Impact of Viral Mutations on SARS-CoV-2 Tests: Evaluation and Monitoring Recommendations

What You Need to Know? 👇

How do viral mutations affect COVID-19 test performance?

Viral mutations can cause false negative results in molecular, antigen, and serology tests. Molecular tests may fail to detect mutated viral RNA, antigen tests may not recognize altered viral proteins, and serology tests may miss antibodies to changed proteins.

What monitoring frequency does FDA recommend for SARS-CoV-2 mutations?

FDA recommends periodic sequence alignment of test primers/probes with publicly available SARS-CoV-2 genomes in databases like GISAID. Developers should monitor mutations appearing in >5% of sequences or variants with credible reports of clinical impact.

When should test developers notify FDA about mutation impacts?

Developers must notify FDA via supplemental EUA request if mutations cause >3-fold difference in limit of detection or potentially change the benefit-risk profile. This includes performance reductions of 5% or more from established baselines.

What design strategies minimize viral mutation impact on molecular tests?

FDA recommends multiple target designs with appropriate result interpretation criteria. Including highly conserved pan-SARS-CoV targets alongside SARS-CoV-2 specific targets can improve resilience against new variants while maintaining test specificity.

How should antigen and serology test developers address viral variants?

Developers should engage early with FDA to discuss monitoring approaches, as assessment methods are less straightforward than molecular tests. They must develop plans to monitor new variants and assess performance impacts using available methodologies.

What labeling requirements exist for COVID-19 tests regarding variants?

Test labeling should include statements about the time period and geographic location of clinical specimens used in evaluation, noting that performance hasn’t been established for all circulating variants and may vary based on prevalent variants.

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What You Need to Do 👇

Recommended Actions

1. Implement routine monitoring of viral mutations through sequence database analysis
2. Design test with multiple targets when possible to minimize impact of mutations
3. Develop and document procedures for:
   • Evaluating impact of new mutations
   • Conducting melting temperature calculations
   • Performing wet testing when needed
   • Notifying FDA of significant findings
4. Update test labeling to include:
   • Limitations regarding variants
   • Time period and location of clinical validation
   • Performance variation statements
5. Create plan for:
   • Routine monitoring of mutations
   • Assessment of mutation impact on test performance
   • Investigation of performance changes
   • Communication with FDA
6. Maintain records of all evaluations and be prepared to submit to FDA upon request
7. Engage with FDA early during test development regarding approach to variant impact evaluation

Key Considerations

Non-clinical testing

• Perform sequence alignment of primer/probe sequences with public SARS-CoV-2 genomes
• Evaluate hybridization changes when mutations are identified
• Conduct melting temperature calculations
• Perform wet testing with clinical samples or synthetic RNA targets when mutations are identified
• Establish limit of detection for both original and mutated targets

Labelling

• Include statements about time period and geographic location of clinical specimens used in evaluation
• Indicate that clinical performance has not been established for all circulating variants
• State that performance may vary depending on variants and their prevalence

Other considerations

• Design tests to minimize impact of viral mutations on performance
• Include multiple targets when possible to provide redundancy
• Routinely monitor for viral mutations that may impact test performance
• Notify FDA if mutations potentially change benefit-risk profile
• Consider impact of mutations on antigen and serology test performance
• Develop monitoring plan for new genetic mutations and variants

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Relevant Guidances 🔗

• Content of Premarket Submissions for Device Software Functions
• Design Controls for Medical Device Manufacturers
• In Vitro Diagnostic Devices for Detection and Differentiation of Influenza Viruses - Performance Testing and Validation Requirements
• Dual Use Molecular Diagnostic Instruments with FDA-Approved and Non-Approved Functions

Related references and norms 📂

• 21 CFR 866.3981: Devices to detect and identify nucleic acid targets in respiratory specimens

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Original guidance

• Impact of Viral Mutations on SARS-CoV-2 Tests: Evaluation and Monitoring Recommendations
• HTML / PDF
• Issue date: 2023-01-12
• Last changed date: 2024-12-30
• Status: FINAL
• Official FDA topics: Medical Devices, Premarket, Coronavirus, IVDs (In Vitro Diagnostic Devices)
• ReguVirta ID: d537c015312b49605abc3b147938cfd6