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CDC releases sequence data for new COVID/Flu multiplex assay




The FDA granted Emergency Use Authorization (EUA) on July 2, 2020 for the CDC Influenza SARS-CoV-2 (Flu SC2) Multiplex Assay. On July 14, 2020 the CDC publicly released the primers & probes at:


https://www.cdc.gov/coronavirus/2019-ncov/lab/multiplex-primer-probes.html


These primers and probes are for Research Use Only and the CDC notes that:

“Reagents manufactured from these sequences may not be used for viral testing under FDA’s authorization of the Flu SC2 Multiplex Assay. Only primers and probes labeled for EUA use and distributed by the International Reagent Resource may be used for viral testing with the Flu SC2 Multiplex Assay.”


Others wishing to use reagents manufactured from these sequences for viral testing will need to go through the FDA’s EUA process, as over 110 entities have done so already to date for PCR assays that only check for SARS-CoV-2.


The CDC’s Flu SC2 Multiplex Assay is only the third multiplex granted EUA status during this pandemic. BioFire and Qiagen have previously added SARS-CoV-2 to their existing approved respiratory panels. The CDC’s Flu SC2 assay will be distributed to public health labs in all the US states and territories in time for the Fall flu season. The CDC should be commended for their rapid public release of the sequence data prior to publication, so that researchers, laboratories, and industry can have sufficient time to adapt them to their platforms and processes prior to the Fall.


This multiplex assay is important for several reasons.

  1. Symptomatic people with the flu will be able to told “You have flu, not COVID-19” instead of being told “You don’t have COVID-19” and be left wondering if their test was a false negative, as is the case now.

  2. The widespread use of this multiplex assay will help restore the ability to do flu testing, tracking and reporting, activities that were often set aside when the pandemic struck.

  3. This adoption of a multiplex assay by the CDC is a huge milestone for them, crossing administrative silos. Perhaps larger symptomatic multiplex panels will also be supported someday?

  4. The public release of the sequence data will create a level playing field for others to provide equivalent assays at the scale that will be needed to deal with the pandemic when cold weather forces people indoors again.

  5. Successful rollout and nationwide usage of this assay could help the CDC to regain some of the public trust that was lost due to the difficulties encountered with their initial SARS-CoV-2 assay earlier this year.

Access the Flu SC2 assay Instructions For Use document here: https://www.fda.gov/media/139743/download

(Tom Slezak had a long career leading bioinformatics at Lawrence Livermore National Lab. He now provides independent consulting to biotechnology companies. In early May 2020 he was honored to be among a small team the CDC asked to review the design of the Flu SC2 Multiplex Assay prior to FDA EUA submission.)

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