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Microbial identification primer/probe sets

qPCR primer/probe sets for rapid microbial and viral identification

Save the time spent designing your own and use our predesigned qPCR primer/probe sets. The following pathogens have been tested with our primer/probe sets on the cobas omni Utility Channel on the cobas® 6800 and 8800 Systems:

  • C. difficile toxin
  • Influenza A, B/RSV
  • HSV-1/HSV-2/VZV
  • PivNG V2
  • MRSA

Primers and probes are HPLC purified and verified by ESI mass spectrometry, delivering batch-to-batch consistency to provide confidence in your data.

Protocol conditions

The primers and probes were tested using the Roche cobas omni Utility Channel Tool v3.0 and the cobas omni Utility Channel Reagent Kit, using the parameters shown in Tables 1 and 2.

Table 1. Suggested experiment parameters.

 C. difficile toxinHSV-1 / HSV-2 / VZVInfluenza A / Influenza B / RSVPivNG V2MRSA
Channel numberChannel 2 (C. diff toxin)Channel 2 (HSV-1)
Channel 4 (HSV-2)
Channel 3 (VZV)
Channel 2 (Influenza A)
Channel 3 (Influenza B)
Channel 4 (RSV)
Channel 4 (NG)Channel 2 (S. aureus)
Channel 3 (SCCmec)
Channel 4 (mecA/C)
Primer/probe set volume480 µL480 µL480 µL480 µL480 µL
MMx-28 mL8 mL8 mL8 mL8 mL
7 mL of the primer-probe and MMx-2 mix transferred to the cobas omni Utility Channel Reagent cassette
Sample type Simple sampleSimple sampleSwab sampleSimple sample or swab sampleSwab sample
Sample input volume200 µL200 µL (CSF)
500 µL (plasma and swab)
400 µL850 µL (simple)
400 µL (swab)
400 µL
RFI min1.5 (C. diff toxin)1.6 (HSV-1)
1.5 (HSV-2)
1.8 (VZV)
1.3 (Influenza A)
2 (Influenza B)
1.2 (RSV)
2.5 (NG)
2.5 (IC)
2.0 (S. aureus)
4.5 (orfX)
2.0 (mecA/C)

Table 2. Cycling conditions.*

 UNG incubationPre-PCR step1st measurement2nd measurementCooling
No. of cyclesPredefined1545Predefined
No. of steps322
Temperature55°C; 60°C; 65°C95°C; 55°C91°C; 58°C 
Hold time120 s; 360 s; 240 s5 s; 30 s5 s; 25 s 
Data acquisitionNoneEnd of each cycleEnd of each cycle 

* Default PCR profile for the cobas omni Utility Channel provided by the Utility Channel software.

Certificates of analysis (COAs)

Find COAs by batch or lot number

*RUO—For research use only. Not for use in diagnostic procedures. Unless otherwise agreed to in writing, IDT does not intend for these products to be used in clinical applications and does not warrant their fitness or suitability for any clinical diagnostic use. Purchaser is solely responsible for all decisions regarding the use of these products and any associated regulatory or legal obligations.

This product and its use is the subject of one or more U.S. patent, and/or other pending U.S. and foreign patent applications owned by IDT. This includes patents and patent applications of IDT related to the right to use oligonucleotide probes labeled with Iowa Black® FQ, Iowa Black RQ, TAO™, and/or ZEN™ quenchers. The purchase of this product conveys to the buyer the non-transferable right to use the purchased amount of the product and components of the product in research and diagnostics for human healthcare conducted by the buyer. The buyer cannot sell or otherwise transfer this product or its components for a third party.

RUO22-1199_001