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EUA for Illumina COVID-19 NGS test opens path to high-volume screening for workplaces, schools

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The first FDA-authorized next-generation sequencing test for COVID-19 could strike the right balance of volume, sensitivity and speed needed for routine screening to help reopen society.

Illumina Inc. (NASDAQ:ILMN) announced Tuesday it received FDA Emergency Use Authorization (EUA) for its Illumina COVIDSeq Test, which detects SARS-CoV-2 RNA from upper respiratory swabs by sequencing the full viral genome.

The company’s workflow, which takes 24 hours to go from sample receipt to result, includes RNA extraction and conversion to DNA, amplification via polymerase chain reaction (PCR), library preparation, sequencing and report generation.

It can fit up to 3,072 samples per run, and can be run on machinery that’s already widely available in diagnostic labs.

According to Illumina’s information-for-use document, the test has a limit of detection (LoD) of 1,000 copies/mL. That puts it in the middle range of sensitivity among FDA-authorized COVID-19 diagnostics, whose LoDs span at least four orders of magnitude (see “Limits of Detection for New Coronavirus”).

The test had a 98.1% positive percent agreement and 97.4% negative percent agreement -- measures of sensitivity and specificity, respectively -- with an undisclosed FDA-authorized PCR test.

In an Illumina-sponsored forum on genomics’ role in COVID-19 surveillance Tuesday, former FDA Commissioner and Illumina board member Scott Gottlieb said NGS testing could enable widespread screening by filling the gap between rapid point-of-care tests that are relatively inexpensive but have lower sensitivity, and PCR-based tests that are more sensitive but have slower turnaround times and are costlier to run for large populations.

Next-generation sequencing could be used for large-scale surveillance of large populations by using pooled samples, Gottlieb said.

Illumina’s test is available at a limited number of early access sites, and is planned to become more broadly available this summer.

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