Yesterday that FDA granted an emergency use authorization (EUA) for the first COVID-19 diagnostic test that uses next-generation sequencing (NGS) technology. The EUA was issued to Illumina, Inc. for its COVIDSeq Test.

“Throughout the COVID-19 pandemic, we have seen the ingenuity that results from the FDA working in partnership with the private sector. Having a next generation sequencing diagnostic tool available will continue to expand our testing capabilities,” said FDA Commissioner Dr. Stephen Hahn, M.D. in an agency release. “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.”

The test performs qualitative detection of SARS-CoV-2 RNA from a respiratory sample taken from a patient suspected of having COVID-19. The sample is taken via nasopharyngeal (NP) swabs, oropharyngeal (OP) swabs, anterior nasal swabs, mid-turbinate nasal swabs, nasopharyngeal wash/aspirates, nasal aspirates, and bronchoalveolar lavage (BAL) specimens. Through NGS, the test can generate information about the virus’ genomic sequence. This information can also be used for research, which means scientists can compare sequencing results to assess if or how the virus mutates.

As stated in FDA’s EUA letter to Illumina, “positive results do not rule out bacterial infection or co-infection with other viruses”, and “negative results do not preclude SARS-CoV-2 infection and should not be used as the sole basis for patient management decisions.” The letter advises that negative results be combined with “clinical observations, patient history and epidemiological information”.