Common Hospital PCR Test Affected by Viral Variant
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One of the most popular SARS-CoV-2 molecular test brands used in U.S. hospital labs has been added to an FDA list of tests with potentially compromised accuracy for viral variants.

Three PCR tests made by Cepheid — the Xpert Xpress, Xpert Xpress DoD, and Xpert Omni — look for both the N2 and E target regions within viral RNA. But two independent single point mutations “reduce the test’s sensitivity for detecting the N2 target,” according to the FDA.

Since the E target can still be detected, a test that reads out positive for E but negative for N2 would be a “presumptive positive,” the agency said.

FDA said the altered readout should not result in false positives, but the agency was providing the information “out of an abundance of caution.”

Christina Wojewoda, MD, chair of the College of American Pathologists’ microbiology committee and director of the microbiology lab at the University of Vermont Medical Center, said she didn’t find the Cepheid results concerning given that the test does have multiple targets.

“Even if there’s a change in the viral sequence that affects one of the primer-probe combinations, the other primer-probe combination is usually unaffected, and the test will still flag as positive,” Wojewoda told MedPage Today. “On the Cepheid package insert, it says if only one of the two targets is detected … it should be reported as a presumptive positive.”

Wojewoda noted that test manufacturers developed their tests based on genes that would be less likely to change over time: “The N1, N2, and E regions didn’t seem to have as much of a selection advantage,” she said.

FDA says it continues to “gather additional information and work with the manufacturer to address this issue.” Cepheid did not return a request for comment from MedPage Today as of press time.

On Jan. 8, FDA issued a similar communication about three other brands of commonly used molecular tests: TaqPath made by Thermo Fisher; Linea by Applied DNA Sciences; and Accula from Mesa Biotech.

The TaqPath, which is also a top choice of hospital labs, detects three target regions of viral RNA, including the region encoding the spike protein. That target now has reduced sensitivity, particularly for the B.1.1.7 variant, FDA said.

Still, the test should be able to detect the virus using the other two targets in combination with the “S-gene drop out.”

“If local or state clinical laboratories have access to quick turnaround whole genome sequencing services, such as those using the EUA-authorized Illumina COVIDSeq Test, these labs should consider further characterizing the specimen with genetic sequencing when this pattern is identified,” FDA stated.

Linea by Applied DNA Sciences looks for two targets within the genes for the virus’s spike protein, S1 and S2, according to company spokesperson Sanjay Hurry. Detection of the S2 portion has been impacted by certain mutations, including one of the mutations in B.1.1.7, Hurry said.

“If S1 and S2 are positive, you have COVID,” he said. “If you are positive for S1 and have S2 drop out, you’re positive, and it indicates B.1.1.7.”

Similar to TaqPath, FDA advised following up with whole-genome sequencing for such results with Linea if labs have such access.

Finally, for Mesa Biotech’s Accula molecular test, FDA noted that samples with a mutation at position 28881 (GGG to AAC), which affects the viral nucleocapsid (N) protein, could be impacted. It’s not clear how widespread that mutation is, and Mesa did not return a request for comment as of press time.

FDA created the new page for the impact of viral mutations on COVID-19 tests, which it says will be updated as new information becomes available. While the agency has previously acknowledged that variants could also have impacts on antigen and antibody tests, it has not yet issued any warnings about affected readouts for those tests.

The agency also issued a policy for evaluating the impact of viral mutations on COVID-19 tests in February.

  • Kristina Fiore leads MedPage’s enterprise & investigative reporting team. She’s been a medical journalist for more than a decade and her work has been recognized by Barlett & Steele, AHCJ, SABEW, and others. Send story tips to k.fiore@medpagetoday.com. Follow

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