FDA Sets the Bar on Specimen Pooling & Asymptomatic Screening for SARS-CoV-2 Test Development

On June 16, the US Food and Drug Administration (FDA) issued new guidance addressing two key issues related to SARS-CoV-2 testing: validation processes for test pooling of samples for test development and Emergency Use Authorization (EUA) purposes and screening of asymptomatic persons.

The Diagnostic Challenge: Pooling of Samples

Pooling is a technique that involves mixing aliquots, i.e., sub-samples extracted from individual samples into a pool or “batch” that can be tested with a single test. If the entire pool returns a positive result, the individual samples are retested to locate the source of the positive; but if the batch tests negative, all of the constituent samples are also deemed to be negative.

Historically, developers of EUA tests have used pooling to modify how those tests are used. In the context of the current pandemic, pooling offers the advantage of conserving testing resources that have been in short supply. The downside of pooling is that it dilutes the nucleic acids produced by the SARS-CoV-2 virus, creating the risk of false negatives. As a result, test producers who use pooling must account for the false negative effect in validating the modified use.

The FDA Guidance on Pooling

The new FDA guidance, which is not freestanding but takes the form of additions to the pre-existing template for molecular diagnostic tests, outlines the agency’s “validation expectations” for the use of specimen pooling either to develop a new test for EUA or modify the use of one that has already received EUA clearance:

For Tests that Have Not Previously Been Authorized: Developers should establish the pool size for the claim and perform a clinical validation study large enough to ensure that at least 30 samples test positive with a comparator method. They must also test samples individually.

For Tests that Have Previously Been Authorized: Adding pooling to an already authorized test requires a clinical study large enough to include 20 positive samples.

For Both: The FDA recommends that developers collect samples at a minimum of three geographically diverse sites; but in the context of an EUA, the agency will consider data from one or two sites. The guidance also indicates that developers can use either archived or prospectively collected samples.

The Diagnostic Challenge: Asymptomatic Screening

During the reopening process, broad screening of asymptomatic individuals for COVID-19 has become an important measure used by airports, schools, employers and others to protect the health and safety of others. While SARS-CoV-2 tests that have received EUA clearance can be used for such purposes, the FDA has not actually given an EUA to any test for such use. “Broad screening using a highly sensitive test, especially given the asymptomatic testing pool, leads to the most accurate results, which is why the FDA has provided validation recommendations designed to establish high sensitivity for tests intended for broad screening in the updated templates,” noted the agency.

The FDA Guidance on Asymptomatic Screening

Again, the changes to the molecular diagnostic tests template distinguish between EUA and non-EUA tests:

For Tests that Have Not Previously Been Authorized: To support EUA for a broad asymptomatic screening test, the test should be evaluated in a clinical study of the intended population. The number of patients should be enough to detect 20 positive samples, with a positive percent agreement (PPA), with a comparator test of 95 percent, and negative percent agreement (NPA) of 98 percent.

For Tests that Have Previously Been Authorized: To add asymptomatic population screening to a test that already has an EUA, a post-authorization study may be appropriate, with a minimum of 20 asymptomatic positive specimens and at least 100 negative specimens. The FDA expectation is that PPA should be 95 percent or greater, and NPA should be 98 percent or greater.

Takeaway

Asymptomatic screening and specimen pooling for purposes of developing new laboratory tests and expanding the use of previously approved ones is nothing new, of course. Historically, while the FDA “has encouraged all test developers to reach out to the agency to discuss appropriate validation approaches,” it has not made any specific recommendations on the subject. So, the decision to add guidance on specimen pooling and asymptomatic screening to its template is a significant policy change, one Jeffrey Shuren of the Center for Devices and Radiological Health at the FDA describes as a “step forward. . . to help facilitate the preparation, submission, and authorization under an” EUA. In the larger context, the move represents a continuation of the agency’s strategy of backing away from its initial laissez faire approach to COVID-19 testing quality in favor of a more active regulatory strategy.