Updating COVID-19 Tests to Address Mutations and Variants

On February 22, FDA issued a new Guidance for COVID-19 test developers entitled “Policy for Evaluating Impact of Viral Mutations on COVID-19 Tests: Guidance for Test Developers and Food and Drug Administration Staff.” The Guidance is designed to address the spread of several major variants carrying multiple mutations, the effects of the mutations on existing tests, and the resulting potential for an increase in the number of false negatives.

As described in our recent Alert, “Novel Coronavirus Mutations and Variants – What Do They Mean for Us?” there are currently three variants of major concern circulating in the United States, colloquially referred to as the UK, the South African and the Brazil(ian) variants; all carry multiple mutations with the potential to affect the results of not only molecular (PCR) tests but also those of antigen tests and serological (antibody) tests. Of these three, the UK variant, with at least 23 mutations, is expected to become the predominant form of the novel coronavirus in the United States during March 2021. In addition, there appear to be other, “home-grown,” variants emerging across the country.

Molecular (PCR) tests are designed to recognize a certain region or regions of the RNA-based genome of the novel coronavirus (SARS-CoV-2). When mutations change one or more of those regions, the test may no longer recognize the coronavirus and may deliver a false negative result, although tests designed to detect multiple regions of the genome may be less susceptible to the effects of a few mutations.

Since certain regions of the genome code for the targets of antigen tests, such as the spike protein that attaches to the ACE-2 receptors on human cells, mutations in those regions may produce variations in the amino acid sequence of the protein that cause antigen tests to fail to recognize them, again producing a false negative result. Furthermore, if a serology test is designed to detect antibodies produced as a response to a particular protein, changes in that protein as a result of mutations may give rise to antibodies that are no longer recognized by the test.

FDA’s new Guidance includes a set of recommendations for developers of all three types of tests. For molecular diagnostic tests, FDA recommends that developers design their tests to minimize the effect of viral mutations on test performance, routinely monitor for mutations that may impact the performance of existing tests, and clearly convey any test limitations in the test’s labeling. FDA further expands on these recommendations in the Guidance. Such recommendations include periodic alignment of sequences targeted in the tests with coronavirus genome sequences published in databases such as GISAID (discussed in our recent Alert on mutations and variants), to determine the extent to which the mutations may affect test performance.

FDA notes that monitoring the impact of variants on antigen and serology tests is less straightforward than for molecular tests. The Agency is currently considering how best to assess this impact, e.g., by directly testing known variants, by testing clinical specimens from individuals infected with the variants, or by using computer or in vitro modeling. In general, however, developers of these tests should consider the impact of currently recognized mutations and variants, and develop a plan to routinely monitor for new mutations and variants and assess their potential impact on existing tests.

The Guidance can be found here.