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FDA: New COVID-19 mutations can affect tests and result in false negatives

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Aakash Molpariya
Aakash started in Nov 2018 as a writer at Revyuh.com. Since joining, as writer, he is mainly responsible for Software, Science, programming, system administration and the Technology ecosystem, but due to his versatility he is used for everything possible. He writes about topics ranging from AI to hardware to games, stands in front of and behind the camera, creates creative product images and much more. He is a trained IT systems engineer and has studied computer science. By the way, he is enthusiastic about his own small projects in game development, hardware-handicraft, digital art, gaming and music. Email: aakash (at) revyuh (dot) com

The U.S. Food and Drug Administration warned in a statement that false negative result may occur, and it can impact any molecular test, approved for the detection of SARS-CoV-2 if a mutation occurs in the part of the virus genome evaluated by that test.

The U.S. regulators warned of the potential risk of false negatives with molecular testing for SARS-CoV-2 due to mutations such as variant B.1.1.7 of the recently detected virus.

The risk of these mutations affecting the overall accuracy of the tests is low, but the FDA is taking additional steps to ensure that the authorized evidence remains accurate, the agency said in a statement. These steps include working with test developers and continuing data analysis to evaluate all currently authorized molecular tests.

Like all viruses, SARS-CoV-2 was expected to mutate over time, as seen with the emergence of variant B.1.1.7, the FDA said.

As these efforts continue, we are working with authorized test developers and reviewing incoming data to ensure that health care providers and clinical staff can quickly and accurately diagnose SARS-CoV-2-infected patients, including those with emerging genetic variants, Stephen Hahn, MD, the FDA commissioner said.

However, he added that “at this time, we believe that the data suggest that currently authorised COVID-19 vaccines may still be effective against this strain.”

In its statement to healthcare workers, the FDA said it has to date identified three molecular tests that have received emergency use authorization in the United States, whose performance could be affected by genetic variants of SARS-CoV-2.

Accula SARS-CoV-2 test

FDA analysis, including additional information provided by the manufacturer, Mesa Biotech Inc, indicates that the performance of this test may be affected when testing a patient sample with the SARS-CoV-2 virus that has a genetic variant at position 28881 (GGG to AAC).

“While the impact does not appear to be significant, the FDA is providing this alert to healthcare providers as a precaution as we continue to collect additional data and work with the manufacturer,” the agency noted. 

The FDA also cautioned that healthcare professionals should be aware of the updated instructions for the use of the Accula SARS-CoV-2 test. These now include the exact location of the variant, in silico analysis of the binding of the primer and the impact of the observed performance compared with the aim of perfect match.

TaqPath COVID-19 Combo Kit and Linea COVID-19 Assay Kit

The FDA cautioned that the detection pattern that appears with the TaqPath and Linea diagnostic tests when certain genetic variants are present can help with early identification of new variants to reduce the spread of infection.

“The recently identified B.1.1.7 variant has been associated with an increased risk of transmission, therefore early identification of this variant in patients can help reduce the spread of infection,” according to the agency.

The agency also advised healthcare professionals to be aware of the detection pattern associated with certain mutations, including the B.1.1.7 variant, specifically a pattern of 2/3 positive targets that show dropout of the S gene (sensitivity reduced with the S-genetic target), when using the TaqPath COVID-19 Combo Kit, and a pattern of 1/2 positive targets showing loss of the S gene when using the COVID-19 Line Assay Kit.

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