CDC’s Influenza SARS-CoV-2 Multiplex Assay and Required Supplies

Summary of Recent Changes

The CDC Influenza SARS-CoV-2 (Flu SC2) Multiplex Assay is a real-time reverse-transcription polymerase chain reaction (RT-PCR) test that detects and differentiates RNA from SARS-CoV-2, influenza A virus, and influenza B virus in upper or lower respiratory specimens. The assay provides a sensitive, nucleic-acid-based diagnostic tool for evaluation of specimens from patients in the acute phase of infection.

Learn more about the benefits of the CDC Flu SC2 Multiplex Assay.

The US Food and Drug Administration (FDA) granted Emergency Use Authorization (EUA) for this test on July 2, 2020.

The CDC Flu SC2 Multiplex Assay FDA-authorized Instructions for Useexternal icon contains information about the test and its intended use, the test procedure, and the test performance characteristics. The FDA Letter of Authorizationexternal icon for the CDC Flu SC2 Multiplex Assay can be found on the EUA websiteexternal icon. The letter defines the authorized use and the conditions of authorization that apply to CDC and other testing laboratories that use this test. Manufacturers and test developers interested in the right of reference to the CDC Flu SC2 Multiplex Assay performance data are encouraged to read these FAQs.

On November 20, 2020, FDA granted an amendmentexternal icon to the EUA for the CDC Flu SC2 Multiplex Assay to expand the list of extraction instruments that may be used to prepare samples for testing. Included in this amendment:

• Addition of four automated nucleic acid extraction instrument options
  • QIAcube HT
  • KingFisher Flex
  • MagNA Pure Compact
  • NucliSENS^® easyMAG^®
• Recommendation to use the JOE filter instead of the VIC filter to view the InfB signal with standard 7500 Fast Dx calibration
• Clarification of verification instructions and dilutions

On January 8, 2021, FDA granted an amendmentexternal icon to the EUA for the CDC Flu SC2 Multiplex Assay to expand the list of extraction instruments that may be used to prepare samples for testing and to add an additional authorized manufacturer of primer and probe reagents for use with the test. This amendment will enable more laboratories to use the test with automated, high throughput specimen preparation instruments, potentially increasing the speed and throughput of testing and will increase manufacturing capacity of primer and probe reagents by adding a second authorized manufacturer. Included in this amendment:

• Addition of two automated nucleic acid extraction instrument options
  • Maxwell® RSC 48
  • Maxwell® CSC 48
• Addition of another authorized manufacturer of primer and probe reagents for use with the CDC Flu SC2 Multiplex Assay

On July 21, 2021, FDA granted an amendment to the EUA for the CDC Flu SC2 Multiplex Assay to update the in silico analysis of assay primer/probe sequences against available genomic sequences of SARS-CoV-2 viruses/variants circulating in the US and globally.

How Public Health Laboratories Order the CDC Flu SC2 Multiplex Assay

CDC’s International Reagent Resource (IRR)external icon provides multiplex kits to IRR-registered state and local public health laboratories. IRR does not supply clinicians, hospitals, or healthcare professionals with testing kits directly.

During the COVID-19 pandemic, state public health laboratories can authorize county or city laboratories in their state to perform testing. These laboratories must be certified under the Clinical Laboratory Improvement Amendments (CLIA) to perform high complexity tests, have appropriate laboratory equipment and training, and demonstrate testing proficiency under their state laboratory’s stewardship to maintain their status as an IRR-registered laboratory. A list of commercially available primers and probes for use with this test is not available at this time. However, CDC has shared the primers and probes sequence specifications, so other laboratories and companies may manufacture their own reagents.

Materials included in the assay

The CDC Flu SC2 Multiplex Assay is a four-in-one assay that includes:

• One primer mix and one probe mix. Primers and probes target:
  • Virus nucleocapsid (N) gene for specific detection of SARS-CoV-2
  • Matrix (M1) gene for specific detection of influenza A virus
  • Nonstructural 2 (NS2) gene for specific detection of influenza B virus
  • RNase P gene (RP) for specific detection of human nucleic acid that serves as an internal control
• Positive controls: SC2PC and Seasonal Influenza Positive Control (SIPC), that together confirm all four targets in the assay are working correctly

Other materials needed to perform the assay

The CDC Flu SC2 Multiplex Assay requires the use of additional authorized materials that are not included with the test. These materials include RT-PCR reagents, equipment, and supplies commonly used in laboratories such as a microcentrifuge, microcentrifuge tubes, pipettes, and pipette tips. Materials are described in the authorized CDC Flu SC2 Multiplex Assay Instructions for Useexternal icon. Two control materials are also required but not provided. These control materials must produce expected results for a test to be considered valid, as outlined in the CDC Flu SC2 Multiplex Assay Instructions for Use. The controls are the following:

• Human specimen control (HSC): A human cell culture preparation used as an extraction procedural control to demonstrate successful recovery of nucleic acid, as well as extraction reagent integrity. Acceptable alternatives to HSC are listed in the Instructions for Use.
• No template control (NTC): Nuclease-free water included in each run. This control monitors for reagent and system contamination.

More Resources for the Flu SC2 Multiplex Assay

• Processing of Sputum Specimens for Nucleic Acid Extraction pdf icon[128 KB, 1 page]
• Research Use Only Primers and Probes

Fact Sheets for the Flu SC2 Multiplex Assay

• Patient Fact Sheetexternal icon
• Healthcare Provider Fact Sheetexternal icon

More Resources for Diagnostic Testing for COVID-19 and Flu

• Request 2019-nCoV Grown in Cell Cultureexternal icon
• Emergency Use Authorizations for Medical Devices (FDA)external icon
• FDA FAQs on Testing for SARS-CoV-2external icon
• Overview of Testing for SARS-CoV-2 (for healthcare providers)
• Testing for COVID-19 (for the public)
• Information for Clinicians on Influenza Virus Testing
• Diagnosing Flu (for the public)