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Illumina Snares First FDA Emergency Use Authorization for NGS-Based SARS-CoV-2 Test

NEW YORK – Illumina said late Tuesday evening that its next-generation sequencing based test for COVID-19 has been issued Emergency Use Authorization by the US Food and Drug Administration, making it the first NGS test to receive such designation for detecting SARS-CoV-2.

The Illumina COVIDSeq Test is a high-throughput, in vitro diagnostic that uses upper respiratory specimens, such as nasopharyngeal or oropharyngeal swab, to provide results in 24 hours. The test is for use with the NovaSeq 6000 Sequencing system, and according to the San Diego-based firm, the design of the test includes 98 amplicons that target the full SARS-CoV-2 genome. COVIDSeq is currently available to a limited number of early-access sites and will become more broadly available in the summer.

Illumina said the workflow accommodates up to 3,072 samples per run on the NovaSeq. It leverages the S4 flow cell and includes steps for viral RNA extraction RNA-to-cDNA conversion, PCR, library preparation, sequencing, and report generation. The firm added that other components leveraged in the workflow include the Illumina Tagmentation library preparation technology and the Dragen COVIDSeq Test Pipeline for rapid reporting.

Illumina CEO Francis deSouza said in a statement that in addition to diagnostic testing, the company and some of its customers "are exploring NGS-based workflows to enable high-volume screening to support a return to work and school."

Illumina has also developed a research-use-only Respiratory Virus Oligos Panel, which contains hybridization capture probes to detect SARS-CoV-2 and about 35 other viral pathogens, including recent flu strains and other human coronaviruses.

While COVIDSeq is the first NGS test to get EUA from the FDA, several firms, as well as academic groups, have been working on viral genome sequencing assays to complement other methods for detecting SARS-CoV-2. Fulgent Genetics and Clear Labs, for example, have submitted applications for EUA for their assays.

Researchers from Baylor College of Medicine also recently published a preprint describing their whole-genome SARS-CoV-2 diagnostic assay called Pathogen-Oriented Low-Cost Assembly & Resequencing.