Important update: Healthcare facilities
CDC has updated select ways to operate healthcare systems effectively in response to COVID-19 vaccination. Learn more
UPDATE
Given new evidence on the B.1.617.2 (Delta) variant, CDC has updated the guidance for fully vaccinated people. CDC recommends universal indoor masking for all teachers, staff, students, and visitors to K-12 schools, regardless of vaccination status. Children should return to full-time in-person learning in the fall with layered prevention strategies in place.
UPDATE
The White House announced that vaccines will be required for international travelers coming into the United States, with an effective date of November 8, 2021. For purposes of entry into the United States, vaccines accepted will include FDA approved or authorized and WHO Emergency Use Listing vaccines. More information is available here.

CDC’s Influenza SARS-CoV-2 Multiplex Assay

CDC’s Influenza SARS-CoV-2 Multiplex Assay
Updated Nov. 14, 2022

Summary of Recent Changes

Overview

The CDC Influenza SARS-CoV-2 (Flu SC2) Multiplex Assay is a real-time reverse-transcription polymerase chain reaction (rRT-PCR) laboratory test that can simultaneously detect and differentiate between influenza A, influenza B, and SARS-CoV-2 in upper or lower respiratory specimens. The test is a highly accurate, nucleic acid-based diagnostic tool to evaluate specimens from patients who are in the acute phase of infection.

Why the CDC Flu SC2 Multiplex Assay is Important

  • Diagnoses infection with the SARS-CoV-2, influenza A, and/or influenza B viruses in one test
  • Allows laboratories to conserve important testing materials and process more tests in a given time period
  • Gives public health officials information they need to control the spread of COVID-19 and flu
  • Allows for ongoing flu surveillance while also testing for SARS-CoV-2

How Public Health Laboratories Order the CDC Flu SC2 Multiplex Assay

CDC’s International Reagent Resource (IRR) provides CDC Flu SC2 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 the SARS-CoV-2 (Flu SC2) Multiplex Assay 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. CDC has shared the primers and probes sequence specifications so that laboratories and test developers may manufacture their own reagents. Refer to description of kit contents below.

Emergency Use Authorizations

The U.S. Food and Drug Administration (FDA) issued an Emergency Use Authorization (EUA) for use of the Flu SC2 Multiplex Assay on July 2, 2020. The EUA process enables FDA to consider and authorize the use of unapproved but potentially lifesaving medical or diagnostic products during a public health emergency. The U.S. Secretary of Health and Human Services declared SARS-CoV-2 to be a U.S. public health emergency justifying the authorization of emergency use of drugs and biologic products, including in vitro diagnostics, on February 4, 2020.

Primers and Probes (Research Use Only)

Not for diagnostic testing use: Reagents manufactured from the sequences listed below may not be used for diagnostic testing under FDA’s authorization of the CDC Flu SC2 Multiplex Assay. Only primers and probes labeled for EUA use and distributed by the International Reagent Resource may be used.

Primer and Probe Kit Description

Tube 1: Flu SC2 Multiplex Assay: Forward (For) and Reverse (Rev) Primers

Flu SC2 Multiplex Assay: Forward (For) and Reverse (Rev) Primers
Name Description Oligonucleotide Sequence (5’ to 3’) Concentration
InfA-F InfA For1 CAA GAC CAA TCY TGT CAC CTC TGA C 3.33 µM
InfA For2 CAA GAC CAA TYC TGT CAC CTY TGA C 3.33 µM
InfA-R InfA Rev1 GCA TTY TGG ACA AAV CGT CTA CG 5.00 µM
InfA Rev2 GCA TTT TGG ATA AAG CGT CTA CG 1.67 µM
InfB-F InfB For TCC TCA AYT CAC TCT TCG AGC G 6.67 µM
InfB-R InfB Rev CGG TGC TCT TGA CCA AAT TGG 6.67 µM
SC2-F SC2 For CTG CAG ATT TGG ATG ATT TCT CC 6.67 µM
SC2-R SC2 Rev CCT TGT GTG GTC TGC ATG AGT TTA G 6.67 µM
RP-F RNase P For AGA TTT GGA CCT GCG AGC G 6.67 µM
RP-R RNase P Rev GAG CGG CTG TCT CCA CAA GT 6.67 µM

Tube 2: Flu SC2 Multiplex Assay: Probes

Flu SC2 Multiplex Assay: Probes
Name Description Oligonucleotide Sequence (5’>3’) Concentration
Option 1: IDT Probes
InfA-P InfA Probe [1] 5’-/FAM/TGC AGT CCT /ZEN/ CGC TCA CTG GGC ACG/3IABkFQ/-3’ 1.67 µM
InfB-P InfB Probe [2] 5’-/YakYel/CCA ATT CGA/ZEN/ GCA GCT GAA ACT GCG GTG/3IABkFQ/-3’ 1.67 µM
SC2-P SC2 Probe [3] 5’-/TexRd-XN/ATT GCA ACA/TAO/ ATC CAT GAG CAG TGC TGA CTC/3IAbRQSp/-3’ 1.67 µM
RP-P RNase P Probe [4] 5’-/CY5/TTC TGA CCT /TAO/ GAA GGC TCT GCG CG/3IAbRQSp/-3’ 1.67 µM
Option 2: Biosearch Probes
InfA-P InfA Probe [5] 5’-/FAM/TGC AGT CCT /Nova/ CGC TCA CTG GGC ACG/BHQ-1/-3’ 1.67 µM
InfB-P InfB Probe [6] 5’-/CIV-550/CCA ATT CGA/BHQ-1/ GCA GCT GAA ACT GCG GTG/C3/-3’ 1.67 µM
SC2-P SC2 Probe [7] 5’-/CalFluor610/ATT GCA ACA/Nova/ ATC CAT GAG CAG TGC TGA CTC/BHQ-2/-3’ 1.67 µM
RP-P RNase P Probe [8] 5’-/Quasar670/TTC TGA CCT /Nova/ GAA GGC TCT GCG CG/BHQ-2/-3’ 1.67 µM

Note: Oligonucleotide sequences are continually monitored to ensure performance and may be subject to future changes as the SARS-CoV-2 virus evolves.

Resources

Previous Updates

As of September 30, 2021

  • Added information on CDC amendment granted by FDA on August 5, 2021

As of February 2, 2021

  • Added information on CDC amendment granted by FDA on January 8, 2021

As of December 11, 2020

  • Added information on CDC amendment granted by FDA on November 30, 2020