Research Use Only CDC Influenza SARS-CoV-2 (Flu SC2) Multiplex Assay Real-Time RT-PCR Primers and Probes

Research Use Only CDC Influenza SARS-CoV-2 (Flu SC2) Multiplex Assay Real-Time RT-PCR Primers and Probes
Updated July 14, 2020

NOT FOR VIRAL TESTING USE

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.

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These sequences are intended to be used for the purposes of respiratory virus surveillance and research. The recipient agrees to use them in compliance with all applicable laws and regulations. Every effort has been made to assure the accuracy of the sequences, but CDC cannot provide any warranty regarding their accuracy. The recipient can acknowledge the source of sequences in any oral presentations or written publications concerning the research project by referring to the Genomics and Diagnostics Team, Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
DDIDNCIRDRespiratoryPanelSARS2FluAB@cdc.gov

Tube 1: Flu SC2 Multiplex Assay: Forward and Reverse Primers
Name Description Oligonucleotide Sequence (5’ to 3’) Concentration/Tube
InfA-F InfA For1 CAA GAC CAA TCY TGT CAC CTC TGA C 3.33 µmol
InfA For2 CAA GAC CAA TYC TGT CAC CTY TGA C 3.33 µmol
InfA-R InfA Rev1 GCA TTY TGG ACA AAV CGT CTA CG 5.00 µmol
InfA Rev2 GCA TTT TGG ATA AAG CGT CTA CG 1.67 µmol
InfB-F InfB For TCC TCA AYT CAC TCT TCG AGC G 6.67 µmol
InfB-R InfB Rev CGG TGC TCT TGA CCA AAT TGG 6.67 µmol
SC2-F SC2 For CTG CAG ATT TGG ATG ATT TCT CC 6.67 µmol
SC2-R SC2 Rev CCT TGT GTG GTC TGC ATG AGT TTA G 6.67 µmol
RP-F RnaseP For AGA TTT GGA CCT GCG AGC G 6.67 µmol
RP-R RnaseP Rev GAG CGG CTG TCT CCA CAA GT 6.67 µmol
Tube 2: Flu SC2 Multiplex Assay: Probes
Name Description Oligonucleotide Sequence (5’>3’) Concentration/Tube
InfA-P InfA Probe1 5’-/5FAM/TGC AGT CCT /ZEN/ CGC TCA CTG GGC ACG/3IABkFQ/-3’ 1.67 µmol
InfB-P InfB Probe2 5’-/5YakYel/CCA ATT CGA/ZEN/ GCA GCT GAA ACT GCG GTG/3IABkFQ/-3’ 1.67 µmol
SC2-P SC2 Probe3 5’-/5TexRd-XN/ATT GCA ACA/TAO/ ATC CAT GAG CAG TGC TGA CTC/3IAbRQSp/-3’ 1.67 µmol
RP-P RnaseP Probe4 5’-/5CY5/TTC TGA CCT /TAO/ GAA GGC TCT GCG CG/3IAbRQSp/-3’ 1.67 µmol

1 Probe labeled at the 5′ end with the reporter molecule 6-carboxyfluorescein (FAM), with a ZEN™ quencher between the 9th and 10th nucleotide, and with an Iowa Black FQ quencher (IABkFQ ) at the 3′ end (Integrated DNA Technologies, Coralville, IA). InfA probe and primer sequences are identical to InfA sequences in the FDA-cleared CDC Human Influenza Real-Time RT-PCR Diagnostic Panel (K200370).

2 Probe labeled at the 5′ end with the Yakima Yellow (YakYel), with a ZEN™ quencher between the 9th and 10th nucleotide, and with an Iowa Black FQ quencher (IABkFQ) at the 3′ end (Integrated DNA Technologies, Coralville, IA). Probe and primer sequences are identical to InfB sequences in the FDA-cleared CDC Human Influenza Virus Real-Time RT-PCR Detection and Characterization Panel (K080570).

3 Probe labeled at the 5′-end with the Texas Red-XN (TexRd-XN), with a TAO quencher between the 9th and 10th nucleotide, and with an Iowa Black RQ quencher (IAbRQSp) at the 3′ end (Integrated DNA Technologies, Coralville, IA).

4 Probe labeled at the 5′-end with the CY5 reporter, with a TAO quencher between the 9th and 10th nucleotide, and with an Iowa Black RQ quencher (IAbRQSp) at the 3′ end (Integrated DNA Technologies, Coralville, IA).

 

Note: Oligonucleotide sequences are subject to future changes as the SARS-CoV-2 viruses evolve.