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First NGS-based COVID-19 diagnostic

In June, the US Food and Drug Administration granted Emergency Use Authorization (EUA) for Illumina’s next-generation sequencing (NGS) test for COVID-19, the first such authorization for a NGS diagnostic. The COVIDSeq test can be scaled up for high-volume screening, anticipating increasing demand as countries and municipalities reopen. It is a modified version of the tests developed by the ARTIC Network, a Wellcome Trust collaborative set up to speed surveillance during outbreaks. It employs 98 DNA fragments, or amplicons, to cover the roughly 30 kilobases in the SARS-CoV-2 genome. By multiplexing the reaction, upwards of 3,000 tests of nasopharyngeal or oropharyngeal samples can be run in one go with a 24-hour turnaround. Company literature states that the test requires at least 1,000 copies of the viral genome per milliliter and displays 98% sensitivity and 97% specificity. Although the test has EUA, it has yet to receive approval from the FDA.

Presently only a few sites are equipped to run the test; in addition to Clinical Laboratory Improvement Amendments (CLIA) certification, labs must be trained on Illumina’s NovaSeq6000 sequencing platform. However, the company plans in the coming months to increase the number of sites. Investing in the Ginkgo Bioworks, a synthetic biology foundry company, could facilitate this expansion. In May, Illumina led a $70 million series E funding round that Ginkgo will use to create the infrastructure for large-scale testing at its Boston lab.

Rapid and large-scale testing is considered key to safely opening schools and workplaces, as well as surveilling for new hotspots. Furthermore, having sequence information will inform public health officials on the route of transmission and mutation rate of the virus. Although rapid, large-scale diagnostics are also in the works, they will mainly be used for detecting and managing COVID-19 clinically.

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First NGS-based COVID-19 diagnostic. Nat Biotechnol 38, 777 (2020). https://doi.org/10.1038/s41587-020-0608-y

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