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Microbial identification assays

qPCR assays for rapid, sensitive microbial and viral detection

Save time spent designing primers and probes by using predesigned assay sets. The following assays have been tested on the cobas omni Utility Channel on the Roche cobas® 6800 and 8800 Systems:

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

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

Ordering

Assay validation

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. Experimental conditions.

 C. difficile toxinHSV-1 / HSV-2 / VZVInfluenza A / Influenza B / RSV
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)
Primer/probe set volume480 µL480 µL480 µL
MMx-28 mL8 mL8 mL
7 mL of the primer-probe and MMx-2 mix transferred to the cobas omni Utility Channel Reagent cassette
Sample type selectedSimple sampleSimple sampleSwab sample
Sample input volume200 µL200 µL (CSF)
500 µL (plasma and 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)

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.

Specificity information

Tables 3–5 provide information on the organisms the C. diff, HSV/VZV, and Influenza qPCR Assays can specifically identify.

Table 3. Assays for Clostridium difficile (C. difficile).

 C. difficile
Quality control panel (all panel members correctly identified)

Qnostics C. difficile Panel (March 2016), including C. difficile ribotypes 027 (Toxin: A+/B+) and 017 (Toxin: A-/B+)

ZeptoMetrix NATrol C. difficile Verification Panel (including ribotypes 002, 017, 078, 027-1, and 027-2)

Culture fluids (all organisms correctly identified)None
No cross-reactivity (none of the organisms generated false positive results)
Bacteria
Campylobacter jejuni
Cryptosporidium parvum
Cyclospora cayetanensis
Enterobacter cloacae
Escherichia coli
Escherichia coli O157 :H7
Shigella sonnei
Salmonella enteritidis
P. sordelli (formerly C. sordelli)
Viruses
Enterovirus 71
Hepatitis A virus
Human adenovirus type 7a
Human adenovirus type 41

Table 4. Assays for herpes simplex virus, types 1 and 2 (HSV-1, HSV-2), Varicella-zoster virus (VZV).

 Herpes simplex virus, types 1 and 2 (HSV-1, HSV-2), Varicella-zoster virus (VZV)
Quality control panel (all panel members correctly identified)INSTAND e.V., Virus Genome Detection—Herpes Simplex Virus Type 1/Type 2 (363) ( June, 2014)
Culture fluids (all organisms correctly identified)
HSV-1 culture fluid strains
Isolates 1 to 21
MacIntyre
HSV-2 culture fluid strains
Isolates 1 to 21
MS
VZV culture fluid strains
Isolates A, B, D
Strain 82
Strain 275
Strain 1700
Strain 9939
Strain Ellen
No cross-reactivity (none of the organisms generated false positive results)
Bacteria
Chlamydia trachomatis
Escherichia coli
Neisseria gonorrhoeae
Staphylococcus aureus
Staphylococcus epidermis
Streptococcus pyogenes
Treponema pallidum
Ureaplasma parvum
Viruses
Cytomegalovirus (CMV)
Epstein-Barr Virus (EBV)
Enterovirus 71
Human adenovirus type 1
Human adenovirus type 7a
Human adenovirus type 31
Human Coxsackievirus A9
Human Coxsackievirus A16
Human Coxsackievirus B3
Human Echovirus 6
Human Herpes Virus Type 6a
Human Herpes Virus Type 7
Human Herpes Virus Type 8
Human Parvovirus B19
Human Polyomavirus JC
Human Polyomavirus Type 1 (BKV)
Simian virus 40
Fungi
Candida albicans

Table 5. Assays for Influenza A, Influenza B, and Respiratory syncytial virus (RSV).

 Influenza A, Influenza B, and RSV
Quality control panel (all panel members correctly identified)Qnostics Influenza A/B panels (including H1N1, H3N2, and H5N1) and RSV panel (RSV-A and RSV-B)
Culture fluids (all organisms correctly identified)
Influenza A culture fluid strains
Influenza A H1N1
Brisbane/59/07
Influenza B culture fluid strains
Influenza B Florida/04/06
B/Brisbane/33/08
B/Brisbane/60/08
B/Massachusetts/2/2012
Utah/9/14
Florida/07/04
Texas/2/13
B/Florida/04/06
Brisbane/9/14
Brisbane/36/12
Phuket/3073/13
Victoria/2/87
Wisconsin/1/10
Yamagata/16/88
B/Florida/02/06
Lee/40
Brisbane/3/07
Brisbane/46/15
B/Texas/6/2011
B/Panama/45/90
RSV culture fluid strains
RSV-A strain 2006 Isolate
RSV-B strain 12/2014 Isolate #1
No cross-reactivity (none of the organisms generated false positive results)
Bacteria
Bordetella parapertussis
Bordetella pertussis
Chlamydophilia pneumoniae
Escherichia coli
Corynebacterium striatum
Haemophilus influenzae
Legionella pneumophilia
Moraxella catarrhalis
Staphylococcus aureus
Staphylococcus epidermis
Streptococcus pyogenes
Mycoplasma pneumoniae
Neisseria meningitidis
Pseudomonas aeruginosa
Streptococcus pneumoniae
Viruses
Bocavirus
Coronavirus 229E
Coronavirus OC43
Human adenovirus type 1
Human adenovirus type 3
Human adenovirus type 5
Human adenovirus type 7a
Human Metapneumovirus 8 type B2
Human Metapneumovirus 27 type A2
Human parainfluenza virus 1
Human parainfluenza virus 2
Human parainfluenza virus 3
Human rhinovirus type 1A

Certificates of analysis (COAs)

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