions of technicians in white coats roll carts of test tubes through mazes of hallways. Thousands of other samples in tubes lined up on metal shelf racks, labeled “overflow,” wait for their barcodes to be scanned when they are also loaded into the system.

On long white benches, rows of machines add tiny drops of chemicals and heat to extract genetic material from each swab sample and divide it into smaller and smaller sections. This information is ultimately converted into digital data that MacInnis and his colleagues examine for clues as to how the virus is progressing and whether those changes signal a more potent threat.

Broad and other sequencing operations rely on nasal swabs, called PCR tests, which are processed in the laboratory.

But on Thursday, President Biden unveiled a plan that he hopes will curb the transmission of the virus by making rapid home COVID-19 testing more widely available by forcing private insurers to cover their costs.

A machine used pipettes to take tiny fluid samples only from samples on the pan that are positive for COVID-19 and meet a specific concentrated viral load threshold, for testing at the Broad Institute.
A machine used pipettes to take tiny fluid samples only from samples on the pan that are positive for COVID-19 and meet a specific concentrated viral load threshold, for testing at the Broad Institute. Jessica Rinaldi / Globe Team

While the plan may make testing more accessible, it raises concerns about the potential weakening of the country’s genomic surveillance system, as home testing is typically rejected and not reported to public health officials or sent. to laboratories to be processed and sequenced.

Scientists are now working to address this concern. Michael Mina, a former Harvard epidemiologist and vocal critic of the country’s COVID testing system, recently left academia to become chief scientist of eMed, a biotechnology software company.

Mina said eMed had partnered with a rapid home testing company for a COVID test that would report the results to local health departments. Now he plans to include a postage-paid envelope in the test kits so that users can send positive swab samples to nearby sequencing sites.

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

The United States is catching up with other countries in the large volume of tests processed. But some public health experts fear that the system, which selects the samples with the highest concentrations of the virus, may miss early warnings of local or regional outbreaks.

“We might be doing enough in total, but it’s not targeted at the right places,” said Dr Kavita Patel, a non-resident researcher at the Brookings Institution and a primary care physician at community health centers in Maryland. and Washington, DC

Patel said the surveillance system should regularly examine samples from infected people despite vaccination, because even though the amount of virus in their test samples may be below the sequencing threshold, they may provide an early warning on a more strain. transmissible or not protect against vaccines.

Dr Nathan Grubaugh, associate professor of epidemiology at the Yale School of Public Health who works with New England states on sequencing, fears sampling is disproportionately lower in rural areas and others with testing rates Weaker COVIDs, potentially missing important trends.

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

As the number of COVID-19 cases rose in Massachusetts to numbers not seen since last winter’s outbreak on Friday, the Broad said it was adding more people to its sequencing operation to respond to the request, and aimed to shorten the turnaround time to less than a week from when a test is performed.

“There was no mandate to set up genomic surveillance for a good faith response to COVID before… early January with the [more contagious] The alpha and beta variants appeared for the first time, ”MacInnis said. “We didn’t think it would become as essential a part of the arms race as it has.”

Kay Lazar can be reached at [email protected] Follow her on Twitter @GlobeKayLazar.

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