FDA spots 26 tests where omicron detection requires further confirmation

An initial analysis by the FDA of commonly used COVID-19 tests found that while the omicron variant may produce an identifiable pattern in their results, that pattern alone is not enough to make a definitive omicron diagnosis.

In a missive to healthcare providers, the agency recommended that after spotting that particular reading in a molecular-based PCR test—known as an S-gene dropout—clinical laboratory staff should prioritize the full sequencing of those samples to determine whether it was caused by the quickly spreading strain.

S-gene dropouts are caused due to a specific single deletion in the code that makes up the coronavirus’s spike protein, which allows it to enter human cells and serves as a focal point for many tests, vaccines and antibody treatments. While the omicron variant houses about 30 mutations in its spike protein, that one deletion can cause a test to return a negative result.

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To get around this—and the potential for the virus to develop additional mutations in the future—many tests query multiple regions of the coronavirus’s genome at once. The dropout signal emerges when other targets report a positive result, while the S-gene returns as negative.

The use of S-gene dropouts as an early proxy method for determining whether a positive sample can be traced back to omicron has also been recommended by the World Health Organization.

According to the FDA, S-gene dropouts are typically not found in the delta variant—which has been the predominant strain circulating in the U.S. since late this summer—but it has been observed in other variants and is not specific to omicron.

The agency listed 26 tests that it found to display S-gene dropouts. However, the FDA said that since they detect multiple genetic targets, their overall accuracy should not be affected. 

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They include Thermo Fisher’s TaqPath kits—S-gene dropouts from which helped identify an early string of new omicron cases in South Africa—as well as molecular diagnostics developed by Verily, Helix, the Cleveland Clinic and other organizations. 

The agency previously listed tests that already known variants may have impacted, such as the alpha variant, also known as B.1.1.7, which was first identified in the U.K. in late 2020.