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FDA Announces First EUA for SARS-CoV-2 Testing Using Next-Generation Sequencing Technology

FDA maze of regulations

New EAU for SARS-CoV-2 diagnostic testing using NGS technology is another first for COVID-19 research and testing.

The US Food and Drug Administration (FDA) announced in a June 10, 2020, press release that the agency has issued an emergency use authorization (EUA) to Illumina Inc. for the first COVID-19 diagnostic test using next-generation sequencing (NGS) technology. This technology can be used for qualitative detection of SARS-CoV-2 RNA from respiratory specimens. 

According to the FDA press release, “Using next generation sequencing means that the test can generate information about the genomic sequence of the virus present in a sample, which can be also used for research purposes.” This new testing method allows for high-throughput testing. According to the Illumina product website, “The Illumina COVIDSeq Test can be scaled up or down to accommodate different numbers of samples. Up to 3,072 results can be processed in 12 hours.”

With this announcement, FDA Commissioner Stephen Hahn, MD, said that having a next-generation sequencing diagnostic tool available will continue to expand COVID-19 testing capabilities. “Additionally, genetic sequencing information will help us monitor if and how the virus mutates, which will be crucial to our efforts to continue to learn and fight this virus,” Hahn added.

Those Collecting Sequences Urged to Post

During a recent virtual FDA Town Hall meeting June 3, Timothy Stenzel, MD, PhD, FDA Director of the Office of In Vitro Diagnostics and Radiological Health in the Office of Product Evaluation and Quality, characterized NGS as “coming forward,” and the sequence information potentially important. 

The FDA’s virtual Town Hall meetings are for clinical laboratories and commercial manufacturers that are developing or have developed diagnostic tests for SARS-CoV-2. Here, they have the opportunity to ask technical questions about development and validation. The June 3 call included laboratory developed tests using NGS technology.

“We are absolutely seeing developers interested in this area and as required or as helpful we will update the molecular template for NGS sequencing as we know large batches, high-throughput sequencing can be done,” Stenzel said during the call.

Additionally, Stenzel urged those collecting sequence information from SARS-CoV-2 to post the information where appropriate so that test developers can survey the sequence information and keep track of mutations where they occur. 

June 3 Virtual Town Hall Gets Specific About NGS and COVID-19

“The recommendations are likely going to be very similar to the current molecular recommendation for LDTs,” Stenzel added. “We expect that the performance be established on actual patient samples, that the performance be very high, at least 95% relative to another molecular test.”

Clinical laboratories and manufacturers can access the entire Virtual Town Hall call, as well as the NGS portion of the call, specifically, on YouTube.

“We see this technology as being able to provide an accurate positive/negative result for SARS-CoV-2 and, in addition, provide sequence information as wanted and desired by those who run the testing or who order the testing. But better expectations for the performance would be no less than the net for any other molecular test, and so our molecular template for LDTs is a really great place to start,” according to Stenzel.

Related Resources:

Coronavirus (COVID-19) Update: FDA Authorizes First Next Generation Sequence Test for Diagnosing COVID-19

June 9, 2020, FDA NGS EUA Letter

Virtual Town Hall Series: Immediately in Effect Guidance on COVID-19 Diagnostic Tests June 3, 2020, via YouTube

NGS Town Hall Segment, via YouTube

June 3, 2020, Transcript: Virtual Town Hall Series – Immediately in Effect Guidance on Coronavirus (COVID-19) Diagnostic Tests

FDA EUA Webpage

Virtual Town Hall Schedule