The U.S. FDA granted San Diego-based Illumina Inc. an emergency use authorization (EUA) for the first COVID-19 diagnostic test that uses next-generation sequencing (NGS). In addition to diagnosing infection with SARS-CoV-2, the COVIDSeq test can help researchers track mutations in the coronavirus.

So far, the FDA has granted more than 120 EUAs for COVID-19 tests, but this is the first to leverage the powerful NGS technology. The test is available now to a limited number of labs equipped with Novaseq 6000 Systems, Dragen, and PCR equipment, though the company expects it to be more broadly available later this summer.

“Having a next-generation sequencing diagnostic tool available will continue to expand our testing capabilities,” said FDA Commissioner Stephen Hahn. “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.”

Understanding the rate and type of mutations that develop in the virus is critical to developing a vaccine as well as for monitoring changes in the virulence of the virus that might indicate the need for more aggressive control measures or permit relaxation of efforts to limit its spread.

“Next-generation sequencing (NGS) has the unique ability to support scientists, researchers, public health officials and health care professionals on the front lines,” Illumina CEO Francis deSouza told BioWorld. “It helps us understand transmission routes, comorbidities, mutation rates, serves as a foundation for vaccine development and therapies, and ultimately helps predict and prevent future outbreaks.”

While the molecular diagnostic tests currently in use detect the presence of the virus by matching snippets of its RNA, COVIDSeq “provides a detailed view of the viral genome itself, enabling valuable insights into viral function and biology,” explained Susan Tousi, Illumina’s senior vice president of product development.

The test includes 98 amplicons, DNA or RNA markers, that target the full SARS-CoV-2 genome. An internal control consisting of 11 human mRNA targets is included in every sample to monitor for errors.

“The ability to generate and share, for example in GISAID, near-complete sequence data of viral genomes allows for collaborative global implementation of effective viral surveillance strategies to prevent further transmission and infection,” Tousi added.

GISAID is a cooperative global science initiative created to track the genomic data of influenza viruses, and now widely used to facilitate rapid sharing of SARS-CoV-2 genomic sequences. The database hosts more than 45,000 genomic sequences of the virus from around the world with hundreds more added daily.

The test

The COVIDSeq Test detects SARS-CoV-2 RNA in upper respiratory specimens obtained through nasopharyngeal or oropharyngeal swabs.

The high-volume test runs on Illumina’s Novaseq 6000 Sequencing system with results available within 24 hours from receipt of sample. The workflow accommodates up to 3,072 samples per Novaseq run, and includes steps for viral RNA extraction, RNA-to-CDNA conversion, PCR, library preparation, sequencing, and report generation. Each run takes 12 hours.

“Large-scale or widespread testing for COVID-19 is critical to recovery but continues to be a challenge,” deSouza noted. “Some forecasts say we should be testing millions of people every day to catch the new infections, but many clinical labs can’t scale up due to resource and capacity constraints. We believe sequencing can diversify testing and help fill this gap by enabling sites to test at high volumes, using equipment they already own.”

The test is available for performance evaluation only in European countries that rely on CE mark. A research use only (RUO) version of the test is also available to labs elsewhere for research, such as detecting strain or viral sequences.

“COVIDSeq is our first step, and the first high-throughput NGS solution in the market, offering U.S customers with experience sequencing at high volumes, a sequencing-based diagnostic for the virus that causes COVID-19,” said deSouza. “Beyond diagnostic testing, Illumina and a number of our customers are exploring NGS-based workflows to enable high-volume screening to support a return to work and school.”

In May, the company reported that it was providing more than $10 million in philanthropic and in-kind donations for instruments and consumables used in surveillance, sequencing, and monitoring of the disease and to mitigate the impact on students of school closings in San Diego during the pandemic. Illumina also offered a free SARS-CoV-2 Data Toolkit to researchers to detect and identify the viral sequence in their samples and supply their findings to public databases to promote understanding of the disease.

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