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FDA Lists SARS-CoV-2 MDx Tests Potentially Impacted by Omicron Variant

This story has been updated to include additional impacted assays.

NEW YORK – The US Food and Drug Administration said on Friday that it has updated its website tracking the potential impact of SARS-CoV-2 variants on molecular diagnostic tests to include tests likely affected by the Omicron variant.

The updated site lists 26 assays from 23 developers and manufacturers "whose performance may be impacted by mutations in the SARS-CoV-2 Omicron variant."

For each of the tests, the FDA's bioinformatics analysis suggests that one genetic target will have significantly reduced sensitivity due to a mutation in Omicron.

"A specific deletion in the spike (S) gene (Δ69-70) results in an S-gene dropout, also referred to as an S-gene target failure (SGTF), where the genetic target that covers the portion of the S-gene where the deletion occurs fails to detect the virus," the agency wrote.

The listed assays will still be able to detect SARS-CoV-2 infection, however.

"Since these tests are designed to detect multiple genetic targets, the overall test sensitivity should not be impacted," the FDA said.

The agency recommended that clinical lab staff and healthcare providers using the listed tests be aware of the potential for SGTF.

Furthermore, as SGTF is typically not observed in the Delta variant — which is the primary variant currently circulating in the United States — specimens "with an S-gene dropout detection pattern may potentially be Omicron variants and should be prioritized for sequencing confirmation," the FDA said.

On Monday, the FDA added one additional molecular assay to the list of tests that show SGTF, bringing the total to 27.

The agency also disclosed an Emergency Use Authorized test from developer Tide Laboratories that targets a single region in the N gene which is mutated in the Omicron variant.

Called the DTPM COVID-19 RT-PCR test, it is currently used by 33 labs in 16 states. 

"Since this is a single target test, the test is expected to fail to detect the SARS-CoV-2 Omicron variant, resulting in false negative results in patients with the Omicron variant," FDA wrote.

However, the nine-nucleotide deletion of positions 28370-28362 appears to be specific to the Omicron variant. "Therefore, based on initial bioinformatics analysis, the performance of the [Tide Laboratories] test is not expected to be impacted for other known SARS-CoV-2 variants," the agency also said.

The FDA advised health care providers and lab staff to be aware of the labs listed on its site that are performing the Tide Laboratories assay, noting as well that the test "is not believed to be used for high volume testing."