Updates to FDA’s COVID-19 Test EUA Templates for Asymptomatic Screening, Pooled Samples & Home Collection

Continuing our series covering market access requirements for COVID-19 tests, the FDA remains diligent in communicating their performance expectations for COVID-19 tests marketed by laboratories and manufacturers in the U.S. They have now provided validation expectations for at-home specimen collection, asymptomatic screening, and use of pooled samples, discussed in more detail below.

The FDA has also been quite busy authorizing a variety of COVID-19 devices to meet the demands of clinicians and patients, including Everlywell’s COVID-19 Test Home Collection Kit for home collection of specimens by patients and Illumina’s COVIDSeq Test, the first EUA test using Next Generation Sequencing for high throughput testing.

At-Home Testing for COVID-19

On May 29, 2020 FDA released a new emergency use authorization (EUA) template for at-home sample collection kits. The template outlines FDA’s expectations for validating specimen collection kits where patients self-collect specimens and ship these to specified testing laboratories. The template clarifies that these validation expectations are specific for specimens collected for use with molecular SARS-CoV-2 tests and includes requirements for usability studies and detailed stability studies to cover anticipated user and shipping scenarios.

Asymptomatic Screening for COVID-19

On June 16, 2020 FDA updated the molecular diagnostic templates for both manufacturers and laboratories to add performance expectations for molecular tests used “for screening of asymptomatic individuals” for COVID-19. Previously, FDA only authorized molecular diagnostic tests for “individuals suspected of having COVID-19 by their healthcare provider.” FDA provided validation expectations for new tests not yet authorized and for adding an asymptomatic screening indication to already authorized tests.

To gain authorization for this intended use for a test not yet authorized, manufacturers will need to conduct a clinical study in the intended asymptomatic population with the following considerations:

• The number of enrolled patients should be sufficient to ensure at least 20 positive samples are prospectively collected in the intended use population and be sufficient to demonstrate the following minimum performance:

  PPA ≥95% (Lower Bound of the two-sided 95% confidence interval >76%)

  NPA ≥98% (Lower Bound of the two-sided 95% confidence interval >95%)

  The total number of samples needed will depend on the prevalence of SARS-CoV-2 in the intended use population.

• Samples for the candidate test should be collected according to the instruction for use.
• Samples for comparator method testing should be healthcare settings, provider collected NP swabs. If an NP swab cannot be collected, a nasal swab may be used, however, both anterior nares should be sampled with the same swab. Sampling for the candidate test and comparator method should occur within a short timeframe to avoid biological variability in viral load.
• If available, FDA recommends selecting a comparator assay that has established high sensitivity with an internationally recognized standard or the FDA SARS-CoV-2 Reference Panel. Please contact CDRH-EUA-Templates@fda.hhs.gov to discuss options to establish the sensitivity of your test.
• In general, we recommend that you collect samples at a minimum of three geographically diverse sites, especially if you are planning to use the same data to support a subsequent De novo/510k submission. If this is not possible, FDA will consider samples collected at one or two sites in the context of an EUA. 
• It may be possible to use archived samples that were collected from asymptomatic patients. We recommend you contact FDA to discuss such an approach prior to initiating your study.

   

  Use of Pooled Samples for COVID-19 Testing

  Also on June 16, 2020 FDA updated the molecular diagnostic templates for both manufacturers and laboratories to outline validation expectations for using pooled patient samples for molecular tests. This was done in order to preserve testing resources by allowing labs to mix several samples together in a “batch” or pooled sample and then test the pooled sample with a diagnostic test. For example, four samples may be tested together, using only the resources needed for a single test. If the pooled sample is negative, it can be deduced that all patients were negative. If the pooled sample comes back positive, then each sample needs to be tested individually to find out which was positive.

  Just as with the asymptomatic screening indication, FDA provided validation expectations for new tests not yet authorized and for adding pooled sample testing to already authorized tests. Validation recommendations for not previously authorized tests include:

  You should establish the number of samples, n (e.g. samples collected at home. ., n=4), to be combined in one pool for testing and this number (n) should be established for each specimen type in your pooling claim.

  To establish performance of your test for pooling, FDA recommends conducting a clinical validation study in the intended use population.

  Please consider the following when designing your clinical validation study:

• The number of enrolled patient specimens should be sufficient to ensure at least 30 comparator method positive samples are collected from the intended use population.
• Samples for the candidate test should be collected according to the instructions for use. Depending on the sample volume required for your test, a single specimen collected from each study participant may be sufficient for individual and pooled sample testing.
• All samples should be individually tested by the comparator assay and individually tested by the candidate assay.
• Those with positive results by the candidate assay should each be pooled with n-1 (e.g., where n=4, n-1=3) randomly selected comparator method negative samples. The resulting pools should be tested by your candidate assay.
• Samples for comparator method testing should be healthcare provider collected NP swabs. If an NP swab cannot be collected, a nasal swab can be used however both anterior nares should be sampled with the same swab. Sampling for the candidate test and comparator method should occur within a short timeframe to avoid biological variability in viral load.
• If available, FDA recommends selecting a comparator assay that has established high sensitivity with an internationally recognized standard or the FDA SARS-CoV-2 Reference Panel. Please contact CDRH-EUA-Templates@fda.hhs.gov to discuss options to establish the sensitivity of your test.
• To confirm that samples with comparator method negative results remain negative in n-sample pools, we recommend testing 30 pools each consisting of n (e.g., n=4) comparator method negative samples.
• In general, we recommend that you collect samples at a minimum of three geographically diverse sites, especially if you are planning to use the same data to support a subsequent De novo/510k submission. If this is not possible, FDA will consider samples collected at one or two sites in the context of an EUA. 
• It may be possible to use archived positive samples that were collected from the intended use population. We recommend you contact FDA to discuss such an approach prior to initiating your study.

  You should report estimates of positive and negative agreement comparing performance of pooled samples to individual samples. Using a study design with 30 positives, all samples that were identified individually as positive by your test should still be positive when tested in pools with n-1 negative samples. Additionally, you should provide an analysis of Ct values of each target detected by your test. We recommend presenting the Ct values for the sample pools on the Y axis and Ct values for the individually tested samples on the X axis. The clinical validation study should demonstrate that individual positive samples with viral load close to the assay’s LoD (i.e., weak positives) are accurately detected by your test in a pool of negative samples.

   

  Additional Updates to the EUA Molecular Diagnostic Templates

  A quick comparison between the previous molecular diagnostic EUA template (last updated May 13, 2020) and the newly released template (June 16, 2020) reveals additional updates not specifically related to adding indications for asymptomatic screening and pooled testing, including:

• Software/ System Validation - The addition of a software validation section where FDA specifies that if you are introducing a system onto the market which has not been previously reviewed by FDA, they recommend providing evidence that the software has been validated. Further, if this evidence is not available prior to authorization, they may be incorporated into the conditions of authorization. As part of this validation, they are looking for manufacturers to:
  • Perform electromagnetic compatibility (EMC) testing to International Electrotechnical Commission (IEC) 60601-1-2 Edition 4.0:2014 [if new system includes hardware];
  • Evaluate cybersecurity of your system to ensure user and patient safety in the intended use environment;
  • Complete validation of all systems and software to ensure that all functions of the system perform as labeled. For more information on system validation please see the following FDA guidance documents and resources:
    • Guidance for the Content of Premarket Submissions for Software Contained in Medical Devices;
    • General Principles of Software Validation; Final Guidance for Industry and FDA Staff;
    • Off-The-Shelf Software Use in Medical Devices; and
    • 21 CFR 820.30 Subpart C – Design Controls of the Quality System Regulation.
• Limit of Detection – Clarified the required use of actual clinical matrix collected from SARS-CoV-2 negative individuals for use in creating test dilutions as well as the requirement to demonstrate the claimed LoD by first determining a preliminary LoD concentration at which 100% of the samples are positive then testing 20 individual extraction replicates at the preliminary LoD to achieve a minimum of 19 of 20 positive replicates.
• Inclusivity – Added the requirement where sequences with less than 100% homology with any of the primers and probes in the test are identified to provide a risk assessment on how such mismatches may impact the performance of the test.
• Specimen type – Several updates were also made throughout to accommodate different specimen types, i.e., common upper respiratory tract specimens, common lower respiratory tract specimens, upper and lower respiratory matrices, and alternate respiratory specimens (e.g., saliva, oral fluid, buccal swab, etc.). The updates provide clarification for how each should be tested for each assay performance characteristic.

To stay current with FDA’s thinking on SARS-CoV-2 diagnostic tests, follow FDA’s COVID-19 IVD-specific FAQ page and tune into their weekly town hall series for which they also post past transcripts.

FDA Guidance for COVID-19 IVDs

Policy for Diagnostic Tests for Coronavirus Disease-2019 during the Public Health Emergency

FAQs on Diagnostic Testing for SARS-CoV-2

Emergency Use Authorizations, COVID-19 IVDs

Molecular Diagnostic Template for Manufacturers (Updated June 16, 2020)

Molecular Diagnostic Template for Laboratories (Updated June 16, 2020)

Serology Template for Manufacturers (unchanged from May 4, 2020)

Serology Template for Laboratories (unchanged from May 4, 2020)

Antigen Template for Manufacturers (new May 11, 2020)

Home Specimen Collection Molecular Diagnostic Template (new May 29, 2020)