What the Coronavirus Variants Mean for Testing

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“You could run into a situation where you just got unlucky with where you chose to target your test, and something popped up there that then made your test less effective,” said Nathan Grubaugh, a virologist at Yale University.

The gene for the virus’s characteristic spike protein, known as the S gene, has been particularly prone to mutation, and tests that target this gene may miss certain variants. For instance, Thermo Fisher’s TaqPath test fails to detect the mutated S gene of the B.1.1.7 variant, which was first identified in Britain and is now spreading rapidly through the United States.

But the test does not rely on the S gene alone; it has three targets and can still return accurate results by detecting two other stretches of the coronavirus genome.

Just 1.3 percent of molecular tests rely solely on an S gene target, according to calculations performed by Rachel West, a postdoctoral associate at the Johns Hopkins Center for Health Security. The rest either target more stable regions of the genome, which are less likely to mutate, or have multiple target sequences, which makes them less susceptible to failure. “It’s very unlikely that you’re going to get mutations in all of them,” Dr. Lillis said.

The F.D.A. has listed four different molecular tests “whose performance could be impacted” by the variants, but notes that the tests should still work. Three of the tests have multiple targets; a fourth may be slightly less sensitive when the virus has one particular mutation and is present at very low levels. (The four tests are the TaqPath Covid-19 Combo Kit, the Linea Covid-19 Assay Kit, the Xpert Xpress and Xpert Omni SARS-CoV-2, and the Accula SARS-CoV-2 Test.)

“We don’t think that those four assays are significantly impacted,” said Dr. Tim Stenzel, who directs the F.D.A.’s office of in vitro diagnostics and radiological health. “It was more out of an abundance of caution and transparency that we made that information public.”

Antigen tests are less sensitive than molecular tests, but they are typically cheaper and faster, and they are being deployed widely in coronavirus screening programs. These tests detect specific proteins on the outside of the virus. Some genetic mutations could change the structure of these proteins, allowing them to escape detection.

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