Reports of multiple new variants of the SARS-CoV-2 virus have emerged, raising questions about the efficacy of vaccines, but also regarding the utility of diagnostic and other tests. The U.S. FDA’s Tim Stenzel said single-target tests are thus at a greater risk of returning a false negative result, adding that these developers “should consider this carefully” in surveillance of their tests.

Stenzel, director of the Office of In Vitro Diagnostics and Radiological Health (OIR), addressed the two safety communications issued by the agency the week of Jan. 4 on the agency’s Jan. 13 COVID-19 testing town hall. One of these alerts was for the Curative test, which should be used only for patients who are symptomatic, and within the first 14 days of the onset of symptoms. Off-label use of this test should be avoided, and because of the risk of false negative findings, any such findings would call for a retest if that test had been conducted in the previous 14 days. This assumes that the clinical picture warrants a retest.

Tighter scrutiny of tests recommended

The recently disclosed mutations of the SARS-CoV-2 virus, including the so-called B.1.1.7 variant discovered in the U.K., “have been a hot topic for a little bit now,” Stenzel said. He asked all developers to conduct in silico analyses of their tests to establish the degree of inclusivity of their tests for all known variants. In mid-summer 2020, the FDA began more active surveillance of EUA tests with this objective in mind, and Stenzel noted that the FDA has routinely checked several databases, such as the Global Initiative for Sharing All Influenza Data (GISAID) database, for new variants.

The emphasis in these GISAID searches is on variants that have reached a prevalence of at least 5%, a threshold selected because this would suggest a corresponding drop in sensitivity of 5%, a topic of special interest for molecular tests. Stenzel said the agency is contacting developers to examine the impact of the U.K. or the South African variant on their tests. There is some concern about the South African variant, which presents a genetic variant at position 28881 on the SARS genome (GGG to AAC amino acid sequence). This had been reported in India as early as May 2020.

Any test that was affected by the U.K. variant, which features an amino acid (69/70) deletion has had some impact on more than one test, but Stenzel said both authorized tests affected by this deletion are multi-target assays, and thus “we don’t expect there would be a decrease in sensitivity” associated with these tests.

However, Stenzel said there is more than one variant that feature the 69/70 deletion, another reason to engage in sequence confirmation when such a virus is detected. Some local labs are equipped to handle sequencing, but the CDC is also sequencing these variants.

The agency has authorized a sequencing test that covers the entire genome, Illumina Inc.’s SARS test, and Stenzel asked that developers and labs forward as many variants as they can to a lab that runs the Illumina test. The objective is to compile as many sequences as possible to develop a clearer picture of the prevalence of each variant.

Mesa Biotech Inc.’s test, a single-target test, may have been affected by the GGG-AAC mutation, Stenzel said, adding that the company has updated the label, although the effect “seems relatively minor,” Stenzel said. There is no expectation of a large effect on sensitivity of the Mesa test, but he emphasized that the risk of false negatives is applicable to all tests.

Still, Stenzel said single-target assays are at a decided disadvantage due to the greater risk of a false negative thanks to the multiple variants of the virus. Developers should carefully examine the potential impact on their tests, he said, and should continue to monitor their tests and be proactive about any signals regarding test performance. He asked developers and labs to contact the FDA immediately if an issue arises.

Faster turnaround of EUAs, but backlog still a problem

The surge of FDA resources for EAU reviews has allowed the agency to make significant progress on EUA filings, but the agency is still receiving about 40 filings a week. “We’re focused on a net decrease in open [EUA] applications,” Stenzel said, although he did not say how large the backlog is at present. However, he said there is a significant impact on the net closure rate as evidenced by more frequent authorizations, adding that the agency is making a lot of decisions at a faster clip than in times gone by.