QuantiFast Pathogen +IC Kits

For sensitive and reliable detection of viral RNA/DNA and bacterial DNA, including internal control

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QuantiFast Pathogen PCR +IC Kit (100)

Cat. No. / ID: 211352

For 100 x 25 µl reactions: Master Mix, lyophilized Internal Control Assay, lyophilized Internal Control DNA, ROX Dye Solution, High-ROX Dye Solution, RNase-Free Water, Nucleic Acid Dilution Buffer, Buffer TE

KitControl

QuantiFast Pathogen Kit

Internal Control

Type

RT-PCR

PCR

Reactions

100

400

Inquire

See trademarks.

QuantiFast Pathogen +IC Kits are intended for molecular biology applications. These products are not intended for the diagnosis, prevention, or treatment of a disease.

✓ 24/7 automatic processing of online orders

✓ Knowledgeable and professional Product & Technical Support

✓ Fast and reliable (re)-ordering

Features

Simultaneous detection of pathogen target and internal control
5x master mix for higher sensitivity with more sample input
Correct interpretation of negative results for increased process safety
Clear detection of weak positive target signals
Fast, universal protocol on both standard and fast cyclers

Product Details

The QuantiFast Pathogen +IC Kits are designed for sensitive and rapid real-time PCR or one-step RT-PCR detection of pathogen nucleic acids using sequence-specific probes. To enable high process safety through correct interpretation of negative detection results, each kit contains reagents for multiplex real-time detection of up to 4 user-defined pathogen targets (e.g., virus, bacteria, fungi etc.) plus the Internal Control (IC). Two kit formats are available: The QuantiFast Pathogen RT-PCR +IC Kit for detection of viral RNA, which contains an internal RNA control template, plus the Internal Control primer/probe set, or the QuantiFast Pathogen PCR +IC Kit for detection of viral, bacterial, or fungal DNA, which contains an internal DNA control template, plus the Internal Control primer/probe set. With both kits, ROX is supplied in 2 tubes of different concentrations, enabling use on virtually any real-time instrument. For convenience, the master mix can be stored at 2–8°C.

Performance

QuantiFast Pathogen +IC Kits enable simultaneous detection of viral RNA or DNA targets plus the supplied Internal Control over a wide linear range without loss of sensitivity when multiplexing (see figures Sensitive detection of Norovirus on the Rotor-Gene Q and High linearity and precision of singleplex and duplex detection). The protocol has been developed to run fast cycling experiments on most cyclers with high reliability (see figures " Sensitive detection of BHV-1 on the Rotor-Gene Q" and " Sensitive detection of BHV-1 on the ABI 7500"). Combined amplification of pathogen target and the Internal Control using the QuantiFast Pathogen +IC Kits increases process safety of the pathogen detection workflow by ensuring the correct interpretation of negative results (see figure " Correct interpretation of negative results").

QuantiTect Nucleic Acid Dilution Buffer, supplied with the kits, stabilizes RNA and DNA standards during dilution and reaction setup and prevents loss of nucleic acids on plastic surfaces, such as tubes or pipet tips. It enables reliable dilution of standards used to quantify viral nucleic acids, giving a wide linear range, from low to high C_T values. The buffer ensures longer storage of standards without degradation (see figure " Reliable dilution and storage of RNA standards").

See figures

Sensitive detection of Norovirus.

High linearity and precision of singleplex and duplex detection.

Sensitive detection of BHV-1 on the Rotor-Gene Q.

Sensitive detection of BHV-1 on the ABI 7500.

Correct interpretation of negative results.

Reliable dilution and storage of RNA standards.

Principle

To enable high process safety through the correct interpretation of negative results, each QuantiFast Pathogen _IC Kit contains reagents for multiplex, real-time detection of a user-defined pathogen target with the Internal Control. Amplifying control and target genes in the same reaction, instead of separate reactions, increases the reliability of gene quantification by minimizing handling errors.

QuantiFast Pathogen +IC Kits provide sensitive and rapid real-time multiplex PCR or one-step RT-PCR detection of pathogen nucleic acids on the first attempt (see flowchart " QIAGEN multiplex kits"). The optimized master mix ensures that PCR products in a multiplex reaction are amplified with the same efficiency and sensitivity as PCR products in a corresponding single-amplification reaction. The specially developed fast PCR buffer contains the novel additive Q-Bond, which significantly reduces denaturation, annealing, and extension times (see figure " Fast primer annealing"). A balanced combination of K⁺ and NH₄⁺ ions as well as unique synthetic Factor MP, promote stable and efficient annealing of primers and probes to the nucleic acid template, enabling high PCR efficiency (see figure " Unique PCR buffer"). In addition, the unique formulation of Sensiscript Reverse Transcriptase ensures highly sensitive reverse transcription of viral RNA, while HotStarTaq Plus DNA Polymerase provides a stringent hot start, preventing the formation of nonspecific products.

Components of the QuantiFast Pathogen +IC Kit
	Kit component	Features	Benefits
5x QuantiFast Pathogen PCR Master Mix	Concentrated master mix	Highly concentrated and optimized for sensitive pathogen detection	Larger volumes of template can be added to the assay for increased sensitivity
	HotStarTaq Plus DNA Polymerase	5 min activation at 95ºC	Set up of qPCR reactions at room temperature
	QuantiFast Pathogen Buffer	Balanced combination of NH₄⁺ and K⁺ ions	Specific primer annealing ensures reliable PCR results
		Synthetic Factor MP	Reliable multiplexing analysis of up to 4 genes in the same tube
		Unique Q-Bond additive	Faster PCR run times, enabling faster results and more reactions per day
Internal Control Assay	Internal Control template	Internal Control DNA template in the QuantiFast Pathogen PCR +IC Kit	A universal DNA amplification control that can be used with different pathogen assays
	Internal Control template	Internal Control RNA in the QuantiFast Pathogen RT-PCR +IC Kit	A universal RNA amplification control that can be used with different pathogen assays
	Internal Control Assay	Premixed primer/probe set (TaqMan® probe) labeled with MAX (equivalent to HEX, VIC, etc.)	Will not interfere with primers against the pathogen-target
Additional kit components	QuantiFast Pathogen RT Mix*	Contains a unique formulation of Sensiscript Reverse Transcriptase	Optimized for highly sensitive detection of pathogen RNA
	ROX Dye Solution	Separate tube of passive reference dye for normalization of fluorescent signals on Applied Biosystems 7500 real-time PCR systems. Optional: Can be used on Stratagene instruments from Agilent	Precise quantification on cyclers that require ROX dye. Does not interfere with PCR on any real-time cycler
	High-ROX Dye Solution	Separate tube of passive reference dye for normalization of fluorescent signals on Applied Biosystems 7900 and StepOne real-time PCR systems
	QuantiTect Nucleic Acid Dilution Buffer	Proprietary buffer formulation for dilution and storage of nucleic acid standards	Stabilizes RNA and DNA standards during dilution and reaction setup and prevents loss of nucleic acids on plastic surfaces, such as tubes or pipet tips

* Included in QuantiFast Pathogen RT-PCR +IC Kits only

See figures

QIAGEN multiplex kits.

Fast primer annealing.

Unique PCR buffer.

Procedure

QuantiFast Pathogen +IC Kits provide a simple procedure for the detection of a user-defined pathogen and the Internal Control. They contain a ready-to-use master mix for the real-time detection of viral RNA (1-step RT-PCR) or viral, bacterial, and fungal DNA (PCR). There is no need for optimization of reaction and cycling conditions. Simply mix the supplied master mix with the pathogen assay (primers and probe) and the supplied Internal Control Assay and the Internal Control DNA or RNA. Alternatively, if the Internal Control has been added to the sample purification procedure, add RNase-free water instead of Internal Control DNA or RNA to the reaction mix. Then add your sample DNA or RNA and start the reaction on any cycler. The kit handbook contains optimized protocols for use with TaqMan® probes on a wide range of cyclers. It also contains recommendations for selection of dye combinations.

Each QuantiFast Pathogen +IC Kit includes the Internal Control Assay and Internal Control DNA or RNA for use as an amplification control via direct addition to the reaction mix. Alternatively, the IC can be added to the purification procedure to control both the purification process and amplification. For addition of the Internal Control to the purification procedure, highly concentrated Internal Control DNA or RNA (High conc.) can be ordered separately (see figure " QIAGEN Internal Control").

See figures

QIAGEN Internal Control.

Applications

QuantiFast Pathogen +IC Kits provide sensitive real-time PCR or one-step RT-PCR using sequence-specific probes for detection of pathogen DNA and/or RNA including an internal control. The kits can be used on a wide range of real-time cyclers, including cyclers from QIAGEN, Applied Biosystems, Bio-Rad, Roche (except for capillary cyclers), and Agilent.

Supporting data and figures

Correct interpretation of negative results.

Duplicates of two concentrations of a viral RNA target were co-amplified with the Internal Control in the presence of different amounts of a PCR inhibitory substance (humic acid) on the Rotor-Gene Q. [A] No template controls (NTCs) serve as a reference for Internal Control signal. [B] Amplification of viral RNA target and Internal Control confirms successful amplification. [C] The Internal Control indicates the presence of a low amount of inhibitors. [D] Failure to detect the Internal Control shows the failure of the amplification reaction through presence of inhibitors.

Specifications

Features	Specifications
Applications	Pathogen Detection: Real-time PCR of viral, bacterial or fungal DNA (QuantiFast Pathogen PCR +IC Kit) or one-step RT-PCR for detection of viral RNA (QuantiFast Pathogen RT-PCR +IC Kit)
Sample/target type	QuantiFast Pathogen PCR +IC Kit: viral, bacterial or fungal DNA; QuantiFast Pathogen RT-PCR +IC Kit: viral RNA
Single or multiplex	Duplex
Reaction type	Real-time PCR or one-step RT-PCR including of an internal control (IC)
Real-time or endpoint	Real-time
SYBR Green I or sequence-specific probes	Sequence-specific probes
Thermal cycler	For most standard and fast real-time cylcers compatible with duplex PCR/RT-PCR, e.g. Rotor-Gene Q or cyclers from Agilent, Applied Biosystems, BioRad, Roche
With or without ROX	Master Mix is provided without ROX dye, but 2 separate ROX solutions are included: High-ROX Dye Solution for use with ABI cyclers except ABI 7500, ROX Dye Solution (low ROX conc.) for use with ABI 7500 and other suppliers

Resources

Now with even more applications!

FAQ

The detection limit for the QuantiFast Pathogen RT-PCR and PCR kits is < 10 copies.

FAQ ID -2453

Ensure PCR amplicons are as short as possible, ideally 60–150 bp. Always use the same algorithm or software to design the primers and probes. For optimal results, only combine assays that have been designed using the same parameters.

Check the functionality of each set of primers and probes in individual assays before combining the different sets in the multiplex assay. Choose compatible reporters and quenchers based on a specific instrument. See How do I select appropriate reporter and quencher combinations for multiplex PCR.

FAQ ID -9093

The DNA IC is a non-linearized plasmid. The RNA IC is an in vitro transcript. Both are naked nucleic acids. The size (base pair length) of both templates is sufficient to allow for efficient purification with standard methods for nucleic acid extraction.

FAQ ID -2450

Replicates in real-time PCR may have different plateau heights due to differences in the reaction kinetics for each sample. Even though replicates start out with identical template amounts, the rate at which reagents are being depleted, and the point when exponential accumulation of PCR product stops and becomes linear, differ between replicates. This will result in different plateau heights, the stage where PCR reactions have come to a halt, and little or no additional PCR product is being amplified. You can find further information in Chapter 'Quantification of target amounts' of our Brochure "Critical Factors for Successful Real-Time PCR".

FAQ ID -539

The QuantiFast Pathogen PCR +IC Kit and the QuantiFast Pathogen RT-PCR +IC Kit are supplied with master mixes that do not contain ROX. Instead, 2 different ROX concentrations are supplied in separate tubes. “High-ROX Dye Solution” is suitable for use with all ABI cyclers except ABI 7500, and “ROX Dye Solution” is suitable for use with ABI 7500 and, optionally, instruments from Stratagene (Agilent). Recommendations are provided in the handbook.

FAQ ID -2605

Using the QuantiFast Pathogen + IC kits on the Rotor-Gene Q:

RT-PCR
40 cycles	~95 minutes
45 cycles	~100 minutes

PCR
40 cycles	~75 minutes
45 cycles	~80 minutes

FAQ ID -2452

No. UNG treatment does not provide any advantage for the QuantiFast and Rotor-Gene PCR kits because the mastermixes do not contain dUTP. Use the QuantiTect kits if you intend to use the UNG treatment.

FAQ ID -9092

The QuantiFast Pathogen PCR + RT-PCR +IC Kits can be used on all leading block cycler platforms, but not on capillary systems (e.g., LightCycler 2.0).

FAQ ID -2596

No calibration for MAX is needed if the instrument is calibrated for VIC. Use the FAM/SYBR Green filter for the pathogen assay and the VIC/JOE filter for the IC assay. To detect the Internal Control (MAX) in the VIC/JOE filter, create a new detector (e.g., “MAX/IowaBlack”). Assign “VIC” as the reporter dye and “None” for the quencher dye.

FAQ ID -2610

Please follow the instructions in the handbook. Briefly, use gain optimization “Before First Acquisition” for the pathogen assay (FAM) in the Green channel, and use a fixed gain of 9 for the Internal Control Assay (MAX) in the Yellow channel.

FAQ ID -2608

If the extra peaks seem irregular or noisy, do not occur in all samples, and occur at temperatures less than 70 ºC, then these peaks may not represent real PCR products and instead may represent artifacts caused by instrument settings.

Usually extra peaks caused by secondary products are smooth and regular, occur reproducibly in most samples, and occur at temperatures greater than 70 ºC. Characterization of the product by agarose gel electrophoresis is the best way to distinguish between these cases. If only one band appears by agarose gel then the extra peaks in the dissociation curve are instrument artifacts and not real products. If this is the case, refer to the thermal cycler user manual, and confirm that all instrument settings (smooth factor, etc.) are set to their optimal values.

FAQ ID -90990

The REST 2009 (Relative Expression Software Tool) software applies mathematic models that compensate for the different PCR efficiencies of the gene of interest and reference genes. In addition, the software can use multiple reference gene normalization to improve the reliability of result, as well as provides statistical information suitable for robust comparison of expression in groups of treated and untreated. QIAGEN offers the REST 2009 software free of charge.

FAQ ID -9095

MAX can be detected using the same channels or filters as for HEX, JOE, or VIC.

FAQ ID -2597

The Ct or threshold cycle value is the cycle number at which the fluorescence generated within a reaction crosses the fluorescence threshold, a fluorescent signal significantly above the background fluorescence. At the threshold cycle, a detectable amount of amplicon product has been generated during the early exponential phase of the reaction. The threshold cycle is inversely proportional to the original relative expression level of the gene of interest.

FAQ ID -2682

No, the Internal Controls used in the QuantiFast Pathogen PCR +IC Kit and the QuantiFast Pathogen RT-PCR +IC Kit are an artificial sequence that is not present in biological sample material.

FAQ ID -2598

Check the template quality and integrity by amplifying an endogenous control gene. Check the amplicon by QIAxcel Advanced system or agarose gel electrophoresis to show that amplification was successful.

Determine whether the gene of interest is expressed in your sample. See How can I find out if my gene of interest is express in a specific tissue type or cell line. Ensure the assay setup and cycling conditions are correct, and that the data collection channel matches the emission wavelength of the fluorescent dye used. Use a control sample in which the gene of interest is definitely expressed.

If the issue persists, please send the original run file to QIAGEN Technical Services.

FAQ ID -9091

For duplex analysis, using non-fluorescent quenchers (e.g., Black Hole Quencher^®) is preferred over fluorescent quenchers (e.g., TAMRA fluorescent dye). For triplex and 4-plex analysis, QIAGEN strongly recommends using non-fluorescent quenchers. Generally, use the green channel, the yellow channel, and the orange and crimson channels to detect the least abundant target, the second least abundant target, and the two most abundant targets, respectively. For instrument-specific recommendations, please see the handbooks for the QuantiTect Multiplex PCR kit, QuantiFast Multiplex kit or Rotor-Gene Multiplex kit.

FAQ ID -9094

No, the QuantiFast Pathogen PCR +IC kits are designed for use with hydrolysis probes (also known as TaqMan® probes) only.

See trademarks.

FAQ ID -2595

Typically, the target-specific probe should be labeled with FAM as the reporter dye and a non-fluorescent quencher (e.g., Dark Quencher, Black Hole Quencher [BHQ] or Iowa Black Quencher). Other reporter dyes than FAM, detected in a different detection channel than MAX, may also be suitable. It is not recommended to use fluorescent quenchers (e.g., TAMRA fluorescent dye). Due to their own native fluorescence, fluorescent quenchers contribute to an overall increase in background and reduce the signal-to-noise ratio.

FAQ ID -2594

No, the Internal Control template DNA or RNA must be added to the lysis buffer or to the lysate in order to prevent the loss of Internal Control template thorough matrix effects.

FAQ ID -2602

In the “Filter Gain Settings” dialog box, set the filter gain to a value of 4 for both the FAM/SYBR Green and HEX/JOE/VIC filters. See the Mx instrument/software manual for details.

FAQ ID -2609

The gDNA wipeout buffer incubation step can be skipped when the total RNA is free from genomic DNA. However, the gDNA wipeout buffer is still required to be added because the reverse transcription step is optimized in the presence of components in the gDNA wipeout buffer.

FAQ ID -9098

Make sure that template, primers, probes, and amplification reagents are stored correctly and avoid multiple freeze–thaw cycles for oligonucleotides and template. Check the performance of your real-time instrument as some instruments require the halogen lamp to be frequently replaced. Lasers must also be replaced occasionally.

FAQ ID -589

Both membrane and magnetic bead-based kits have been tested (e.g., QIAamp MinElute Virus Kit, QIAamp Viral RNA Kit, DNeasy kits, RNeasy kits, QIAsymphony Virus/Bacteria kits, QIAxtractor Vx Reagents).

FAQ ID -2606

Store the standards at a high concentration in aliquots at -20^oC to -70^oC. If using low concentrations, stabilize standards with carrier nucleic acid. It is always best to use freshly diluted standards for each experiment. If possible, use siliconized tubes for standard (and target) dilutions. This will prevent any unspecific binding of nucleic acids to the plastic.

FAQ ID -9099

Reliable HRM analysis results depend on template quality, highly specific HRM PCR kit with a saturation dye, a real-time instrument with HRM capability, and powerful software package. Factors critical for successful HRM analysis are:

Use the same genomic DNA purification procedure for all samples being analyzed by HRM. This avoids variation due to differing composition of elution buffers.
DNA template concentrations should be normalized using the same dilution buffer. Ensure the C_T values are below 30 and differ no more than 3 C_T values across individual samples.
Design assays with amplicon length 70–350 bp. For SNP analysis, use amplicon length 70–150 bp.
Always start with 0.7 µM primer concentration

For more details, please refer to the HRM Technology – FAQs and the Critical Success Factor for HRM performance.

FAQ ID -9097

Principally, yes. However, additional factors influencing the CT are:

1. Extraction efficiency, which depends on extraction method and sample material.

2. Volume of the eluate used for PCR.

Examples: Use of the Internal Control according to handbook instructions (0.1µl per 1µl elution volume) for two different workflows.

Workflow 1: High extraction efficiency: use of 5 µl of the eluate for PCR results in a CT value of 29-30.
Workflow 2: High extraction efficiency: use of 10 µl of the eluate for PCR results in a CT of 28-29.

Depending on the workflow, the amount of Internal Control to be added to the extraction might have to be adjusted to more than 0.1 µl per 1 µl elution volume, or to less than 0.1 µl per 1 µl elution volume, in order to achieve a CT value within the expected range.

Running the Internal Control DNA/RNA provided with the QuantiFast Pathogen +IC Kit in a separate reaction can serve as a reference for adjusting the amount of Internal Control DNA/RNA (High conc.) to be added to the extraction.

FAQ ID -2604

On the Rotor-Gene Q, setting the threshold in the Yellow channel to an absolute value of 0.05 will give satisfactory results in most cases.

FAQ ID -2607

The QuantiTect Virus Kit and the new QuantiFast Pathogen +IC Kits are based on similar reaction chemistry and show identical sensitivity but as a new feature, the QuantiFast Pathogen kits include an Internal Control template and the corresponding primer/probe set for duplex amplification of a user-defined pathogen target with the provided Internal Control. Additional new features are pack size, kit variants, ROX variants, and speed.

FAQ ID -2448

In the QuantiFast Pathogen + IC kit, the probe is labeled with MAX-NHS ester (MAX) as the reporter dye which has a spectrum equivalent to HEX, JOE or VIC dyes. IowaBlack is used as the quencher dye. IowaBlack is a non-fluorescent quencher (dark quencher).

FAQ ID -2449

Yes, the Internal Control RNA (High conc.) and Internal Control DNA (High conc.) templates are available under a separate catalog number. After reconstitution according to the description in the handbook, these IC templates have a 10x higher concentration than the Internal Control templates provided in the kits. They are sufficiently concentrated to be spiked into the sample prep without replacing too much of the sample input volume.

**Please note that there is no assay (primer/probe set) for amplification of the IC included in these separate catalog numbers. The assay is only included in the QuantiFast Pathogen PCR +IC Kit and QuantiFast Pathogen RT-PCR +IC Kit. The ICs cannot be used with the QuantiTect Virus kits because the assay (primer/probe set) for the detection of the IC is provided with the QuantiFast Pathogen Kits only.

FAQ ID -2451

After reconstitution according to handbook instructions, the Internal Control (IC) templates provided with the kits have a ready-to-use concentration for direct use as an amplification control in PCR or RT-PCR. For each 25 µl reaction, 2.5 µl of the IC are added, resulting in an expected CT value of approximately 29-30.

In order to achieve the same CT value when using the IC as an extraction control, more IC template has to be spiked in before extraction. The exact amount depends mainly on the elution volume. For each 1 µl of elution volume, 0.1 µl of the IC High conc. should be added to each of the extraction samples. This should result in a CT value in the PCR or RT-PCR reactions of approximately 29-30.

Examples: For 100 µl of elution volume, 10 µl of the IC, per sample, should be added to the lysis buffer or lysate. For 50 µl of elution volume, 5 µl of the IC, per sample, should be added to the lysis buffer or lysate.

FAQ ID -2603

Depending on primer design and copy number of target, primer-dimer may occur and its signal might be detected. Typical strategies against this are to optimize PCR conditions and/or redesign the assay.

Alternatively, an additional data-acquisition step can be added to the 3-step cycling protocol. First, determine the melting temperatures (T_m) for both the amplicon and the primer-dimer. Then, add a 15 second data-acquisition step with a temperature that is higher than the primer-dimer T_m, but approximately 3ºC lower than the specific amplicon T_m.

FAQ ID -9096

The Internal Control templates can be freeze-thawed for up to 6 times without decrease in performance. However, great care should be taken to avoid inadvertently introducing RNAses/DNAses into the Internal Control template solutions. In general, in order to avoid repeated freeze-thaw cycles, we recommend preparing aliquots of the Internal Control templates.

FAQ ID -2599

When the IC is added to the amplification reaction mix, the IC signal confirms that PCR amplification has been successful. When it is added at the extraction step to the lysis buffer or lysate, the IC signal confirms that nucleic acid purification and PCR amplification have been successful.

FAQ ID -2600

Yes, the Internal Control RNA will only give the expected signal when both the reverse transcription and the PCR reactions have been successful.

FAQ ID -2601