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T-cell screening launched to detect previous coronavirus infections

UPDATED: Wed., Feb. 24, 2021

This electron microscope image made available by the U.S. National Institutes of Health shows a human T cell, in blue, under attack by HIV, in yellow, the virus that causes AIDS. The virus specifically targets T cells, which play a critical role in the body's immune response against invaders like bacteria and viruses. Colors were added by the source.  (Seth Pincus, Elizabeth Fischer and Austin Athman/National Institute of Allergy and Infectious Diseases)
This electron microscope image made available by the U.S. National Institutes of Health shows a human T cell, in blue, under attack by HIV, in yellow, the virus that causes AIDS. The virus specifically targets T cells, which play a critical role in the body's immune response against invaders like bacteria and viruses. Colors were added by the source. (Seth Pincus, Elizabeth Fischer and Austin Athman/National Institute of Allergy and Infectious Diseases)
By Emma Court and Dina Bass Bloomberg

Adaptive Biotechnologies has launched a test that uses machine-learning technology from Microsoft to detect previous coronavirus infections, aiming to fill a gap left by standard antibody screening.

The screening, called T-Detect COVID, searches for T-cell responses against SARS-CoV-2, the virus that can cause the disease COVID-19, rather than the immune proteins detected by conventional tests.

Seattle-based Adaptive says its product may help people who believe they’ve been infected but have not tested positive with currently available analyses. That includes long-haulers – patients who suffer lingering COVID-19 symptoms, often for months.

“Some of these people were never diagnosed,” Lance Baldo, Adaptive’s chief medical officer, said in an interview last month. “Sometimes their physicians are wondering, and – frankly, this is where it gets ugly – sometimes their insurers are wondering.”

Antibody tests from Abbott Laboratories, Roche and other manufacturers are inexpensive and plentiful, but they face questions about accuracy in long-past infections.

Meanwhile, U.K. research suggests that a characteristic T-cell response remains in the body six months after a coronavirus infection, potentially longer than antibodies.

T-cell responses arise quickly and “have this long tail,” Baldo said. “It’s those biologic properties of T-cells that make them a really excellent target for trying to track disease and for a diagnostic.”

A way to test after the fact

T-Detect COVID extracts and sequences DNA from T-cells in a person’s blood sample. It uses machine-learning software developed with Microsoft to determine whether the collection of T-cells in the body is consistent with a past coronavirus infection.

The test costs $150, not including blood draws and a physician consultation, and it has not been cleared by the Food and Drug Administration. Available online with a prescription, it’s a new technology for Adaptive, whose stock has climbed more than 66% in the past year amid a wider surge of interest in diagnostics.

The company has signed partnerships with concierge medical groups who want to offer the test to patients. Public health officials and employers are interested in using it to look at coronavirus exposure among their groups, Baldo said.

“Anyone who has had either flu-like symptoms or thinks they might have had COVID” could be a customer, said Mark Massaro, managing director and senior equity research analyst at BTIG. “We’re talking millions of people.”

Because T-cell responses correlate with disease severity, T-Detect COVID may be used to predict a person’s vulnerability to the coronavirus, Baldo said. “That’s probably the Holy Grail,” Baldo said.

Research is not peer reviewed

T-cell responses can vary among people, making it challenging to define their response to a specific pathogen, said Alessandro Sette, a lead researcher at the La Jolla Institute for Immunology in California. Research on the Adaptive test is scant, and none of it is peer reviewed, said Sette, and more independent evaluation is needed.

Research by Sette and colleague Daniela Weiskopf evaluating the immune system’s response to SARS-CoV-2 suggests there might be overlap, or cross-reactivity, with responses to other coronaviruses that cause the common cold.

“It is difficult to resolve exactly which response is coming from where,” Sette said.

T-Detect COVID did not show evidence of cross-reactivity in a study submitted to the FDA for emergency-use authorization, Baldo said in a statement.

Looking past COVID-19 to other illnesses

T-Detect COVID is the first product to come out of the biotech’s partnership with Microsoft. The companies foresee using the T-Detect platform for other conditions including Lyme and Crohn’s disease.

The companies connected years ago when colleagues gave Peter Lee, now vice president for research and incubations at Microsoft, a copy of a paper from Adaptive, a spinoff from Seattle’s Fred Hutchinson Cancer Research Center.

The study showed how a simple analysis of a small snippet of T-cell DNA could predict the immune cell’s target. The company used “college-level machine learning and got these amazing results,” Lee recalled.

Lee was intrigued about what kinds of results the company could obtain using more advanced techniques, and in 2017 Microsoft invested $45 million in Adaptive.

Even though Adaptive has expanded its work to several diseases, Lee said he was initially wary of taking on the coronavirus so soon.

“On our research timeline, we were still more than a year away from being able to look at re-targeting the machine learning,” Lee said.

Prodded on by Adaptive CEO Chad Robins, “we tried it and, damn, it worked, in just a small number of weeks,” he said.

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