The FDA has its hands full with the impact of the mutations to the SARS-CoV-2 virus, but test developers can count on an ever-increasing base of data for those viruses thanks to a new contract taken by the CDC. The CDC indicated recently that its sequencing efforts and that of other organizations churned out nearly 14,000 sequences for the week of April 3, but Aegis Sciences Corp., of Nashville, Tenn., announced April 7 that it had undertaken an agreement to perform next-generation sequencing of samples from all 50 states and Puerto Rico, ensuring plenty of access to up-to-date information on those mutations.

The latest update from the CDC suggests that the agency struggled to gather a large volume of samples for sequencing until the week of Feb. 20, when the agency sequenced more than 9,600 samples. This volume, when combined with another 2,361 samples from other sources, breached the 12,000-sample mark for the first time in the U.S., a metric that has been nearly matched or surpassed four times in the intervening weeks. The volume of more than 13,700 for the week of April 3 stands as the new high-water mark for volume of samples sequenced, with more than two thirds of those samples having been processed by the agency.

In an April 7 statement, the Rockefeller Foundation unveiled an initiative to provide training for deployment of testing protocols designed to restore in-school learning for K-12 students, a program in which Aegis will participate. Aegis took the opportunity to announce that it had taken a contract with the CDC to perform next-generation sequencing of de-identified samples, although the company did not specify the volume of samples it would be able to process. This addition to the national sequencing volume arrives at a time when concerns continue to rise regarding the ability of mutated variants of the SARS-CoV-2 virus to evade antibody neutralization.

E484K mutation the latest source of consternation

According to a study published April 7, 2021, in The Lancet Microbe, the so-called E484K mutation of the virus’s spike protein, is seen principally in the B.1.351 and P.1 lines of the virus. An experiment run on sera from 34 subjects, along with five other individuals who had been vaccinated with the Pfizer-Biontech vaccine, indicate that this mutation may thwart the binding process for polyclonal neutralizing antibodies, suggesting that those who have been vaccinated may be unprotected from these mutations.

The dilemma has hardly been lost on the FDA, which recently provided an updated set of advisories. This advisory constitutes a refresh of the February 2021 communique with recommendations for specific tests. The agency reiterated that molecular tests that key on multiple genetic targets are less likely to be affected by the mutations now in circulation, although a repeat test with a different set of genetic targets is still advised if the clinician suspects the patient is infected despite a negative test result.

For the Linea COVID-19 assay kit, the FDA observed that the sensitivity of one of the targets of this test suffers due to “certain mutations,” including that found in the B.1.1.7 variant, first disclosed in the U.K. Still, the agency said overall test sensitivity should not be adversely affected, a conclusion based in part on information provided by the developer, Applied DNA Sciences Inc., of Stony Brook, N.Y.

The B.1.1.7 variant is also a factor in the advisory about the use of the Taqpath COVID-19 combo kit by Thermo Fisher Scientific Inc., of Waltham, Mass. Two of the targets of this three-target test are unaffected by the mutation in question, but the reduced sensitivity for the S-gene target prompted the FDA to advise that any sample that is suspected as a B.1.1.7 virus be sent for sequencing at a nearby lab. There were two other tests included in this update, the Accula test by Mesa Biotech Inc., of San Diego, and three tests in the line of Xpert tests developed by Cepheid Inc. of Sunnyvale, Calif.

Tim Stenzel, the director of the FDA’s Office of In Vitro Diagnostics and Radiological Health (OIR), said on the agency’s March 30 testing town hall that the agency is still unaware of any significant effect of the mutations on test performance. Stenzel added that there are reports of breakthrough infections of those who have been vaccinated, although all such instances were accompanied by no more than mild symptoms. There is also a remaining question as to whether viral loads in these instances are different from those who have not been vaccinated, a question that testing may answer shortly.

T cell question lingers for negative antibody tests

Toby Lowe, associated director of OIR, said the science is still not clear on the significance of a positive or a negative antibody test result for those who have been vaccinated. This problem is still confounded by the prospect that T-cell response might be protective in the absence of antibodies, but Lowe reminded that a vaccination will not trigger a positive result in a test that does not target the antibodies generated by that vaccine. Each of the first three vaccines authorized by the FDA is designed for spike protein immunity, and thus a serology test that fails to target a spike protein is of little or no use in assessing the impact of vaccination.

Lowe said the agency prefers that developers of tests for over-the-counter use provide pictures and diagrams with their instructions for use to ensure proper utilization. These instructions should be written for comprehension for a seventh-grade reading level, and instructions are more likely to be useful if they do not run more than two pages.

While the FDA is still unwilling to require that at-home tests come with a mechanism to report the results to public health authorities, the agency would prefer that test developers provide this function. Despite considerable interest from test developers, Lowe said the agency has no timetable for drafting of a template for at-home serology testing, although she confirmed that the test would have to be validated in a study performed in the home.