This article was first published August 20, 2020 and updated on April 29, 2021
The Food and Drug Administration (FDA) has granted Illumina a second amendment to the previous Emergency Use Authorization (EUA), expanding the installed base of next-generation sequencing (NGS) systems that can run Illumina’s COVIDSeq Test, a diagnostic test for COVID-19. With this amendment, even more labs can embrace NGS scalability and accuracy to help diversify and expand current FDA (EUA) approved COVID-19 diagnostic testing capabilities and genome reporting for surveillance for research use only (RUO).
The first amendment leveraged a broad NextSeq install base in CLIA-certified labs and further simplified the workflow by giving customers more equipment options to use, alleviating critical supply bottlenecks. In addition to the NovaSeq 6000, NextSeq 550, and NextSeq 550Dx (in RUO mode) systems, the FDA has now authorized Illumina’s newest mid-throughput platform, the NextSeq 2000 to run the COVIDSeq diagnostic test.
“COVIDSeq for the NextSeq 2000 System expands COVID-19 diagnostic testing and surveillance capabilities for mid- and high-throughput laboratories. This gives patients more timely and accurate diagnostic results while simultaneously providing public health entities valuable information about the variant mutations that are circulating."
The second amendment further expands COVIDSeq testing capabilities to NextSeq 2000 sequencing system and additional NovaSeq reagent chemistry configurations making it faster and more cost-effective for customers. Additional changes include updates to the thermocycler specification, providing customers with the flexibility to use different thermocycler platforms and a 63°C annealing temperature at the PCR step improving variant analysis. Software analysis for COVIDSeq can be performed using the DRAGEN COVIDSeq Test v 1.3 installed on the local DRAGEN server or using the DRAGEN COVIDSeq Test App on BaseSpace Sequencing Hub.
The first amendment expanded the initial EUA authorization on the NovaSeq 6000 sequencing system from the S4 flow cell to include the SP flow cell, allowing labs to process a minimum of 768 and up to 3,072 samples in a single run. Together, the two amendments ensure COVIDSeq is available to mid- and high-throughput sequencing labs to ensure adequate testing is accessible.
COVIDSeq has not been FDA cleared or approved. This test is authorized by FDA under an EUA for the duration of the declaration that circumstances exist justifying the authorization of emergency use of in vitro diagnostics for detection and/or diagnosis of COVID-19. COVIDSeq is only authorized for use in laboratories in the U.S., certified under the Clinical Laboratory Improvement Amendments of 1988 (CLIA), 42 U.S.C. §263a, to perform high complexity tests. Outside the U.S., COVIDSeq will be labeled either as Research Use Only (RUO), or with labeling aligned with local regulations.