Guidance on Evaluating Impact of Viral Mutations on COVID-19 Tests and Lessons Learned Thus Far

Published: April 2, 2021

Dr. Timothy Stenzel
Dr. Timothy Stenzel

As part of our March 18 COVID-19 Diagnostics Evidence Accelerator Collaborative meeting, Dr. Timothy Stenzel, Director of FDA’s Office of In Vitro Diagnostics and Radiological Health detailed the impact of viral mutations on COVID-19 testing and answered key questions posed by meeting participants. In light of new FDA guidance on monitoring and responding to emerging variants and diagnostic test performance, his insight is particularly informative. Below are highlights from that discussion.


Dr. Stenzel began with an overview of the impact of viral mutations on testing and then answered questions from Accelerators.

  • Viral mutations present a risk to the effectiveness of diagnostic tests and vaccines. If vaccines lose their effectiveness against variants, diagnostic testing (and test performance) becomes more important in the pandemic response.
  • At the beginning of the pandemic, developers were encouraged to develop multitarget assays. However, due to the shortage of tests, the recommendations for a multitarget assay were modified to allow for a single target assay. Because the FDA expected mutations in the virus, the Agency asked manufacturers to conduct an analysis of known viral mutations at the beginning of the pandemic, and now developers focus on the US primarily, to assess whether the test will perform with the known mutations.
  • With the growing number of variants and access to the primers and probe sequences for Emergency Use Authorized tests, the FDA conducted their own analysis to see if the variants had an impact on the test. This led the FDA to release safety communications where they described three tests that are impacted by viral mutations.
  • In  guidance released on February 22, 2021, FDA describes working with developers where they will consider current and future mutations that may impact their tests and develop new tests as needed. Also, the guidance described the ongoing efforts to monitor the current tests and describe improvements that can be made to existing and new tests. [See also additional information published by FDA on March 30, 2021.]

Questions and Answer Session

Question: Are there any questions or feedback that the FDA/CDRH has been getting from test developers about the new guidance?

Answer: Developers have been engaged in the public comment aspect of the new guidance. The guidance was issued to make the process for developers clear and transparent about what the FDA/CDRH wants to do.

Question: Will the results report be required to include “sensitivity” to known major variants?

Answer: To date, there is no significant decrease in overall test sensitivity, therefore there is no need to report sensitivity to variants, though EUA labeling is usually updated with relevant information. Increased occurrence of false negative results will trigger further investigation. In the event of a false negative, it will be important to know whether the patient was exposed to a variant. FDA/CDRH has prioritized sequencing based assays and will begin prioritizing genotyping based assay. This will be important to evaluate diagnostic testing, therapeutics, and vaccines.

Question: What incentives are in place to have developers review performance of their assays for different variants?

Answer: There are no defined incentives. However, developers want to ensure that their test continues to perform well, which motivates them to continue to review performance of their assay for different variants. FDA is interested in helping assure that test performance remains high. As such, we work with diagnostic companies to facilitate assay tests for new variants.

Question: Test developers are sequencing; however, they are struggling to decided what to report out. Should they report out on the spike variant or the lineage?

Answer: The value of sequencing is for public health planning and action. For FDA/CDRH, the prevalence of variants, particularly variants of concern, provides context for trends in COVID-19 presentation and transmission. There is limited evidence that mutations need to be reported for patient care; though this may be needed in the future. The FDA is accepting submissions for tests that will allow genotyping information to be collected and reported. The FDA encourages such advancements to fight the pandemic.

Question: Do you see a role for multi-target testing and variant calling in a distributed setting, or do you feel that sequencing will continue to be the tool to track prevalence of variants?

Answer: The FDA is open to the genotyping strategy. Challenges arise with additional variants of the virus. The concern is that genotyping assays will not be as useful as sequencing. We want to capture what mutations and variants are possible and design assays for those variants that will prove to be beneficial.

Questions: Development requires samples of the different kinds of variants, spiking works for the variant testing but is not necessary for the immune response - are there sample repositories that can be used for development?

Answer: This is part of the Pandemic response to partner with other governmental agencies. However, the challenge that occurs is the identification of which samples to put in the repositories. The FDA is ready to engage stakeholders to address this.